A few elements of the anthophyte hypothesis (J. A. Doyle and Donoghue 1986, 1987) and classic research by Arber and Parkin (1907), Edgar Anderson (1934), Ehrlich and Raven (1964), Raven and Kyhos (1965), Takhtajan (1969, 1976), and Raven (1977), dovetail with- and potentially support a coevolutionary hypothesis on the origin of flowering plants.
Why include Takhtajan's often criticized proposal on a "neotenous" origin of flowering plants (1969, 1976, and previous papers) as a paramount synthesis?
"... Equally puzzling is that despite intense interest in the origins of seed plants and angiosperms throughout the entire last century, few have looked at the problems from a life cycle evo-devo perspective, with perhaps one exception (Takhtajan 1976), who alluded to neoteny as one of the possible mechanisms contributing to the origin of angiosperms."
The above quotation is from page 296 of Y.-L. Qiu (2008), Phylogeny and evolution of charophytic algae and land plants. Journal of Systematics and Evolution 46(3): 287-306.
Based on my review of the literature and leaving out progenesis of reproductive modules from immediate consideration in the origin of angiosperms (J. A. Doyle 1978), neoteny expressed as paedomorphic heterochrony (Gould 1977) might have an evo-devo basis, potentially involving shared repetitive DNA sequences at the heart of molecular coevolution of the homeodomain protein Engraled and LFY.
I intend on developing this idea later in this essay. James A. Doyle (1978) and Robert Thorne (1992) then, are probably too critical of Takhtajan's broadly defined and strangely predictive concept of a neoteny as a way to explain the evolution of angiosperm flowers from fertile spur shoots of ancient seed plants.
The LFY gene duplication hypothesis by Albert et al. (2002), and out-of-male and out-of-female hypotheses involving floral quartets in compartments of meristematic cells of developing SAMs of bisexual cone axes (Theißen Saedler 2001, Becker and Theißen 2003, Baum and Hileman 2006, Theißen and Melzer 2007, Melzer et al. 2010) provide a demonstrably solid evo-devo foundation for continuing debate and evaluation of molecular evolution of angiosperms from unknown gymnosperm ancestors.
Support for MMT and the gamoheterotopic hypotheses from the research perspective of gene expression in conifers (Vásquez-Lobo et al. 2007) and Gnetum (Shindo et al. 2001) and the biochemical logic of deeply conserved cone and floral tool kits (Melzer et al. 2010), is equivocal, especially when studies of conifer cone abnormalities are considered (Flores-Rentería et al. 2011, Rudall et al. 2011) together with phylogenetic tests.
Having compared and discussed some of the previous hypotheses on the origin of flowering plants the next section reevaluates published clues gleaned from geochemical data that might help paleontologists to focus on the interval in geologic time necessary to solve a riddle of angiosperm beginnings.
First Clues on the Origin of Angiosperms:
The first clue that sheds light on the shadowy origin of flowering plants comes surprisingly from study by oil and gas explorers and geochemists of taxon-specific biomarkers (TSBs) and molecular traces which are recoverable from mud logs of well boreholes, or from coal balls, compressions, and permineralizations (Moldowan and Jacobson 2002).
The picture of the rock slab to the left is of an indeterminate pentamerous fossil rosid flower (Celastrales, Rosanae) collected by Professor David L. Dilcher from the Lower Cretaceous Dakota Formation of North America. The image was captured in 1981 while the author was visiting Indiana University.
Molecular tracers include naturally occurring but fossilized triterpenoids known as oleanone triterpanes (oleananes). Oleananes, together with ursenes, lupenes, and taraxerenes are important TSBs that belong to a class of Β-amirin triterpenoids (Moldowan and Jacobson 2002).
Oleananes occur in fossilized leaf material of certain gigantopterids, bennettitaleans, and flowering plants (Moldowan and Jacobson 2002), but are absent from samples of several other fossil seed plants (D. W. Taylor et al. 2006).
Mud-loggers are able to ascertain higher plant input into a core segment of a stratigraphic horizon pulled-up from the well-site gas chromatography and mass spectrometry, and microscopic analysis of animal and plant microfossils including pollen and vascular plant fragments in core samples.
Oleanane-containing gigantopterids are rarely discussed in published forums as possible ancestors or relatives of flowering plants because paleobotanists have only just begun to find and describe permineralizations of these enigmatic seed plants.
For example, none of the work on Permian gigantopterids published to date convincingly demonstrates physical connections between reproductive structures, stems, roots, and leaves. Whole plant morphologies are incompletely known for this group of Paleozoic seed plants (pages 758-763, T. N. Taylor et al. 2009).
I now state a coevolutionary hypothesis on the origin of flowering plants and certain holometabolous insect antagonists:
[ Coevolutionary Hypothesis ]
Coevolution between phytophagous insect antagonists and Carboniferous, Permian, and Triassic seed plant hosts at the level of their respective developmental tool kits with focus on selective forces that drive the logic of transcriptional regulation is proposed to explain the origin of angiosperms and certain clades of holometabolous insects.
I advance Takhtajan's ideas on flowering plant origins (1969, 1976) from 21st century research perspectives of evolutionary-developmental (evo-devo) biology, melded with rethinking of the paleontology of detached, fossilized remains of overlooked Paleozoic seed plant organs that might potentially be derived from massive, developmentally plastic, shoot apical meristems (SAMs) of gigantopteroid shrubs, vines, or small trees.
During the hypoxic late Frasnian-Famennian ice-house (DeCARB), invertebrate Hox proteins, hemocyanin (Hc) respiratory enzymes, and certain nuclear receptors of plecopteran (stonefly) ancestors diverged, leading to novel multimeric proteins in several hemimetabolous and holometabolous clades of late Paleozoic insects.
Candidates for the early insect developmental tool kit may also include certain homeotic selector genes of the Hox complex such as homologs and paralogs of abdominal A (abd-A), Abdominal B (Abd-B), Hox3, proboscipedia (pb), sex combs reduced (Scr), and Ultrabithorax (Ubx), the compartment-selector gene engraled; also including the proteins these genes encode such as Ubx and Engraled, the ecdysone hormone signaling machinery, Hcs, hexamerins (Hxs), and nuclear receptor proteins.
At the same time that homeotic genes and transcription factors (TFs) were diverging in early Carboniferous insect clades, key vascular plant developmental genes including AP2, ARF, Class I and II TCP, Class III HD-Zip, GRAS, KNOX, LEAFY (LFY), MIKC-type MADS-box, PIN, TIR, and YABBY, and their modular TFs, were evolving into molecular novelties in Paleozoic seed plant lineages.
Coevolution of insect helix-turn-helix (HTH) homeodomain proteins, seed plant HTH LFY proteins, other phytophagous insect- and seed plant host developmental cis-regulatory modules (CRMs), and their respective developmental tool kits, potentially occurred during the DeCARB and/or end-Guadalupian carbon cycle event (GuCCE), with local hypoxia and temperature extremes as underlying and potentially powerful selective forces.
Global oxygen levels declined to 13% during the course of millions of years following the DeCARB. Resident chewing, crawling, ovipositioning, piercing, siphoning, sponging, stinging and sucking insects probably became dependent on host seed plant shrubs and trees for food, oxygen gas; and shelter from predators, cold temperatures, and ultraviolet radiation. Phytophagous insect associates of Permo-Carboniferous vegetation potentially coevolved with their oxygen generating plant hosts.
The GuCCE and associated global hypercapnia reinforced the already close association between Permian plants and protocoleopterans, weevils, and other hemi- and holometabolous insects, ostensibly established after the DeCARB. Resident phytophagous insect associates of developmentally plastic Permian seed plant shrubs including populations and species of Vojnovskyales and gigantopteroid seed plants, allowed stressed hemimetabolous insect mutualists to survive hot, hypoxic (low pO2) environments.
Permo-Triassic seed plants were probably confined to small isolated populations indigenous to fragmented biomes and fitness landscapes resulting from the deleterious effects of the end-Permian extinction (EPE). Surviving insects of the EPE and Triassic-Jurassic boundary carbon cycle event (TrCCE) fed, reproduced, and might have secreted biologically active molecules or infected growing points and reproductive modules with LTR retrotransposons while chewing, ovipositioning, scraping, sponging, stinging, and trampling the surfaces of SAMs and accessory bisexual cone axes.
Signaling molecules such as jasmonates and volicitins originating in the bodies of phytophagous insect associates of Permo-Triassic shrubs and trees, when applied to growing points of the host plant with mechanical force might have affected biosynthesis of certain phytohormones including gibberellic acid (GA). Transduction of biologically active insect signaling molecules potentially stimulated biosynthesis of GA, activating, modifying, and upregulating homeotic selector and meristem identity genes affecting developmental switches in expanding bisexual cone axes.
Phytoecdysones originating in tissues of Carboniferous and Permian seed plants could have signalled the Hc respiratory and Hx storage protein manufacturing machinery of eggs and instars of phytophagous insect antagonists profoundly affecting their development and body size.
Based on a trail of biochemical clues gleaned from studies of vegetative growth and SAM organization in extant model lignophytes and monilophytes, when combined with insight gained from molecular phylogenetic analyses of Class III homeodomain leucine zipper (Class III HD-Zip) genes and KNOTTED1 homeodomain proteins at least two (possibly three or more) evo-devo programs might have existed in early diverging Devonian progymnosperm and/or seed plant populations.
Many of the supposed homologies of leaves, sporophylls, and ectopic structures including reproductive axes and ovular integuments could be incorrect based on the possibility that a fundamental dichotomy in the evolution of SAM development emerged in Devonian vascular plant stock. Pteridosperm cupules and Mesozoic Caytoniales probably had nothing to do with the origin of flowers and the origin of angiosperms.
I propose that modern models of SAM trafficking of mobile cis-acting homeodomain TFs and certain promoters, enhancers, messenger RNAs, and phytohormones may be used to simplify morphological phylogenetic analysis of progymnosperms and seed plants, or to conduct certain cladistically-based experiments.
If this proposal is correct then traditional ideas on the homology of leaf and sporophyll characters, which are gene expression products of TFs downstream of the SAM patterning developmental tool kit, should be reconsidered.
Bisexual cone axes consisting of inner (terminal) Phasmatocycas bridwellii megasporophylls and an outer ring of microsporophylls subtended by a spirally-arranged perianth of tepals and colored andropetals potentially existed in populations of poorly understood Paleozoic seed plants described as gigantopteroids and Vojnovskyales, groups omitted from most phylogenetic analyses.
Flower-like hermaphroditic organs (protoflowers) certainly existed in Vojnovskyales and possibly unrelated gigantopteroid seed plants. Further, no "assembly" (page 816, J. A. Doyle 2008) of perianth parts, microsporophylls, and megasporophylls was needed during early stages of angiosperm evolution prior to the EPE. It is likely that flowers evolved "first" instead of "organs" during the late Paleozoic, which is the reverse of a recent proposal by D. W. Taylor (page 156, 2010).
I hypothesize that insect-mediated natural hybridization among Vojnovskyales and gigantopteroid seed plants might have been a method through which MIKC-type MADS-box genetic novelties were recruited into populations of ancestral angiosperms during the Permo-Carboniferous approximately 300 million years ago (MYA).
Enormous protoflowers known only from fragments and detached megasporophylls were probably modifications of developmentally plastic bisexual cone axes representing divergent clades of several Permian gymnosperms that survived the end-Permian apocalypse.
Carpel, floral, and ovular transcriptional regulation in extant angiosperm model organisms does not preclude derivation of evo-devo models that explain curling, inrolling, and fusion in 260- to 300 million year old ovule-bearing gigantopteroid Phasmatocycas bridwellii leaves to form carpels, ovaries, and pistils.
Paedomorphic heterochrony to include condensation of vojnovskyalean and gigantopteroid protoflowers is the most simple evo-devo process to explain the origin of reproductive organs in Mesozoic crown group angiosperms and extant basal Amborellanae, Austrobaileyanae, Nymphaeanae, and Magnolianae from a putative 160 million year old ghost lineage.
Reproductive traits of certain developmentally plastic Paleozoic seed plants including early Mesozoic flowering plants are ostensibly intertwined with 200 to 300 million year old gene duplications and subsequent molecular evolution of cis-acting floral protein quartets and progenesis essential to meristem, organ, and reproductive module identity.
At the same time that gene duplications led to the evolution of floral quartets in Paleozoic shrub lifeboats, certain phytophagous insect associates underwent a second burst of molecular evolution of Hx storage proteins. Molecular evolution comprising the second burst of Hx diversification led to Coleoptera (bees), Diptera (flies), Hymenoptera (bees and wasps), and certain Lepidoptera (moths).
Moulting in developmentally plastic insect mutualists of Permian seed plant shrub lifeboats was probably affected by phytoecdysone hormones manufactured by the host seed plant. Signaling of respiratory protein genes and transposable elements (TEs) of the insect genome by the plant, and mechanical and secretory activities of insect antagonists leading to signaling of host plant homeotic genes in SAMs, were likely hallmarks of Permo-Carboniferous and Permo-Triassic coevolutionary compartments.
Enveloped and surrounded by an acidified hypoxic desert, shrub lifeboats were venues where reciprocal, simultaneous, and specialized communication between insect antagonist and seed plant host took place at the molecular level possibly by way of baculovirus vectored transmission of TEs. Insect Hxs might have been hypoxia-inducible moulting storage proteins of the developmental tool kit of the larger-bodied insects of Carboniferous and Permian time. Insect bodies became smaller in plant-dwelling populations that survived the EPE and TrCCE.
Innovative traits of Permo-Triassic seed plants possibly included double fertilization, encapsulation of female gametophytes inside hardened ovules, folding of megasporophylls into carpels, and development of staminodes and stamens from laminar microsporophylls, but critical fossil evidence is needed. Populations of Permo-Triassic seed plants were ostensibly subjected to the vagaries of genetic drift, gene flow, meiotic drive, mutation, and natural selection of phenotypes resulting from developmental recombination, genetic accommodation, and gene duplications potentially leading to evolutionary change and possible angiospermization.
Permo-Triassic shrubs and trees ostensibly developed anatomical and biochemical defenses against both invertebrate and vertebrate herbivores possibly ameliorating mechanical damage to SAMs and accessory fertile meristems. Dependence of insect colonies on seed plant shrubs and trees might have been reinforced by paleoclimatic changes triggered by global catastrophe.
Selection pressures in populations of Carboniferous and Permo-Triassic seed plant populations were probably much greater than believed. An herbaceous origin of flowering plants cannot be explained by mutualism and coevolution of insects and seed-bearing shrub hosts alone. A Late Jurassic aquatic origin for flowering plants is incongruent with likely deleterious effects of sulfuric acid poisoning of lakes, shorelines, and wetlands, caused by basalt outpouring from the Central Atlantic Magmatic Province (CAMP), which is associated with the TrCCE.
Assuming coevolution of phytophagous coleopterans with angiosperms various proposals on rapid diversification of flowering plants during the Albian Age of the Gallic Epoch of the early Cretaceous Period are inconsistent with molecular based phylogenies of Coleoptera that suggest a Triassic origin of certain non-chrysomelid beetle lineages. Concomitantly, existence of a 160 million-year-old angiosperm ghost lineage is likely. Therefore, extant basal flowering plants such as Amborella trichopoda are probably highly derived species, essentially semaphoronts at the ends of very long branches.
Further, the origin of flowering plants and their coevolving insect hosts is potentially traceable to hybridization between unrelated Vojnovskyales and gigantopteroid seed plants about 300 MYA. When supported by future phylogenetic analyses a monophyletic origin of flowering plants becomes less likely.
When taking into account the cyclic nature of angiospermization, flowering plants as traditionally defined, might be an amalgam of paraphyletic evolutionary lines traceable to surviving geographically disparate early Triassic remnants of already divergent gigantopteroid Permian seed plant lineages.
[ Discussion of a Coevolutionary Hypothesis ]
I now consider and discuss evidence drawn from studies of insect- and plant anatomy and development, ecology, evolution, physiology, genetics, and phylogenetics, which is critical in understanding the origin of flowering plants.
While composing the three essays on the origin and evolution of flowering plants, I integrated data from many scientific disciplines, which was key to possibly solving the riddle of the origin of angiosperms and certain coevolving Holometabola from disparate research perspectives. This challenging and daunting approach was facilitated by ready access to several world class research libraries at the University of California, Berkeley.
Anatomic and Developmental Considerations:
The following chapter of the essay considers evidence drawn from the research perspectives of insect- and plant anatomy and development.
The image to the right is the passive insect trapping flowering plant, Darlingtonia californica (Sarraceniaceae, Ericales, Asteranae), photographed by the author at a seep on Eight Dollar Mountain located in the Klamath Region of western North America.
Studies of evolving allometries and body plans might help us understand a possible coevolutionary origin of angiosperms and certain clades of holometabolous phytophagous insect antagonists.
Evolutionary development of arthropod- and plant organs and molecular tool kits is "highly dynamic in evolutionary time" involving the evolution of cis-acting promoters (page 83, Baum 1998).
The evo-devo research perspective followed throughout the essays posted on the Gigantopteroid Dot Org Web Site may be help us to decipher more than 400 million years of insect and seed plant evolution and the enigmatic origins of flowering plants and Holometabola.
"The idea is that plants have a plastic and modular developmental system such that simple changes in regulatory genes need not lead to inviability but can generate novel, potentially favored phenotypes."
The preceding quotation is from page 83 of D. A. Baum (1998), The evolution of plant development. Current Opinion in Plant Biology 1(1): 79-86.
According to a reviews by Meyerowitz (2002) and Becker and Theißen (Figure 1, page 468, 2003), the developmental systems of animals, fungi, and plants were derived independently over the course of more than a billion years of organic evolution. Homeodomain proteins are critical to genetic regulation of many developmental systems in animals, fungi, and plants.
"Ontogeny in land plants can be viewed as a complex, partly hierarchical, series of developmental processes, which together with their underlying genetic controls, provide the raw material for morphological innovation. Ontogeny is thus the creative force behind botanical diversification, and small modifications at the genetic level may have a disproportionate effect on plant form as their consequences cascade and multiply through development. Plant evolution occurs as variation in genetic and epigenetic developmental processes is winnowed by ecology..."
The preceding quotation is from page 161 of P. R. Crane and P. Kenrick (1997), Diverted development of reproductive organs: a source of morphological innovation in land plants, Plant Systematics and Evolution 206: 161-174.
Logically, understanding the structure of cis-regulatory elements (CREs), cis-regulatory modules (CRMs), specific transcription factors (TFs), modular cone and floral homeotic protein quartets, developmental regulatory networks, communication conduits, and signaling systems of extant phytophagous arthropod- and seed plant- tool kits might allow us to better interpret morphologic transformational series in fossils.
This line of reasoning is necessary to decipher character homologies and to solve the mystery of angiosperm origins within a coevolutionary and phylogenetic context. Homology assessments (see section on character analysis and homology assessment) should take into account comparisons between animal and plant genetic, developmental, and transcriptional regulatory systems at the highest levels (Arthur 2002, Meyerowitz 2002, Niklas 2006).
Students of angiosperm evo-devo and character homologies should begin with Volume 107, Number 9 of the Annals of Botany (2011), which is a Special Issue on Evolution and Development.
Body plans and allometric scaling. From the research perspectives of insect- and floral biology, and paleoentomology and floral origins, allometric scaling data might be applied to understanding potentially interesting aspects of escape and radiation at the interface between development and ecology (Enquist et al. 2007).
Sean B. Carroll (1995), Rogers et al. (1997), Gellon and McGinnis (1998), and S. B. Carroll et al. (2005) review molecular evolution of homeotic genes and homeodomain TFs needed to understand regulation of body ground plan development in phytophagous arthropod antagonists. Molecular control over arthropod growth varies among the major clades of insects (Grimaldi and Engel 2005).
A key paper on the control of insect body size (Nijhout 2003) outlines the molecular mechanisms (involving cis-acting TFs and hormones) and environmental controls (nutrition and temperature) behind growth and cell division in hemimetabolous and holometabolous insects.
Several neurosecretory hormones play an important part in mechanisms that regulate cell division and growth including insulin-like peptides (Drosophila insulin-like proteins [DILPs] and bombyxins), chitenase-derived imaginal disk factor proteins, the steroid hormone ecdysone, local autocrine and paracrine TFs, and brain neurosecretory prothoracicotropic hormone (PTTH) (Nijhout 2003).
Cessation of growth in holometabolous insects leading to a new moulting cycle is triggered by PTTH that initiates the ecdysone growth regulatory cascade. Prothoracicotropic hormone and/or ecdysone secretion in Holometabola is negatively controlled by juvenile hormone (JH) (Truman and Riddiford 2002). Once JH circulating in the hemolymph is destroyed by juvenile hormone esterases, then PTTH secretion resumes under circadian (22-24 hour) photoperiodic control (Nijhout 2003). On the other hand, certain hemimetabolous bugs (Hemiptera) possess abdominal stretch receptors that activate secretion of PTTH (Nijhout 2003).
Arthropod body allometry is intertwined with development of larval and imaginal disc tissues (Stern and Emlen 1999, Shingleton et al. 2008) and assembly of chitin and cuticle proteins into the exoskeleton (Charles 2010, Moussian 2010). Studies on Drosophila melanogaster eggs, specifically, artificial size-selection experimentation, affects larval patterning and body allometry (Miles et al. 2011).
Do host seed plant brassinolides and other hormones affect insect antagonist egg size, potentially controlling larval tissue patterning?
If the answer to the preceding question is "yes," how does this evo-devo mechanism affect arthropod antagonist body allometries and population ecology?
The evo-devo of insect caste polyphenism is reviewed by Emlen and Nijhout (2000).
A review of neotenous development in termites is available (Korb and Hartfelder 2008). Isoptera (termites) are hemimetabolous insects (Grimaldi and Engel 2005).
Insect developmental tool kit. The insect developmental tool kit is comprised of certain homeotic selector genes (including Hox genes), zygotic (gap- maternal-, and pair-rule-) genes, field-specific selector genes, compartment selector genes, cell-type-specific selector genes, and segment polarity genes; and the TFs they encode (Rosenberg et al. 2009). In addition, the insect developmental tool kit is comprised of controlling factors behind the cessation of insect growth including bioactive PTTH, JH, juvenile hormone esterases, and ecdysone steroids (Truman and Riddiford 2002, Nijhout 2003, S. B. Carroll et al. 2005).
Thummel and Chory (2002) point to a possible coevolutionary connection between the 20E-ecdysone/cytochrome P450 biosynthetic machinery of insect antagonists and seed plant hosts. Structurally similar to bioactive plant brassinosteroids, 20E-ecdysone induces a cascade of TF biosynthesis important in the regulation of insect development (Truman and Riddiford 2002, De Loof 2008).
Juvenile hormone biosynthesized in the corpora allata of the insect brain is a sesquiterpenoid epoxide methyl ester (Hartfelder 2000). Interestingly, many naturally-occurring plant sesquiterpene esters and lactones are bioactive and exhibit insecticidal properties. Juvenile hormone and its homologs are integral in vitellogenesis (Hartfelder 2000), regulation of moult cycles (Truman and Riddiford 2002), and caste development and behavior in social Hymenoptera (Guidugli et al. 2005).
Were bioactive brassinolides and sesquiterpenes manufactured by Paleozoic seed plants used as chemical warfare agents to affect growth, development, and behaviour of herbivorous insects?
Another important reason for students of insect-seed plant coevolution to be conversant with arthropod tool kits is that evo-devo of the anterior (head) segment is linked to feeding, pollinating, and sensory perception. Labandeira (2010) states:
"The most obvious feature of an insect that reveals consumption of nectar or pollen, or the existence of a pollinator association, is the mouthparts and head structure ..."
The aforementioned passage is from page 471 of C. C. Labandeira (2010), The pollination of mid-Mesozoic seed plants and the early history of long-proboscid insects, Annals of the Missouri Botanical Garden 97(4): 469-513.
Several developmental gene families, TFs, and enzymes involved in hormone signaling cascades are known in invertebrates based in part, on experimental studies of the Drosophila model arthropod (S. B. Carroll et al. 2005, Hittinger and S. B. Carroll 2008, Rosenberg et al. 2009).
Key elements of the Drosophila genetic tool kit are:
Achaete-Scute [AS-C] complex (four-gene complexes encoding TFs critical for bristle patterning and neural cell development)
apterous [ap] (compartment-selector gene encoding Apterous protein needed for subdivision of imaginal discs into dorsal and ventral compartments)
bicoid [bcd] (maternal effect gene necessary for anterior embryo development)
caudal and nanos (maternal effect genes needed for posterior development of the embryo)
decapentaplegic [dpp], short-gastrulation [sog], snail [sna], twist [twi], and zerknüllt [zen] (maternal effect genes involved in subdivision of cells in the dorsiventral axis of larvae)
distal-less [dll] (field-specific selector gene necessary for limb [antennae, genitalia, mouthparts, legs] development)
engraled [en] (compartment-selector gene encoding the homeodomain protein Engraled, which determine the posterior identity of embryos and wings).
even-skipped, fushi-tarazu [ftz] (encodes Ftz protein [Merebet and Hudry 2011]), hairy, and paired (pair-rule genes which act in the periodicity of double segments)
eyeless [ey] (encodes Ey protein, a DNA TF which regulates other field-specific genes)
giant, huckebein, hunchback, knirps, Krüppel, and tailless (gap genes that regulate larval segmentation)
hedgehog and wingless (segment polarity genes which organize the orientation and patterns of cells within the anteroposterior axis of each larval segment)
Hox genes (clusters of eight linked homeotic selector genes absolutely required for embryo, larval, and adult development)
Runx genes (clusters of homeotic selector genes that regulate development)
scalloped [sd] and vestigial [vg] (field-specific selector genes required for haltere and wing development)
tinman (field-specific selector gene that controls development of the insect heart)
Evolution of the Hox complex. Molecular diversification of the Hox gene complex over the course of 600 million years of metazoan evolution is analogous to the 400 million year old molecular evolution of MIKC-type MADS-box genes and related cis-acting TFs of land plants (Theißen et al. 2000, Theißen 2001, and Theißen and Becker 2004).
Evolution of the Hox complex probably involved small gene duplications, WGDs, divergence of homeodomains, disintegration of the Hox cluster at breakpoints, and rapid changes in the nucleotide sequence of homeodomains (S. B. Carroll et al. 2005, Negre et al. 2005). Further, changes in the arthropod homeodomain and evolution of new protein motifs led to new Hox developmental tool kit functions in certain insect lineages (S. B. Carroll et al. 2005).
The homeotic selector genes (S. B. Carroll et al. 2005, among others) of the Drosophila Hox complex are:
abdominal A [abd-A] (selects the developmental fate of the front-middle parts of the abdomen)
Abdominal B [Abd-B] (selects the developmental fate of the rear-middle part of the abdomen)
antennapedia [ANTb] (affects development of the middle legs and middle part of the thorax)
deformed [Dfd] (affects development of the upper part of the head)
labial [lab] (selects the developmental fate of the labium of the head)
proboscipedia [pb] (affects development of the lower half of the head)
sex combs reduced [Scr] (selects the developmental fate of the most posterior region of the head, labial segment, front legs, prothorax, and front and anterior portions of the thorax) (Rogers et al. 1997)
ultrabithorax [Ubx] (selects the developmental fate of the rear legs and thorax and front of the abdomen; regulator of dipteran haltere morphogenesis [Pavlopoulos and Akam 2011])
Ancestral arthropods possess two additional homeotic selector genes of the Hox cluster that together comprise the HOM-C, ten gene complex (see discussion in Negre et al. 2005). These additional genes are:
fushi-tarazu [ftz] (encodes Ftz protein [Merebet and Hudry 2011]), and
Genomic analyses suggest that derived winged insects lost functional copies of ftz and Hox3 through disintegration of the HOM-C complex (Negre et al. 2005). Duplication of the Hox3 gene of ancestral Cyclorrhaphan flies gave rise to two maternal effect genes, bcd and zen (Stauber et al. 2002). Based upon this study it is important to include Hox3 as part of the ancestral diverging insect developmental tool kit.
Early divergent arthropod developmental tool kit. Possible candidates for the early divergent insect developmental tool kit might include certain homeotic selector genes of the Hox complex such as homologs and paralogs of abd-A, Abd-B, Hox3, pb, Scr (Rogers et al. 1997), Ubx (Pavlopoulos and Akam 2011), and the field-specific selector gene necessary for limb development in Drosophila (Diptera) known as dll (S. B. Carroll et al. 2005).
The importance of Ubx protein encoded by the Ubx gene in the early divergent insect developmental tool kit cannot be neglected in the present analysis since significant changes in the carboxy-terminal (C-terminal) region (Galant and Carroll 2002) and serine/threonine phosphorylation sites (Ronshaugen et al. 2002) are probably behind many insect body plan novelties seen in the paleontologic record of the past 400 million years of arthropod and crustacean evolution (Pavlopoulos and Averof 2002, Pavlopoulos and Akam 2011).
Fushi-tarazu protein encoded by the ftz gene, intracellular tertiary enzyme structure folding environments, and the apparent flexibility of Ftz and other Hox proteins in the evolution of arthropods, are discussed in a recent review by Merebet and Hudry (2011). Another Hox protein Abd-B, when combined with the Dsx enzyme, represses expression of the wg gene in fruit flies (W. Wang et al. 2011).
These studies, among others underway or already published by Sean Carroll and colleagues, underscore the importance of Hox proteins in evolution of the arthropod tool kit.
I also add hexamerin moulting storage proteins which are related to hemocyanin respiratory enzymes (Burmester et al. 1998, Burmester 2001, Burmester et al. 2006, Burmester and Hankein 2007), JH esterases, vitellogenin genes and yolk proteins (Isoe and Hagedorn 2007), pheromone chemoreceptors (Robertson and Wanner 2006), and certain nuclear receptor proteins (Bonneton et al. 2003, Bonneton et al. 2008) including ultraspiracle, and ecdysone inducible TFs to the list of molecular developmental tools among early diverging arthropod lineages.
Respiratory enzymes, specifically hemocyanins and hemoglobins, and moulting storage proteins (hexamerins) are key elements of the early divergent arthropod developmental tool kit that tie-in with the evolution of insect legs and wings from bilaterian gills. Ancient insect wings probably functioned as respiratory organs. Wings, halteres, arachnid spinnerets, and insect legs are all organs that develop from limb fields of cells where Ubx expression is prevalent (S. B. Carroll et al. 2005).
Further, hexamerins are also implicated as silencers of JH signaling in neotenous castes of hemimetabolous termites (X. Zhou et al. 2006, X. Zhou et al. 2007) and caste polyphenism in holometabolous wasps (J. H. Hunt et al. 2007).
Insect developmental tool kits and a Paleozoic origin of the Holometabola. Understanding the nature and timing of early molecular diversification of homeotic selector genes, developmental proteins, nuclear receptor proteins, and cis-acting TFs of both invertebrate antagonists and vascular plant hosts might be a critical first step in understanding the Paleozoic origin of holometabolous insects and their putative coevolution with the earliest angiosperms.
The place and time to begin a molecular phylogenetic analysis is the late Frasnian-Famennian Age hypoxic icehouse that extended into the Tornaisian Age of the Carboniferous Period.
Molecular model systems used as tools in beetle genomic research and phylogenetic studies include proteins central to development (JH esterases), diapause proteins, heat shock proteins, ultraspiracle (an ecdysone nuclear receptor protein), cuticle proteins, hexamerins, genes encoding vitellogenin, and apolipophorins, among others (see review by Gómez-Zurita and Galián 2005).
Several insect systematists studying beetle (Coleoptera) evolution are employing some genes and proteins of the insect development tool kit in their phylogenetic analyses (Gómez-Zurita and Galián 2005). Gómez-Zurita and Galián (2005) discuss the utility of molecular phylogenetic characters appearing in the entomological literature in a review paper, which is organized along the lines of Floyd and Bowman (2007) for land plants (see section below).
Land plant developmental tool kit. Understanding the land plant developmental tool kit and gene regulation from a deep time research perspective ties-in with models of cone and floral organization, cell geometry and regulation of growth from SAMs, paleobiology of homeodomain TF trafficking, phyllotaxis, leaf development, and morphogenesis of fertile organs.
Evolutionary development of early land plants was probably intertwined with regulatory changes in polycomb repressive 2 gene complexes and other stem cell factors as evidenced from studies of the extant model bryophyte Physcomitrella (Okano et al. 2009).
Floyd and Bowman (2007) are the first workers to estimate the developmental tool kit of early land plants including Paleozoic seed plant homeotic genes potentially important in the later evolution and diversification of angiosperms and origin of the first flowers from bisexual cone axes sensu Melzer et al. (2010).
The work by Floyd and Bowman (2007) focuses on a molecular phylogenetic analysis of Chara (a green alga), Physcomitrella (a moss), Selaginella (a lycophyte), Arabidopsis (angiosperm malvid), Antirrhinum (angiosperm asterid), Oryza (angiosperm monocot), Populus (angiosperm fabid), Picea (gymnosperm conifer), and Pinus (among others).
Is unique architecture and branch patterning in progymnosperms traceable to differentiation and growth of cells from meristematic tissue fields other than axillary buds?
Were certain seed plant morphologies exploited by respiring insect eggs, larvae, instars, and adults?
Can we identify plant adaptations that helped shield insect eggs and instars from hypoxia, temperature extremes, and ultraviolet (UV) radiation in paleoenvironments?
Are there TFs in the land plant tool kit that act as oxygen sensors?
What are the kinds of miniature seed-plant fitness landscapes exploited by insects?
Did the architecture of some Paleozoic seed plants provide critical, oxygenated habitat for phytophagous insect and tetrapod associates?
Was the development and form of pollen and seed cones (strobili) affected by wind currents in Triassic fitness landscapes?
Are some seed plant morphologies, such as ovule placement (adaxial or abaxial) on the surfaces of large, leathery leaves a consequence of the mechanostimulatory effects of grazing tetrapods on expanding SAMs of seed plant monopodia?
A review of plant homeobox genes and homeodomain proteins offers additional insight into critical elements of the land plant developmental tool kit (Mukherjee et al. 2009).
Many developmental gene families and TFs have been identified in land plants (Glover 2007, Langdale 2008, Mukherjee et al. 2009, Specht and Bartlett 2009, Licausi 2011, among others). These genes, and their TFs, together with phytohormone biosynthetic and regulatory factors, homeotic selector genes, and certain microRNAs, comprise the developmental tool kit of land plants including lignophytes. The main developmental and regulatory gene tools of focus are:
APETALA 2 (AP2) (see euAP2, below)
ARF (auxin response factor gene family)
ARP (KNOX regulating genes ASYMMETRIC LEAVES1, ROUGHSHEATH2, PHANTASTICA [ARP])
AS2 (LOB family genes that function in lateral organ formation in SAMs)
Class III HD-Zip (a family of SAM maintenance genes and upstream controllers of leaf development)
Class I KNOX (essential genes to meristem maintenance and SAM formation affected by auxins and gibberellins)
Class I TCP (leaf sculpting genes and cell division controllers)
Class II TCP (genes that determine leaf shape, floral symmetry, and flower patterns)
CUC (important genes in embryo and flower development)
ERF ethylene responsive factor genes encode ERF proteins that potentially reprogram metabolic pathways and morphologies affected by hypoxia (low pO2) (Licausi 2011)
euANT (regulating genes involved in lateral organ development)
euAP2 (SAM maintenance and timing of flowering including APETALA 1 [AP1]and AP2)
GRAS (a family of genes necessary for radial patterning of roots and shoots and axillary meristem development [HAIRY MERISTEM, LATERAL SUPRESSOR, SCARECROW], and in mediation of gibberellic acid (GA) responses during flowering and development of trichomes [DELLA genes])
KANADI (GARP family transcriptional regulators antagonistic to Class III HD-Zip genes important to leaf and integument development)
LEAFY [LFY] and FLORICAULA [FLO] (controllers of the downstream expression of several genes including MIKC-type MADS-box genes)
MIKC-type MADS-box genes (developmental genes that control organogenesis in seed plants) encode MIKC-type MADS-box proteins that regulate cone and floral development, among other functions
MYB genes encode MYB homeodomain proteins necessary for lignin biosynthesis, secondary wall thickening, and petal morphogenesis
NAC genes encode NAC TFs necessary for secondary cell wall biosynthesis (Zhong et al. 2010)
PIN (auxin related genes needed in land plant architecture)
TIR (auxin related genes)
UFO (stem cell maintenance gene)
WOX Class genes including WUSCHEL [WUS] (essential genes for stem cell maintenance in organizing centers of SAMs) that encode WOX and WUS homeodomain proteins (Nardmann et al. 2009)
YABBY (seed plant specific family of genes that promote differentiation of abaxial tissues and leaf growth)
Based on a molecular phylogenetic analysis by Floyd and Bowman (2007) the ancestral land plant tool kit genes of our focus to deduce the timing of the origin of the first flower should be AP2, ARF, Class I and II TCP, Class III HD-Zip, GRAS, KNOX, LFY, MIKC-type MADS-box, PIN, TIR, and YABBY genes. Genes that encode the other conserved homeodomain proteins (MYB, WOX, WUS) might also be important to consider in floral tool kit studies.
All available evidence suggests deep conservation in the xylem transcriptome of vascular plants (X. Li et al. 2010), which is consistent with Floyd and Bowman's findings (2007).
Cell geometry of shoot apical meristems (SAMs). Much progress has been made on understanding developmental biochemistry and hormonal controls behind the anatomy and cell geometry of SAMs and accessory fertile meristems of a number of diverse flowering plants and gymnosperms (Glover 2007, Busov et al. 2008). The best studied example is the diminutive mouse-ear cress (Arabidopsis thaliana [Brassicaceae, Brassicales, Rosanae]), an extant, highly derived annual species of malvid mustards (Kwiatkowska 2006).
Floral meristem identity and integrator genes of massive SAMs of the oil palm (Elaeis guineensis [Arecaceae, Arecales, Lilianae]) have also been studied (Adam et al. 2007).
Biomechanics is a fertile area of research in botany (Niklas 1992, Niklas 2000, Rowe and Speck 2005, Niklas et al. 2006, Read and Stokes 2006, Masselter et al. 2009). Basic to biomechanics are the biochemical pathways in plant cells (e.g. lignin biosynthesis) that result in secondary thickening of vascular tissues of the procambium and secondary cambium. Secondary cell wall biosynthesis involves MYB homeodomain proteins and NAC TFs (Zhong et al. 2010).
Can the experiments drawn from principles of geometry and engineering answer some of the basic questions posed by Coen et al. (2004)?
"Whatever the detailed mechanism for aligning cell axes with gradients [of morphogen flow], these considerations indicate that morphogens play two distinct roles in the generation of shape. The first is a regionalizing role, involved in elaborating differences between regions [of meristems], such as levels of gene activity, growth rate, or anisotropy. The second is a polarizing role involved in specifying directions of cell axes. Morphogens with a regionalizing role often act by influencing transcription factors, which in turn can affect parameters such as growth rate and anisotropy. Cells respond only to the overall concentration of these morphogens, not to the direction of their gradient. Morphogens with a polarizing role, influence the orientation of cell axes and can determine the principal directions of growth. Cells respond to the highest slope of the morphogen gradient or to the direction of morphogen flow. Such responses [of plant cells] are unlikely to be mediated by transcription factors, as the directional information would be lost through conversion to a gene expression level."
The preceding quote is from E. Coen, A.-G. Rolland-Lagan, M. Mathews, A. Bangham, and P. Prusinkiewicz (2004), The genetics of geometry, Proceedings of the National Academy of Sciences 101(14): 4728-4735. The phrases in brackets  are mine.
Certain anatomical and enzymatic tools of the land plant hormone signaling machinery align cell axes and control morphogen flow. Some of these affect SAM development and phyllotaxis in both morphospace and time resulting in evolutionary change.
"Evolutionary changes in developmental tissue geometry, in our terminology, are the result of heterotopy."
The preceding sentence is quoted from M. L. Zelditch and W. L. Fink (1996), Heterochrony and heterotopy: stability and innovation in the evolution of form. Paleobiology 22(2): 241-254.
Shoot apical meristem (SAM) organization. The SAM, stem cell geometries, and fertile SAM phyllotaxis figure prominently in several evo-devo hypotheses on the origin of cones and flowers (Theißen Saedler 2001, Becker and Theißen 2003, Baum and Hileman 2006, Theißen and Melzer 2007, Melzer et al. 2010).
Reviews of SAM development in model flowering plants are available (Bäurle and Laux 2003, Aida and Tasaka 2006 [two papers], Carraro et al. 2006, Barton 2010), which tie together aspects of tool kit genes and the TFs they encode (previous sections) with phyllotaxis (next section).
The SAM of angiosperms and certain other seed plants is layered consisting of the tunica (surface layer) and tissues within (corpus). This character has been employed in many seed plant phylogenetic analyses.
Development of the model malvid Arabidopsis thaliana SAM operates three ways (Bäurle and Laux 2003):
local maintenance of stem cells
amplification of stem cell daughters
initiation of organ primordia
The essential gene WUS and the homeodomain TF this gene encodes operates in the organizing center of the eudicot SAM (Mayer et al. 1998). At the periphery of the central zone, partitioned pre-founder cells and founder cells determine how lateral organs grow and the position of reproductive modules.
Partitioning of cells of the central SAM in model malvids leads to discernable boundary layers: the meristem-organ primordium (M-O) boundary and a region between developing organs known as the O-O boundary (Aida and Tasaka 2006).
Morphogenesis at the boundary cells between developing organ primordia and the SAM daughter cells is regulated by several classes of genes. Further, plasmodesmata of the boundary cells of the SAM potentially regulate flow (traffic) of small proteins and other TFs (see review by Aida and Tasaka 2006). Physiology of homeodomain TF trafficking is discussed in a later section.
At every step of the way cells of the developing and expanding SAM exhibit discreet gene expression patterns. Further, early biochemical events in regulation of transcription, and post-transcriptional modification of mRNA, translation, and post-translational protein folding, potentially lead to canalized morphologies of lateral organs of the seed plant shoot (Carraro et al. 2006, Johnson and Lenhard 2011, among others).
Shoot apical meristem maintenance and patterning genes and TFs of the land plant developmental tool kit including WUS (Vásquez-Lobo et al. 2007, Nardmann et al. 2009) may affect downstream phyllotactic patterns.
Did early WGDs early on in the evolution of vascular plants and progymnosperms affect the expression of WUS genes and their TFs resulting in fundamental changes in the way SAMs were organized in diverging seed plant lineages?
Phyllotaxis. Phyllotactic patterns of extant flowering plants are of ongoing interest to paleobotanists and plant systematics who seek to understand the origin of the angiosperm flower from an evo-devo research perspective (J. A. Doyle and Endress 2000, Endress and J. A. Doyle 2007). Floral phyllotaxis is distinct from vegetative phyllotaxis.
Extant basal angiosperms including the Magnoliales exhibit both spiral and whorled floral phyllotactic patterns (J. A. Doyle and Endress 2000, Ronse De Craene et al. 2003, Staedler et al. 2007). When floral phyllotactic characters in basal angiosperms are subjected to phylogenetic analyses, reversals from spiral to whorled and whorled to spiral become apparent (Ronse De Craene et al. 2003, Endress and J. A. Doyle 2007).
Phyllotaxis is reviewed by Kuhlemeier (2007). The most recent Arabidopsis model suggests that in addition to PIN proteins, the family of AUX1 LAX auxin influx carrier enzymes stabilize spiral phyllotaxis (Bainbridge et al. 2008).
An earlier model of developmental phyllotaxis and initiation of procambial strands leading to vasculature in the SAMs of extant flowering plants implicates auxins, ATPIN1, mRNA transcripts such as ATHB8-GUS, and other auxin related developmental genes (R. S. Smith et al. 2006). Development of phyllotactic geometric patterns and vasculature in SAMs of some modern flowering plant species may be traced to a common genetic and physiologic mechanism (Dengler 2006).
Lignification of conducting cells may occur in concert with secondary growth. Biosynthesis of lignin, a class of phenylpropane polymers, involves activation of key developmental switches, a cytochrome P450 (CYP)-dependent monooxygenase, CYP hydroxylase, and MYB TFs (Zhao et al. 2010). Syringyl subunits of lignin polymers may be angiosperm specific (Zhao et al. 2010).
Genomic studies of conifers point to deep conservation of the xylem transcriptome (X. Li et al. 2010).
A recent review of vascular cambia and secondary growth in lignophytes written from an evo-devo research perspective, is available (Rachel Spicer and A. Groover 2010).
Were the possibly conserved mechanisms of SAM differentiation that underlie geometric patterning in sporophytes operating the same way in long extinct progymnosperm and seed plant species?
According to Floyd and Bowman (2007) the answer to the second question is "yes." Orthologues of PIN and ARF, auxin related genes and TFs needed in land plant architecture and phyllotaxis, were part of the ancestral land plant developmental tool kit according to Floyd and Bowman (2007).
Floyd and Bowman (2007) identified several "PIN-like" genes from expressed sequence tag (EST) studies of moss gametophytes belonging to Physcomitrella. Five PIN genes were identified in sporophytes of extant Selaginella, and eight additional PIN genes were found in Arabidopsis (Floyd and Bowman 2007).
"If the hypothesis that increasing complexity of auxin metabolism, transport, and perception was related to the increased sporophytic complexity accompanying land plant evolution, then we might expect these particular gene families to be less complex in the moss and lycophyte lineages than in angiosperms, as indeed appears to be the case."
The preceding quote is from page 22 of Sandra K. Floyd and John L. Bowman (2007), The ancestral developmental tool kit of land plants, International Journal of Plant Sciences 168(1): 1-35.
Did auxin exist in Paleozoic vascular plants? Yes, as evidenced by paleobotanical data (Rothwell and Lev-Yadun 2005, Rothwell et al. 2008).
Macromolecular secretions (microRNAs, bioactive peptides, and other small sized molecules) when applied to the surfaces of SAMs by chewing, crawling, ovipositing, piercing, and sucking resident, phytophagous insects, could potentially signal the host plant genome and affect phyllotaxis and other developmentally plastic traits but experimental studies are needed to support this hypothesis.
Leaf development. Evolutionary development of leaves is a critical body of evidence necessary to decipher paleophysiology and the origin of reproductive organs unique to flowering plants: carpels and stamens.
There are three reviews of leaf development (Braybrook and Kuhlemeier 2010, Efroni et al. 2010, and Galtier 2010).
Knowledge of long extinct whole plants and paleopopulations often exists only as detached compressed or permineralized foliar organs traditionally described by paleobotanists as morphotype species. An underappreciated paleontologic problem is that detached perianth parts and vegetative leaves having different venation patterns and cell sizes, thus exhibiting heteroblasty, might have belonged to the same mother plant.
Several books and review papers place leaf development of vascular plants including angiosperms in a paleontologic context including Melville (1969), J. A. Doyle (1978), Melville (1983), (J. A. Doyle and Donoghue 1986, 1987), Stewart and Rothwell (1993), Trivett and Pigg (1996), Sinha (1999), Beerling et al. (2001), Roth-Nebelsick et al. (2001), Boyce and Knoll (2002), Boyce (2005), Feild and Arens (2005), Harrison et al. (2005), J. A. Doyle (2006), Beerling and Fleming (2007), Brodribb et al. (2007), Sanders et al. (2007), Boyce et al. (2009), and Brodribb and McAdam (2011), among many others.
According to a review by Boyce and Knoll (page 74, 2002), " ... the gigantopterids bore the most complex and morphologically distinctive leaves of any plants in the Paleozoic ... "
The Permian gigantopteroid seed plant Delnortea abbottiae possesses leaves with four orders of veins, and certain cells of the leaf hypodermis are sclerotic (pages 1423 and 1424, Fig. 36 on page 1420, Mamay et al. 1988), which is anatomically transitional to the two means of water distribution in leaves described by Brodribb et al. (2007).
The image to the left is a piece of rock slab containing the largest known Delnortea abbottiae leaf compression collected by the author and colleagues (USNM 387473, Fig. 10, page 1413, Mamay et al. 1988). The piece of fossil leaf was photographed by the writer on the day it was pulled from the rock layer in the Lower Permian (Leonardian) Cathedral Mountain Formation, Del Norte Mountains of southwestern North America in 1982.
Was the paleophysiology of gigantopterid and gigantopteroid plants as expressed by the presence of two anatomical innovations to maximize leaf hydraulics somehow linked with the success of these plants in arid Permian paleoenvironments?
"Just as the early steps of marginal meristem evolution were constrained by the scope of developmental possibility, the ultimate range of possible leaf morphologies must have been constrained by available developmental mechanisms."
This quote is from page 78 of C. K. Boyce and A. H. Knoll (2002), Evolution of developmental potential and the multiple independent origins of leaves in Paleozoic vascular plants. Paleobiology 28(1): 70-100.
Land plants possess two leaf hydraulic strategies as expressed by their anatomy and morphology (Brodribb et al. 2007). According to Brodribb et al. (pages 1894 and 1895, 2007), the first hydraulic method is to branch the system of veins to deliver water to the site of transpiration (this is the method employed by many flowering plants). The second method seen in some members of the gymnosperm clade is to modify hydraulics by lignifying certain cells of the leaf mesophyll thus channeling water to the stomates.
Can these same leaf traits be found in later Mesozoic seed plants? Yes, according to work by Taylor Feild and coworkers (see later chapter on Physiologic Considerations).
Ongoing research on the anatomy and cell biology of leaf development from meristematic cells of SAMs, nuclei, and genetic tool kits is incrementally reviewed by Sinha (1999), Roth-Nebelsick et al. (2001), Bharathan et al. (2002), Boyce and Knoll (2002), Engström et al. (2004), Fleming (2005), Piazza et al. (2005), Aida and Tasaka (2006), Brodribb et al. (2007), Champagne et al. (2007), and Hasson et al. (2010).
Regulation leaf development in the malvid flowering plant Arabidopsis thaliana is explained by a model (Bilsborough et al. 2011).
Development of leaves depends on the activity of Class III HD-ZIP genes (Floyd and Bowman 2007), and a KNOX/ARP genetically based, modular switch mechanism (Beerling and Fleming 2007). At least two and probably several land plant evo-devo programs existed in deep time. Several classes of homeotic genes, homeodomain proteins, and other TFs are probably involved.
Whether the KNOX genetic switch is on or off depends on the activity of ARP protein repressors (see review by Piazza et al. 2005), and may lead to the development of different leaf forms e.g. pinnate, palmate, or compound (Beerling and Fleming 2007).
Abaxial-adaxial leaf organ development in angiosperms begins in the SAM. Adaxial faces of leaf primordia are positioned toward the SAM while the abaxial surface is orientated away from the SAM. The genetic basis of cell polarity in Arabidopsis SAMs is reviewed by Engström et al. (2004) and Carraro et al. (2006), among others.
Three classes of TFs establish adaxial-abaxial leaf organ identity in Arabidopsis: Class III HD-Zip (PHA, PHAV, REV), KANADI, and YABBY proteins (Floyd et al. 2006, Nole-Wilson and Krizek 2006). Class III HD-Zip TFs operate on the adaxial side of organ bulges in the SAM. Kanadi and Yabby proteins are active in the abaxial domain (Carraro et al. 2006, among others).
James A. Doyle discusses YABBY within the context of ovule tissue layers and attachment point (abaxial or adaxial) to carpels and leaves in Amborella, a basalmost angiosperm (J. A. Doyle 2006).
AINTEGUMENTA gene expression in certain extant flowering plants determines which cells of the SAM "leave the meristem to form lateral organs" (page 983, Nole-Wilson and Krizek 2006). Further, ANT and AP2 are TFs of focus in phylogenetic analyses of seed plants (Floyd and Bowman 2007) and the origin of angiosperms (S. Kim et al. 2006, among others).
Fertile leaves of seed plants are termed sporophylls. The two kinds of sporophylls potentially derived from the ancient land plant developmental tool kit of SAMs are: megasporophylls (ovule-bearing leaves) and microsporophylls (microsporangium bearing leaves).
Sporophylls and their fertile regions may be viewed as kinds of reproductive modules (see next section). Based on studies of MIKC-type MADS-box genes (Zahn et al. 2005) and MIKC-type MADS-box B protein heterodimers (Hernández-Hernández et al. 2007), a WGD occurring around the time of the angiosperm-gymnosperm split roughly 300 MYA, was a critical macroevolutionary step in the origin of the first flowers from bisexual cone axes (Melzer et al. 2010, among others).
Reproductive modules. Modular development as it pertains to seed plant reproduction may be viewed at the cellular or organ level. Aggregations of cells (tissue fields and compartments) and whole organs are also potentially modular from an evo-devo research perspective.
Paleontologic evidence of ovule development in bennettitalean seed plants suggests early innovation in the production of these reproductive modules (Rothwell and Stockey 2002).
Cellular and anatomic details of sexual reproduction in extinct seed plant groups are sometimes "accessible" contrary to statements in the literature (page 145, Williams 2009) but require tedious preparation of rare permineralizations (e.g. Nishida et al. 2004, Rothwell et al. 2009).
The image to the right is the permineralized nucellus (the megasporangium wall of a fossilized ovule) of Eoantha zerikhinii (from a gnetalean "pre-flower") from the Baisian Assemblage, early Cretaceous Period, of Transbaikalia in central Asia. The fossilized ovule contains a female gametophyte with a pollen chamber filled with Ephedrites-type pollen (this picture is from an original image provided by Professor Valentin Krassilov, posted here with his permission).
Several key papers and reviews are devoted to the study of reproductive structures in seed plants as an approach to gain a better understanding of evolution of gymnosperms and the origin of flowering plants (Friedman 1992 [two papers], Crepet and Nixon 1996, Crane and Kenrick 1997, Labandeira 2000, Eckardt 2002, Lord and Russell 2002, Friedman et al. 2004, Friedman and Williams 2004, Williams and Friedman 2004, Friedman et al. 2008, Friedman and Ryerson 2009, Williams 2009, among others).
Friedman and Ryerson (2009) in a recent review of megagametogenesis in angiospermous seed plants argue that the female gametophyte of flowering plants consists of a modular quartet of cells.
Curious molecular and developmental similarities of angiosperm reproductive modules with animal germ lines (Dickinson and Grant-Downton 2009) require further study.
Reproductive modules are specific organs, tissue fields, or cells derived from a SAM or cone axis. Evolutionary development and genetics of the female reproductive tract is reviewed by B. C. W. Crawford and Yanofsky (2008). The bulleted list below includes some key references:
archegonia (haploid tissue receptacles in certain gymnosperms that contain the egg and accessory cells)
carpel (an inrolled [conduplicately folded] ovule-bearing leaf) (Scutt et al. 2006, Vialette-Guiraud and Scutt 2009, among others)
central cell (female haploid cell of the embryo sac involved in double fertilization) (Bemer et al. 2008, Berger et al. 2008, R. J. Scott et al. 2008, among others)
eggs or egg nuclei (female haploid cells or nuclei, respectively) (Berger et al. 2008, R. J. Scott et al. 2008)
embryo (an often tiny [usually dormant] diploid daughter plant [complete with a basal cell, suspensor, and growing point] that develops from the fertilized egg, usually housed within a mature ovule or ripened seed) (Tobe et al. 2000, Forbis et al. 2002, Holloway and Friedman 2008, among others)
endosperm (diploid, triploid, or polyploid nutritive cells or nuclei usually housed inside of ovules and embryo sacs) (Baroux et al. 2002, Raghavan 2003, Rudall et al. 2009, Cailleau et al. 2010, among others)
interseminal scale (modified female organs of bennettitaleans possibly used to house toxins needed as defense against potential herbivores)
megasporangia (multicellular sacs that produce megaspore mother cells and megaspores)
megaspore mother cells (female diploid cells where meiosis occurs)
megaspores (female haploid products of meiosis)
megagametophytes (cellular or acellular haploid tissues derived from cell- and/or nuclear divisions in megaspores [termed modular quartets of cells in flowering plants]) (Yadegari and Drews 2004, Tobe et al. 2007, Blanvillain et al. 2008, Friedman et al. 2008, Madrid and Friedman 2008, Friedman and Ryerson 2009, Madrid and Freidman 2009, W.-C. Yang et al. 2010, among others)
microgametophytes (Russell 1991, Rudall and Bateman 2007, Blanvillain et al. 2008, Borg et al. 2009, Zobell et al. 2010, among others)
microsporangia (diploid multicellular sacs that produce diploid microspore mother cells, haploid microspores, and haploid pollen) (Russell 1991, Furness et al. 2002, among others)
microspore mother cells (male diploid meiotic cells) (Russell 1991, Furness et al. 2002, among others)
microspores (male haploid products of meiosis) (Russell 1991, Furness et al. 2002, Nadot et al. 2008, among others)
ovary (an organ of the mother plant consisting of one or more carpels; contains one to several ovules)
ovule (a complex organ of the mother seed plant that contains sterile diploid protective tissues termed integuments [often hardened by lignified cell walls], a vestigial megaspore wall [nucellus], megaspores; and at later stages of development: megagametophytes, other nutritive tissues in some seed plants [endosperm], archegonia [in certain seed plants], and eggs [to include accessory cells and synergids in some seed plants]) (Skinner et al. 2004, Scutt et al. 2006, Colombo et al. 2008, Kelley et al. 2009, Skinner and Gasser 2009, R. H. Brown et al. 2010, Endress 2011, among others)
polar nuclei (haploid nuclei of the embryo sac) (Berger et al. 2008, among others)
pollen grain (an endosporic microgametophyte that consists of a hardened microspore containing haploid male nuclei and/cells [Borg et al. 2009, Lora et al. 2009]; the exine layer of the pollen cell wall contains sporopollenin [Ariizumi and Toriyama 2011, among others])
pollen tube (a living tubular cell derived from the male [micro] gametophyte, which is lined with callose in extant flowering plants) (Russell 1991, Williams 2008, Cai and Cresti 2009, Dresselhaus and Márton 2009, Williams 2009, Michard et al. 2011, among others)
seed (a ripened ovule that contains an embryo, see a review by Linkies et al. 2010, among others)
sperm or sperm nuclei (male haploid cells [sometimes motile] or nuclei, respectively) (Berger et al. 2008)
stamen (a complex, highly modified male branch or grouping of fused male [micro] sporophylls that contains one or more microsporangia [and pollen when ripe]) (Alves-Ferreira et al. 2007, among others)
staminode (a sterile, often leaf-like module derived from the male [micro] sporophyll or stamen) (Walker-Larsen and Harder 2000)
stigma (the pollen receptive surface of a carpel)
style (an organ located midway between the ovary and stigma through which the pollen tube may penetrate) (J. P. Alvarez et al. 2009, among others)
suspensor (an often linear array of diploid cells [often containing endoreduplicated nuclei] of the embryo)
synergids (specialized cells of the embryo sac that interact with the pollen tube during double fertilization) (Sandaklie-Nikolova et al. 2007, among others)
Sporophylls. Fertile leaves (sporophylls) of heterosporous seed plants are of two kinds: 1) megasporophylls (these are leaves that bear ovules later maturing into seeds, a morphological condition termed phyllospermy) and, 2) microsporophylls (microsporangium-bearing, polleniferous leaves). The sporophylls of some Permo-Triassic shrubs were flattened and photosynthetic.
Sporophylls in early diverging populations of Paleozoic seed plants were often clustered together on spur shoots, essentially fertile simple cones and proanthostrobili. Further, prevailing models of cone and floral organization of sporophylls (Theißen Saedler 2001, Becker and Theißen 2003, Baum and Hileman 2006, Theißen and Melzer 2007, Melzer et al. 2010) posit that the MRCA possessed a hermaphroditic (bisexual) strobilus (Specht and Bartlett 2009, Rudall and Bateman 2010).
The diagram below illustrates a Paleozoic megasporophyll and microsporophyll (actual size), which are artistically "detached" from a hypothetical seed plant mother shrub. Certain Paleozoic seed plants e.g. Vojnovskyales might have possessed many sporophylls that were arranged on bisexual spur shoots.
Generalized seed plant reproductive organs (microsporangia, pollen, ovules, and seeds) are shown not to scale. Note the retuse, petal-like tips of these detached foliar organs: a character which may help paleobotanists piece together whole proanthostrobili from fossilized fragments in the bedding plane.
The Carboniferous and Permian Periods were times of seed plant innovations and adaptive radiation including a rich fossil history and considerable paleodiversity in detached seed plant reproductive organs and leaves. However the morphology of whole plants such as Paleozoic gigantopteroid seed plants is unknown or poorly understood (T. N. Taylor et al. 2009).
Did angiosperm carpels evolve from megasporophylls as first suggested by Mamay (1976) in his classic paper on the Paleozoic Origin of Cycads?
David W. Taylor and Kirchner state that the angiosperm carpel (page 116, 1996) is "... one of the defining characteristics of flowering plants," yet neglect to cite Mamay's defining proposal on carpel evolution published 20 years earlier.
Since publication of the book chapter by D. W. Taylor and Kirchner (1996), research advances on the evo-devo of the angiosperm carpel are incrementally reviewed by Friedman et al. (2004), J. A. Doyle (2006), Endress and J. A. Doyle (2009), and Vialette-Guiraud and Scutt (2009), among others.
A starting point for an evaluation of the origin, evolution, and homologies of the angiosperm stamen is a paper by Canright (1952). Incremental reviews are available in Cronquist (1968), Takhtajan (1969), Stebbins (1974), Crepet and Nixon (1996), Endress (1996), and Hufford (1996). Research advances on the evo-devo of stamens and staminodes are summarized by Ronse De Craene and Smets (2001).
Ovules. Certain paleobotanists focus on the origin of bitegmic (having a two-layered integument), anatropous (reflexed) ovules from Caytoniales or other unknown gymnospermous ancestors (page 458, Stewart and Rothwell 1993, J. A. Doyle 2006).
Ovules of flowering plants are composed of the embryo sac (megagametophyte), a nucellus (old megasporangium wall), and sterile integuments. Integuments are generally regarded as modified leaves. Many but not all angiosperms possess two integuments. It is important therefore, to understand the evo-devo genetics of integuments and details of ovule ontogeny (Skinner et al. 2004, Scutt et al. 2006, Skinner and Gasser 2009) as a prerequisite to understanding certain character homologies (Friedman et al. 2004).
Frohlich (2003) offers additional discussion on the origin of ovule integumentation and placement on leaf surfaces from the standpoint of YABBY signaling from SAMs. James A. Doyle discusses YABBY within the context of ovule tissue layers and attachment point (abaxial or adaxial) to carpels and leaves in Amborella, a basalmost angiosperm (J. A. Doyle 2006).
Kelley et al. (2009) conclude that there are similarities between expression and transcriptional regulation of Class III HD-Zip, KANADI, and YABBY genes of integuments and leaves of the malvid Arabidopsis. Based on biochemical studies of ovule polarity determinants, these workers state:
"Although these organs [integuments and leaves] have distinct evolutionary origins, a common set of polarity determinants appears to have been serially utilized in both sets of structures. The differences in the precise roles and interactions of the determinants of each structure may represent differences dating from their origin, or alternatively, differences arising from subsequent structural diversifications."
This quote is from page 1062 of D. K. Kelley, D. J. Skinner, and C. S. Gasser (2009), Roles of polarity determinants in ovule development. The Plant Journal 57(6): 1054-1064.
Seeds. Seeds are ripened ovules that often contain nuclear and cytoplasmic products of fertilization (e.g. zygotes, embryos and nutritive cells, free-nuclei, and/or tissues including endosperm). A review on the evolution of seeds by Linkies et al. (2010) is a potential starting point for discussion.
The treatise by Linkies and company is especially important to questions of angiosperm origins from paraphyletic lineages of the great Upper Paleozoic gymnosperm divergences since the paper discusses the evolution of seeds from evo-devo and paleoecological research perspectives.
Megagametophytes. Despite the importance of the megagametophyte in hypotheses of the origin of angiosperms almost nothing is known of the anatomy of female haploid stages in Paleozoic gymnosperms. Only recently have paleobotanists begun to understand the anatomy and morphology of female gametophytes of Mesozoic seed plants (Stockey and Rothwell 2003, Rothwell et al. 2009). Preserved megagametophytes of unequivocal stem group flowering plants are unknown.
Additional insight has been gained from studies of megagametogenesis in evolutionarily derived extant gymnosperms including Gnetum (Gnetales) (Friedman and Carmichael 1998). Now that molecular systematists converge on the root of phylogeny of extant flowering plants, plant anatomists have turned their research focus to studies on the reproductive anatomy of basal angiosperms including magnoliids.
Anatomical studies of megagametophytes of basal flowering plants have been conducted by Friedman and Williams (2003), Madrid and Friedman (2008), Friedman and Ryerson (2009), and Madrid and Freidman (2009). The angiosperm female gametophyte consists of a basic modular quartet of cells according to Friedman and Ryerson (2009).
In 2006 Friedman described an unusual eight-celled and nine-nucleate female gametophyte in the basal flowering plant Amborella trichopoda (Amborellaceae, Laurales, Magnoliidae), a shrubby species indigenous to New Caledonia in the southwest Pacific. While discussing the peculiar four-celled egg apparatus (consisting of three synergids and one egg cell) of Amborella, in comparison with the common seven-celled, eight-nucleate Polygonum-type female gametophyte of angiosperms, Friedman states:
"Ironically, it is now evident that none of the most ancient lineages of flowering plants produces a seven-celled, eight-nucleate female gametophyte, a stark reminder that much remains to be discovered or correctly circumscribed for the earliest angiosperms."
The preceding quote is from page 339 of W. E. Friedman (2006), Embryological evidence for developmental lability during early angiosperm evolution, Nature 441: 337-340.
Historically the seven-celled, eight-nucleate female gametophyte, also known as the Polygonum-type, was regarded as the plesiomorphic state for flowering plants. Tobe et al. (2000) reported this anatomical type in Amborella. However, in 2006 Friedman discovered a peculiar eight-celled, nine-nucleate Amborella-type female gametophyte in this same group of New Caledonian angiosperms.
Detailed anatomical studies of Austrobaileya (Austrobaileyales) by Tobe et al. (2007), Illicium (Austrobaileyales) by Williams and Friedman (2004), Kadsura (Austrobaileyales) by Friedman et al. (2003), and Nymphaeales (including Nuphar and Hydatellaceae [Hydatella and Trithuria]) (Williams and Friedman 2002, Friedman 2008, Rudall et al. 2008), reveal a four-celled, four-nucleate, Nuphar-type or Schizandra-type female gametophyte.
According to the review by Friedman and Ryerson (2009) the three types of female gametophyte development in basal clades of extant flowering plants are:
Amborella-type (known only from Amborella trichopoda (Amborellaceae)
Nuphar/Schizandra-type (common to all Austrobaileyales and Nymphaeales), and
Polygonum-type ("ancestral" to magnoliids, Ceratophyllaceae, Chloranthaceae, eudicots, monocots)
Further, Friedman and Ryerson propose that a four-celled egg apparatus consisting of an egg cell, two synergids, and a central cell is the most plesiomorphic character state for the angiosperm female gametophyte. Concomitantly, these authors suggest that either a one-module megagametophyte (i.e. in Austrobaileyales and Nymphaeales) or a two-module female gametophyte (i.e. among magnoliids, Ceratophyllaceae, Chloranthaceae, eudicots, monocots) could be the plesiomorphic condition in two different parsimony analyses (Friedman and Ryerson 2009).
Did species of the long extinct stem group of flowering plants possess a many-celled (i.e. more than 16-celled) megagametophyte compartmentalized into two or more modular octets of cells, or some other gametophytic configuration and combination of female modules?
A concerted effort by paleobotanists is needed to unearth, painstakingly prepare, and to describe the anatomy of female gametophytes of Carboniferous and Permo-Triassic ovules and details of attachment to the mother plant.
Pollen-containing male gametophytes. Considerable insight on the questions of the origin, evolution, and radiation of angiosperms has been gained from the recovery and study of fossil pollen (Wing and Boucher 1998, Lupia et al. 1999, J. A. Doyle 2005, Zavada 2007, Zavialova and Gomankov 2009).
Preserved pollen inside fossilized insect guts is a potential source of paleobiological data (Krassilov 1997, Labandeira 2000). Ultrastructural details of fossilized pollen and spores are known from many vascular plants (T. N. Taylor et al. 1996). Further, angiospermous pollen of the perforate-reticulate and/or columellate type is known from Permian, Triassic, and Jurassic rocks (Cornet 1989, Hochuli and Feist-Burkhardt 2004, Zavada 2007).
Evolution and anatomical diversity of seed plant male gametophytes (also termed microgametophytes) is reviewed by Friedman (1993) and T. N. Taylor et al. (2009). A recent review of pollen exine development and genetic regulation of sporopollenin biosynthesis is available (Ariizumi and Toriyama 2011).
Focused studies of the male gametophytes of seed plants have been underway for several years including investigations of Ginkgo (Ginkgoales) (Friedman 1987 [two papers]), Ephedra (Gnetales) (Friedman 1990), and the malvid Arabidopsis (Friedman 1999). Several MIKC* MADS-Box proteins are very important in development of the male gametophyte in the model malvid Arabidopsis (Zobell et al. 2010).
Microgametophytes and sperm are often poorly preserved in the fossil record with the notable exception of Permian glossopterids (Nishida et al. 2003, Nishida et al. 2004). More often than not, the only evidence of male gametophytes in the fossil record consists of empty permineralized sporopollenin casings termed palynomorphs (T. N. Taylor et al. 2009).
The World Pollen Database is an important online resource.
The biology and diversity of pollen modules and pollination syndromes as this relates to the origin of angiosperms is discussed by several authors including Hughes (1976), J. Müller (1984), Hotton (1991), Cornet and Habib (1992), T. N. Taylor et al. (1996), Krassilov (1997), Labandeira (2000), Ramanujam (2004), J. A. Doyle (2005), Zavada (2007), Friedman and S. C. H. Barrett (2008), J. A. Doyle (2009), T. N. Taylor et al. (2009), Tekleva and Krassilov (2009), Zavialova and Gomankov (2009), and J. A. Doyle (2010).
Evolutionary development of the seed plant progamic phase. The progamic phase of seed plant reproduction is defined as, "the life history period between pollination and fertilization" (page 144, Williams 2009). The flowering plant diplophase and male and female haplophases coordinate development of pollen tubes through maternal tissues to ovules at the same time that female gametophytes develop from a megaspore mother cell. Biochemical interactions between cells of sporophytic and gametophytic reproductive modules that underlie orchestration of the progamic phase, vary widely among the angiosperms (Williams 2009).
Solitary carpels of the "primitive" magnoliid tree, Degeneria vitiensis (Degeneriaceae, Magnoliales), are shown on either side of the text. The left image is a scanning electron micrograph of a portion of the stigmatic secretion of a carpel. A tiny, thread-like pollen tube emanates from a single boat-shaped monosulcate pollen grain, which is just visible on the left-hand surface of the secretory plug. The pollen grain adheres to the secretory surface, ×30.
The pollen tube probably penetrates the flared stigmatic secretion and would eventually be guided to the egg of a modular female gametophyte inside one of several ovules within the carpel.
The right hand image is a cutaway view revealing a row of ovules with cellular detail of the carpel, a thin placenta, and the stigmatic secretion, ×15.
Both samples were field fixed in 1986 and later dissected from a flower collected in the canopy of a tagged and vouchered Degeneria tree, Naitaradamu Study Area, Viti Levu, Fiji. The scanning electron micrographs were prepared by Al Soeldner, Director, Oregon State University Electron Microscopy Laboratory. I thank the National Geographic Society for providing research funding for this study.
Extant crown group flowering plants including basal angiosperms exhibit remarkable diversity in pollen tube development (Williams 2008). Yet, nothing is known of microgametophyte development and the progamic phase in long extinct individuals and populations of the stem group.
Recent reviews of the angiosperm progamic phase, evo-devo of pollen tubes and pollen tube transmitting tissues, and the biology of pollination of the basal crown groups of flowering plants are published by Sage et al. (2009), Thien et al. (2009), Williams (2009), and Michard et al. (2011).
A study by Michard et al. (abstract, 2011) reveals "a novel plant signaling mechanism between male gametophyte and pistil tissue similar to amino acid mediated communication commonly observed in animal nervous systems."
Fertilization and embryology of seed plants. Friedman (1992, 1994) and Dumas and Rogowsky (2008), outline and discusses the large body of scientific literature on the reproductive biology of seed plants including fertilization, development of nutritive tissue (megagametophytes discussed above), endosperm, and embryogenesis. Questions of reproductive success of flowering plants are discussed in several later reviews (Friedman 1995, 1999, 2001 [two papers], Rudall et al. 2009).
Double fertilization has historically been regarded as one of the hallmarks of angiospermy (Cronquist 1968, Takhtajan 1969, Stebbins 1974). Yet, later studies reveal that certain extant gymnosperms also possess this syndrome.
Specific studies of double fertilization in gymnosperms belonging to the anthophyte clade sensu J. A. Doyle and Donoghue (1986, 1987) have been carried out by Carmichael and Friedman (1995, 1996) and Friedman and Carmichael (1996) on Gnetum gnemon (Gnetales).
Many studies of double fertilization, endosperm formation, and embryology appear in the extensive literature on extant basal angiosperms (Rudall et al. 2009) including magnoliids. These include papers on endosperm development (Floyd and Friedman 2000, Rudall et al. 2009) and embryogenesis (Arias and Williams 2008).
"Endosperm is a key feature of angiosperms, yet its homologies and evolutionary origin remain enigmatic."
The preceding quote is from page 1592 of P. J. Rudall, T. Eldridge, J. Tratt, M. M. Ramsey, R. E. Tuckett, S. Y. Smith, M. E. Collinson, M. V. Remizowa, and D. D. Sokoloff (2009), Seed fertilization, development, and germination in Hydatellaceae (Nymphaeales): implications for endosperm evolution in early angiosperms American Journal of Botany 96(9): 1581-1593.
Historically the seven-celled, eight-nucleate female gametophyte, also known as the Polygonum-type, was regarded as the plesiomorphic state for flowering plants. Tobe et al. (2000) reported this anatomical type in Amborella. In 2006 Friedman discovered a peculiar eight-celled, nine-nucleate Amborella-type female gametophyte in this same group of New Caledonian angiosperms.
An important goal toward a better understanding of coevolution with insect antagonists and the early angiosperm reproduction might be to elucidate anatomical and evo-devo interactions between insects and megasporophylls, pollen and megasporophylls, pollen and female pollen receptive surfaces, pollen tubes and ovaries (when present), pollen and carpels (including secretions), and pollen tubes and ovules.
Reviews by Lord and Russell (2002), Bernhardt et al. (2003), Bernasconi et al. (2004), Nasrallah (2005), Friedman et al. (2008), Cai and Cresti (2009), Sage et al. (2009), Thien et al. (2009), and Williams (2009), among others, form a basis for opening new lines of research and later discussion from other perspectives.
Did biomechanical and secretory activities of animal antagonists affect evolutionary development of megasporophylls (and carpels), microsporophylls (and stamens) through reciprocal selection in paleopopulations?
Thigmomorphogenesis. Thigmomorphogenesis involves mechanostimulation, mechanoperception, signal transduction, and cellular differentiation (Jaffe 1973). Mechanostimulation may be passive (caused by wind currents, flowing and freezing water, and scraping effects of soil particles and moving rocks) or active, triggered by touching animals, fungi, and neighboring plants (Braam 2005).
Several reviews of thigmorphogenesis (Jaffe et al. 2002, Braam 2005, D. Lee et al. 2005, Fluch et al. 2008, Chehab et al. 2009) open a door to potentially new ways of thinking about evo-devo and ecology. Surveys of the mechanical forces that shape plant organs are also available (Mirabet et al. 2011).
This section of my essay was the starting point of a six-year-long review of the origin and paleobiology of flowering plants that began in 2005. I initially coined the name "thigmomorphogenetic hypothesis" to explain a coevolutionary origin of angiosperms and Holometabola but soon realized that this "fringe" idea scared too many colleagues in population ecology.
Mechanostimulation of the plant cell surfaces is perceived by the plant cytoskeleton (mechanoperception). Transduction of thigmo- (touch) stimuli by plant cells and tissues may signal certain touch-inducible (TCH) genes (Braam and Davis 1990, Lee et al. 2005), and potentially trigger developmental switches and differentiation, and change the shape and function of developmentally plastic organs (morphogenesis).
Volatile organic compounds (VOCs) are often released by plants when mechanically stimulated by chewing, crawling, egg-laying, and sucking herbivores (Hare 2011, among many other papers).
The diagram below illustrates how an instar of a Permo-Triassic insect might convey biochemical and mechanical signals to nuclei of dividing cells of the host plant SAM. Mechanostimulation of cell walls, plasmalemmas, protoplasts, and the cytoskeleton of the plant SAM by the insect antagonist may involve a signal transduction cascade that potentially leads to de-repression of DELLA chromosomal proteins and switching on or off of meristem identity genes, differentiation, and thigmomorphogenesis.
Strobilus formation in club mosses (Selaginella) a modern evolutionary derivative of certain Paleozoic lycopods, is a thigmo response (Jaffe et al. 2002, Braam 2005, Read and Stokes 2006).
Based on morphological and evo-devo studies of extant club mosses, were indeterminate membrane receptors, microtubule enzymes, and TCH genes and TFs tied-in with the developmental tool kit of early land plants?
An almost completely unexplored and potentially important phenomenon is whether insect bristles are capable of mechanically stimulating plant cell surfaces and the cytoskeleton, and inducing thigmorphogenesis in host plant organs. Arthropod bristles are innervated while hairs are not. Both types of insect organs are under developmental control and require the activity of the AS-C complex and svb/ovo gene, at least in Drosophila (S. B. Carroll et al. 2005).
Could the potential mechanostimulatory effects of insect bristles on seed plant cell surfaces of SAMs and floral meristems affect homeodomain TF trafficking, leading to differentiation and morphogenesis?
The engineering approach is used to study chewing in grasshoppers and locusts (acridids) and caterpillars of butterflies and moths (lepidopterans) (Clissold 2008), and to ascertain the magnitude of mechanical force potentially applied by ants (Paul and Gronenberg 1999), and other insects to artificial surfaces (Zhendong et al. 2002, Barbakadze et al. 2006). With the exception of in vivo x-ray analytical techniques there are few experimental studies in the literature to date that explore biomechanics of insect body parts and application of physical force to plant cell surfaces in a behavioral context (Clissold 2008).
At the cellular level, mechanostimulation of plant cells and protoplasts in the laboratory affects movements of their nuclei (Qu and M.-X. Sun 2007). Mechanostimulation of Arabidopsis plants by air currents or touch may also alter gene expression by upregulating TCH genes (Braam and Davis 1990).
Dennis Lee et al. (2005) found that 589 genes are upregulated in Arabidopsis thaliana by touch including those of the cytochrome P450 family, genes encoding calmodulin-related proteins, AP2, and WRKY TFs. The AP2 gene encodes one of the class A cis-acting TFs in the ancestral developmental tool kit of land plants (Floyd and Bowman 2007).
Transduction of signals that originate from abiotic and biotic sources in environments external to the stationary plant body potentially involves cell walls, the plasmalemma, Hechtian strands, microtubules, calcium-binding proteins, and expression of genes of the CAM/CML and XTH gene families (Lee et al. 2005, Braam 2005). Microtubules in plant cells convey signals from the cell wall, plasmalemma, and cytoplasm to other parts of the cell, including the nuclear envelope and endoplasmic reticulum (Wasteneys 2004).
Did extinct plants have the anatomical machinery to convey mechanostimulatory and hormonal signals from insect bodies rubbing against cell walls, to adjoining membranes, microtubules, and the nucleus? Yes.
Intact protoplasm containing fossilized plastids and secondary plant substances has been identified in the cells of Paleogene "green-leaf" fossils of "dicotyledonous" flowering plants (Giannasi and Niklas 1981, Niklas and Brown 1981, Niklas 1982). Calcium carbonate permineralizations of pteridophyte (Tubicaulis fern) sieve elements yield fine cell wall structure (Smoot and Taylor 1984).
Is there anatomical evidence preserved in the fossil record that cells have responded to touch? Possibly.
When fossilized leaves containing chew marks and punctures are permineralized, the preserved plant remains exhibit thicker cells surrounding the damaged tissues (Labandeira 1998).
Wind currents and moving parts of large herbivorous animals potentially had thigmomorphogenic effects on development of pollen dispersing reproductive modules (microsporophylls, microsporangia, synangia, stamens) and ovular points of attachment (abaxial or adaxial) on large, seed-bearing leaves, but paleontologic evidence in support of this idea is lacking.
Exposure to wind currents results in endogenous biosynthesis of ethylene and signaling of primary and secondary meristems in some seed plant species, leading to differentiation, morphogenesis, and wood formation (Rowe and Speck 2005).
Certain geometries of ovule-bearing shoots in extant gnetophytes (among other plant groups) affect the aerodynamics of pollen, possibly resulting in differential reproductive success (Niklas et al. 1986).
Thigmomorphogenesis in plants is incompletely understood but some progress has been made in understanding the effects of touch stimuli on plant differentiation and the derivation of plant growth forms (Pruyn et al. 2000, Pigliucci 2002, Lee et al. 2005, Rowe and Speck 2005, Telewski 2006, Fluch et al. 2008).
The next chapter discusses paleoecologic, paleoclimatic, and geochemical aspects of global mass extinctions which had potentially profound effects on ancient animal and plant interactions at all levels (biomes, species, paleopopulations, plant-herbivore compartments, organisms, and tissues and cells).
Was angiospermization a consequence of coevolution between seed plants and resident insect mutualists, reinforced by global ecologic catastrophe, temperature extremes, or hypoxia?
The image to the right is my imaginary apocalyptic but artistic reconstruction of an early Triassic landscape a few thousand years following the end-Permian global hiatus. The Hercynian Mountains are in the distance and the dark regions to the left are decayed remains of coastal gigantopteroid mangrove at the edge of the Panthalassa Sea. Lighter areas on land represent acidified ground probably unsuitable to mycorrhizal fungi and some vascular plants.
"To begin to connect ecology to the early radiation of angiosperms, we must understand the ecological starting point for angiosperm evolution."
The preceding statement is quoted from page 385 of T. S. Feild and N. C. Arens (2005), Form, function and environments of the early angiosperms: merging extant phylogeny and ecophysiology with fossils, New Phytologist 166: 383-408.
Paleoecology of global catastrophe. Among the planet's untold episodes of climatic and ecologic catastrophe (including fire, flood, glaciation, drought, global warming, and volcanism) several events stand-out as "extinction-level" global cataclysms.
The six most severe planetary apocalypses were the Frasnian-Famennian boundary extinction extending from the Upper Devonian Period to the Tornaisian Age of the Carboniferous Period, the carbon cycle anomaly marking the end of the Guadalupian Epoch, the end-Permian extinction also known as the "Great-Dying", the Triassic-Jurassic boundary carbon cycle event, the early Cretaceous end-Barremian biogeochemical perturbation, and the Cretaceous-Paleogene asteroid impact.
"Many paleontologists persist in using the number of species (or higher taxa) present as a metric of recovery. But the response to a mass extinction is above all an ecological one, and the number of taxa is only an indirect measure of evolutionary activity. Understanding these events requires an ecological approach. What are the dynamics and interactions between species? How well were ecosystems functioning? How complex were food webs and other ecological services during the survival and recovery intervals? Perhaps most importantly, how does the structure of the ecosystem facilitate the speciation involved in biotic recovery?"
The preceding quotation is from page 241 of D. H. Erwin (2006), Extinction: How Life on Earth Nearly Ended 250 Million Years Ago, Princeton, Princeton University Press, 306 pp.
Paleoclimatology is the subject of active research (Berner 1999, Berner and Kothavala 2001, Beerling and Berner 2002, Huey and Ward 2005, McElwain et al. 2005, Ward et al. 2006, Lamarque et al. 2006, A. C. Scott and Glasspool 2006, Knoll et al. 2007, McElwain and Punyasena 2007, Cleveland et al. 2008, Retallack 2009, Wignall et al. 2009, Payne et al. 2010, S. V. Sobolev et al. 2011, McElwain et al. 2011, L. G. Stevens et al. 2011, among others [see below]).
Refinements in the global oxygen level curve from reanalysis taking into account the effects of weathering of sulfur-containing iron pyrites on atmospheric free oxygen "... may have an important, relatively unrecognized relation to animal evolution." (page 5663, Berner 2006).
A review of paleobotanical data by McElwain and Punyasena (2007) reveals that the Earth's last three major mass extinction episodes since the Paleozoic did little to affect survivability of vascular plant families and orders. Retallack (2009) reports that refined stomatal indices seen in fossil leaves referable to the Ginkgoales are proxies "for past CO2 spikes."
Paleoatmospheric oxygen content has profoundly affected the incidence of wildfire with possible consequences to late Paleozoic divergences of angiosperm, conifer, cycad, ginkgophyte, and gnetophyte lineages. Papers published by Belcher et al. (2010) and Glasspool and Scott (2010) are gateways to the literature on paleowildfire.
Based on studies of charcoal in sediments Glasspool and Scott (abstract, 2010) conclude "that variation in pO2 was not the main driver of the loss of faunal diversity during the Permo-triassic and Triassic-Jurassic mass extinction events."
Frasnian-Famennian boundary extinction (DeCARB). One of the greatest mass extinctions on Earth occurred at the boundary of the Frasnian and Famennian Age during the Devonian Period, 375 MYA (McGhee 1996, Ward et al. 2006, Bishop et al. 2009). During the late Devonian Period island fragments and a chunk of Gondwana were clustered south of the equator and in the south polar region.
A developing ice house that began 375 MYA and extended to at least the Tornaisian Age of the Lower Carboniferous 345 MYA, apparently was accompanied by low pO2 (hypoxic) conditions with oxygen levels at 13% (Berner 1999, Berner and Kothavala 2001, Huey and Ward 2005) during the time interval known as Romer's Gap (Ward et al. 2006). The warm interval preceding the DeCARB was the first phase of the expansion of invertebrate arthropod herbivores in terrestrial environments (Labandeira 2006).
According to Ward et al. (page 16820, 2006) "no new clades" of arthropods occurred during the low oxygen interval demarcating Romer's Gap. Adaptive radiation of arthropods, land plants, and early limbed vertebrates (stegocephalians) occurred on land during the millions of years following Romer's Gap (Ward et al. 2006). As the late Paleozoic ice-house Earth slowly warmed during the Carboniferous Period, global oxygen concentration increased to levels exceeding 31% (Berner and Kothavala 2001, Ward et al. 2006), coinciding with the second phase of arthropod herbivore expansion (Labandeira 2006).
"While mass extinction and recovery, accommodation to new habitats, and body-plan modernization have all been factors in the evolution of life, atmospheric O2 level also has been a major, if underappreciated, driver in the major features of life's history. These features include origination, diversity levels, and probably absolute size increases through time."
The preceding quotation is from page 16821 of P. Ward, C. Labandeira, M. Laurin, and R. A. Berner (2006), Confirmation of Romer's Gap as a low oxygen interval constraining the timing of initial arthropod and vertebrate terrestrialization. Proceedings of the National Academy of Sciences 103(45): 16818-16822.
While certainly not applicable to events following Romer's Gap, I suggest that evolutionary biologists should consider decreases in insect body size and cone- (or floral-) axis length as likely adaptations emerging in coevolving species pairs resulting from the selective forces of the two Paleozoic mass extinctions and later Triassic-Jurassic carbon cycle event.
The Permian Period, despite evidence of episodic glaciation, saw a continuation of climatic warming, which was punctuated by at least two global mass extinctions (see next section). Evidence from the study of fossil soils (paleosols) supports stratigraphic division of the Permian Period into three epochs: Cisuralian (299-270 MYA), Guadalupian (270-260 MYA), and Lopingian (260-251 MYA) (Retallack 2005).
End-Guadalupian carbon cycle event (GuCCE). Retallack et al. (2006) present evidence of a global carbon isotope anomaly coinciding with the close of the Guadalupian Epoch of the late Permian Period. Oxygen levels in Earth's atmosphere declined significantly in the final days of the Guadalupian triggered by ignition of coal seams with hot igneous intrusions and extruding lava (Lai et al. 2008), and by expulsion of carbon monoxide and carbon dioxide into the atmosphere (Retallack et al. 2006, Retallack and Jahren 2008).
Stratigraphic evidence from Laibin and the Emeishan carbonates and volcanics of Asia coupled with magnetostratigraphic findings supporting the Illawara Reversal (Wignall et al. 2009 [two papers], Isozaki 2009), implicate a trigger for the GuCCE. Methane clathrates stored in cold undersea sedimentary layers were disrupted by volcanic activity releasing gigatons of ozone-damaging CH4 into the atmosphere (Knoll et al. 2007).
Earth slowly became a hot house with far-reaching ecological effects on late Permian terrestrial ecosystems, as determined from study of the geochemistry of fossil soils and coals and biostratigraphy of plant and vertebrate fossils (Retallack et al. 2006). Additional details on paleoclimatic effects on late Permian floras are covered in a reviews by Looy et al. (1999), Looy et al. (2001), McElwain and Punyasena (2007) and L. G. Stevens et al. (2011).
Prolongation of the biotic crisis is suggested by a gradual decrease in marine invertebrate biodiversity from the Wordian to end of the Changhsingian, about 253 MYA (Clapham et al. 2009).
Pictured below is a chart that illustrates the rise and fall of oxygen levels (expressed here as percent; in the scientific literature as atmospheric partial pressure [pO2]) in Earth's atmosphere, timing of the DeCARB, and later great mass extinctions (see below).
The graph below is based on several data sets (Berner 1999, Huey and Ward 2005, Ward et al. 2006) including GEOCARB III (Berner and Kothavala 2001) and GEOCARBSULF (Berner 2006 [two papers]). The graphic does not show the geologic interval of the Neoproterozoic snowball Earth, or periods of less severe global temperature swings (ice-house to hot house and vice-versa, except the DeCARB), and the Oligocene-Eocene cooling interval of the Paleogene Period.
At the Permian-Triassic (PTr) boundary, global oxygen levels on the shores of the Panthalassa Sea further declined to a level of free atmospheric oxygen less than 12% (Ward et al. 2006). Carbon dioxide levels in the atmosphere were elevated with profound effects on the physiology of aquatic and terrestrial animals (Knoll et al. 2007).
When taking into account supposed adaptations of terrestrial animals to pre-Guadalupian high oxygen levels of 31%, and effects of altitudinal compression, animals might have experienced hypoxia comparable to the higher Himalaya or the summits of Kilimanjaro and Mount McKinley (Huey and Ward 2005). Low pO2 at sea level, and in the Hercynian Mountains was probably exacerbated by carbon dioxide and sulfur dioxide outgassing linked to catastrophic volcanism that led to hotter climates within 600,000 years of the global apocalypse marking the close of the Paleozoic Era (Retallack et al. 2006).
End-Permian extinction (EPE). Global catastrophe caused extinction of most life at the close of the Permian Period, 251.3 MYA (Erwin 2006, Knoll et al. 2007). The Great Dying coincides with a 2,000,000 million year interval of volcanic unrest causing heating of Tunguska Basin sediments (Svensen et al. 2009), and extrusion of epicontinental lava lakes known as the Siberian Traps dated precisely 250.3 MYA (Reichow et al. 2009).
Geochemical studies of at least one subvolcanic intrusive rock formation associated with the Siberian Traps reveal high levels of sulfur contamination of the magma which potentially exacerbated the effects of SO2 outgassing on the atmosphere (C. Li et al. 2009). Mantle plume thermomechanical models proposed by S. V. Sobolev et al. (abstract, 2011) postulate that "massive degassing of CO2 and HCl, mostly from the recycled crust in the plume head, could along trigger a mass extinction."
Several other hypotheses have been proposed that might explain the greatest of all of Earth's mass extinctions. These include collision of the Earth with a bolide, comet, or icy dwarf; episodic release of thousands of gigatons of methane gas from methane clathrate deposits in the undersea bed (de Wit et al. 2002), methane gas derived from burning coal measures ignited by volcanic activity (Retallack and Jahren 2008), disruption of the Earth's magnetosphere by galactic dust and gas clouds, or catastrophic atmospheric disturbances attributable to solar flaring (Benton and Twitchett 2003).
No single event listed in the preceding paragraph explains the oceanic δ13 data gleaned from paleogeochemical and isotopic studies of carbonates in sediments bracketing the Permian-Triassic (PTr) boundary (Berner 2002, Payne et al. 2010, Luo et al. 2011). Lipid biomarkers suggest a prolonged period of ecological disruption in marine environments preceding and following the main global kill event (Cao et al. 2009).
Important insight on the effects of the EPE "trigger and kill" mechanisms (page 296, Knoll et al. 2007) on early Triassic aquatic and terrestrial ecosystems, has been gained from detailed biostratigraphic, paleoclimatic, and paleophysiologic studies (Z.-Q. Wang and Zhang 1998, Looy et al. 1999, Z.-Q. Wang 2000, Rees 2002, Rees et al. 2002, Berner 2005, Gastaldo et al. 2005, Erwin 2007, Sahney and Benton 2008).
Recovery of biota on land probably took a very long time relative to other global extinctions according to the review by Grauvogel-Stamm and Ash (2005). Recovery and later radiation of arthropod clades following the EPE is even more nebulous due to a general lack of meaningful paleontologic data (Béthoux et al. 2005).
Discoveries of insect galls on Lower Triassic fossilized leaves of corystosperms "... indicate that herbivory and reproductive strategies involving galling and foliar ovipositioning were re-established relatively soon after the end-Permian mass extinction event that saw major turnovers in both the [Gondwanan] flora and insect fauna." (McLoughlin, abstract 2011). The word in  is mine.
Kozur and Weems (abstract, 2011) suggest that the EPE and associated Siberian Traps volcanism "... coincide with a rapid collapse of tropical rain forest environments (disappearance of the highly diverse Gigantopteris flora) ..." "...caused by global cooling due to a volcanic winter event ..."
Palynological data from oil and gas exploratory drill holes off the northern coast of Europe suggest multiple climatic shifts at the Permo-Triassic boundary (Hochuli et al. 2010). Blooms of cyanobacteria are associated with massive volcanism in Asia at the PTr boundary (Xie et al. 2010).
Zi-Qiang Wang and co-workers in a series of papers report that Cathaysian floras were reduced to isolated, fungal-enriched refugia dotted within arid, desolate landscapes by late Permian time. Some of the Upper Permian sedimentary red beds studied contained only charcoal fragments of vascular plants while some stratigraphic sequences up to 70 meters thick were devoid of plant fossils (Z.-Q. Wang 2000).
A later paper by Peng and Shi (2009), which is based on detailed biostratigraphic data from continuous sections across the PTr boundary, suggests uneven recovery of the Cathaysian Gigantopteris flora following the EPE. These findings are complicated by results of yet another study of Wuchiapingian paleofloras extending across the PTr boundary by Xiong and Q. Wang (2011).
When seed plant compressions of gigantopterids were found the fossilized leaves had thick cuticles suggestive of drought conditions in Cathaysia. Based on biostratigraphic and taphonomic data cycads, peltasperms, ferns, ginkgos, and certain other conifers were represented in the fossil record on both sides of Permo-Triassic boundary (Z.-Q. Wang 2000).
Paleogeochemical data show a rise in the proportion of rate of burial of sulphur and iron containing pyrite over organic carbon burial rate at the PTr boundary, 251.3 MYA, which was probably attributable to forest decline at that time (Fig. 4, page 3214, Berner 2005). Some estimates based on geochemical data suggest a catastrophic drop in atmospheric oxygen over a 20 million year period following the end-Permian apocalypse (Berner 2006, Bond and Wignall 2010).
The EPE was marked by increased levels of erosion and sedimentation rate, lower pH levels in rain, and higher precipitation which was probably a result of habitat destruction on land according to studies by Algeo and Twitchett (2010) and S. G. Thomas et al. (2011). Biostratigraphic studies of Late Permian and earliest Triassic (Scythian Age) rocks in East Greenland by Looy et al. (2001) suggest spatial and temporal variability in ecosystem recovery.
Proportional changes in the relative amounts of oxygen (pO2), carbon dioxide (pCO2), methane (pCH4), and sulfur dioxide (pSO2) at the ground surface, when accompanied by temperature swings, might have affected low-elevation terrestrial biomes with far-reaching global paleoclimatologic and paleoecologic consequences (Looy et al. 1999, Huey and Ward 2005, Retallack et al. 2006).
Paleontologic evidence from climatic and geophysical phenomena listed above includes data gleaned from studies of fossil soils (paleosols) of Antarctica, southwestern North America, and southern Africa (Retallack 2005, Retallack et al. 2005, Pace et al. 2009), taphonomical investigations of fossorial therapsids and paleosols preserved in Permian rocks (Retallack et al. 2003), and from reports of marine foraminifers in packstone and framestone carbonate facies (Song et al. 2009).
Conditions on land following the EPE were probably inhospitable to insects, tetrapods, and plants (Z.-Q. Wang 2000, Retallack et al. 2006), but more data are needed. Reinterpretation of channel fill deposits in the Bethulie region of the Karoo Basin of South Africa suggest that the EPE was a non-event (Gastaldo et al. 2009).
In conclusion, the DeCARB, GuCCE, EPE, and Triassic-Jurassic boundary carbon cycle event (TrCCE) had a common thread: significant fluctuation in global carbon dioxide and oxygen levels (Berner and Kothavala 2001, Huey and Ward 2005, Berner 2006, Ward et al. 2006).
Triassic-Jurassic boundary carbon cycle event (TrCCE). The end-Triassic mass extinction was preceded by a global increase in temperature followed by severe climatic disruption over many millions of years (Cleveland et al. 2008 [two papers]). Many studies suggest that the mass extinction was prolonged and connected with at least two intervals of higher carbon dioxide levels in the atmosphere during the Rhaetian Age preceding the TrCCE (Cleveland et al. 2008, Ruhl et al. 2009), and "extremely elevated CO2 concentrations at the Triassic/Jurassic boundary" (title, Steinthorsdottir et al. 2011).
Hallam (2010) suggests that the Triassic-Jurassic mass extinction on land was prolonged and not sudden.
Relatively little is known of the effects of the TrCCE on terrestrial vegetation and biodiversity (Bonis et al. 2009, Götz et al. 2009, Mander et al. 2010, Lucas et al. 2011). Studies on the classic Triassic floras of Greenland suggest that tropical forests of this boreal region began to change in composition and stratification at the onset of global warming well before the TrCCE (McElwain et al. 1999, McElwain et al. 2007).
Data gleaned from paleoecological and taphonomic studies of the Whitmore Point Member of the Moenave Formation of southwestern North America by Lucas et al. (2011) shed light on the effects of the TrCCE on terrestrial extinction across the Triassic-Jurassic boundary.
Beerling and Berner (2002, abstract) state that "the end-Triassic mass extinctions represent one of the five most severe biotic crises in Earth history, yet remain one of the most enigmatic." Further, Beerling and Berner (abstract, 2002) propose that global warming, "due to a buildup of volcanically derived CO2," triggered "destabilization of seafloor methane hydrates and the catastrophic release of CH4 [Pálfy et al. 2001]."
The two papers by Beerling and Berner (2002, 2004) present data and findings that disruption of the global carbon cycle at the end of the Triassic Period resulted in the release of up to 9,000 gigatons of carbon (as carbon dioxide gas) during the Central Atlantic Magmatic Province (CAMP) basalitic eruptions (Cirilli et al. 2009), and an additional 5,000 gigatons of methane released from methane hydrates imbedded in the seafloor.
Major perturbation of the global carbon cycle at the Triassic-Jurassic boundary (Beerling and Berner 2004, Whiteside et al. 2010, Črne et al. 2011, Ruhl and Kürschner 2011, Ruhl et al. 2011, Schaller et al. 2011) is coincident with anomalies in marine sulfur cycling (Williford et al. 2009), increases in unradiogenic osmium from the CAMP mantle source (Kuroda et al. 2010), and flood basalt volcanism (Schoene et al. 2010).
Early Cretaceous end-Barremian biogeochemical perturbation (BaCCE). Biogeochemical evidence exists suggesting that a global atmospheric and climatic perturbation occurred in the Late Barremian (Neocomian, early Cretaceous). The BaCCE might have accelerated the diversification of early magnoliid flowering plants and possibly monocots (Heimhofer et al. 2005).
Paul M. Barrett and Katherine J. Willis (page 437, 2001) report that elevated levels of carbon dioxide in Earth's atmosphere during the Cretaceous Period coincide with "... emergence of the major plant groups ..." and "... increasing rates of species turnover ..." Further, the initial radiation of flowering plants may be attributable to carbon dioxide build-up in the atmosphere according to an interesting hypothesis by P. M. Barrett and Willis (2001).
Implications of the BaCCE and other thermal maximums toward the colonization of ice free landscapes, and diversification and speciation of flowering plants and their invertebrate and vertebrate antagonists, is discussed by P. M. Barrett and Willis (2001) and Friis et al. (2006).
Cretaceous-Paleogene (K-Pg) asteroid impact. Also known as the Chicxulub asteroid impact, the Cretaceous-Paleogene (K-Pg) extinction has been the subject of much discussion with respect to the demise of dinosaurs. Older literature refers to the K-Pg or Chicxulub event as the Cretaceous-Tertiary (K-T) mass extinction.
The insect and plant paleoecological literature on the K-Pg event is vast and some important papers include Labandeira et al. (2002), Nichols and Johnson (2008), Sepúlveda et al. (2009), and Schulte et al. (2010), among others.
Discussion of the Chicxulub event marking the close of the Cretaceous Period and beginning of the Paleogene Period of the Cenozoic Era is outside the scope of this essay.
Ecology of Paleozoic seed plants. Paleozoic seed plants did not possess flowers and fruits. Rather ovules and seeds (ripened ovules) of some species were probably phyllospermous and attached to fertile leaves termed megasporophylls.
A detached megasporophyll of extant Cycas revoluta (Cycadaceae, Cycadales) is pictured on the right-hand side of the page. The hairy megasporophyll bears a pair of bright red ripened seeds and one brownish immature ovule on the lower edges of the dissected leaf. Ovules of cycads mature into bright red seeds (see image) that contain diploid embryos (offspring) which are protected by an indurate sarcotesta.
Each ovule consists of a single diploid integument, pollen chamber, a multicellular megasporangium (cells at the tip of this structure disintegrate into a colloidal pollination droplet), archegonial chamber (this space receives flagellated sperm which are discharged from the pollen-grain end of the pollen tube), and a multicellular, haploid megagametophyte. The female gametophyte serves as nutritive tissue for the embryo.
The best example of a Paleozoic megasporophyll is probably Phasmatocycas bridwellii (Axsmith et al. 2003), but anatomical details are unknown due to poor preservation of the fossils. Paleobotanists do not know the whole plant morphology or taxonomic relationships of the gymnosperm to which Phasmatocycas leaves were attached.
This question is one of many paleobotanical challenges discussed in the second essay.
"... Nonetheless, it is possible that co-expression of AP3- and PI-homologs of MIKC-type MADS-box B genes, (see chapter on Genetics Considerations) mediated the evolutionary innovation of animal-attractive, petal-like organs well before the appearance of flowers."
The preceding passage is quoted from page 361 of D. E. Soltis, H. Ma, M. W. Frohlich, P. S. Soltis, V. A. Albert, D. G. Oppenheimer, N. S. Altman, C. dePamphilis, and J. Leebens-Mack (2007), The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends in Plant Science 12(8): 358-367. The phrase in brackets  is mine.
Early phytophagous insects and herbivorous tetrapods probably used seed plant reproductive modules including fertile leaves (megasporophylls), ovules, seeds (ripened ovules), pollen-making sacs (microsporangia), and pollen as a source of food (Tiffney 1992, Zavada and Mentis 1992, P. M. Barrett and Willis 2001, Tiffney 2004).
What was the extent of pollen flow in Paleozoic seed plant shrub populations?
Phytophagous insects developed host specificity during the Permo-Triassic and this might explain the evolution of "pollinator faithfulness" (page 126, Zavada 2007). Further, host plant secondary plant biochemical pathways leading to the production of antifeedents were probably developed by the Permian Period (Zavada and Mentis 1992).
Microsporangia, pollen, and ovules were a likely source of food for phytophagous insects including paleodictyopterans, bugs, and early beetles.
Seeds which are the products of sexual reproduction, probably rained from early Triassic shrub- and tree-like survivors of the EPE. Small, burrowing vertebrate animals probably ate many of the ovules and seeds, adversely affecting seed plant fecundity. Trampling and digging around these shrubs and small trees by fossorial vertebrates probably affected recruitment from the seed bank.
During the first several thousand years following the global collapse of ecosystems at the PTr boundary, acidified substrates of fragmented biomes probably limited the germination of seed recruited from the seed bank.
Vertebrate habitats. I use the term habitat in the context used by wildlife biologists. This subsection describes vertebrate habitats and the likely ecological effects of tetrapods on the paleoecology of the first angiosperms. Tiffney (1992) outlines the fossil history of amphibians and reptiles to create a better understanding of the effects of these animals on the evolution and diversification of land plants. Additional references on vertebrate herbivory include Regal (1977), Wing and Tiffney (1987), Coe et al. (1987), Weishampel and Jianu (2000), P. M. Barrett and Willis (2001), Labandeira (2002), Tiffney (2004), Eriksson (2008), Butler et al. (2009 [two papers]), Butler et al. (2010), and Sander et al. (2010), among others.
In glossopterids manifestations of vertebrate interactions with these plants include increased indigestible carbon content of plant tissues, increase in the biosynthesis and secretion of natural plant defense substances, reduction in leaf size, increased production of secondary tissues (greater woodiness), and morphological adaptations to protect ovules and pollen (Zavada and Mentis 1992).
Key evidence on the fate of dicynodonts and therapsids following the EPE, based on study of fossil bones, paleosols, and depositional environments, is presented by Retallack et al. (2003). All paleontologic, paleopedologic, and paleoclimatic data gathered to date suggests that the mechanical activities of herbivorous dinosaurs had far-reaching effects on the evolution of seed plants including angiosperms (P. M. Barrett and Willis 2001).
Grazing and trampling of the landscape by massive archosaurian dinosaurs, creating openings in conifer forests, probably favored the spread and diversification of flowering plants into these disturbed biomes. Indurate seeds with red sarcotestae may have been adapted to withstand digestive cavities of herbivorous dinosaurs. Mesozoic angiosperms that colonized vertebrate-disturbed landscapes probably evolved antiherbivory traits including production of deleterious natural plant products, spines, leathery leaves, small-sized leaves, thorns, woody trunks (Tiffney 1992, Zavada and Mentis 1992, P. M. Barrett and Willis 2001, Tiffney 2004).
Duckbill dinosaurs, hadrosaurians, and ceratopsians probably fed on the foliage of woody angiosperm eudicots and conifers such as Gingko (Fricke and Pearson 2008). Fossils of the giant sauropod Alamosaurus co-occur in the same beds as fallen, permineralized logs of extinct dilleniid angiosperms (Wheeler and Lehman 2000).
Based on anatomical studies of petrified stumps in situ and fallen whole logs, Wheeler and Lehman (2000) suggest that angiosperm tree species with extensive ray parenchyma might have been better adapted to survive browsing and trampling by large dinosaur herbivores in Cretaceous times. Coprolites, which are a potential measure of vertebrate herbivory, reveal fragments of Pennistemon (Friis et al. 2006), an early Cretaceous (Neocomian) monocotyledonous flowering plant (Friis et al. 2000).
Insect associations with vegetation. The idea that invertebrates coexisted with extinct vascular plants (including those producing seeds) and with primitive angiosperms is not a new one (Meeuse 1978, Thien et al. 1985, Labandeira 1997, Labandeira 1998, Labandeira 2000, Zherikhin 2002, Krassilov et al. 2003). Sidney Ash (1997) reports fossil evidence of interactions between arthropods and seed plants from the Upper Triassic.
By the Jurassic Period bisexual flower-like organs were common among certain Gnetales. Friis et al. (page 254, 2006) suggest that interactions between seed plants and insects (phytophagy and pollination), "appeared earlier, and perhaps independently, in other groups."
Labandeira (2006), in a review of insect associations, recognizes four phases of terrestrial herbivore expansion during the geologic past that may be linked with global environmental change.
The first phase of expanding herbivores on land was associated with transformation of the Silurian hot house world into the late Devonian-early Carboniferous ice-house.
Phase 2 led to a resurgence of herbivores on land coinciding with melting of the global icehouse during the Carboniferous and the rise of oxygen levels in the atmosphere to 31% (Labandeira 2006). As a Permian hot house Earth developed, oxygen levels declined to less than 12% culminating with the EPE (Labandeira 2006, Knoll et al. 2007).
The image to the left is a 280 million year old calcitic and limonitic permineralization of the midrib of the abaxial leaf surface of Delnortea abbottiae (USNM 372427) with possible preserved tissue damage or uneven weathering (actual size). The tiny pits on the midrib of the leaf may be bite marks or ovipositor traces.
The fossil was collected from the Lower Permian (Leonardian) Cathedral Mountain Formation, Del Norte Mountains of southwestern North America (Mamay et al. 1988), photographed by the author on the day the fossil was found.
Herbivore Expansion 2 and developing hypoxia of the Permo-Triassic "may explain major turnover of Permian plant clades," according to Labandeira (page 423, 2006). The third phased expansion began during the late Triassic and continued through the Jurassic Period ending in the middle of the Cretaceous. Finally, Herbivore Expansion 4 occurred from mid-Cretaceous times ending with the present (Labandeira 2006).
Elegant studies of the reproductive biology of extant cycads suggest that an ancient association might have existed between beetles and pollination of ovules (Norstog et al. 1986, Norstog and Fawcett 1989); and thrips as cycad pollinators (Terry et al. 2004, Terry et al. 2007). I regard individual cycad plants as miniature fitness landscapes exploited by invertebrate antagonists.
Beetles, weevils, and ants are often closely associated with palms (monocotyledonous flowering plants), but the nature of pollination and phytophagy in specific species is relatively unstudied (Uhl and Dransfield 1987).
Rasnitsyn (2002) reviews the fossil history of the phytophagous insect groups. Key papers include Labandeira et al. (1994), Krassilov et al. (1997), Labandeira (2000), Labandeira (2002), Labandeira et al. (2002), Krassilov et al. (2003), Gandolfo et al. (2004), Labandeira (2007), Labandeira and E. G. Allen (2007), Krassilov (2008 [two papers]), Crepet and Niklas (2009), and Labandeira (2010).
Another attribute of seed plants is the ability to raise ambient temperature in the immediate spaces between sexual organs, sheathing leaf bases, and wood, cavities and crevices by increasing cell metabolism. This physiologic process is termed thermogenesis. Morphological adaptations are termed thermogenic plant tissue shelters (Meeuse 1978).
Thermogenesis has been identified in developing cones of extant cycads (Tang et al. 1987, Terry et al. 2004), in beetle-pollinated, large-flowered angiosperms (Davis et al. 2008), and extant aroid monocots (Ito-Inaba et al. 2008, Ivancic et al. 2008). Flowers of certain Nymphaeales, a basal order of angiosperms, maintain temperatures in line with optima favored by beetles (Seymour and P. G. D. Mathews 2006).
The next chapter briefly outlines aspects of coevolution, developmental tool kit plasticity, fitness landscapes, mutualism, and reciprocal selection as a framework to consider evolutionary ecology of seed plants and phytophagous arthropod antagonists in deep time.
In the preceding two chapters that considers evidence from anatomy and development and ecology, and in the following two chapters on physiology and genetics, numerous research findings of my colleagues shed light on the developmental plasticity of certain plant reproductive structures critical toward an understanding of the origin and diversification of seed plants with flowers.
Studies on extant seed plant laboratory MIKC-type MADS-box genes of flowering plants including gymnosperm orthologues of MIKC-type MADS-box genes and their modular protein TFs demonstrate with little doubt the labile nature of expanding SAMs, cones, and flowers.
Tremendous advances have been made in the last decade on understanding the molecular basis of cone and floral organization from studies of the MIKC-type MADS-box gene family (Theißen et al. 2000, Theißen 2001, Theißen and Melzer 2007, Melzer et al. 2010, among many other papers).
Based on genetic studies and evo-devo work on gymnosperm orthologues of MIKC-type MADS-box genes (P. Zhang et al. 2004), the MIKC-type MADS-box family of TFs has probably been conserved for some 300 million years (Becker et al. 2000), at least since the Gzelian Age of the Carboniferous Period.
Molecular and genomic studies of the homeotic gene family in vascular plants when subjected to phylogenetic analysis (Bowers et al. 2003) point toward the occurrence of several independent gene duplication events (or one massive doubling of the whole genome) just a few million years prior to divergence of angiosperms from the MRCA (Zahn et al. 2005).
Were certain gene duplications and/or the doubling of whole genomes in Permo-Triassic shrub lifeboat hosts somehow connected with coevolving resident insect colonies at molecular and organismal levels?
Can we integrate insight gained from elucidation of cross-Kingdom signaling networks, genome parasitism, and the protein biochemistry of transcriptional regulation into a mechanistic view of real time coevolution?
How can we better appreciate coevolution of animals, fungi, and plants in deep-time by studying their paleoecologies?
The image on the right-hand side of this page is a native Fijian iguana Brachylophus vitiensis (Iguanidae, Reptilia), photographed by the late John R. H. Gibbons, Ph.D., which is a vertebrate herbivore indigenous to certain islands of the southwest Pacific.
Insect-plant mimesis. Cases of arthropods mimicking plants are encountered by ecologists rather often, especially in habitats where insects seek cover against flying carnivores such as bats, birds, and predatory insects. Fully-developed insects sometimes possess segments and appendages with bizarre modifications of the exoskeleton that are suggestive of bark, leaves, and twigs.
Gene expression studies of the evo-devo of modified insect body parts manufactured by the animal to look like plant organs might shed light on cross-talk of homeotic TFs and hormones. Fossil evidence suggests deep conservation in the insect tool kits once used for crypsis, aposematism, and mimicry. Cis-regulatory evolution of TFs controlling expression of optix may be responsible for mimicry in certain butterflies (Reed et al. 2011).
The fossil history of insects masquerading as plants is reviewed by Sonja Wedmann (2010). Recent studies of fossilized lacewings (Neuroptera) from the Middle Jurassic document ancient mimesis of bennettitalean and cycadalean leaf pinnation by insects (Y. Wang et al. 2010).
Mutualisms. A brief discussion of the evolutionary history of cross-Kingdom mutualisms might be relevant to questions having to do with the great late Paleozoic seed-plant divergences and Mesozoic explosive diversification and adaptive radiation of flowering plants. Further, there are implications of mutualisms toward a better understanding of the mechanisms that underpin coevolution (see the illustrated discussion in the next section).
Mutualisms include those between fungi and plants, arthropods and plants, and tetrapods and plants, among others. Interactions among sympatric, juxtaposed species belonging to different kingdoms in the Tree-of-life might have been important in the evo-devo of signaling networks, immune systems, and molecular tool kits. Why?
Cell-to-cell connections between two interacting organisms in paleopopulations might be one way to explain past episodes of horizontal gene transfer and genome parasitism. These ideas are discussed in the last section of the chapter on Genetic Considerations.
While discussing an inherent "multifaceted" capacity of angiosperms for "reinvention" within the evolutionary and paleobiological context, Crepet and Niklas (2009) conclude:
"... It is clear that plant-animal interactions were critical to the success of the earliest flowering plants in light of a reciprocal driving mechanism for angiosperm and animal diversifications."
The preceding statement is quoted from page 378 of W. L. Crepet and K. J. Niklas (2009), Darwin's second "abominable mystery": Why are there so many angiosperm species? American Journal of Botany 96(1): 366-381.
Fungal-plant connections. The fossil history of fungal-plant interactions is well-documented in the paleobotanical literature (Chapter 3, T. N. Taylor et al. 2009). Mycorrhizal mutualisms are of particular importance in seed plant paleoecology (page 103, T. N. Taylor et al. 2009).
Mycorrhizal fungi probably played an important ecological function in the recovery of terrestrial vegetation following the Paleozoic mass extinctions. More paleoecological studies are needed with possible focus on interacting ground dwelling fungal mycelia and gymnosperm root- and rhizome systems.
Insect-plant mutualisms. Insect-plant mutualisms involve a mobile organism (the insect) and a stationary one (the plant host). Such mutualisms evolved multiple times in many flowering plant groups. Mutualisms are often gained and then lost over time (Bernhardt 2000, Bronstein et al. 2006).
Further, traits seen among interacting insect- and plant-mutualists are often mismatched (B. Anderson et al. 2010).
Plant cavities and organs are used by insects for breeding, feeding, and shelter (G. N. Stone et al. 2008). For example, saproxylic beetles were prevalent in the Mesozoic and late Paleozoic eras (Kirejtshuk 2003).
Fossil evidence of mutualistic associations between specific insect groups such as beetles, nitidulids, bees, and wasps; and early Mesozoic and Paleozoic seed plants is sparse but intriguing (Krassilov et al. 1997, Krassilov and Rasnitsyn 1997, Ponomarenko 1998, Beck and Labandeira 1998, Labandeira 1998, Zherikhin 2002, Krassilov et al. 2003, Scott et al. 2004, among others). Controversial reports of fossilized hives possibly belonging to ancestors of hymenopterans, which are commonly associated with modern flowering plant pollination and herbivory, predate the appearance of fossil flowers by more than 100 million years (Hasiotis et al. 1998).
Sometimes hints of past insect activities on plants come from the study of ichnofossils e.g. indirect evidence of egg-laying inside leaf fossils from the Upper Permian (Vassilenko 2011).
The most complete review to date of insect-seed plant mutualisms in Mesozoic time is a landmark paper by Labandeira (2010).
Whether plant-insect mutualisms lead to coevolution of the plant host and insect antagonist is problematic. While discussing cospeciation in fig pollination mutualisms, Bronstein et al. (page 422, 2006) suggest "... that evolution has been relatively one-sided in many of these mutualisms ..." and "... that we have not always been looking at the right insect traits."
Coevolutionary studies of insects and their fig plant hosts employ living systems (Jousselin et al. 2003, Cook et al. 2004, Machado et al. 2005). Questions on the paleobiology of coevolution may be difficult to answer except from a molecular phylogenetic research perspective.
Interactions between insects and seed plants (Futuyma and Keese 1992, Labandeira et al. 1994, Krassilov et al. 1997, Labandeira 1998, Labandeira 2000, Gorelick 2001, Zherikhin 2002, Krassilov 2002, Labandeira 2002, Cornell and Hawkins 2003, Krassilov et al. 2003, A. C. Scott et al. 2004, Labandeira 2010) are well-documented in the literature.
Animal and plant mutualisms in Upper Paleozoic time were not just confined to arthropods, myriapods, and lignophytes, but also included interacting tetrapods and plants. This subject is discussed in the next subsection.
Tetrapod-plant interactions. There has been considerable attention paid to the paleoecology of tetrapod-seed plant mutualisms in discussions of the origin, dispersal, and adaptive radiation of angiosperms, gymnosperms, and plant-eating dinosaurians (Tiffney 1992, Zavada and Mentis 1992, Weishampel and Jianu 2000, P. M. Barrett and Willis 2001, Labandeira 2002, Tiffney 2004).
Dinosaurians and seed plants interacted in their ancient habitats but the relationship was diffuse (Weishampel and Jianu 2000, P. M. Barrett and Willis 2001, Labandeira 2002, Tiffney 2004). The oldest evidence of vertebrate gut contents containing identifiable plant material (i.e. conifer ovules) is from fossilized food boluses of Permian tetrapods (Munk and Sues 1993).
Posit a late Paleozoic or early Triassic origin of flowering plants, and taking into account potentially important (if not critical) Upper Paleozoic divergences of the main clades of gymnosperms (i.e. conifers, cycads, gigantopterids, gigantopteroids, gnetophytes, ginkgophytes), might convince at least some students of paleoecology to look for evidence of diffuse coevolution in sympatric populations of Permo-triassic tetrapods and spermatophytes.
Temnospondyls are a possible candidate group of late Paleozoic tetrapods for focused paleoecological studies (Sanchez et al. 2010). The poster-baby of evo-devo studies of tetrapod paedomorphism and neoteny is the axolotl (S. J. Gould 1977), which is the evolutionary offshoot of Permo-triassic Temnospondyli.
Astonishingly, a species of extant salamander (Ambystoma maculatum) is mutualistic with a green alga (Kerney et al. 2011). Did green algal cells form mutualisms with late Paleozoic temnospondyls?
If supported by paleontological evidence, did algal-vertebrate mutualisms lead to episodes of horizontal transfer of plastidic DNA and tetrapod host cell mitochondria?
In the next section I discuss potential coevolution of animals, fungi, and seed plants during the Carboniferous and Permian periods of the Paleozoic Era as a possible contributing factor in the origin and evolution of flowering plants.
Coevolution. This section briefly mentions studies on extant coevolutionary networks and some aspects of escape and radiation with the hope that ideas might be applied to answering questions in deep time.
"It is clear that plant-animal interactions were critical to the success of the earliest flowering plants in light of a reciprocal driving mechanism for angiosperm and animal diversifications."
The preceding quotation is from page 378 of Crepet and Niklas (2009), Darwin's second "abominable mystery": Why are there so many angiosperm species? American Journal of Botany 96(1): 366-381.
What was the reciprocal mechanism sensu Crepet and Niklas (2009) that led to the diversification of the stem lineage(s) of flowering plants, certain tetrapods, and holometabolous insects?
A review of Cretaceous records for clumped angiosperm pollen and its bearing on coevolution with insect pollinators is available (D. W. Taylor et al. 2010).
Coevolutionary theory was developed from hypotheses tested using extant plant and animals in their native biomes, communities, and habitats (J. N. Thompson 1989, Grehan 1991, Futuyma and Keese 1992, Cornell et al. 2003, B. Anderson and S. D. Johnson 2008). Habitats are viewed by students of coevolution as nested and antagonistic networks of interacting species (Bascompte et al. 2003, Guimarães et al. 2006, Bastolla et al. 2009).
A conceptual framework for the Geographic Mosaic Theory of Coevolution is outlined and discussed by J. N. Thompson (2005). This theory is structured by several "assumptions," "evolutionary hypotheses," and "general ecological predictions" (page 98, Table 6.1, J. N. Thompson 2005) outlined below:
coevolving species pairs are comprised of genetically differentiated populations
interacting species pairs do not always have identical geographic ranges
such pairs of coevolving species are phylogenetically conservative in their interactions
these coevolutionary relationships are held together for a long time
ecological outcomes in interacting species pairs differ from one plant community to another
coevolving species become locally adapted to local populations of other species
coevolution is potentially rapid
natural selection on interacting species pairs varies from place to place but reproductive success (fitness) of one species depends on the other
coevolutionary "hotspots" involve species interactions which are subject to reciprocal selection
"hotspots" are often imbedded among "coldspots" which are dominated by non-reciprocal selection
traits are remixed as a consequence of mutation, gene flow across landscapes, and drift and saltation, resulting in shifts of the geographical mosaic
phenotypes of coevolving species pairs are shaped by their interactions matched within plant communities
very few coevolved traits become fixed due to differential selection
Aspects of the geographic mosaic theory of coevolution might be applied to deep time animal, fungal, microbial and viral pathogen, and plant interactions, including interactomes at all levels from molecules to populations, but mathematical models are generally wanting in the literature.
Coevolution of pathogenic microbes and viruses with arthropods and land plants. Two important reviews are available on the subject of coevolution of wasp parasites, hosts, and pathogenic viruses with implications on the manipulation of insect behavior and the coevolution of seed plant and insect tool kits (Lovisolo et al. 2003, Grimaldi and Engel, page 427, 2005).
Students of coevolution should pay attention to clues pertaining to gene flow mechanisms involving both vertical and horizontal transfer of DNA, which are buried in the extensive literature on pathogenic baculoviruses. Baculovirus genes are incorporated into genomes of gypsy moth hosts causing large behavioral phenotypic effects. "Gypsy moths infected by a baculovirus climb to the top of trees to die, liquefy, and 'rain' virus on the foliage below to infect new hosts" (abstract, Hoover et al. 2011).
Are baculoviruses one potential source of cross-Kingdom mobile, genome parasites e.g. LTR retrotransposons, which are able to freely move from fungal and/or insect vectors to plant hosts within one of J. N. Thompson's coevolutionary compartments?
Implications of cross-Kingdom horizontal transfer of bits and pieces of tool kit DNA from accumulating LTR retrotransposons originating in fungal and/or insect bodies to genomes of seed plant hosts, are understandably profound.
In the next two chapters, the reader should realize the potential importance of tool kit coevolution in unraveling the mysterious origins of flowering plants and their holometabolous insect antagonists.
Coevolution of arthropods and land plants. This subsection places on the table questions having to do with possible coevolution of arthropods and lignophytes in deep time from molecular phylogenetic and paleophysiologic research perspectives.
What molecular phylogenetic aspects of arthropod antagonist/seed plant host developmental regulation should paleobiologists study?
Studies of the HTH DNA-binding motif of the malvid angiosperm Arabidopsis thaliana by Hamès et al. (2008) report similarities to the active motif of Drosophila Engraled homeodomain protein. Molecular phylogenetic and biophysical studies of seed plant LFY enzyme and insect engraled protein may shed light on coevolution at the molecular level.
It might also be important to consider the paleophysiology of homeodomain proteins and other enzymes when developing explicit hypotheses on a possible coevolutionary origin of angiosperms and certain holometabolous insects.
The "right insect traits" (page 422, Bronstein et al. 2006) might be HTH proteins encoded by the compartment-selector gene engraled and certain homeotic selector genes of the Hox complex (e.g. homologs and paralogs of abd-A, Abd-B, Hox3, pb, Scr, and Ubx). Bronstein and company's traits of focus might also include enzymes belonging to the respiratory, moulting, and vitellogenin developmental tool kit.
Coevolution between phytophagous insect associates of certain land plants may have been affected by the two rounds of slow decline in atmospheric oxygen levels during the Paleozoic Era. The first round coincided with the late Devonian-early Carboniferous ice-house (Berner and Kothavala 2001), and a second was initiated by the GuCCE (Retallack et al. 2006) and high carbon dioxide and methane levels in the atmosphere, culminating with "trigger and kill mechanisms" (page 296, Knoll et al. 2007) associated with the EPE.
Based on global atmospheric and biogeochemical crises, specific invertebrate respiratory proteins of potential evolutionary interest are probably hemocyanins, hemoglobins, and hexamerins (Van Holde et al. 2001, Burmester 2004, Burmester and Hankein 2007, Hagner-Holler et al. 2004, Hagner-Holler et al. 2007).
The diagram below illustrates how signals originating in the bodies of phytophagous insects might potentially affect the biochemical machinery of differentiating cells in SAMs of certain developmentally plastic, late Paleozoic host seed plants. Transposable elements might have moved from the insect genome to the host plant genome or vice versa within the confines of a shrub lifeboat (see next section).
Further, host plants might have manufactured phytoecdysones (including brassinolide hormones) that potentially signaled the developmental, respiratory, and storage protein biosynthetic machinery of insect antagonists inhabiting Paleozoic and early Mesozoic vegetation compartments.
Clues on whether or not low pO2 is a selective force come from ecologic, physiologic, and rearing studies of extant insects (Gorr et al. 2006). The Holometabola exhibit complete metamorphosis of the fertilized egg to a wingless larval stage, a quiescent pupal stage, culminating with reproductively mature adults (page 331, Grimaldi and Engel 2005).
Hypoxia in extant terrestrial environments is defined as an oxygen concentration below ca. 20% (Hoback and Stanley 2001). Adaptations to hypoxia in holometabolous insects are specific to developmental stages. According to the review by Hoback and Stanley (2001), several kinds of extant insects are adapted to hypoxic environments including Coleoptera (beetles and weevils), Collembola (springtails), Diptera (flies), Isoptera (termites), Lepidoptera (butterflies and moths), and Orthoptera (grasshoppers and katydids).
Tenebrio molitor beetles exhibit 80% larval mortality, decreased instar body mass, and an increased number of moults when reared in an atmosphere of 10% oxygen in a nitrogen (Greenberg and Ar 1996). Aquatic insects are generally more susceptible to hypoxia than terrestrial insects (Hoback and Stanley 2001). Hoback and Stanley (page 540, 2001) conclude "... that the developmental plasticity of insects facilitates morphological changes in respiratory systems in chronically hypoxic situations."
Choice of hemocyanins and hexamerins as some of the right insect traits to study ties-in with the evolution of insect legs and wings from bilaterian gills. Ancient insect wings probably functioned as respiratory organs. Wings, halteres, arachnid spinnerets, and insect legs are all organs that develop from limb fields of cells where Ubx expression is prevalent (S. B. Carroll et al. 2005).
Escape-and-radiate or oscillate. The "escape-and-radiate" hypothesis was discussed in Chapter 7 of J. N. Thompson's book on coevolution to recapitulate Ehrlich and Raven's (1964) suggestion that reciprocal selection may produce "higher-level patterns of diversification within phylogenetically conserved interacting lineages" (page 150, J. N. Thompson 2005).
Competing "escape-and-radiate" and "oscillate" hypotheses are reviewed by Fordyce (2010). The two hypotheses discussed by Fordyce might be applied to a couple of intractable or difficult questions in population paleoecology:
Was there a potential for genetic release of insect induced molecular effects on the seed plant developmental machinery attributable to shifts of arthropod antagonists away from the plant host to other oxygen-enriched shrub lifeboat habitats and lignophyte hosts?
What specific kinds of paleontologic and molecular phylogenetic data may be used to shed light on the paleobiology of insect-seed plant coevolutionary compartments?
To my knowledge the notion of genetic release in a host plant-insect antagonist coevolutionary relationship at successively complex levels of transcriptional regulation, repetitive ("junk") DNA, genome dynamics, and neo-Goldschmidtian saltation is rarely discussed to explain observations seen by ecologists who study fitness in extant populations.
Since Ehrlich and Raven's classic paper (1964) many colleagues have enthusiastically supported proposals on a coevolutionary origin and/or diversification of flowering plants based on co-radiations between specific groups of animals and seed plant hosts of the Cretaceous Period (Grehan 1991, Crepet and Niklas 2009).
Aspects of coevolution of Mesozoic arthropods and seed plants which have a bearing on the origin and diversity of angiosperms were proposed by Takhtajan (1969), Raven (1977), Thien et al. (1985), Farrell (1998), Labandeira (1998), Grimaldi (1999), Wilf et al. (2000), and S. Hu et al. (2008).
Some of these studies however, focus on possible coevolution of arthropods and the first angiosperms during the Jurassic or Cretaceous periods of the Mesozoic Era, not the Carboniferous or Permian periods of the Paleozoic Era.
There are problems associated with Cretaceous co-radiations of angiosperms and insects brought to light by phylogenetics (Wheat et al. 2007). Presumed co-radiations are often out-of-sync, suggesting that evolution of clades of late Mesozoic phytophagous ants, bees, beetles, butterflies, flies, and moths is independent of the explosive origin and spread of eudicot orders and families.
Coevolution and cospeciation between butterflies and host plants are probably more dynamic than appreciated (Wheat et al. 2007).
Molecular phylogenies of chrysomelid leaf beetles suggest a younger age of the group than previously realized (Gómez-Zurita and Galián 2005, Gómez-Zurita et al. 2007). These findings contradict earlier proposals on a coevolutionary origin of angiosperms during the Cretaceous Period (Farrell 1998, Grimaldi 1999, Wilf et al. 2000).
Shifting pollinators. Ecological studies and phylogenetic analyses of extant species groups with divergent floral characters point toward reciprocal selection and recurring pollinator shifts in the evolutionary history of certain parallel lineages (see review by Fenster et al. 2004).
The recent literature contains several key articles on this subject (P. Wilson et al. 2007, S. D. Smith et al. 2008, J. D. Thomson and P. Wilson 2008, Muchhala and J. D. Thomson 2009, Pauw et al. 2009, Des Marais and Rausher 2010).
Des Marais and Rausher (2010) place an interesting suggestion on the table that might explain in biochemical and genetic terms the mechanism underlying floral color polymorphisms and shifting pollinators. Regulation of flavonoid biosynthesis by flavonol-3'-hydroxylase is affected by cis-regulatory changes in the gene encoding this enzyme.
A study by Ramírez et al. (2007) sheds light on the time of origin of a specific orchid and its pollinator. In follow-up work Ramírez et al. (2011) explore peculiar asymmetries in bee and orchid pollination mutualisms possibly involving sensory behaviour.
Based on a possibility that insect "sensory bias" might affect co-diversification with plant hosts (abstract, Ramírez et al. 2011), could studies of insect pollinator and flowering plant mutualisms from research perspectives of horizontal transmission of tool kit transposable elements shed light on underlying "evolutionary processes" in pollination ecology and shifts?
Coevolution of seed plants and dinosaurian tetrapods. Weishampel and Jianu (2000), in an extensive review of dinosaurian herbivory, cast doubt on the coevolutionary-based idea that ornithischian tetrapods had an effect on the rapid radiation of flowering plants during the Cretaceous Period. Dinosaurians probably did not play a key role in the contrived Cretaceous Terrestrial Revolution (G. T. Lloyd et al. 2008).
According to Weishampel and Jianu (page 137, 2000), three geologic intervals of diversification of euornithopod transverse grinders occurred during the Cretaceous Period "with the middle peak arguably associated with the origin of angiosperms." However, when ghost lineages are added to the cladistic analyses "the middle peak disappears" (page 137, Weishampel and Jianu 2000).
"Whatever coevolutionary interactions may have existed between flowering plants (angiosperms) and ornithischian dinosaurs, they are not apparent at the onset of the evolutionary radiation of angiosperms, as least as far as diversity patterns are concerned."
The preceding quotation is from page 139 of Weishampel and Jianu (2000), Chapter 5, Plant-eaters and ghost lineages: dinosaurian herbivory revisited. Pp. 123-143 In: H.-D. Sues (ed.), Evolution of Herbivory in Terrestrial Vertebrates: Perspectives from the Fossil Record, Cambridge: Cambridge University Press, 256 pp.
Tiffney (2004), in an extensive review of vertebrate dispersal of seed plants, concludes that tight coevolution between animal dispersers and plant is rare. Biotic dispersal of seed plant propagules probably arose through "transfer of function," according to Tiffney (page 6, 2004). Further, he suggests that "the Mesozoic dynamic was dominated by reptile-gymnosperm interactions to which the angiosperms were newcomers" (page 20, Tiffney 2004).
Fitness landscapes. Niklas (1997) expands and modifies Wright's fitness landscape concept in a review of the evolution of early land plants.
How do we apply Sewall Wright's adaptive (fitness) landscape concept toward a better understanding of evolutionary ecology of biome fragments, paleohabitats, seed plant shrubs, trees, mycorrhizal fungi, vertebrate herbivores, and resident phytophagous insects of Pangaea?
Shrub lifeboats. Pockets of air trapped by sheathing, leathery photosynthetic leaves of a monopodium and other crevices in organs of arborescent and herbaceous seed plant species might have had higher amounts of oxygen gas than the surrounding atmosphere of Devonian, Carboniferous, Permian, and Triassic time.
I name the individual seed plant shrubs and small trees of hypoxic late Devonian-early Carboniferous, Permian, and Triassic fitness landscapes that house herbivorous insect antagonists in oxygenated air spaces and crevices, shrub lifeboats.
A higher partial oxygen pressure within the air spaces between host plant leaves could potentially protect resident insect mutualists from atmospheric disruption and hypoxic conditions attributable the DeCARB, GuCCE, EPE, TrCCE, and BaCCE. Trapped oxygen gas of air pockets in the host shrub might have been critical for the survival and metamorphosis of instars (fertilized eggs, larvae, pupae).
Optimal thermogenic microhabitats cast from food-bearing, sheathing leaves and woody tissues could have sustained a resident insect and tetrapod population during times of temperature extremes, hypoxia, and high ultraviolet radiation levels.
The diagram on the left side of the page illustrates a hypothetical seed plant shrub lifeboat. The monopodium with its SAM and large, leathery sheathing leaves is shown from an overhead view. The resident insect colony of eggs and instars (or larvae, pupae, and adults) shown as red-colored objects occupies the oxygenated air spaces that surround the growing tip and hollows formed by clasping leaves of the shrub.
Invoking coevolutionary nomenclature drawn from studies of extant biomes, a shrub lifeboat might also be viewed as a compartment housing antagonists (herbivores and predators) in a locally hot, hypercapnic, hypoxic, Permo-Triassic fitness landscape.
Did perennial seed plant shrubs furnish respiring insects with cavities and air spaces having a higher pO2 than the surrounding hypoxic oxygen desert?
Were ancient baculoviruses a source of cross-Kingdom genome parasites able to move from animal bodies and/or fungal mycelia to reproductive modules and/or growing points of seed plant hosts comprising Permo-triassic shrub lifeboat coevolutionary compartments?
What happened to complex food webs, plant communities and habitats of early Triassic time following the disruptive and extirpatory forces of the EPE?
Some early Paleozoic forests of conifers, ferns, lycophytes, and sphenopsids were stratified and contained complex food webs involving decomposers, primary producers, mycorrhizal fungi, and populations of invertebrates and amphibians (Z.-Q. Wang 2000).
Were elevated carbon dioxide levels and volcanic gases in the atmosphere of late Permian time when combined with low pO2, a selective force in plant and animal populations, including terrestrial arthropod invertebrates and vertebrate tetrapods?
A recent paper by L. G. Stevens et al. (2011) provides some answers to this question, among others.
Knoll et al. (2007) review the possible physiological effects of hypercapnia on animals and plants in connection with the end-Permian global apocalypse and biotic recovery of early Triassic aquatic and terrestrial landscapes. Geochemical studies suggest that late Permian and early Triassic air of Pangaean shorelines had oxygen levels comparable to the highest summits (>5000 meters) of most modern mountain ranges (Huey and Ward 2005).
Based on studies of fossils, paleosols, and geochemistry it was possible that during millions of years of Paleozoic global climate changes, complex networks of generalist and antagonist animal and plant species broke down and/or were disrupted (Retallack et al. 2003, Retallack et al. 2005).
Hypoxic ice-house late Devonian-early Carboniferous fitness landscapes. The ice-house terrestrial paleoenvironments of the DeCARB might have been challenging to the respiratory systems of invertebrates including ancient plecopteran insects (Labandeira 2006). The DeCARB was also a time of seed plant innovation (Rothwell et al. 1996).
Early arthropods exhibited an explosive radiation of molecular novelties of the hemocyanin class of gas-binding respiratory enzymes during the hypoxic DeCARB. At least seven clades of hemimetabolous and holometabolous insects diverged from the thawing ice-house as evidenced by molecular clock estimates of hexamerin moulting storage proteins (Hagner-Holler et al. 2007).
Was the burst of evolution of insect hexamerin proteins from hemocyanins somehow linked to low temperature and low oxygen levels in late Devonian-early Carboniferous terrestrial paleoenvironments?
Are there TFs in arthropod and land plant tool kits, respectively that act as oxygen sensors? Possibly.
Hypoxia-inducible factors (HIFs) are unexpectedly diverse in invertebrates (Rytkönen et al. 2011). Specific HIFs are not yet known from the land plant tool kit but the ERF and AP2 family of TFs might be key players (Licausi 2011, Licausi et al. 2011).
Hypoxic and hypercapnic hot-house Permo-Triassic fitness landscapes. High carbon dioxide levels in the atmosphere and water column preceding and immediately following the EPE might have had profound effects on the physiology of animals (Knoll et al. 2007). Several unanswered questions remain:
How did terrestrial invertebrates and vertebrates cope with high carbon dioxide content and low levels of oxygen in the global atmosphere (<12%) following the GuCCE and EPE?
Was pO2 lower at higher altitudes in, for example, the Hercynian Mountains?
What was the effect of low pO2 and elevated carbon dioxide (hypercapnia), methane, and hydrogen sulfide levels on animals and plants indigenous to aquatic and terrestrial environments?
Two important book chapters compiled by McElwain and coauthors explore the potential effects of hypercapnia on angiospermization, diversification, and rates of speciation in land plants (McElwain et al. 2005, McElwain et al. 2011).
According to Andy Knoll et al. (page 302, 2007), "... hypercapnia can reduce respiratory capacity, exacerbating the physiological effects of environmental oxygen limitation."
"It is possible, therefore, that the high CO2 [Silurian] concentrations acted as an environmental 'barrier' that prevented the origination and spread of large megaphylls. Once that environmental barrier was removed, ecological processes, especially competition between species for light, soil and water nutrients, would have driven both the co-evolution of the root and shoot and the well-documented increase in plant height (Beerling and Berner 2004)."
The previous statement is quoted from page 10 of David J. Beerling and Andrew J. Fleming (2007), Zimmermann's telomb theory of megaphyll leaf evolution: a molecular and cellular critique, Current Opinion in Plant Biology 10: 4-12.
Did Paleozoic seed plant shrubs and trees (or even herbs) furnish respiring insect larvae with cavities and air spaces having a higher pO2 than the surrounding hypoxic landscape?
Could plant organs, tissues, and waxy cuticles shield insect eggs and instars from potentially deleterious UV solar radiation?
The EPE marking the beginning of the Triassic Period of the Mesozoic Era also had devastating effects on growing substrates including extirpation of mycorrhizal fungi and certain soil bacteria. Global terrestrial and aquatic environments became acidified by 600,000 years of global volcanism and more than a million years of precipitation containing dissolved sulfur dioxide (SO2) outgassed from magma underlying the Siberian Traps, a name applied by geologists to early Triassic epicontinental lava lakes.
The art board below shows a community of potentially coevolving animal antagonists that inhabit shrubs and trees of a biome fragment of an hypoxic late Permian fitness landscape based on descriptions by DiMichele and Hook (1992). A biome fragment near a water source in an otherwise arid landscape is depicted with overstory conifers and understory scrub, which is punctuated by dicynodont burrows. Herbivorous dicynodonts were probably the most common vertebrate animals of such late Permian landscapes (DiMichele and Hook 1992).
Did certain Triassic seed plants possess functional underground mycorrhizal nodules? Yes, according to Schwendenmann et al. (2011).
The vertebrate tetrapod population resided with the oxygen generating vegetation consisting of seed plant shrubs and coniferous trees, and an understory of bryophytes, ferns, horsetails, lycopsids, and seed ferns. Seeds rained on to the floor of the biome forming a seed bank sensu Harper (1977), and bisaccate pollen was transported to other shrubs and trees. Insect colonies and free-living invertebrates (antagonistic generalists and predators) are shown in dark red.
Free living insects and certain generalists were probably only able to crawl, fly, or hop short distances from the oxygenated crevices of one shrub lifeboat to another. The surrounding hypoxic desert might have been lethal to most respiring animals. The increasingly small body size of Triassic invertebrates and larger lung cavities of certain tetrapodial vertebrates might have been adaptations of these animals to withstand oxygen deprivation.
The preceding diagram emphasizes a possible fate of one biome fragment immediately following the EPE. In this case, the biome fragment is dominated by antagonistic networks of interacting plants and animals compartmentalized around oxygen generating vegetation including shrub lifeboats. Several questions may be posed:
What were adaptations of land plants available for exploitation by resident insect colonies?
Were these invertebrate colonies subject to predation by insectivorous amphibians and reptiles?
How did the activities of dicynodonts, therapsids, and archosaurian dinosaurs (among other vertebrates) affect the evolution, diversification, and dispersal of seed plants and their angiospermization?
Paleoecological processes in Paleozoic animals and plants were probably not homologous to living systems. Inextricably linked to paleosuccession in Permo-Triassic terrestrial ecosystems following disturbance was the feeding behavior of herbivorous and insectivorous amphibians and early reptiles including archosaurians, dicynodonts, and therapsids, among other tetrapods (Tiffney 1992).
Hypocapnic and hyperoxic Cretaceous fitness landscapes. Impacts of hyperoxic oxygen levels in the atmosphere of Permo-Carboniferous time are reviewed by Beerling and Berner (2000) and Scott and Glasspool (2006). McElwain et al. (2005) in a review chapter on the effects of atmospheric carbon dioxide on angiosperm origin, radiation, and paleodiversity conclude:
"It is likely, therefore, that a long-term trend of CO2 decline through the Cretaceous period may have played an extremely important role in the diversification of angiosperms ..."
The previous phrase is quoted from page 158 of J. C. McElwain, K. J. Willis, and R. Lupia, 2005, Chapter 7. Cretaceous CO2 decline and the radiation and diversification of angiosperms. Pp. 133-165 In: J. R. Ehleringer, T. E. Cerling, and M.-D. Dearing, A History of Atmospheric CO2 and its Effects on Plants, Animals, and Ecosystems. New York: Springer, 530 pp.
Cretaceous angiosperm diversification might have been triggered by abiotic effects of carbon dioxide decline (hypocapnia) on the physiology of flowering plants as McElwain et al. suggest. However, a concomitant rise in atmospheric oxygen content probably also had physiologic effects on insect antagonists of early Aptian angiosperms.
Coevolutionary arms race. The scientific literature on the coevolutionary arms race ("Darwin's race" title, Pauw et al. 2009) is vast and beyond the scope of this essay. Key references include published work by I. T. Baldwin (1998, among numerous other publications), Cornell et al. (2003), J. Wu and I. T. Baldwin (2010) and Hare (2011). High points of this line of scientific inquiry are stated in this section and in the next chapter.
A coevolutionary arms race at the molecular level between populations of coevolving flowering plant hosts and insect antagonists is supported by real-time experimental studies. Further, evo-devo studies using biochemically altered probes, genetically-engineered TFs, and microRNAs demonstrate the lability of flowers and insect bodies.
Insects are unable to manufacture cholesterol ring systems required for the biosynthesis of 20E-ecdysone, an important steroid in endocrine signaling, but must obtain precursor molecules from digested products of animal and plant tissues, which are then assembled by cytochrome P450 enzymes (Truman and Riddiford 2002).
A recent review of the evolutionary history of the cytochrome P450 protein family is available (Nelson and Werck-Reichhart 2011).
Certain enzymes of lepidopteran insect guts are able to isomerize biosynthetic precursors of oxylipin phytohormones (Dabrowska et al. 2009). Jasmonic acid oxylipins, which are biosynthesized as a response to mechanostimulation (wounding) of tissues by herbivores (I. T. Baldwin 1998, among others), affect stamen- and pollen tool kits (Devoto and Turner 2003), and induce nectar biosynthesis (Heil 2011). Other VOCs are released by plants when attacked by herbivores (Hare 2011).
Experimental evidence on the efficacy of arthropod digestive enzymes to alter the molecular structure of ingested phytohormone precursors may have implications toward an understanding of coevolutionary arms race dynamism.
Plants manufacture many small polypeptides that affect reproductive development (BRICK, CLAVATA3-like/embryo-surrounding [ESR], CLE, cyclotide mini-proteins, and Dresselhaus proteins) or operate in defense and wounding responses (systemins), or in molecular mimicry. Some of these possess insulin-like (e.g. leginsulin) or neuropeptidal (e.g. plant atrial natiuretic peptides) properties that affect insect development and physiology (Germain et al. 2006).
Does the inherent lability of floral and insect organs inferred from laboratory studies have a molecular genetic basis applicable at the population level to coevolving plants and animals?
"Coevolution is a well characterized process that takes place at all biological levels, from ecosystems to molecules."
The preceding quotation is from page 934 of Juan et al. (2008), High-confidence prediction of global interactomes based on genome-wide coevolutionary networks, Proceedings of the National Academy of Sciences 105(3): 934-939.
Understanding the selective forces behind molecular coevolution of insect and seed plant DNA-binding TFs and CRMs in deep time i.e. hundreds of millions of years, might be an important first step in unraveling the enigmatic origin of angiosperms, evo-devo of the first flower, and adaptive radiation of certain clades of coevolving Holometabola.
The next two chapters consider scientific evidence drawn from plant physiology and genetics critical toward a greater understanding of the putative Paleozoic beginnings and later Mesozoic adaptive radiation of the first angiosperms.
This chapter considers evidence from the physiology of interacting plants and insects from a different research perspective. A discussion of phytohormones and defense substances and insect developmental and respiratory proteins, hormones, and neurotransmitters is necessary to understand possible molecular coevolution of insect and seed plant developmental tool kits, animal-plant signaling, and the ongoing coevolutionary arms race (Becerra et al. 2009, Pauw et al. 2009).
Some of the topics covered here are discussed by the contributing authors to chapters in a book edited by Hemsley and Poole (2004) and papers authored by Feild et al. (2003), Feild et al. (2004), Brodribb et al. (2007), Feild and Arens (2007), and Feild et al. (2011 [two papers]), among others.
The time in geologic history to consider paleoecophysiology of early angiosperms should be coincident with findings suggested by molecular phylogenetic inference (Magallón 2010, S. A. Smith et al. 2010), which is the Permian Period of the late Paleozoic Era and Triassic Period of the early Mesozoic Era.
Work published by Boyce and Knoll (2002) and Boyce et al. (2009) offers firm footing for the slippery slope of later optimistic conclusions on a supposed rapid rise of angiosperms and their adaptations under early Cretaceous climatic and ecological regimes (Feild and Arens 2005).
Insect development is apparently controlled by cis-acting TFs (S. B. Carroll et al. 2005) and hormone signals acting in regulatory networks and cascades (Bonneton et al. 2008). Further, structural similarities exist in the trihelical bundle of certain HTH cis-regulatory homeodomain proteins of the model insect Drosophila melanogaster and angiosperm malvid Arabidopsis thaliana.
The image to the right is a 20 × 20 cm polyamid thin layer chromatogram representing successive gel filtration column fractions from a mixture of floral flavonoids (x-axis), partitioned in an aqueous solvent mixture (y-axis) by TLC. Development of the thin layer chromatogram and treatment with Natural Products Reagent A reveals a separation of flavonol mono-, di-, and triglycosides, viewed under long wave UV light and captured on ASA 25 kodachrome film. The yellow-orange spot to the right is a standard sample of quercetin-3-O-glucoside, a flavonol monoglycoside.
Natural products, phytohormones, and signaling. This section briefly discusses the high points of a great body of literature in plant physiology, which is devoted to bioactive secondary plant products. Certain natural products are natural insecticides and phytohormones.
According to Floyd and Bowman's phylogenetic analyses (2007) the auxin, ethylene, and gibberellin metabolic pathways are highly conserved and involve several ancient land plant enzyme systems including AP2/ARFs, DELLAs (TFs of the GRAS family), and ERFs.
Did Paleozoic seed plants manufacture bioactive plant natural products and phytohormones and signal moulting insect instars residing in oxygenated crevices and leaf bases of massive SAMs?
Likewise, did phytophagous insect antagonists of Permo-Carboniferous and Permo-Triassic seed plants signal the homeotic genetic machinery of host plants affecting SAM development and morphology?
An important clue comes from naturally occurring but fossilized triterpenoids known as oleanone triterpanes (oleananes) and class 1c components of fossilized resins (amber).
Oleananes, together with ursenes, lupenes, and taraxerenes are important TSBs that belong to a class of Β-amirin triterpenoids (Moldowan and Jacobson 2002). Class 1c resin constituents associated with Mesozoic angiosperm amber are known from 320 million year old (Paleozoic) amber samples (Bray and K. B. Anderson 2009).
Do TSBs provide indirect evidence that certain Paleozoic seed plants once manufactured steroids and terpenoids?
Were Vojnovskyales and gigantopteroid seed plants a source of angiosperm-like class 1c components of Carboniferous amber deposits?
Natural products. Plants manufacture thousands of natural plant substances. The main groups of biologically active micromolecules are alkaloids (including betalains), amino acids and small polypeptides, anthocyanins and flavonoids (B. A. Bohm 1998), polyacetylenes (Lersten and Curtis 1989), steroids (Suzuki et al. 2006), terpenoids (Cheng et al. 2007, S. Lee and Chappell 2008), and lipids and waxes, which are necessary in plant protection and signaling.
The study of anthocyanins and other flavonoids as chemotaxonomic markers in plants dominated the literature in systematic botany for almost two decades (B. A. Bohm 1998). Flavonol aglycones are biosynthesized by the flavonol synthase enzyme (Owens et al. 2008).
A few members of the cytochrome P450 gene family are implicated in flavonoid metabolism together with R2R3 MYB TFs (Rosinski and Atchley 1998, Boudet 2007, Nelson and Werck-Reichhart 2011). The MYB-related TF MIXTA is important in epidermal cell patterning of flower petals that contain UV-absorbing flavonoids compounds visualized by insect pollinators (Baumann et al. 2007).
Some flavonoids are antioxidants that inhibit auxin efflux carriers. Many flavonoids are implicated in hormone signaling, plant defense, and regulation of gene expression (Koes et al. 2005, Owens et al. 2008).
Biosynthesis of chalcone synthetase is affected by the hormone gibberellic acid in some flowering plants. Chalcone synthetase manufactures many classes of flavonoids involved as antioxidants, bee-violet attractants in flowers such as Rudbeckia hirta, and as UV shields.
Steroids are well-known natural products manufactured by plants for use in defense and signaling (Truman and Riddiford 2002).
Phytohormones. Perception of environmental stimuli by coevolving insects and plants and transduction of signals back and forth to insect antagonist and host plant genomes were probably hallmarks of shrub lifeboat compartments in Paleozoic times. Plant and insect physiologists employing extant organisms as research subjects publish data each year that indirectly supports this hypothesis.
Coevolution between developmental tool kits of insect herbivores and host seed plants might require that communication take place at all levels from interacting populations to molecular systems. The plant cytoskeleton, touch receptors, and phytohormones (Bari and Jones 2009); and insect secretions and sensory receptors may play key roles in communication between plant and animal and vice versa.
Are herbivorous insects capable of inducing morphological changes in the plants they eat or use for shelter and rearing of offspring?
Can insect derived cues affect geometric patterns in SAMs?
Auxins. Auxin down-regulates Class I KNOX genes in developing SAMs of extant flowering plant experimental systems permitting gibberellic acid activity in leaf primordia and promoting growth (Weiss and Ori 2007). Membrane proteins known as efflux and influx carriers control auxin movement from cell to cell in the SAM.
Phyllotaxis is apparently regulated by the differential translocation of auxin phytohormones in SAMs in at least some extant species (R. S. Smith et al. 2006). Auxin biosynthesis catalyzed by TAA oxidase mediates cross talk with ethylene in etiolated Arabidopsis seedlings. Auxin gradients in floral meristems affect tissue patterning and the expression of YUCCA genes (Stepanova et al. 2008).
Auxin is "a major regulator of organogenesis" (title, Bohn-Courseau 2010).
Further, ARF genes encode cis-acting ARF proteins that bind to auxin responsive genes (Busov et al. 2008, Delker et al. 2008, R. S. Smith 2008). Auxin response factors figure prominently in the regulation of leaf morphology and belong to the ancestral developmental tool kit of land plants (Floyd and Bowman 2007).
The MIKC-type MADS-box TF SEP3 interacts with ARF and other elements of several hormone signaling cascades in Arabidopsis (Kaufmann et al. 2009).
Clues on the possible existence of polar auxin flow in woody stems have been uncovered in comparative anatomical studies of a 375 million-year-old fossilized progymnosperm known as Archaeopteris and modern conifers (Rothwell and Lev-Yadun 2005). The fossil record reveals that auxin regulation of secondary growth was a conserved physiologic process (Rothwell et al. 2008).
Based on the phylogenetic analysis of Class I KNOX genes (Floyd and Bowman 2007), paleobotanical evidence of polar auxin flow in Devonian plant fossils (Rothwell and Lev-Yadun 2005), and deep conservation in terpenoid enzymology (S. Lee and Chappell 2008) needed to biosynthesize diterpenes including gibberellic acid, it is not unreasonable to add auxins and gibberellins to the regulatory tool kit of early diverging land plants.
Brassinosteroids. Brassinolides (BRs), are structurally similar to 20E-ecdysone, a potent insect steroid moulting hormone. Brassinolides are also implicated in endogenous ethylene production (J. Li and Chory 1999, Thummel and Chory 2002, Zullo and Adam 2002).
A recent review of brassinolide metabolism in plants is available (T.-W. Kim and Z.-Y. Wang 2010).
Cytokinins. Zeatin and other cytokinins are modified nucleotide phytohormones that induce the expression of WUS genes in CLAV pathways in developing SAMs (Gordon et al. 2009), among other profound regulatory effects on plant growth and development.
Ethylene. Ethylene is a gaseous hormone with profound effects on plant growth, development, and responses to biotic stress including herbivory. A family of five membrane bound receptor proteins perceives ethylene molecules from the external environment. The ethylene signaling cascade crosstalks with the biosynthetic machinery of most other phytohormones including abscisic acid (ABA), auxins, BRs, and gibberellins (Y. F. Chen et al. 2005).
For example, ethylene adversely affects gibberellic acid by activating DELLA repressing proteins. In turn, DELLAs repress the floral integrator genes LFY and SOC1 resulting in delayed flowering in Arabidopsis (Achard et al. 2007). Ethylene and gibberellic acid (GA) biosynthesis in plants is enhanced by insect neurotransmitters such as catecholamines (Schultz 2002).
Gibberellins. Key diterpenoid hormones of the developmental tool kit of extant plants include gibberellins (Weiss and Ori 2007). The effects of nuclear regulatory growth repressing DELLA proteins that belong to the GRAS family of transcriptional regulators are relieved by GA via the ubiquitin 26S proteasome biosynthetic pathway (Yu et al. 2004, Axtell and Bartel 2005, Lu et al. 2005, Jiang and Fu 2007, Weiss and Ori 2007, Gao et al. 2008, Hartweck 2008).
Studies of the malvid Arabidopsis provide evidence that GA controls the development and morphology of trichomes on leaves, flowers, and shoots by de-repressing DELLAs (Gan et al. 2007). Whether the mechanism of GA action on the negative effects of nuclear regulatory growth repressing DELLA proteins on glandular hair and trichome development in other seed plants is the same as Arabidopsis is not known. Trichomes and glandular hairs play an important role in defense against herbivores.
DELLAs restrain plant growth and development under adverse environmental conditions in extant flowering plants, and repress the accumulation of reactive oxygen species (Achard et al. 2008).
Did these nuclear repressing proteins play a role in the diversification and adaptive radiation of flowering plants in fluctuating paleoclimates?
The ubiquitin 26S proteasome pathway is employed by animals and plants to control levels of- and degrade regulatory proteins such as gibberellin sensitive plant DELLAs and certain ethylene regulatory enzymes (Y. F. Chen et al. 2005).
Several other plant hormones including ABA, auxin, cytokinins, and ethylene, interact with GA. Some of hormone interactions with GA are negative and reciprocal. For example, when rice is grown under hypoxic conditions, culm and internode elongation requires both ethylene and GA. Knotted 1 homeodomain proteins induce the production of cytokinins in SAMs that in turn inhibit the biosynthesis of GA (Weiss and Ori 2007).
Oxylipins. Jasmonic acid (JA) and related esters belong to the oxylipin family of molecules (Wasternack 2007, Chico et al. 2008). Jasmonates are hormones implicated in conserved but specific biochemical- and plant-morphogenetic effects (I. T. Baldwin 1998, Biondi et al. 2001, Balbi and Devoto 2008, Katsir et al. 2008).
Specific effects include the ability of oxylipins to reprogram expression of JA-inducible genes (Pauwels et al. 2009). Jasmonates, biosynthesized as a response to mechanostimulation (wounding) of tissues by herbivores (I. T. Baldwin 1998) orchestrate plant defense (Ballaré 2011) and affect development of stamens and pollen (Devoto and Turner 2003).
Further, JA induces nectar formation in tissues of extant seed plants (Heil 2011).
Salicylic acid. Salicylates (SAs) is a well known natural signaling molecule that a play key role in activating genes for defense and integrating WRKY transcription factors during plant responses to herbivory and wounding (Wasternack 2007, Balbi and Devoto 2008, Blanco et al. 2009).
Simple gases. Nitric oxide (NO) is a gas with profound mediating effects on phytohormone cross talk, development of flowers and pollen tubes, defense, and signaling (Perazzolli et al. 2006, Besson-Bard et al. 2008 [two papers], Palavan-Unsal and Arisan 2009, Gupta et al. 2011). Nitric oxide activates protein kinase G (PKG) in mammals. Both molecules are important to survival of insects in artificial hypoxic environments (Wingrove and O'Farrell 1999, Hoback and Stanley 2001).
Interestingly, NO also binds to hemoglobins, a class of oxygen-binding enzymes found in plants (Perazzolli et al. 2006), and vertebrates and invertebrates including certain species of the insect orders Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera (Van Holde et al. 2001, Burmester and Hankein 2007). Further, both NO and PKG enhance the survival of Drosophila larvae when deprived of oxygen in the laboratory (Wingrove and O'Farrell 1999).
Were Paleozoic insect antagonists attracted to potential NO emissions by host plants (where NO possibly played a role in ameliorating the detrimental effects of local hypoxia on egg and larval development)?
Carbon dioxide is also a gaseous signaling molecule, which is perceived by the olfactory receptors of blood sucking, meat eating, and herbivorous insects. At certain concentrations CO2 becomes an odor to Manduca moths (Goyret et al. 2008).
How did hypercapnic paleoenvironments following the GuCCE, EPE, TrCCE, and BaCCE affect molecular evolution of insect olfactory receptor proteins and coevolution of stem group angiosperms and their pollinators?
Strigolactones. Carotenoid-derived hormones implicated in negative repression of axillary bud growth include strigolactones (Dun et al. 2009, Rameau 2010). Potential biological activity of strigolactones in insect antagonist and host plant systems should be researched.
Signaling by herbivory and wounding. The mechanism of action of hormone signals in SAMs is an active area of research in plant physiology. Volatile organic compounds are often released by plants when attacked by herbivores (Hare 2011, among others).
Through a process termed signal transduction, biochemical signals originating in the insect exoskeleton manipulate and control the genetic machinery needed for orderly, or disorderly growth and expansion of shoots and other organs of the plant (Pandey et al. 2008).
Molecular studies on the herbivorous sphingid moth, Manduca sexta by Ian Baldwin and students, demonstrate several molecular interactions between the insect and the wild tobacco plant host Nicotiana attenuata (Solanales, Asteranae) that potentially affect the ecology and development of both organisms. The activities of the specialized insect herbivore induces "... a dramatic ethylene release, a jasmonate burst, and a suppression of nicotine accumulation ..." in simulations of herbivory on the host plant (abstract, Winz and I. T. Baldwin 2001). Further, plant mRNAs accumulate "... in response to insect-derived cues" (title, Schittko et al. 2001).
Gall forming insects inject plant cells with modified transfer RNAs (tRNAs), which are in fact, cytokinins. Injected cytokinins biosynthesized by phloem feeding insects cause rapid differentiation and disorderly growth in plant tissues resulting in gall formation (Schultz 2002).
Small CSE polypeptides biosynthesized in the esophageal glands of parasitic nematodes when injected through feeding stylet into plant cells, affect development of floral meristems (Germain et al. 2006). The historically elusive flowering hormone florigen is now known to be a small protein that is transported through the phloem of angiosperms (Shalit et al. 2009).
Do hormones secreted by parasitic invertebrates or insect instars and larvae upregulate or repress homeotic genes in host seed plant SAMs?
Possibly, at least based on a recent review by J. Wu and I. T. Baldwin (2010).
Plant light receptors. Phytochrome, an enzymatic light receptor implicated in several physiological processes in plants, including flowering, affects regulation of MIKC-type MADS-box genes. Issue Number 12 of Volume 58 (2007) of the Journal of Experimental Botany is devoted to photomorphogenesis.
Further discussion of photoreceptors in plants is beyond the scope of this essay although phytochrome genes figure prominently in early attempts to unravel angiosperm phylogeny (Mathews and M. J. Donoghue 1999).
Mathews et al. (2010) present new data and valuable insight on the timing of major events in flowering plant evolution based on amino acid sequences of the phytochrome enzyme.
Insect hexamerins (Hxs): molecular evolution of hemocyanins (Hcs). As the Neoproterozoic snowball Earth slowly warmed during the Cambrian and Ordovician periods global oxygen concentration increased. Photosynthesis in the chloroplasts of aquatic algae, protozooans, and land plants was the source of oxygen gas (Berner 1999, Berner and Kothavala 2001).
Hemocyanins (Hcs) of invertebrate circulatory systems evolved during the early Paleozoic as a class of gas-binding, copper-containing enzymes needed in respiration (Burmester and Hankein 2007, Pick et al. 2009). Iron-containing hemoglobins (Hgs) of animals also evolved and diversified during this time (Burmester et al. 1998, Van Holde et al. 2001, Burmester 2004).
Molecular evolution of copperless insect storage Hxs from Hcs of invertebrate copper containing enzymes may be linked with the late Devonian/early Carboniferous ice-house cooling of the Earth, accompanied by a drop in oxygen levels to 13% (Berner and Kothavala 2001, Ward et al. 2006). Protein storage macromolecules of the Hc family of enzymes are termed Hxs (Burmester 2001, Moreira et al. 2004).
Thorsten Burmester and coworkers (1998) describe the molecular evolution of Hx hemolymph protein subunits from the Hc family of enzymes in two important reviews (Burmester 2001, Burmester et al. 2006). Hexamerins are moulting storage proteins composed of multimeric polypeptide chains. Each Hx enzyme subunit has a molecular weight of about 80,000.
Hemocyanins including Hxs are critical to developing and respiring entognathous hexapods and true (ectognathous) insects, being necessary for instar development and successive moults (Hagner-Holler et al. 2004, Pick et al. 2009). Larvae digest Hx storage proteins to release certain amino acids required for development (Moreira et al. 2004).
Hexamerins are also implicated as silencers of JH signaling in neotenous castes of hemimetabolous termites (X. Zhou et al. 2006, X. Zhou et al. 2007) and caste polyphenism in holometabolous wasps (J. H. Hunt et al. 2007).
Moulting food storage proteins, homeotic selector genes including Hox genes, zygotic genes, field specific selector genes, compartment selector genes, cell-type-specific selector genes, segment polarity genes, and controlling factors behind the cessation of insect growth (brain neurosecretory PTTH, JH, and ecdysone steroids) comprise key elements of the developmental tool kit of insects (Truman and Riddiford 2002, S. B. Carroll et al. 2005).
Trans-acting chromatin proteins and cis-regulatory TFs of eukaryotic genomes respond to oxygen levels in controlled environments. For example, lowering oxygen concentration in controlled environments affects levels of nonubiquitinated proteins and activates hypoxia-responsive genomic DNA elements (HREs) (Flück et al. 2007). Further, "hypoxia regulated gene expression very likely reflects an ancient adaptive trait that was established in primitive eukaryotes in response to alterations in levels of oxygen" (page 529, Flück et al. 2007).
The below graphic is a crude plot of changing oxygen levels in Earth's atmosphere over geologic time based on GEOCARB III (Berner and Kothavala 2001), and other work (Beerling and Berner 2002, Huey and Ward 2005, Ward et al. 2006). I superimposed an evolutionary tree showing cladogenesis of insect Hxs from invertebrate Hcs, which is based on the most recent molecular clock estimates by Hagner-Holler et al. (2007) and morphological data. In addition, I plotted three of the four insect herbivore expansion phases outlined by Labandeira (2006) on the graph.
The preceding plot is redrawn from Figure 6 on page 1072 of Hagner-Holler et al. (2007), Diversity of stonefly hexamerins and implication for the evolution of insect storage proteins, Insect Biochemistry and Molecular Biology 37: 1064-1074, with additional data added from GEOCARB III (Berner and Kothavala 2001), GEOCARBSULF (Berner 2006), and Labandeira (2006).
Three bursts of molecular evolution of insect Hxs are apparent from the Hagner-Holler et al. data (2007). The first of the Hx molecular evolutionary radiations roughly corresponds with the DeCARB, 360 to 320 MYA (Hagner-Holler et al. 2007) and the initiation of Insect Herbivore Expansion Phase 2 (Labandeira 2006). During hypoxic intervals of the DeCARB seven clades of Hxs diverge from primitive Plecoptera (stoneflies) leading to many derived hemimetabolous and holometabolous insect orders (Hagner-Holler et al. 2007).
A second burst of insect Hx evolution occurs prior to the GuCCE and a decline in atmospheric oxygen levels from 31% to 12% (Berner and Kothavala 2001, Ward et al. 2006). During this interval, Hxs diverged into clades leading to the Coleoptera (beetles and weevils), Hymenoptera (bees and wasps), and Diptera (flies), and certain Lepidoptera (butterflies and moths). This interval of Hx diversification corresponds with Insect Herbivore Expansion Phase 2 (Labandeira 2006).
The point of divergence between the Hx class belonging to beetles and those Hxs belonging to bees and wasps roughly coincides with the second burst of Hx evolution.
Was the second explosion of molecular evolution of insect Hx protein subunits driven by developing hypoxia following the GuCCE of the late Permian, or did diversification occur before the GuCCE as the data suggest?
Dipteran Hxs diverged roughly about the same time as oxygen levels in Earth's atmosphere declined to 12%. The third burst of Hx evolution leading to blattarians (cockroaches) and Isoptera (termites) occurs at a point in geologic time coincident with the TrCCE (Beerling and Berner 2002).
Rough estimates of molecular divergence times of insect Hxs published by Hagner-Holler et al. (2007) could be refined to include GEOCARB III data and calibrated with fossils.
A more detailed synthesis of invertebrate gene duplications and later molecular evolution of Hxs and vitellogenins in populations of coevolving insect antagonists and Permo-Triassic seed plants is possible. Precise molecular phylogenetic and isotope studies are needed to implicate global hypoxia as an underlying selective force in the evolution of insect Hxs. Insect Hgs remain relatively unstudied in this context. Several questions come to mind:
Were Paleozoic changes in atmospheric oxygen concentration the selective force driving the molecular evolution of gas-binding Hc respiratory enzymes and moulting storage proteins of Permian insects?
Are Hxs hypoxia inducible Hx storage proteins of insects?
What was the role of NO in mediating developmental and physiologic effects of hypoxia on Paleozoic insects living with plants?
Did certain steroid hormones manufactured by Permo-Triassic seed plant host shrubs act like ecdysones while sending signals to the genetic machinery of developing eggs, instars of phytophagous insects inhabiting shrub lifeboats?
At the same time that Hx molecules were probably evolving in insect populations and colonies of shrub lifeboats, trampling and secreting insect antagonists might have sent signals to the genetic machinery of SAMs of host plants. Signals, secretions, and genetic parasites originating in the bodies of phytophagous insects could have had affected developmentally plastic SAM tool kits of Permo-Triassic seed plant hosts.
Insect sensing and hormone signaling. Arthropods manufacture several classes of hormones that regulate development and together with anatomically modified appendages, they facilitate communication among individuals, within castes of social insects, or possibly with plant hosts.
Some of the hormones produced by insects which are active in signaling and sensing include ecdysone steroids, epoxide methyl esters of sesquiterpenoids, peptides and polypeptides, and pheromones (Robertson and Wanner 2006).
Insect olfactory and gustatory chemoreceptors (Abdel-latief 2007) and innervated bristles are of potential interest with respect to plant to insect, insect to insect, and insect to plant communication by biomolecules and thigmo.
Nicholas Strausfeld (2009) reviews the deeply conserved evo-devo of arthropod mushroom bodies in the biochemical and phylogenetic context. Mushroom bodies are paedomorphic neuropils of insects and firebrats that function in control of behavior, and in olfactory perception (Strausfeld et al. 1998, S. M. Farris 2005, S. M. Farris and Schulmeister 2011).
Olfactory organs and chemoreceptors (Ray et al. 2008) allow certain insects to sense minute concentrations of pheromones, NO, carbon dioxide, and other VOCs in the air. Beetles exhibit many adaptations to smell and taste and this is reflected in considerable anatomical, biochemical, and morphological diversification in sensillae of antennae, legs, mouthparts, and wings (Abdel-latief 2007).
The scanning electron micrograph shown above is the anterior front part of the head of Haptoncus tahktajanii (Nitidulidae, Coleoptera), the cucujiform phytophagous associate of the primitive magnoliid flowering plant Degeneria vitiensis (Degeneriaceae, Magnoliales, Magnoliidae). Some of the gustatory, olfactory, and visual sensory organs of the nitidulid beetle are visible including antennae, sensillae, compound eyes, mandibles, maxillae, and labia.
Nitidulids were collected by the author from flowers clipped from the canopy of Degeneria trees at the Mount Naitaradamu Study Area, Viti Levu, Fiji Islands in 1986. The National Geographic Society is acknowledged for providing research funding for this work. The photograph is by Al Soeldner of the Oregon State University Electron Microscope Laboratory, × 100.
Certain insect hormones exhibit bioactivity in plants, and some natural plant substances are bioactive agents in insects. Many bioactive substances were probably integral components of the early diverging arthropod developmental tool kit.
Further, genomic analyses and indirect proteome computational modeling reveal numerous insect specific olfactory proteins implying a rich and conserved evolutionary history (G. Zhang et al. 2007).
Several neurosecretory hormones play an important part in mechanisms that regulate cell division and growth including insulin-like peptides (Drosophila insulin-like DILPs and bombyxins), chitenase-derived imaginal disk factor proteins, the steroid hormone ecdysone, local autocrine and paracrine TFs, and PTTH (Nijhout 2003).
Juvenile hormone biosynthesized in the corpora allata of the insect brain is a sesquiterpenoid epoxide methyl ester (Hartfelder 2000). Interestingly, many naturally-occurring plant sesquiterpene esters and lactones are bioactive and exhibit insecticidal properties. Juvenile hormone and its homologs are intertwined with vitellogenesis (Hartfelder 2000), regulation of moult cycles (Truman and Riddiford 2002), and caste development and behavior in social Hymenoptera (Guidugli et al. 2005).
Vitellogenins play a central role in insect female reproductive development. High levels of vitellogenin inhibit the production of JH. It is widely believed that such interactions are highly conserved ancient features of female insect physiology (Guidugli et al. 2005).
Ecdysone steroids play a central role in regulation of growth and development of moulting insects comprising the Holometabola (Grimaldi and Engel 2005). In Manduca sexta (Lepidoptera), PTTH is released by the insect brain to initiate a moult. In turn, PTTH triggers the ecdysone cascade and the larva develops into the pupa, and so forth (Truman and Riddiford 2002).
Are natural plant substances including BRs and sesquiterpene lactones capable of regulating the expression of insect Hox genes including Ubx and pb?
Based on Drosophila melanogaster (Diptera) work, 20E-ecdysone signals are received by cis-acting EcR isoforms. The functional EcR is a heterodimer made-up of usp and EcR. Further, the ligand binding domains (LBDs) of EcR isoforms is unusually divergent in holometabolous clades of insects (Truman and Riddiford 2002, Watanabe et al. 2010).
Interestingly, the "sudden divergence" of dipteran and lepidopteran LBDs of the EcR (page 847, Truman and Riddiford 2002) coincides with the supposed angiosperm-gymnosperm split, roughly 300 MYA, seen in evolution of MIKC-type MADS-box TFs and LFY protein CRMs.
Is timing of divergence of EcR isoforms, MIKC-type MADS-box TFs, Engraled protein, and LFY enzyme coincidental, or is this an example of possible molecular coevolution of certain elements of insect and seed plant developmental tool kits leading to the origin of flowers and holometabolous insect body plan novelties of butterflies, moths, and flies?
Can we pin-point divergences of insect- and angiosperm tool kit components using fossil calibrated molecular phylogenies? Yes.
Helix-turn-helix (HTH) proteins. There are four major groups of regulatory proteins present in most forms of life that share a similar conserved amino acid sequence in the DNA-binding domain: helix-loop-helix, HTH, leucine zipper, and zinc finger (Rosinsky and Atchley 1999, S. B. Carroll et al. 2005, Feller et al. 2011, among others).
Helix-turn-helix proteins mediate interactions between substrates and the enzymes that bind to DNA, affect cell division, control circadian rhythms, transport and organize DNA, and regulate transcription in bacteria, algae, animals, fungi, and plants. There are several main classes of HTH proteins and many hundreds of structural forms found in most forms of life (Aravind et al. 2005).
Enzymes with a helix-loop-helix and/or HTH DNA-binding motif consisting of a trihelical bundle are termed homeodomain proteins (Aravind et al. 2005). The HTH DNA-binding motif is an important component of developmental CRMs which are critical in insect and plant body patterning (S. B. Carroll et al. 2005, Glover 2007).
Homeodomain proteins are important in animal, fungal, and plant development (Bharathan et al. 1997, Rosinsky and Atchley 1999, Aravind et al. 2005, Baumann et al. 2007). Certain MYB proteins also possess an HTH structure in the DNA-binding homeodomain (Dubos et al. 2010, Feller et al. 2011, among others).
Phylogenetic analyses suggest a possible close evolutionary relationship in deep time between several classes of animal, fungal, and plant homeodomain proteins (Bharathan et al. 1997). Two groups of KNOX homeodomain proteins exist in angiosperms based on phylogenetic studies (Bharathan et al. 1999). These are the BEL1-like and KNOX homeodomain proteins that belong to the TALE family of TFs (Hamant and Pautot 2010).
It may be important to consider the molecular paleobiology and paleophysiology of homeodomain proteins in developing explicit hypotheses on a possible coevolutionary origin of angiosperms and certain holometabolous insects.
Rosinsky and Atchley suggested on page 306 of a 1999 review paper that "the evolution of the HTH family of proteins has been marked by strong evolutionary forces maintaining a specific secondary structure (the HTH structure) and a single function (sequence specific DNA binding)." The specific primary and secondary structures being discussed by these authors were the two alpha helices of the HTH DNA-binding motif, and primary structural amino acid residue 390 (R390), which is lysine.
Hamès et al. (2008) deduced the primary and secondary structure of two alpha helices of the HTH DNA-binding motif of LFY protein.
"The acquisition R390 [of LEAFY protein] might therefore have been important for flower evolution."
The previous statement is quoted from page 2635 of C. Hamès, D. Ptchelkine, C. Grimm, E. Thevenon, E. Moyroud, F. Gérard, J.-L. Martiel, R. Benlloch, F. Parcy, and C. W. Müller (2008), Structural basis for LEAFY floral switch function and similarity with helix-turn-helix proteins. The EMBO Journal 27: 2628-2637. The phrase in brackets  is mine.
Are there structural and functional relationships between the homeodomain proteins of insect antagonists (e.g. Engraled [en]) and homeodomain proteins (Class III HD-Zip and KNOX, among others) of seed plant hosts, which might have a bearing on a coevolutionary origin of hexapods and angiosperms?
Physiology and molecular biology of cone development and flowering. Since the pioneering work of Coen and Meyerowitz (1991) tremendous advances have been made in understanding the physiology and molecular biology of flowering within an evo-devo context (Endress 2006, Irish 2006, D. E. Soltis et al., eds. 2006, Glover 2007, Whitney and Glover 2007, Hileman and Irish 2009, P. S. Soltis et al. 2009, Specht and Bartlett 2009).
Regulation of flowering is reviewed by Specht and Bartlett (2009), Chanderbali et al. (2010), Melzer et al. (2010), Rudall and Bateman (2010), D. W. Taylor (2010), Dornelas et al. (2011), and Rudall et al. (2011).
A compilation of reviews on the biochemistry and genetics of cones and flowers appears in Issue 1 of Volume 21 of Seminars in Cell and Developmental Biology (2010).
Induction of flowering from vegetative SAMs and changes in accessory meristem identity occurs four different ways (Glover 2007):
induction of flowering by perception of photoperiodism
meristem determination and flower formation by DELLA de-repression, the ubiquitin 26S proteasome pathway, and GA
Floricaula and LFY genes and the DNA-binding HTH proteins they encode i.e. Floricaula and Leafy enzymes, are main integrators of the biosynthetic and developmental pathway that leads to organ identity and formation of reproductive modules in the fertile SAMs of seed plants (Becker et al. 2000, Irish 2006, Jack 2004, Theißen and Kaufmann 2006, Theißen and Melzer 2007, Specht and Bartlett 2009, Gramzow et al. 2010, Zobell et al. 2010), but FLC, PAN (a bZIP protein), SEP3 (a MIKC-type MADS-box protein), UFO, and Wuschel [WUS] (a homeodomain protein} are also possibly involved as cofactors and regulators (Vásquez-Lobo et al. 2007, Nardmann et al. 2009, Liu and Mara 2010, Deng et al. 2011).
Development of fertile organs (bract and cone scale complexes, carpels, perianth parts, sporophylls) following the integration and induction of MIKC-type MADS-box genes in bisexual strobili may be divided into four sequential steps:
Response of the SAM to environmental (light, temperature, touch) and endogenous/exogenous biochemical signals (hormones produced by the insect and the plant, polypeptides, and microRNAs) that switches the meristem from vegetative to reproductive
Integration of signals leading to activation of SAM identity genes
Meristem identity genes activate reproductive organ identity genes in specific regions of the expanding SAM
Reproductive identity genes activate organ building genes of the growing SAM
However, ferns and fern allies, carry out development of fertile structures differently (Hasebe et al. 1998, Himi et al. 2001). Floricaula and LFY genes of the fern model organism Ceratopteris "do not directly induce MADS-box genes" (page 1205, Shindo et al. 2001).
Induction of seed plant reproductive structures in the four whorls of monopodial SAMs is under genetic control (Irish 2006, Specht and Bartlett 2009). While the biochemistry and development of expanding cells of SAMs and accessory fertile meristems is just barely understood (and only in a few extant seed plant species), at least two working models on the molecular mechanism of floral control and evolution, either the ABCDE model (Ditta et al. 2004) or floral quartet model (Theißen 2001) have been proposed.
Evidence of the involvement of floral quartets in floral development is supported by in vitro experiments using MIKC-type MADS-box B and E proteins (Melzer and Theißen 2009, Melzer et al. 2009).
Leafy and the biochemical logic behind FLO, LFY, and NLY DNA-binding HTH proteins figure prominently in papers that explore the use of evo-devo approaches in understanding gymnosperm phylogeny, the origin of angiosperms, and floral origins (Frohlich and Parker 2000, Shindo et al. 2001, Albert et al. 2002, Frohlich 2003, Baum and Hileman 2006, Frohlich 2006, Theißen and Melzer 2007, Vásquez-Lobo et al. 2007, Rudall et al. 2009).
Vásquez-Lobo et al. (2007), in an elegant study of FLO/LFY orthologs in Picea (Coniferales), Podocarpus (Podocarpales), and Taxus (Taxales), while employing ultrasensitive radioactive probes and histochemical methods, clearly demonstrate in situ expression of FLO/LFY gene transcripts in all the organs of female fertile SAMs. These findings, when taken together with similar studies by Shindo et al. (2001) on Gnetum parvifolium (Gnetales), disprove MMT.
The ancestral function of LFY, its paralog, NLY, and various orthologs; and the putative arthropod and seed plant biological activity of the DNA-binding HTH proteins they encode remain as enigmatic as ever (see the later subsection on the LFY switch and insect Engraled protein).
DELLA de-repression and GA. What are DELLA nuclear regulatory proteins? The DELLA subfamily of nuclear repressing proteins belongs to the larger family of plant specific GRAS proteins (Bolle 2004). Further, the DELLA subfamily of proteins is gibberellin sensitive and functions in holding-back plant growth and development in cells of floral meristems in extant angiosperms (Jiang and Fu 2007).
Hao Yu et al. (2004) suggest a close relationship between GAs and other indeterminate morphogens and expression of homeotic selector genes. Yu et al. state:
"Taken together, the work presented here suggests that GA promotes normal development of floral organs partly by up-regulating the expression of floral homeotic genes AP3, PI, and AG. Gibberellic acid achieves this effect by suppressing the function of two DELLA proteins, RGA and RGL2."
The preceding phrase is quoted from page 7832 of H. Yu, T. Ito, Y. Zhao, J. Peng, P. Kumar, and E. M. Meyerowitz (2004), Floral homeotic genes are targets of gibberellin signaling in flower development, Proceedings of the National Academy of Sciences 101(20): 7827-7832.
Further, studies of Arabidopsis suggest that DELLA proteins mediate the GA-dependent development of floral organs however, the detailed interactions between DELLAs and the floral meristem organ identity and integrator genes they repress remain incompletely understood (Hou et al. 2008).
It might be important to understand the details of DELLA repression of floral homeotic genes (and relief of repression by GA) in other experimental seed plant systems (and in a molecular phylogenetic context), as floral regulators are probably a key part of the puzzle behind the origin of the angiosperm flower (Theißen and Melzer 2007, Melzer et al. 2010).
A possible relationship exists between the plant gibberellin nuclear receptor GIBBERELLIN INSENSITIVE DWARF (GID1), DELLAs, and hormone specific lipases (HSLs) (Itoh et al. 2008, Murase et al. 2008).
Do certain insect nuclear receptor proteins and HSLs bind to plant GA?
Are gibberellins manufactured by host plants bioactive in developing instars and larvae of insect antagonists?
The LEAFY (LFY) switch and insect Engraled protein. The LFY gene encodes a diffusible 47 kilodalton-sized TF which is unique to plants (Sessions et al. 2000, X. Wu et al. 2003). Leafy protein regulates patterning of cells in developing SAMs of the model flowering plant, Arabidopsis thaliana (Maizel et al. 2005, Moyroud et al. 2009, Moyroud et al. 2010).
The left-hand image is reproduced from Figure 6 on page 2634 of Hamès et al. (2008), "Comparison of LFY-C with paired and homeodomain DNA binding. (A) Two orthogonal views of LFY-C helices α1 - α3 bound to their DNA target site [red] superimposed with the three helical bundle core of the N-terminal subdomain of the paired domain of Drosophila Prd [blue, PDB-id: 1pdn]. (B) Superposition with the homeodomain of Drosophila engrailed bound to DNA [yellow, PBD-id: 1hdd], where the centre of recognition helix α3 inserts into the major groove."
Reprinted by permission from Macmillan Publishers Ltd: The European Molecular Biology Organization (EMBO) Journal, Hamès, C., D. Ptchelkine, C. Grimm, E. Thevenon, E. Moyroud, F. Gérard, J.-L. Martiel, R. Benlloch, F. Parcy, and C. W. Müller. 2008. Structural basis for LEAFY floral switch function and similarity with helix-turn-helix proteins, The EMBO Journal 27: 2628-2637, copyright ©2008.
Leafy protein regulates GA mediated transition to flowering and downstream expression of MIKC-type MADS-box genes that determine floral organ identity (H. Yu et al. 2004, Theißen and Melzer 2007, Hou et al. 2008, among others).
Engraled (en), also spelled "engrailed" in the literature, is an insect compartment selector gene that encodes the Engraled homeodomain TF that determines the posterior identity of embryos and wings of the Drosophila model arthropod. The Apterous (ap) compartment selector gene encodes Apterous protein, which is another TF involved in subdivision of imaginal discs into dorsal and ventral compartments of developing fruit flies (S. B. Carroll et al. 2005).
The structure of the LFY-C protein of Arabidopsis thaliana shown in the image above, consists of a HTH DNA-binding motif with uncanny similarities to the active motif of Drosophila Engraled homeodomain protein, Tc3A transposase, and Hin recombinase enzymes (Hamès et al. 2008).
Now that Hamès et al. (2008) deduced the 3-dimensional crystal structure of LFY-C protein from Arabidopsis, it is possible to formulate explicit hypotheses on the origin of angiosperms and the origin of the first flower involving molecular coevolution of seed plant LFY protein and insect homeodomain proteins including Engraled (Hittinger and S. B. Carroll 2008).
"Our study reveals that the LFY master regulator, which determines flower meristem fate and controls the expression of floral organ identity genes, shares structural similarity with other HTH proteins, indicating that this universal DNA-binding motif has also been adopted in plants to trigger major developmental switches."
The preceding paragraph is quoted from page 2635 of C. Hamès, D. Ptchelkine, C. Grimm, E. Thévenon, E. Moyroud, F. Gérard, J.-L. Martiel, R. Benlloch, F. Parcy, and C. W. Müller (2008), Structural basis for LEAFY floral switch function and similarity with helix-turn-helix proteins. The EMBO Journal 27: 2628-2637.
A focus of the exercise should now be further development of hypotheses on the origin of the angiosperms, the origin of the flower, and MIKC-type MADS-box protein evolution proposed by Theißen and Saedler (2001), Albert et al. (2002), Kaufmann et al. (2005), Maizel et al. (2005), Baum and Hileman (2006), and Theißen and Melzer (2007).
Clusters of hermaphroditic pollen- and ovule bearing leaves known as bisexual strobili are the focus of most of the leading models of cone and floral organization (Melzer et al. 2010). Further, studies of developmental abnormalities in cones of extant conifers offer a window for better understanding the origins of flowers and flower-like organs (Flores-Rentería et al. 2011, Rudall et al. 2011).
Further, phylogenetic analysis suggests that a critical MIKC-type MADS-box gene duplication or WGD occurred in the common seed plant ancestor of angiosperms and gymnosperms at least 300 MYA (Becker et al. 2000, Zahn et al. 2005).
Based upon a brief paleontologic survey of Paleozoic seed plants having bisexual strobili, the prime gymnosperm candidate population for the 300 million year old gene duplication event was among the species and genera of Vojnovskyales, a Paleozoic gymnosperm with bisexual cone axes, and gigantopteroids and their potential intergeneric hybrids.
Evolution in MADS-box proteins is reviewed by Kaufmann et al. (2005), Rijpkema et al. (2007), Veron et al. (2007), Leseberg et al. (2008), Gramzow et al. (2010), Y.-Q Wang et al. (2010), and Dornelas et al. (2011).
Physiology of homeodomain transcription factor (TF) trafficking. Traditional concepts of SAM organization in eudicots are being reevaluated using scanning electron microscopy and fluorescence light microscopic techniques involving fusion of probes with homeodomain proteins. Shoot apical meristems of flowering plants contain two fields of meristematic cells: the central zone and a peripheral zone (Ori et al. 2000, among others).
Further, SAMs produce specialized boundary cells at the interface between meristematic cells of the central zone and organ cells in the peripheral zone where TFs necessary for the regulation of development move from cell-to-cell (Aida and Tasaka 2006).
Certain KNOX homeodomain proteins, FLO/LFY proteins, and other small-sized (<60 kilodalton) TFs and their mRNAs move from cell to cell via plasmodesmata in the SAMs of some of the model eudicot angiosperms studied (Jackson 2002, J.-Y. Kim et al. 2003, Jackson 2005, Xu et al. 2011, among others).
Chaperonins are necessary for homeodomain TF trafficking in SAMs (Xu et al. 2011).
Studies of SAMs in the model malvid species Arabidopsis thaliana using fused green fluorescent protein (GFP) and the 47 kilodalton-sized LFY enzyme, suggest that movement within the SAM through secondary plasmodesmata is by simple diffusion (X. Wu et al. 2003). In contrast MIKC-type MADS-box proteins AP3 and PI do not move from cell to cell between tissues layers.
Does thigmo affect homeodomain TF movements in SAMs of extant model eudicots?
Trafficking of certain homeodomain TFs in SAMs of extant model eudicots is conserved, often unidirectional, developmentally important, and ontogenetically controlled (J.-Y. Kim et al. 2003). The physiology of SAM macromolecular trafficking, when extrapolated to seed plants in deep time is an important component of the prevailing models of cone organization and floral origins (Baum and Hileman 2006, Theißen and Melzer 2007, Melzer et al. 2010).
Baum and Hileman (page 16, 2006) propose that since the GA signaling pathway positively regulates LFY gene expression (and LFY integrates fertile meristem ontogenetic change from vegetative to reproductive), the bisexual cone axis in "... the common ancestor of angiosperms and gymnosperms would have gradually accumulated higher and higher levels of LFY protein during development."
When considering the evo-devo of modular SAM developmental programs in deep time, conceptual models that incorporate chaperonins, movable cis-acting homeodomain proteins, promoters, and enhancers have potentially profound implications toward evolution of progymnosperm and seed plant reproductive axes. My concept of "developmental programs" is probably similar to biological process-based, evo-devo homology concepts suggested by Laubichler (2000) and Brigandt (2003), among others.
Boyce and Knoll (page 70, 2002) reaffirm a common theme that, "Cell walls also prohibit cell migration, constraining the types of development that are possible in plants ...." but neglect to discuss potential cell to cell movements of homeodomain proteins (Jackson 2002), and the implication of this phenomenon toward regulation of transcription and meristematic evo-devo of novel leaf morphologies.
Based on the possibility that two traffic patterns of homeodomain protein movement emerged in meristems of aerial shoots of extinct progymnosperms and seed plants, I split the lignophytes into two groups based on a potential biological process split in diverging Devonian seed plant lineages, prior to a character assessment and phylogenetic analysis.
These biological process ideas on character homology are developed in the second essay from an experimental cladistic perspective as a means to simplify data analysis and to ameliorate vexing problems in seed plant phylogenetic reconstruction raised by J. A. Doyle (2006).
This means that in disparate seed plant groups, traditional ideas and supposed homologies of organs such as ovular integuments (origin by evo-devo splitting of tissues or by incorporation of foliar organs), and position of ovules on the megasporophyll whether adaxial or abaxial (Figures 13 and 14, J. A. Doyle 2006), are called into question.
Further, location and canalization of sporophylls in relation to the SAM or lateral meristems might have evo-devo significance.
Additional evo-devo research on ophioglossoid model monilophytes at the level of homeodomain protein trafficking in meristematic tissues is probably needed, whether or not extant eusporangiate ferns are descendants of Devonian progymnosperms or some other vascular plant stem group. The leptosporangiate fern model organism Ceratopteris richardsonii is probably unsuitable for this purpose.
The next chapter of the essay considers evidence from tool kits and genomics needed to better understand the origin of the first flower and the origin of angiosperms.
In this chapter I discuss molecular evolution of TFs and CRMs, co-option and exaptation, developmental recombination and reprogramming, genetic accommodation, homeotic selector genes, horizontal transfer of genes, chloroplast capture, mobile chromosome parasites, gene duplications, chromosome doubling as a consequence of interspecific hybridization, and paleopolyploidy.
The image on the right is a stained preparation of the chromosomes of Joinvillea plicata (Joinvilleaceae, Poales, Lilianae), a species of grass-like monocots with a fully developed perianth.
Chromosomes in this image were fixed at the moment of metaphase I of meiosis in a microspore mother cell, × 2000. In the living Joinvillea plant, meiotic chromosomes would be identifiable in two places: inside the immature megasporangium of the ovule and within young microsporangia of very young stamens.
In addition, I summarize key research advances in our understanding of the possible effects of signals on whole genomes, homeotic selector genes, gene transcripts such as microRNAs (miRNAs and siRNAs), and cis-regulatory sequences that bind TFs.
"A central concept that is emerging from comparative studies of developmental genes and their interactions is the co-option of these for different functional roles as evolution proceeds."
This quotation is from page 761 of W. Arthur (2002), The emerging conceptual framework of evolutionary developmental biology. Nature 415: 757-764.
Could the application of mechanical force, simple thigmo, and/or secretion of phytohormone signals by chewing, crawling, feeding, ovipositing, and sucking insect mutualists on elongated (or shortened) cone axis SAMs affect movement of homeodomain proteins and trigger developmental switches that determine downstream reproductive organ identity and formation?
"I argue that the origin of species differences can be explained, and the synthesis of Darwinism with genetics can be improved, by invoking two concepts: developmental recombination and genetic accommodation. Developmental recombination, or developmental reorganization of the ancestral phenotype, explains where new variants come from: they come from the preexisting phenotype, which is developmentally plastic and therefore subject to reorganization to produce novel variants when stimulated to do so by new inputs from the genome or the environment. Genetic accommodation, or genetic change in the regulation or form of a novel trait, is the process by which new developmental variants become established within populations and species because of genetic evolution by selection on phenotypic variation when it has a genetic component."
The preceding passage is quoted from page 6544 of M. J. West-Eberhard (2005), Developmental plasticity and the origin of species differences, Proceedings of the National Academy of Sciences 102(Supplement 1): 6543-6549.
These and many other questions are in need of answers:
What is the role of developmental plasticity and genetic accommodation, as underlying processes that lead to co-option, modularity, dissociation, and diverted development of seed plant characters involved in angiospermization?
Were the genes, morphogens, and regulatory factors having to do with mechanoperception and shoot development linked or the same in extinct Permo-Triassic seed plants?
Are phytophagous insects and their secretions a source of signals perceived by the developing plant SAM (including accessory reproductive meristems) and sent to nuclei of cells where they upregulate (or repress) floral integrator and meristem identity genes?
Does mRNA and homeodomain protein trafficking in meristematic tissues of model ophioglossoid monilophytes occur differently than seed plants?
Do certain insect nuclear receptor proteins and HSLs bind to plant GA?
Are miRNAs passed on to male and female reproductive modules (pollen and ovules)?
Can we identify potentially interfertile sources of reproductive modules, and model the flow of pollen and rain of seeds in pre-angiospermous seed plant populations following the EPE and TrCCE?
What were the effects of epigenesis including input of foreign genetic material on developmental plasticity and phenotypic variation in populations of Permo-Triassic seed plants and the first flowering plants?
How has cross-Kingdom signaling and microbial activity including movement of mobile genome parasites in seed plant/arthropod paleopopulations and ancient coevolutionary compartments affected the origin and evolution of angiosperms and the Holometabola?
Do phytophagous insects send biochemical signals via the host plant cytoskeleton and microtubules to the nucleus thereby upregulating SAM maintenance- and floral integrator and meristem identity genes?
Students of neo-Darwinian thought and Goldschmidtian saltation should read the review by Moczek et al. (2011).
"... developmental underpinnings of plasticity increase the degrees of freedom by which environmental and genetic factors influence ontogeny, thereby diversifying targets for evolutionary processes to act on and increasing opportunities for the construction of novel, functional and potentially adaptive phenotypes."
This phrase is quoted from the abstract of A. P. Moczek, S. Sultan, S. Foster, C. Ledón-Rettig, I. Dworkin, H. F. Nijhout, E. Abouheif, and D. W. Pfennig (2011), The role of developmental plasticity in evolutionary innovation. Proceedings of the Royal Society of London, Series B, Biological Sciences 278(1719): 2705-2713.
Homeotic selector genes. Homeotic selector genes are known from metazoans, fungi, and plants. These genes are key regulators in insect and land plant developmental tool kits being important in plant organ or body segment identity (S. B. Carroll et al. 2005, Floyd and Bowman 2007). Homeotic selector genes of insects include Hox genes, zygotic (gap- maternal-, and pair-rule-) genes, field-specific selector genes, compartment selector genes, cell-type-specific selector genes, and segment polarity genes (S. B. Carroll et al. 2005).
Homeotic selector genes of plants include SAM maintenance genes and floral meristem organ identity and integrator genes that encode MIKC-type MADS-box TFs.
Developmental proteins encoded by homeotic selector genes of plants have been the subject of active research by biochemists, plant cell biologists, and molecular systematists for nearly two decades (Coen and Meyerowitz 1991, Theißen et al. 1996, Kramer et al. 1998, Becker et al. 2000, Cubas et al. 2001, Stuurman et al. 2002, Becker and Theißen 2003, Irish 2003, S. Tucker 2003, Yamada et al. 2003, Kaufmann et al. 2009, Melzer et al. 2009, among others).
More recent studies having to do with the origin of the flower, perianth parts, bisexual cone axes, ovules and carpels include Buzgo et al. (2004), Jack (2004), S. Kim et al. (2004), P. Zhang et al. (2004), Adam et al. (2005), Buzgo et al. (2005), Irish and Litt (2005), Kaufmann et al. (2005), S. Kim et al. (2005 [two papers]), Zahn et al. (2005 [two papers]), Baum and Hileman (2006), Cronk (2006), De Bodt et al. (2006), Doerner (2006), Endress (2006), Feng et al. (2006), Irish (2006), S. Kim et al. (2006), Scutt et al. (2006), P. S. Soltis et al. (2006), Kramer et al. (2007), Theißen and Melzer (2007), and Melzer et al. (2010), among others.
Developmental cis-regulatory modules (CRMs). Non enzyme-coding DNA sequences involved in the control of gene expression are termed CRMs (Zinzen et al. 2009, Borok et al. 2010).
Clusters of regulatory DNA spaced at irregular intervals on the chromosomes of diverse eukaryotes sometimes contain enhancer and promoter cis-regulatory sequences that bind TFs (Borok et al. 2010). Promoters are cis-regulatory sequences that affect transcription. Some promoters work together with additional factors termed modular enhancers, which are cis-regulatory elements (CREs) (Rebeiz et al. 2009, Borok et al. 2010).
Modular enhancer CREs of certain insects are subject to mutation. Further mutations in CREs within Drosophila populations potentially lead to adaptive morphological changes with "large phenotypic effect" (abstract, Rebeiz et al. 2009).
"Plant evolution may often entail changes to the promoter/enhancer elements that cause changes in the expression patterns of regulatory genes."
The preceding quotation is from page 59 of D. A. Baum and M. J. Donoghue (2002), Transformation of function, heterotopy, and the evolution of plant development. Pp. 52-69 In: Q. C. B. Cronk, R. Bateman, and J. Hawkins (eds.), Developmental Genetics and Plant Evolution, The Systematics Association Special Volume Series 65. London: Taylor and Francis, 543 pp.
Transcription factors are proteins that bind to cis-regulatory sequences (Wray et al. 2003).
It is increasingly clear that cis-regulatory MADS-box domain TFs interact even with their own promoters. Further, "MADS-box proteins seem to function mostly as subunits of larger protein complexes" (page 34, Rijpkema et al. 2007).
Understanding the selective forces behind molecular coevolution of insect and seed plant developmental CRMs in deep time may be an important first-step in unraveling the enigmatic origin of angiosperms, evo-devo of the first flower, and adaptive radiation of certain clades of coevolving Holometabola.
Evolution of CRMs in relation to animal and plant body plan patterning, development of organs of insects and seed plants, and natural selection is reviewed by Rodríques-Trelles et al. (2003), Wray (2003), Wray et al. (2003), Theißen and Becker (2004), S. B. Carroll (2005), De Bodt et al. (2006), Wittkopp (2006), Hoekstra and Coyne (2007), Wray (2007), and S. B. Carroll (2008).
The diagram below, which is redrawn from Carroll (2005), shows how the cis-regulatory molecular evolution and duplication of genes in insects or plants may potentially increase gene function while minimizing pleiotropy. The blue lines are segments of coding and non-coding DNA. Intron pairs are gray-colored rectangles. Orange circles are cis-regulatory promoters. Finally, asterisks denote mutations.
The first line of "A" illustrates a progenitor gene with its introns and promoter. The second two lines of "A" shows a gene duplication. Potential mutations of the cis-regulatory promoter and gene intron are denoted by asterisks. "B" illustrates expansion of cis-regulatory elements. "C" depicts the genesis of a novel intron and potential splicing sites that may lead to biosynthesis of alternative protein forms without the deleterious effects of mutations.
The above graphic is redrawn from Figure 1 of Sean B. Carroll, 2005, Evolution at two levels: on genes and form, PLoS Biology 3(7): 1159-1166.
A typical promoter consists of fewer than 50 binding sites for less than 15 different TFs. Transcription factor binding sites are about a dozen nucleotide base pairs wide, spaced irregularly along a segment of chromatin. Some promoters may be conserved while others are not.
Shoot apical meristem (SAM) maintenance genes. Function and patterning in the SAM requires several gene families and their cis-acting TFs. The main SAM identity genes are Class III HD-Zip, KANADI, Class 1 KNOX (KNOTTED1-like), and ARP genes (Ori et al. 2000, Reiser et al. 2000, Hake et al. 2004, Di Giacomo et al. 2008, among others).
Class III homeodomain-leucine zipper proteins, which are encoded by Class III HD-Zip genes, include AtHB8, CNA, PHB, PHV, and REV (see reviews by Floyd et al. 2006 and Prigge and S. E. Clark 2006). Class III HD-Zip genes and the enzymes they encode have been isolated from extant flowering plants, gymnosperms, ferns, lycophytes, bryophytes, and charophytes including most of the model photosynthetic organisms used in evo-devo research. All were probably key players in the land plant developmental tool kit of cis-acting genes, TFs, and homeodomain proteins (Floyd and Bowman 2007).
The diagram below is a phylogeny of Class III HD-Zip genes redrawn from Floyd et al. (2006). Cha = Chara (Charophyta), Phy = Physcomitrella (Bryophyta), Pha = Phaeoceros (Anthocerotophyta), Mar = Marchantia (Hepatophyta), Psi = Psilotum (Psilophyta), Cer = Ceratopteris (Pteridophyta), Pse = Pseudotsuga (Coniferophyta), Gin = Ginkgo (Ginkgophyta), Tax = Taxus (Coniferophyta), Ory = Oryza (angiosperm), Zin = Zinnia (angiosperm).
Class III homeodomain-leucine zipper genes are abbreviated on the diagram. The CNA, PHB, PHV, and REV CRMs are principal components of the plant SAM, which are also needed for initiation of axillary SAMs in vascular plants including seed plants (see Floyd et al. 2006).
Many supposed homologies of leaves, sporophylls, and ectopic structures including reproductive axes and ovular integuments could be incorrect based on the possibility that a fundamental dichotomy in SAM evo-devo emerged in Devonian lignophyte populations.
Lateral branches of the Devonian progymnosperm, Archaeopteris (Archaeopteridales) may arise from tissue fields resembling leaf primordia, and not axillary buds (page 481, T. N. Taylor et al. 2009).
Did early diverging Devonian progymnosperms sprout branches without axillary SAMs and buds?
Three of the Class III HD-Zip genes (PHB, PHV, and REV) are needed by the plant for development of leaves and the placement of organs on upper (adaxial) leaf surfaces (Floyd et al. 2006). Additional functions of Class III HD-Zip genes are known (Floyd and Bowman 2007).
Colored bars on the cladogram denote landmark developmental events in vascular plant evolution. Yellow = vascularization of the microphyll of lycophytes, Orange = evo-devo of the sporophyte SAM, Blue = organization of the stele of the vascular plant stem, Light Green = site of lateral organ initiation, Dark Green = evo-devo of adaxial domains.
The preceding diagram is adapted from Figure 7 on page 383 of S. K. Floyd et al. (2006), Evolution of Class III homeodomain-leucine zipper genes in streptophytes, Genetics 173: 373-388. The diagram is placed against a backdrop of changing levels in global atmospheric oxygen concentration (sources: GEOCARB III, Berner and Kothavala 2001 and GEOCARBSULF, Berner 2006) over the course of geologic time (bottom scale).
Six of the planet's greatest mass extinctions are also depicted on the chart of changing global oxygen levels and Class III HD-Zip gene evolution: DeCARB = light blue rectangle, GuCCE = purple stripe, EPE = grey bar, TrCCE = orange rectangle, BaCCE = yellow stripe, and K-T = red bar.
Pteridosperms, which are seed plants often discussed in classic theories on the origin of angiosperms and conifers (J. A. Doyle 1978, Crane et al. 2004, J. A. Doyle 2006, E. L. Taylor et al. 2006, E. L. Taylor and T. N. Taylor 2009, among others), occupy an unknown position in the phylogeny of Class III HD-Zip genes. Absence of data on Class III HD-Zip genes of progymnosperms and pteridosperms probably would explain why cladistic analysis of the REV clade by Floyd et al. (2006) reveal no significant support for gymnosperm monophyly.
A diagram of land plant phylogeny published in a review by Langdale (Figure 2, page 370, 2008) overlooks pteridosperms and neglects to discuss their reproductive morphology within the macroevolutionary context of developmental programs of the SAM.
Molecular phylogenetic analyses of Class III HD-Zip genes by Floyd et al. (2006) illustrate one handicap in phylogenetic inference: no living experimental model progymnosperm and/or pteridosperm organism exists. Therefore, it may be incorrect to assume homology of morphologic characters of anthophytes and pteridosperms derived from two different evo-devo programs of SAM development arising from transcriptional regulation by Class III HD-Zip proteins in early-diverging Devonian lignophytes.
Consequently, it is not possible to fully understand ancient SAM patterning in seedlings and axillary meristems of Paleozoic lignophytes, and deduce the genetics of CNA, PHA, PHAV, and REV in the evo-devo of branches of progymnosperms; and axillary buds, leaves, strobili, synangia, and cupules of pteridosperms, leading to morphological innovation and early radiations of seed plants (Sanders et al. 2007).
Despite this impediment toward increasing our understanding of evo-devo of seed plant lineages in deep-time, tantalizing clues are gained by experimentally manipulating malvid SAMs with synthetic promoters causing misexpression of KNOX genes leading to bizarre pteridosperm-like ectopic shoots on abaxial leaf surfaces (see Reiser et al. 2000).
Knotted1-like homeobox genes are expressed in the actively dividing cell fields in the SAMs of extant seed plants (Ori et al. 2000, among others). Downregulation of KNOX genes occurs in organ primordia founder cells of the malvid SAM and other angiosperms and gymnosperms studied to date (Bharathan et al. 2002). When these genes are not expressed properly in monocots, ectopic shoots grow from new fields of meristematic cells on the abaxial surfaces of leaves or other deformities occur, invoked by experimentally manipulating KNOX cis-regulatory function (Reiser et al. 2000).
Class 1 KNOX genes are necessary components of SAM development in conifers (Guillet-Claude et al. 2004). In seedlings of the gnetophyte Welwitschia mirabilis, Class I KNOX genes are expressed in the SAM but not in primordia of the only two leaves (Pham and Sinha 2003). Movable, small-sized Class I KNOX homeodomain proteins are assembled upon translation of KNOX gene mRNA transcripts in cells of organizing centers of the SAM (Jackson 2002).
Pham and Sinha (2003) do not address potential significance of KNOX homeodomain protein movements from the SAM to leaf primordia, thence to regions of indeterminate growth, when discussing ontogeny of accessory scaly bodies and reproductive organs of Welwitschia.
In vascular plants these genes are organized into KNOX/ARP modules. The SAMs of extant flowering plants typically express KNOX but not ARP (ASYMMETRIC LEAVES1, ROUGHSHEATH2, PHANTASTICA) genes. Conversely expression of ARP genes in leaf primordium cells of the SAM leads to suppression of KNOX function. Whether the KNOX genetic switch is on or off depends on the activity of ARP repressors, and may lead to the development of different leaf forms e.g. pinnate, palmate, or compound (Beerling and Fleming 2007).
Class I KNOX genes are important when considering the genetic basis of land plants and the origin of angiosperms as they figure prominently in discussions of classic theories on telomb transformational series within the evo-devo context (Beerling and Fleming 2007, Sanders et al. 2007). Understanding KNOX genes and their expression may offer clues toward unraveling complex mechanisms behind morphogenetic patterns in flowering plants (Bharathan et al. 1999), among other seed plants.
Cytokinins and gibberellins (see previous chapter) act downstream of Class I KNOX genes in the rice and mouse-eared cress subjects studied (Di Giacomo et al. 2008). Among the many other TFs found in plant meristems, Class II TCP genes encoding TCP proteins are involved in the shaping of leaves and flowers (Cubas 2004, Damerval et al. 2007).
Deep conservation in tool kit gene families in land plants (Floyd and Bowman 2007) such as SAM maintenance genes e.g. Class III HD-Zip and KNOX/ARP CREs and the conserved HTH DNA-binding motifs of homeodomain proteins, illuminates the critical importance of CRMs in the evolution of sporophyte SAMs, axillary SAMs, and lateral organs of ancient seed plants.
Cone and floral meristem organ identity and integrator genes and transcription factors (TFs). The development of perianth parts of the flower involves homeotic cis-acting TFs that act downstream of SAM maintenance genes (Glover 2007, among others).
Pamela S. Soltis et al. (2009), Specht and Bartlett (2009), Chanderbali et al. (2010), Melzer et al. (2010), Rudall and Bateman (2010), and D. W. Taylor (2010), among others, review the developmental genetics and evolution of cones and flowers.
Leafy protein encoded by the LFY gene is a key developmental switch in floral meristems of many angiosperms including Arabidopsis (Glover 2007, Hamès et al. 2008, Moyroud et al. 2009) and Liriodendron (Magnoliaceae, Magnoliales, Magnolianae) (Liang et al. 2011). Floricaula/Leafy proteins are key controllers of cone and bract-scale development in several diverse genera of gymnosperms including Cryptomeria (Cupressaceae, Coniferales) (Shiokawa et al. 2008), Gnetum (Gnetaceae, Gnetales) (Shindo et al. 2001), and Taxus (Taxaceae, Taxales), among others (Vázquez-Lobo et al. 2007, Moyroud et al. 2009).
The main floral meristem organ identity and integrator genes in Arabidopsis include LFY, AG, AP1, AP2, CAL, FLO, SOC1, TFL1, and UFO.
A gymnosperm paralog of LFY termed NLY has been isolated from Pinus [Pinaceae, Coniferales] (Mouradov et al. 1998). Shiokawa et al. (2008) demonstrated that transgenic Nicotiana tabacum (Solanaceae, Solanales, Asteranae) that expressed a CjNdly gene isolated from Cryptomeria japonica possessed stamens expressed as petals. These workers conclude that the gymnosperm CjNdly gene is a homolog of angiosperm FLO/LFY.
The FLO/LFY family of TFs controls the downstream expression of several genes in extant anthophyte seed plants including MIKC-type MADS-box genes (Theißen and Melzer 2007, Melzer et al. 2010, among many other papers).
High points of the extensive work on LFY in seed plants with implications toward MMT, the timing of the angiosperm-gymnosperm split, and the origin of flowering plants, are discussed by Shindo et al. (2001), Baum and Hileman (2006), and Vázquez-Lobo et al. (2007).
Several TFs are implicated in changing the shape and size of flowers (Glover 2007). These include ANT, ARGOS, BB, CYC, DICH, and DIVARICATA (Glover 2007, among others). AINTEGUMENTA is a principal controller of both flower- and leaf size. Further, ANT negatively regulates the expression of the Class C MIKC-type MADS-box gene AG (Krizek 2009). AINTEGUMENTA is a component of the auxin regulated signaling cascade (Busov et al. 2008, Krizek 2009, among others).
Floricaula, which is encoded by FLC represses both FT and SOC1 in the malvid model plant Arabidopsis (Deng et al. 2011).
AINTEGUMENTA and AP2 (and a number of other genes and TFs known from Arabidopsis) comprise the AP2 subfamily, which is part the larger AP2/ERF (ethylene responsive factor) family of TFs (S. Kim et al. 2006). All of these genes including their paralogs, orthologues, and cis-acting TFs, figure prominently in discussions of the ancestral developmental tool kit of land plants (Floyd and Bowman 2007, among others), and in numerous studies of the origin of the angiosperm flower and floral diversification (S. Kim et al. 2006, P. S. Soltis et al. 2009, among others).
In 2006 Baum and Hileman proposed a modification of Theißen and Saedler's (2001) protein quartet model involving genetic interactions of B and C homeotic selector genes, SEP genes, and small-sized growth promoting molecules (phytohormones and other factors) aligned along gradients within a developing seed plant cone axis.
The protein quartet model of floral molecular evolution is now widely accepted among plant biologists (Leseberg et al. 2008). Plant systematists view the expanded ABC model as "the default program" behind the identity of organs of the flower (page 18, D. E. Soltis et al. 2008; page 117, Figure 2, P. S. Soltis et al. 2009). MIKC-type MADS-box E proteins such as SEP3 bind to DNA in the test tube as quartet-like complexes (Melzer et al. 2009).
"Out-of-male" and "out-of-female" hypotheses on the origin of the angiosperm flower (Theißen Saedler 2001, Becker and Theißen 2003) are potential examples of how cis-acting protein modules "might exert their function as transcription factors by binding to the promoters of target genes" (page 132, Theißen and Becker 2004).
While discussing evidence that seed plant class B homeotic selector genes diverged into the two lineages leading to extant gymnosperms and angiosperms 300 million years ago during the late Carboniferous Period following a gene duplication or WGD, Theißen and Becker (2004) state:
"Changes in cis-regulatory elements, typically located in the promoter region of a respective gene, in enhancers or silencers up- or downstream of the coding region, or even in introns, might have rendered B gene expression more susceptible to a hypothetical apical-basal gradient already present within the cone. Such a gradient could be based on a low molecular weight compound such as a phytohormone or on a protein (presumable another TF). The underlying molecular changes within the B gene could range from a simple single nucleotide change to major rearrangements at the B gene locus."
The preceding statement is quoted from page 142 of Günter Theißen and Annette Becker (2004), Gymnosperm orthologues of class B floral homeotic genes and their impact on understanding flower origin, Critical Reviews in Plant Sciences 23(2): 129-148.
Is Theißen and Becker's hypothetical cone concept (2004) applicable to bisexual axes of Carboniferous Vojnovskyales?
MIKC-type MADS-box genes and transcription factors (TFs). Certain MADS-box floral meristem organ identity and integrator genes encode MIKC-type MADS-box TFs that determine development of cones and flowers (Ma and dePamphilis 2000, Theißen et al. 2000, Theißen 2001, Becker and Theißen 2003, Theißen and Melzer 2007, Melzer et al. 2010, among others).
The acronym "MADS" was coined from names of homeotic genes isolated from yeast (MCM1), snapdragon (AG and DEF), and humans (SRF) (Ma and dePamphilis 2000). Protein subunits encoded by the MIKC-type MADS-box genes possess a modular organization that includes a MADS (M) intervening (I), keratin-like (K), and a C-terminal (C) domain (Theißen et al. 2000).
The extreme age of MIKC-type MADS-box genes as controllers of development is supported by numerous biochemical and phylogenetic analyses (Nam et al. 2003, Gramzow et al. 2010, among others). Gymnosperms possess orthologs of certain MADS-box genes. It is not unreasonable to accept the proposal that at least some MADS-box genes operated in more general developmental patterning in Carboniferous seed plants supposedly before the angiosperm-gymnosperm split roughly 300 MYA (Nam et al. 2003).
Further, based on studies of extant Ceratopteris [a monilophyte fern] (Hasebe et al. 1998), Chara (an algal charophyte), Physcomitrella (a moss), and Selaginella (a lycophyte), early land plants probably had two MIKC-type MADS-box genes and that the MADS-box gene family diverged widely after the seed plant/fern split (Floyd and Bowman 2007).
Soltis et al., eds. (2006), Glover (2007), Kramer (2007), P. S. Soltis et al. (2009), Specht and Bartlett (2009), Rudall and Bateman (2010), Melzer et al. (2010), and D. W. Taylor (2010), among others, incrementally review advances in our understanding of the genetics and regulation of flowering.
A compilation of published research on regulation of cone and floral development appears in Volume 21, Number 1 (2010) of the serial Seminars in Cell and Developmental Biology. This issue contains papers by Alvarez-Buylla et al. (2010), Causier et al. (2010), Immink et al. (2010), Litt and Kramer (2010), Liu and Mara (2010), Melzer et al. (2010), Rijpkema et al. (2010), and Sablowski (2010).
There are three fundamental classes of floral organ identity genes, "A," "B," and "C" that comprise the first unifying principle of fertile meristem development (Jack 2004, Causier et al. 2010 [two papers], among others). In extant flowering plants A function is responsible for sepal identity (M.-K. Chen et al. 2008, among others), A + B expression determines the identity of petals (Su et al. 2008, among others), B + C expression affects stamen morphology (Kramer et al. 1998, Piwarzyk et al. 2007, among others), and C gene expression controls the identity of carpels and stamens (Causier et al. 2009, Yellina et al. 2010, among others).
Variations in B gene expression determine the identity, shape, and form of unusual perianth parts in columbines (Kramer et al. 2007, Bharti Sharma et al. 2011), grasses (Whipple et al. 2007), papaya (Ackerman et al. 2008), and potatoes (Geuten et al. 2011).
Gymnosperm orthologues of the B and C genes including AG are known: their conserved evolution is demonstrable (P. Zhang et al. 2004). Apparently gymnosperm "B" genes are only expressed in male cones (Theißen and Becker 2004). The evolution of "B" and "C" genes is recently reviewed by Causier et al. (2010, among others).
Additional classes "D," "E," and "F" been identified in certain extant seed plants. D-class genes apparently operate to determine organ identity in the flowering plant genus Petunia (Solanaceae, Solanales, Asteranae) (Ferrario et al. 2006).
"... the most parsimonious explanation [i.e. differential expression of class B, C, and D genes as the 'primary sex-determination mechanism in all seed plants'] would be that the mechanism of female/male reproductive organ specification/distinction in angiosperms was recruited from a similar system that was already established in the lineage leading to all extant seed plants about 300 MYA (Theißen et al. 2000). At the molecular level, therefore, flower origin seems less mysterious than the morphological difference between flowers and gymnosperm cones or strobili might suggest."
The preceding statement is from page 138 of Günther Theißen and Annette Becker (2004), Gymnosperm orthologues of class B floral homeotic genes and their impact on understanding flower origin, Critical Reviews in Plant Sciences 23(2): 129-148. The phrase and within-context but out of place quote from the original article denoted by brackets  is mine.
There are apparently two of A-class floral meristem identity genes, AP1 and AP2, in Arabidopsis thaliana. The B-class genes of Arabidopsis, including AP3 and PI are specifiers of petaloid organs in whorl two, and staminate organs in whorl three of the SAM (Hileman and Irish 2009). The C-class gene AG integrates the activity of whorl three stamens and carpels of the fourth whorl. C-class genes evidently repress the activity of A-class genes that operate in whorls three and four (Jack 2004).
A fourth class of MIKC-type MADS-box genes known as SEP is implicated in determination of floral identity (Becker and Theißen 2003, Kaufmann et al. 2009, Melzer et al. 2009, among others). Zahn et al. (2005) report SEP homologues in basal angiosperms including Amborella trichopoda.
"The coincidence between the origin and diversification of the SEP subfamily and the emergence of angiosperms suggests that the origin of the SEP subfamily may be part of a hypothesized 'molecular innovation' that made possible the morphological invention of the flower."
The previous quotation is from page 2219 of L. M. Zahn, H. Kong, J. H. Leebens-Mack, S. Kim, P. S. Soltis, L. L. Landherr, D. E. Soltis, C. W. dePamphilis, and H. Ma (2005), The evolution of the SEPALLATA subfamily of MIKC type MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history, Genetics 169: 2209-2223.
Zahn et al. (2005) suggest that since the SEP and SQUA subfamilies of MIKC-type MADS-box genes are not known from gymnosperms the first SEP gene duplication might have occurred after flowering plants diverged from their naked seed plant ancestors some 300 MYA.
SEPALLATA genes are known as MIKC-type MADS-box E genes. The revised Coen and Meyerowitz ABC model, at least for the extant flowering plant species studied to date, states that sepals are specified by A gene activity alone, petals by A + B + E genes, stamens by B + C + E MADS-box factors, and carpels by C + E genes. Higher order MIKC-type MADS-box gene combinations are also now suspect to operate in certain seed plant species but much work remains to be done (Jack 2004), and is underway in many laboratories all over the world.
Study of floral meristem organ identity genes in Persea (Lauraceae, Laurales, Magnolianae) identified "... spatial and temporal shifts in gene expression that coincide with an evolutionary change in perianth morphology." (page 1081, Chanderbali et al. 2006).
Molecular systematists have identified and studied MIKC-type MADS-box genes in basal angiosperms (Aoki et al. 2004, S. Kim et al. 2005, P. S. Soltis et al. 2009, among others). Sangtae Kim and coworkers report several homologs of MADS-box genes including AP3 and P1. These two genes are expressed in all the floral organs of Amborella. APETALA3 and PI were either not expressed at all, or only weakly expressed in several other basal angiosperms.
Broader expression of AP3 and P1 homologs in basal flowering plants suggested that this was the ancestral condition. Other deviations from the Coen and Meyerowitz ABC model were noted by S. Kim et al. (2005) as a basis for a fading borders model (D. E. Soltis et al. 2007, P. S. Soltis et al. 2009).
"Despite numerous genetic-based models for the origin of the flower (e.g. Frohlich and Parker 2000; Albert et al., 2002; Theissen et al., 2002), how that ancestral reproductive program was modified to yield a flower largely remains an abominable mystery itself."
The preceding statement is from page 118 of P. S Soltis, S. F. Brockington, M.-J. Yoo, A. Piedrahita, M. Latvis, M. J. Moore, A. S. Chanderbali, and D. E. Soltis (2009), Floral variation and floral genetics in basal angiosperms. American Journal of Botany 96(1): 110-128.
A novel "Mosaic Theory for the Evolution of the Dimorphic Perianth" proposed by Warner et al. (2009) states that:
sepal and petal identities evolved "early in angiosperm history"
morphological features of tepals may not have been "fixed to particular organs and were primarily environmentally controlled"
later during the evolution of flowering plants "sepalness and petalness became fixed to whole organs in specific whorls, forming distinct sepals and petals, thus removing the need for environmental control in favour of fixed developmental control"
reversals observed in certain eudicots (e.g. Berberis [Berberidaceae] and Hypericum [Hypericaceae]) constitute plesiomorphies
Despite compatibility with the fading borders model the hypothesis proposed by Warner et al. (page 3571, 2009) neglects to account for a possible role of MYB TFs in environmental control of perianth pigmentation and evolution.
Gene and whole genome duplications (WGDs). Consideration of both small gene duplications and WGDs is important in understanding the timing of the origin of angiosperms, radiation of basal flowering plants and eudicots (D. E. Soltis et al. 2007, D. E. Soltis et al. 2009, Jiao et al. 2011, among others), and in the evolution of seed plants (Guillet-Claude et al. 2004, Jiao et al. 2011).
By knowing the interval in geologic deep time when molecular systematists predict divergence of molecular tool kits, paleobotanists might be able to better focus on candidate seed plant groups for detailed anatomical study of permineralized fossils (Crepet 2008).
Van de Peer et al. (2009) and Jiao et al. (2011) discuss the high points of research on WGDs in eukaryotes and the evolutionary consequences of polyploidy. Pamela S. Soltis et al. (2009) review and summarize the role of gene duplications in angiosperm floral diversification.
Phylogenetic analyses suggest that duplications in floral meristem identity genes took place prior to the origin of angiosperms more than 260 MYA (Bowe et al. 2000, Bowers et al. 2003, S. Kim et al. 2004). Mathematical modeling studies of Arabidopsis reveal that diversification of genes involved in signal transduction, SAM development, and the regulation of transcription are attributable to three WGDs during the last 350 million years (Maere et al. 2005).
A phylogenetic analysis of KNOX1 genes by Guillet-Claude et al. (page 2242, 2004) "suggests that three duplication events (D1, D2, and D3) occurred between the split of the lineage leading to conifers from that leading to angiosperms, around 300 m.y.a. ..." and the Cretaceous divergence of pines and spruces.
Jiao et al. (2011) narrow this estimate by employing phylogenetic models to all available seed plant genomic data to "... two groups of duplications, one in the common ancestor of all angiosperms and the other in the common ancestor of all seed plants."
Evolution of the Hox gene cluster and MADS-box genes. Gene duplications were an important part of the assembly of the early bilaterian animal tool kit that led to tetraploidization and the creation of several gene families including the HOM-Hox and Parahox clusters of homeobox genes (Carroll et al. 2005). Homeobox genes are not the same as homeotic MADS-box genes (Meyerowitz 2002).
An ancestral MADS-box gene duplication took place before the divergence of animals, fungi, and plants hundreds of millions of years ago (Alvarez-Buylla et al. 2000), probably before or during the Neoproterozoic snowball Earth or later warming leading to the Cambrian explosion of life. This earliest gene duplication gave rise to the Type 1 and Type II lineages of MADS-box genes (see Figure 1, page 468, Becker and Theißen 2003).
Animal genes such as MEF2 encode certain enzymes involved in muscle differentiation of both invertebrates and vertebrates and wing vein and tracheal development in certain insects. Duplicated MADS-box genes in plants have completely different functions (Meyerowitz 2002).
Some of the better understood duplicated MADS-box floral meristem organ identity and integrator genes encode MIKC-type MADS-box TFs that determine development of cones and flowers (Ma and dePamphilis 2000, Theißen et al. 2000, Theißen 2001, Becker and Theißen 2003, Theißen and Melzer 2007).
An evolutionary history of MIKC-type MADS-box A genes, including gene duplications and functional divergence is reviewed by S. Kim et al. (2006) and Shan et al. (2007). Recent functional analyses of A-class genes in monocots is published by M.-K. Chen et al. (2008).
Irish and Litt (2005) and Irish (2006) review the evolutionary history of B-, C-, and E-class MADS-box gene duplications in plants. The molecular evolution of B-class MADS-box genes has been extensively researched by Kramer et al. (1998), Kramer et al. (2003), Aoki et al. (2004), S. Kim et al. (2004), Zahn et al. (2005), and Hernández-Hernández et al. (2007).
Molecular evolution of MIKC-type MADS-box C genes over the course of 300 million years of seed plant evolution is reviewed by Kramer et al. (2004), P. Zhang et al. (2004), and Irish and Litt (2005).
Finally, the importance of MADS-box gene duplications and the interactions among the proteins they encode toward the evolution and radiation of flowering plants is reviewed by Rijpkema et al. (2007) and Veron et al. (2007).
Paleopolyploidy. A great body of data has been assembled on paleopolyploidy in plants (Bennett and Leitch 2005, J. J. Doyle et al. 2008, Jiao et al. 2011). Evidence from an exhaustive genomic study of the cultivated grape overwhelmingly supports the existence of paleohexaploidy (Jaillon et al. 2007), which is equivalent to the "γ triplication" cited in the recent paper by Jiao et al. (2011).
Volume 66, Number 1 (2011) of The Plant Journal is devoted to evolution of the plant genome.
Douglas E. Soltis et al. (2007) suggest that WGDs were important in the early evolution of the angiosperm stem group.
"It is noteworthy that polyploidy is absent in some ancient plant lineages, such as the cycads, which argues against the proposition that the frequency of polyploidy in a lineage is merely of symptom of lineage age (Fig. 9)."
The preceding quotation is from page 376 of W. L. Crepet and K. J. Niklas, (2009), Darwin's second "abominable mystery": Why are there so many angiosperm species? American Journal of Botany 96(1): 366-381.
Ancient WGDs are implicated in both the common ancestor of eudicots and monocots and in the MRCA (Jiao et al. 2011), roughly coinciding with the DeCARB and TrCCE.
Evidently, WGDs in Permo-Carboniferous and Triassic-Jurassic seed plants were necessary as a building scaffold for developmental recombination and evolution of innovative morphologies (S. Kim et al. 2004, Zahn et al. 2005, Jiao et al. 2011) such as developmentally labile bisexual cone axes (Baum and Hileman 2006, Theißen and Melzer 2007, Melzer et al. 2010).
Nancy Eckardt (2004) in one of many journal article summaries for The Plant Cell reports on a paper by Blanc and Wolfe (2004). Blanc and Wolfe (2004 [two papers]) deduce the timing of gene duplications in several monocots, eudicots, and rosids over the course of the last few million years using mathematical models, which were refined in later studies by Cui et al. (2006) and Jiao et al. (2011).
The genome of the malvid Arabidopsis thaliana has undergone at least three WGDs in its evolutionary history (Proost et al. 2011).
Phylogenetic analyses permit accurate estimates of the divergence times of major eudicot clades (D. E. Soltis et al. 2008), with precision enhanced by including fossil minimum age data mapped on to branch points (Crepet et al. 2004).
Based upon studies of gene and genome duplications in rice (Oryza sativa, Poaceae, Poales, Commelinidae) and mouse-eared cress, Chapman et al. (2006) provide insight on the functional divergence and buffering models for genome duplication. Chapman et al. (page 2734, 2006) suggest that as ancient duplicated genes diverge "... reciprocal buffering presumably erodes with time ..." leading to cyclic genome duplication.
De Bodt et al. (2005) propose that paleopolyploidy created much of the genetic material in modern flowering plants. For example, genes retained in duplicate from WGDs in Arabidopsis over the course of million of years are involved in developmental gene regulation and often do not retain redundant functions (Blanc and Wolfe 2004). Gene duplications result in either neofunctionalization, loss of function thus forming pseudogenes, or provide raw material for divergence in animals (Carroll et al. 2005) and plants (Irish and Litt 2005).
"Given that such genes [developmental, regulatory, and signaling genes] are considered important for introducing phenotypic variation and increase in biological complexity, linking ancient polyploidy events with decisive moments in evolution becomes less speculative and the origin and evolution of angiosperms perhaps less of a mystery."
The above quotation is from page 596 of S. De Bodt, S. Marie, and Y. Van der Peer (2005), Genome duplication and the origin of angiosperms. Trends in Ecology and Evolution 20(11): 591-597. The phrase in brackets  is mine.
Interspecific hybridization. Paleopolyploidy as a consequence of interspecific hybridization and polyploidization of unrelated gymnosperms having two different chromosome base numbers was proposed by Edgar Anderson in 1934. Some aspects of this early work was developed in a paper published in 1965 by Raven and Kyhos.
While G. Ledyard Stebbins (1958) did not agree with specifics stated in Edgar Anderson's hypothesis, he does propose that Cretaceous angiosperms were products of interspecific hybridization between flowering plant prototypes. Stebbins (1958) states:
"Because of this fact [see above], and also because of the possibility that in its early stages the phylogeny of the angiosperms may have been highly reticulate, I believe that no phylogenetic tree which can be constructed on the basis of present day knowledge can express the genetic interrelationships between orders and families of angiosperms with any degree of accuracy ..."
The above quotation is from page 269 of Stebbins (1958), On the hybrid origin of the angiosperms, Evolution (Lancaster) 12: 267-270.
MicroRNAs. MicroRNAs (miRNAs) are tiny ribonucleic acid fragments comprised of about a dozen nucleotides found in animal and plant cells. Their precursors possess a characteristic hairpin loop structure (reviewed by Carraro et al. 2006, Axtell et al. 2007).
A phylogenetic analysis of miRNA164 presents new data needed to disentangle the phylogenetic relationships of major clades of seed plants (Jasinski et al. 2010).
While many microRNA's are deeply conserved in land plants as determined from molecular phylogenetic analyses (S. Kim et al. 2006, Barakat et al. 2007), the birth and death of certain miRNAs may occur within a short evolutionary time span (Axtell et al. 2007).
Are plant microRNAs involved in repressing homeotic genes in growing cells and tissues?
Yes, according to Axtell and Bartel (2005) and Axtell et al. (2007). Most microRNAs are involved in negative regulation of gene expression, specifically in control of transcriptional regulators that affect plant development and morphology (Axtell et al. 2007). They are powerful but negative repressors of key transcriptional regulators in the land plant developmental tool kit (B. Zhang et al. 2006, Floyd and Bowman 2007, Axtell and Bowman 2008).
Some key examples of miRNA regulation of TFs include repression of Class III HD-Zip genes necessary for SAM and leaf development by miR165 and miR166 (Floyd et al. 2006), targeting of AP2 floral development Class A genes by miR172 (S. Kim et al. 2006), repression of scarecrow-like GRAS family genes by miR172, cleavage of GAMYB proteins (positive regulators of LFY gene expression) by miR159, loss-of-function of CUC genes (important in embryo and flower development) caused by miR164, and negative effects on ARF genes by miR160 and miR167 (B. Zhang et al. 2006).
Regulatory effects of miRNAs are modeled by Djuranovic et al. (2011).
MicroRNAs specifically small-interfering RNAs (siRNAs) are implicated in the regulation of plant defense responses to insect herbivore attack. These small RNAs may move through living cells and tissues via plasmadesmata from plant to plant, or from plant to insect and vice-versa (Pandey et al. 2008).
Chloroplast capture and horizontal transfer (HT) of genes. Phylogenetic systematists who study the origin and evolution of angiosperms have identified genes that originated outside of the host plant (Bergthorsson et al. 2004). Foreign chloroplasts and mitochondria (including their genetic material) may be incorporated into new symbionts (seed plants) (Tsitrone et al. 2003, Cho et al. 2004).
Horizontal transfer of genes (HT) occurs in both prokaryotes and eukaryotes including animals, fungi, and plants. According to a recent survey by Richardson and J. D. Palmer (2007), Horizontal transfer involves housekeeping respiratory- or ribosomal protein encoding- mitochondrial genes.
Robert Jansen et al. (2011) report numerous transfers of rpl22, a plastidic sequence, to the nuclear genomes of several rosids.
Transfer of genes from donor epiphytic or saprophytic (or other) species to certain organelles of seed plant hosts is demonstrable. At least 26 mitochondrial genes in the basal angiosperm Amborella trichopoda originated from other plants (Bergthorsson et al. 2004) including nine genes from probably epiphytic mosses, and another 19 from sympatric eudicots (Richardson and J. D. Palmer 2007). This is in contrast to the chloroplast genome of Amborella where no horizontally transferred genes are apparent (Goremykin et al. 2003).
"The horizontal gene transfer concept is potentially of great importance for leading evolutionary thinking beyond the ossified tenets of 'synthetic' theory, first of all, by introducing a long sought - and vigorously denied by traditionalists - mechanism by which macromutations can spread ..."
The passage above is quoted from page 381 of Krassilov (2002), Chapter 29, Character parallelism and reticulation in the origin of angiosperms, Pp. 373-382 In: M. Syvanen and C. I. Kado (eds.), Horizontal Gene Transfer (second edition), San Diego: Academic Press, 445 pp.
Plant pathologists provide important clues on the nature of bioactive substances manufactured by insects and signaling between plant hosts and herbivores. Professor Jack Schultz states:
"We should not be surprised to find that plants and animals employ microbes to manipulate each other's signaling systems. It appears that both symbionts and lateral gene transfer offer such possibilities, and that the origin of some (many?) plant-herbivore interaction traits is neither insect nor plant."
The preceding quotation is from page 460 of Schultz (2002), Shared signals and the potential for phylogenetic espionage between plants and animals, Integrative and Comparative Biology: 42: 454-462.
A well-studied basis of "phylogenetic espionage" is buried in the extensive literature on pathogenic baculoviruses. Insect bodies are often infected by baculoviruses. In certain cases baculovirus genes are incorporated into genomes of lepidopteran hosts causing large behavioral phenotypic effects (Hoover et al. 2011).
Further, it might have been possible for genome parasites such as transposable elements (Venner et al. 2009) to move from fungal-, insect-, or tetrapod genomes to the host plant genome or vice versa by baculovirus vectors in their eukaryotic hosts residing coevolutionary compartments.
Were ancient baculoviruses a source of cross-Kingdom genome parasites able to move from bacterial, animal, and/or fungal hosts and vectors to shrub lifeboats (or vice-versa) of Permo-triassic coevolutionary compartments?
Transposable elements (TEs). One key ingredient left out of the steaming cauldron of past ideas on the origin of flowering plants is a class of mobile chromosome parasites known as transposable elements (TEs). Transposable elements are "pieces of DNA characterized by their ability to move from one locus to another in the genome" (page 537, Schaack et al. 2010).
Good places to gain a basic understanding of transposons within an evolutionary context are reviews by Lovisolo et al. (page 350, 2003), Schaack et al. (2010), and Blumenstiel (2011).
Transposable elements are known from prokaryotes and eukaryotes including animals, fungi, plants, and protozooans (Lovisolo et al. 2003, Tu 2005, de la Chaux et al. 2011). Long terminal repeat (LTR) retrotransposons are eukaryotic DNA sequences "... with homology to retroviruses ..." (page 350, Lovisolo et al. 2003).
Sarah Schaack et al. (page 537, 2010) define several types of TEs:
Autonomous TEs "... encode the proteins necessary to perform a complete transposition reaction on their own i.e. to move from one genomic locus to another"
Class 2 DNA transposons are TEs "... that transpose via a DNA intermediate ..."
Cut-and-paste TEs are Class 2 DNA TEs that "... excise and integrate elsewhere ..." on the chromosome
Retro-TEs are class 2 DNA TEs that "... do not excise ..."
LTR retrotransposons constitute one class of retro-TEs "... comprised of several superfamilies (e.g. Ty1/Copia), some of which produce virus-like particles; characterized by long terminal repeats (LTRs) which are generated upon chromosomal integration"
Non-autonomous TEs are TEs "... that do not encode the transposition machinery and are therefore not able to transpose on their own... "
Non-LTR retrotransposons are a second class of retro-TEs "... also comprised of numerous superfamilies (e.g. L1, RTE, and Alu) ..." "... characterized by the lack of terminal repeats ..."
Class 1 retrotransposons are TEs "that replicate based on the reverse transcription of an RNA intermediate ..."
Some retrotransposons of plants are localized in the centromere of chromosomes (Neumann et al. 2011).
Why should students of the evo-devo of arthropod- and floral tool kits, coevolution, heterochrony, molecular systematics, and paleobotany, and the population ecology of pollination, be concerned with these bizarre mobile genetic parasites?
A promising clue that indirectly suggests transposon activity in putatively coevolving arthropod and seed plant genomes is contained in an important paper by Hamès et al. (2008) published in The European Molecular Biology Organization (EMBO) Journal.
Further, TEs are a potentially unstudied yet ostensibly critical ingredient in genome dynamics with potentially profound effects on transcription, translation, enzyme folding, and coevolution of manufactured homeodomain proteins. Amino acids including lysine residue 390 of the LFY-C primary polypeptide chain, and secondary HTH coiling of homeodomain proteins e.g. Tc3 transposase, Hin recombinase, insect Engraled, and LFY, are noteworthy clues (Hamès et al. 2008) and possible signatures suggesting cross-Kingdom TE activity.
Surprisingly, all the contributors to the Botanical Society of America 2009 Darwin Symposium and 2010 Royal Society of London compilations overlooked the paper by Hamès and company (2008).
Equally important toward a greater appreciation of the role of TEs in the coevolution of angiosperms and holometabolous insects is the landscape evolutionary ecology of dynamic animal, fungal, and plant genomes. Repetitive DNA elements such as LTR-retrotransposons together with "non-protein-encoding sequence types" (i.e. CREs including enhancers and promoters) are responsible for interspecific variation in DNA content of plants (Grover and Wendel 2010).
Did surviving insects of the EPE and TrCCE feed, reproduce, and secrete biologically active molecules on, or infect growing points and reproductive modules with transposons, while chewing, piercing, ovipositioning, scraping, sponging, stinging, and trampling the surfaces of SAMs and accessory bisexual cone axes?
Based on a review of the literature, unraveling the evolutionary complexities behind vertical transmission of viruses in insects, cross-Kingdom horizontal movement of TEs, and coevolution of insect antagonist- and seed plant host tool kits, might be the keys to solving the enigmatic origins of flowering plants and the Holometabola.
Conclusions on the Origin of Angiosperms:
I propose that insect-seed plant interactions at the molecular level led to diversification in seed plant lineages, formation of flowers from bisexual cone axes, and the origin of angiosperms. Molecular coevolution of insect and seed plant developmental CRMs and early diverging developmental tool kits probably took place in shrub lifeboat-phytophagous insect compartments indigenous to biomes of the Carboniferous icehouse and later Permian hothouse Earth.
Despite the observations by developmental biologists that animals and plants evolved their master developmental regulatory systems independently there is a fundamental logic to how the systems operate in SAMs of plants and in dorsal-ventral patterning of developing insects (Meyerowitz 2002).
Therefore, it is not surprising that similarities exist among the HTH DNA-binding motifs of some homeodomain regulatory proteins and the seven-helix fold of the Leafy switch (Hamès et al. 2008). A fertile area for future research might include X-ray crystallographic studies of HTH, helix-loop-helix, and zinc-finger motifs of homeotic and respiratory enzymes, including detailed functional analyses of amino acid sequences at the C-terminal end of certain developmental, regulatory, and signaling proteins.
Is the apparent logic expressed in the evo-devo of modular DNA-binding enzyme systems of coevolving insects and plants supported by experimental data and phylogenetic analyses?
Did natural selection operate in deep time on the proteins and other factors necessary for the assembly of modular cis-regulatory systems of insect antagonists and seed plant hosts?
Based on proteonomics modeling and molecular phylogenetic studies, insect olfactory chemoreceptors and selected nuclear receptor proteins are also potential candidates for study (Abdel-latief 2007, G. Zhang et al. 2007, Bonneton et al. 2008). I also add Hx moulting storage proteins which are related to Hc respiratory enzymes (Burmester et al. 1998, Burmester 2001, Burmester et al. 2006, Burmester and Hankein 2007), JH esterases, vitellogenin genes and yolk proteins (Isoe and Hagedorn 2007), pheromone chemoreceptors (Robertson and Wanner 2006), and ecdysone-inducible TFs as proteins for possible future analyses of proteomes.
Choice of Hcs and Hxs as key elements of the early divergent arthropod developmental tool kit ties-in with the evolution of insect legs and wings from bilaterian gills. Ancient insect wings probably functioned as respiratory organs. Wings, halteres, arachnid spinnerets, and insect legs are all organs that develop from limb fields of cells where Ubx expression is prevalent (S. B. Carroll et al. 2005).
Molecular evolution of invertebrate Hc enzymes and their derived insect Hxs might have been driven by the rise and fall of oxygen in the Earth's atmosphere at two intervals (during the DeCARB and following the GuCCE) of the Paleozoic Era. Phytophagous insects may have used oxygen generating vegetation of hypoxic Paleozoic times as a source of food and for shelter from temperature extremes and UV radiation (Labandeira 2006).
Coevolution of insect antagonist and seed plant host was potentially reciprocal, simultaneous, and specialized.
Evidently, WGDs in Permo-Carboniferous and Triassic-Jurassic seed plants were necessary as a building scaffold for developmental recombination and evolution of innovative morphologies (S. Kim et al. 2004, Zahn et al. 2005, Jiao et al. 2011) such as developmentally labile bisexual cone axes (Baum and Hileman 2006, Theißen and Melzer 2007, Melzer et al. 2010).
Further, trampling and secreting insects on meristems of plastic bisexual cone axes might have affected assembly of homeotic protein quartets and homeodomain protein trafficking in Paleozoic gigantopteroid and vojnovskyalean seed plants. Finally I propose that phytoecdysones secreted by Permo-Carboniferous and Permo-Triassic shrub lifeboats potentially affected body size and moulting time of phytophagous insect antagonists.
Clues gleaned from biochemical studies of vegetative growth and SAM organization in extant model lignophytes and monilophytes, when combined with insight gained from molecular phylogenetic analyses of type III HD-Zip genes and KNOTTED1 homeodomain proteins suggest that at least two (possibly three or more) evo-devo programs potentially existed in early diverging Devonian progymnosperm and seed plant populations.
Theißen and Saedler's (2001), Baum and Hileman's (2006), and Theißen and Melzer's (2007) molecular evolutionary models of cis-acting enzyme quartets is now the most widely accepted explanation for the evolution of floral regulators (Melzer et al. 2010).
Based on cladistic studies of ornithischian tetrapod ghost lineages (Weishampel and Jianu 2000) and paleoecological data it was unlikely that dinosaurians invented flowers (Barrett and Willis 2001).
The origin of angiosperms and certain clades of holometabolous insects is potentially a consequence of coevolution of animal and seed plant CRMs and developmental tool kits.
Transposable elements are a potentially unstudied yet ostensibly critical ingredient in genome dynamics with potentially profound effects on transcription, translation, enzyme folding, and coevolution of manufactured homeodomain proteins. Amino acids including lysine residue 390 of the LFY-C primary polypeptide chain, and secondary HTH coiling of homeodomain proteins e.g. Tc3 transposase, Hin recombinase, insect Engraled, and Leafy, are noteworthy clues (Hamès et al. 2008) and possible signatures suggesting cross-Kingdom TE activity.
Cladogenesis of flowering plants may be traced back in geologic time to the EPE, and to surviving remnants of already divergent Permian seed plant lineages. Coevolving insect antagonists of monopodial Permo-Triassic seed plants potentially inhabited massive SAMs, cone axes, and thermal insulating crevices of leaf bases, bark, and wood.
A Norian Age (late Triassic) of the crown-group basal angiosperms is suggested in relaxed clock phylogenetic analyses (Stephen A. Smith et al. 2010). Magallón (2010) estimates a Permo-Triassic or Permo-Carboniferous origin of the flowering plant stem group. These estimates better correspond with diversification in major clades of phytophagous Holometabola (Grimaldi and Engel 2005), and are consistent with arguments presented by Bruce Cornet (1989) on the origin of flowering plants, palynological evidence (Hochuli and Feist-Burkhardt 2004), and numerous molecular phylogenetic studies of key tool kit enzymes necessary for cone and floral development.
More work is needed to answer the following questions, among others:
Are classic proposals on the origin of the angiosperm outer integument, and carpels from axillary organs of Mesozoic Caytoniales congruent with the deeply conserved evo-devo of floral tool kits and homeodomain proteins?
Could the application of mechanical force, simple thigmo, and/or secretion of phytohormone signals by chewing, piercing, ovipositioning, scraping, sponging, stinging, and trampling insect mutualists affect homeodomain protein movements and developmental switches in cone and floral SAMs?
Did biologically active plant defense substances affect moulting insect instars residing in oxygenated crevices of SAMs of ancient seed plants?
Do hormones secreted by moulting instars upregulate or repress transcription in nuclei of host seed plants?
Did the repetitive actions and long-term activities and secretions of certain Carboniferous, Permian, and Triassic herbivorous insect colonies affect LFY gradients in SAMs and cone axes of host seed plant shrub lifeboats?
What was the role of secreted plant-derived BRs, catecholamines, and peptides in defense against both large and small herbivorous dinosaurs?
Were Paleozoic changes in atmospheric oxygen concentration the selective force driving the molecular evolution of gas-binding Hc respiratory enzymes and moulting storage proteins of arthropods?
Are Hxs hypoxia-inducible storage proteins of insects?
If so, how is the molecular evolution of Hxs tied-in with deep time neoteny in hemimetabolous Isoptera and Mecoptera, and the evolution of caste polyphenism in holometabolous ants, bees, and wasps?
Was hypoxia a driving force in the evolution of insect and plant Hgs?
"But what does the analysis of KNOX gene expression evolution tell us about morphological evolution in plants?" (page 162, Reiser et al. 2000)
Are there structural and functional relationships between the homeodomain proteins and MYB TFs of insect antagonists and their seed plant hosts that might have a bearing on a coevolutionary origin of angiosperms and the Holometabola?
Did genome parasites move from fungal-, insect-, or tetrapod genomes to seed plant genomes (or vice versa) within the confines of hypothetical Paleozoic coevolutionary compartments?
Were Paleozoic insect antagonists attracted to potential emissions of NO of host plants where NO possibly played a role in ameliorating the detrimental effects of local hypoxia?
Could BRs manufactured by Carboniferous, Permian, and Triassic seed plant host shrubs send signals to the EcRs of developing eggs and instars of phytophagous insect antagonists inhabiting shrub lifeboats?
Did surviving insects of the EPE and TrCCE feed, reproduce, and secrete biologically active molecules on, or infect growing points and reproductive modules with transposons while chewing, ovipositioning, scraping, sponging, stinging, and trampling the surfaces of SAMs and accessory bisexual cone axes?
Can changes in the quaternary structure of homeotic protein quartets sensu Baum, Hileman, Melzer, and Theißen over geologic time be integrated with macroevolutionary models explaining origins and co-radiations of flowering plants and holometabolous insect mutualists?
How has the HT of genes including cross-Kingdom movement of TEs, affected tool kits over time, underpinned morphological heterochronies, and somehow been partly responsible for the coevolution of angiosperms and the Holometabola?
Were swarms of WGDs in seed plant populations that occurred prior to the "γ triplication" event in eudicots and monocots a manifestation of wide-crossing events in populations of the MRCA and the first angiosperms?
Can molecular phylogenetics pin-point the timing of WGDs and tool kit divergences when calibrated with fossils?
Is the Aptian (Cretaceous) explosion of flowering plant paleodiversity attributable to the effects of the BaCCE on coevolving angiosperm hosts and insect antagonists?
Selection pressures in populations of Permo-Carboniferous and Permo-Triassic seed plant populations were probably much greater than believed. An herbaceous origin of flowering plants cannot be explained by mutualism and coevolution of insects and seed-bearing shrub hosts alone.
Enormous protoflowers known only from fragments and detached megasporophylls were probably modifications of developmentally plastic bisexual cone axes representing divergent clades of several Permian gymnosperms that survived the end-Permian apocalypse.
Carpel, floral, and ovular transcriptional regulation in extant angiosperm model organisms does not preclude derivation of evo-devo models that explain curling, inrolling, and fusion in 260- to 300 million year old spermopteroid Phasmatocycas bridwellii leaves to form carpels, ovaries, and pistils.
When cast in a phylogenetic framework and tested using Larry Hufford's methods (2001), paedomorphic heterochrony to include condensation of hypothetical gigantopteroid protoflowers is the most simple evo-devo process to explain the origin of reproductive organs in Mesozoic crown group angiosperms and extant basal Amborellanae, Austrobaileyanae, Nymphaeanae, and Magnolianae from a putative 160 million year old ghost lineage.
I conclude that insect mediated intergeneric natural hybridization among populations of Paleozoic gigantopteroids and possibly Vojnovskyales, followed by spontaneous paleopolyploidy, might have been a method through which MIKC-type MADS-box gene duplicates were generated, later spreading molecular novelties in populations of the ancestral early Triassic ghost lineages of angiosperms that survived the EPE.
When supported by fossil calibrated phylogenetic tests of possible heterochrony in floral evo-devo of the unstudied chronocline linking Vojnovskya with Sanmiguelia, would the assertion quoted below be correct?
"... major innovations in floral evolution do not coincide with the recovery stages following mass extinctions ..."
The passage above is quoted from page 124 of J. C. McElwain, K. J. Willis, and K. J. Niklas (2011), 5. Long-term fluctuations in atmospheric CO2 concentration influence plant speciation rates. Pp. 122-140 In: T. R. Hodkinson, M. B. Jones, S. Waldren, and J. A. N. Parnell (eds.), Climate Change, Ecology and Systematics. Cambridge: Cambridge University Press, 524 pp.
Ancient WGDs are implicated in both the common ancestor of eudicots and monocots and in the MRCA roughly coinciding with the DeCARB and TrCCE. Further, an exhaustive genomic study of the cultivated grape overwhelmingly supports the existence of paleohexaploidy (Jaillon et al. 2007), which is equivalent to the "γ triplication" cited by Jiao et al. (2011).
A divergence of angiosperms from the MRCA is probably much older than suggested by paleontologic data. Certainly a Triassic or even older Permian origin of flowering plants is likely (Stephen A. Smith et al. 2010, Magallón 2010). Divergence of putative paraphyletic angiosperm lineages from the MRCA might extend back in time to the oxygen-starved hot house of the GuCCE or EPE, or even earlier, potentially rooted among hybridizing populations of the ice-house DeCARB coincident with the first swarm of seed plant WGDs modeled by Jiao et al. (2011).
When taking into account the cyclic nature of angiospermization, flowering plants as traditionally defined, might be an amalgam of paraphyletic evolutionary lines traceable to surviving geographically disparate early Triassic remnants of already divergent gigantopteroid and vojnovskyalean Permian seed plant lineages.
An early Jurassic aquatic origin for flowering plants is incongruent with likely deleterious effects of sulfuric acid poisoning of lakes, shorelines, and wetlands, caused by basalt outpouring from the CAMP, which is associated with the TrCCE.
Assuming coevolution of phytophagous Coleopterans with angiosperms, various proposals on rapid diversification of flowering plants during the Albian Age of the Gallic Epoch of the early Cretaceous Period are inconsistent with molecular based phylogenies of Coleoptera that suggest a Triassic origin of certain non-chrysomelid beetle lineages (Hunt et al. 2007).
Since some of the interdisciplinary data from paleoclimatology, paleontology, developmental biology, and plant physiology have only just been published in peer-reviewed journals in the last decade, it is not surprising that the origin of flowering plants has been elusive.
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