Towards a synthetic view of axis specification mechanisms in vertebrates: insights from the dogfish

The genetic mechanisms, which control axis specification, apparently extensively diverge across vertebrates. In amphibians and teleosts, they are tightly linked to the establishment of an early dorso-ventral polarity. This polarity has no equivalent in amniotes, which unlike the former, retain a considerable plasticity for their site of axis formation until blastula stages and rely on signals secreted by extra-embryonic tissues for the establishment of their early rostro-caudal pattern. In order to better understand the links between these seemingly highly divergent mechanisms, we have used an evo-devo approach, aimed at reconstructing the gnathostome ancestral state and focussed on a chondrichthyan, the dogfish Scyliorhinus canicula. A detailed molecular characterization of the dogfish embryo at blastula and gastrula stages highlights striking similarities with all vertebrate model organisms including amniotes. It suggests the presence in the dogfish of territories homologous to the hypoblast and extra-embryonic ectoderm of the latter, which may therefore reflect the primitive condition of jawed vertebrates. In the ancestral state, these territories are specified at opposite sides of an early axis of bilateral symmetry, homologous to the dorso-ventral axis of amphibians and teleosts, and aligned with the later forming embryonic axis, from head to tail. Amniotes have diverged from this pattern through a posterior expansion of extra-embryonic ectoderm, resulting in an apparently radial symmetry at late blastula stages. These data delineate the broad outlines of the gnathostome ancestral pattern of axis specification and highlight an unexpected unity of mechanisms across jawed vertebrates. They illustrate the complementarity of comparative and genetic approaches for a comprehensive view of developmental mechanisms themselves. To cite this article: M. Coolen et al., C. R. Biologies 332 (2009).     

Wnt signaling and dorso-ventral axis specification in vertebrates.

The dorso-ventral axis is specified in vertebrates through the formation of a dorsal signaling center known as the Spemann organizer. This process depends on signal transduction by beta-catenin that can be regulated by secreted Wnt proteins. Recent discoveries of new players in this signaling pathway have narrowed down the search for the initial cues for axis specification in vertebrate embryos.     

Mechanism of anteroposterior axis specification in vertebrates. Lessons from the amphibians.

Interest in the problem of anteroposterior specification has quickened because of our near understanding of the mechanism in Drosophila and because of the homology of Antennapedia-like homeobox gene expression patterns in Drosophila and vertebrates. But vertebrates differ from Drosophila because of morphogenetic movements and interactions between tissue layers, both intimately associated with anteroposterior specification. The purpose of this article is to review classical findings and to enquire how far these have been confirmed, refuted or extended by modern work. The "pre-molecular" work suggests that there are several steps to the process: (i) Formation of anteroposterior pattern in mesoderm during gastrulation with posterior dominance. (ii) Regional specific induction of ectoderm to form neural plate. (iii) Reciprocal interactions from neural plate to mesoderm. (iv) Interactions within neural plate with posterior dominance. Unfortunately, almost all the observable markers are in the CNS rather than in the mesoderm where the initial specification is thought to occur. This has meant that the specification of the mesoderm has been assayed indirectly by transplantation methods such as the Einsteckung. New molecular markers now supplement morphological ones but they are still mainly in the CNS and not the mesoderm. A particular interest attaches to the genes of the Antp-like HOX clusters since these may not only be markers but actual coding factors for anteroposterior levels. We have a new understanding of mesoderm induction based on the discovery of activins and fibroblast growth factors (FGFs) as candidate inducing factors. These factors have later consequences for anteroposterior pattern with activin tending to induce anterior, and FGF posterior structures. Recent work on neural induction has implicated cAMP and protein kinase C (PKC) as elements of the signal transduction pathway and has provided new evidence for the importance of tangential neural induction. The regional specificity of neural induction has been reinvestigated using molecular markers and provides conclusions rather similar to the classical work. Defects in the axial pattern may be produced by retinoic acid but it remains unclear whether its effects are truly coordinate ones or are concentrated in certain regions of high sensitivity. In general the molecular studies have supported and reinforced the "pre-molecular ones". Important questions still remain: (i) How much pattern is there in the mesoderm (how many states?) (ii) How is this pattern generated by the invaginating organizer? (iii) Is there one-to-one transmission of codings to the neural plate? (iv) What is the nature of the interactions within the neural plate? (v) Are the HOX cluster genes really the anteroposterior codings?     

Evolution of jaw depression mechanics in aquatic vertebrates: insights from Ghondrichthyes

The widely accepted phylogenctic position of Chondrichthyes as the sister group to all other living gnathostomes makes biomechanical analyses of this group of special significance for estimates of skull function in early jawed vertebrates. We review key findings of recent experimental research on the feeding mechanisms of living elasmobranchs with respect to our understanding of jaw depression mechanisms in gnathostome vertebrates. We introduce the possibility that the ancestral jaw depression mechanism in gnathostomes was mediated by the coracomandibularis muscle and that for hyoid depression by the coracohyoideus muscle, as in modern Chondrichthyes and possibly placoderms. This mechanism of jaw depression appears to have been replaced by the sternohyoideus (homologous to the coracohyoideus) coupling in Osteichthycs following the split of this lineage from Chondrichthyes. Concurrent with the replacement of the branchiomandibularis (homologous to the coracomandibularis) coupling by the sternohyoideus coupling as the dominant mechanism of jaw depression in Osteichthyes was the fusion and shift in attachment of the intcrhyoideus and intermandibularis muscles (producing the protractor hyoideus muscle, mistakenly refereed to as the geniohyoideus), which resulted in a more diversified role of the sternohyoideus coupling in Osteichthyes. The coracohyoideus coupling appears to have been already present in vertebrates where it functioned in hyoid depression, as in modern Chondrichthyes, before it acquired the additional role of jaw depression in Osteichthyes.     

Ventilation and the origin of jawed vertebrates: a new mouth

This study investigates the origin of jaws by re-assessing homologies between the oropharyngeal regions of Agnatha and Chondrichthyes. In accordance with classical theory, jaws are interpreted as the most anterior arches of the ventilatory branchial basket. It is proposed that jaws first enlarged for a ventilatory function, i.e. closing the jaws prevented reflux of water through the mouth during forceful expiration. Next, they enlarged further to grasp prey in feeding. As they enlarged, the jaws tilted forward, squeezing the ancestral oral cavity in front of them ('old mouth') into a slit between the jaws and lips. Simultaneously, the anterior part of the pharynx behind the jaws was pulled forward and became a 'new mouth' (the buccal part of the buccopharyngeal cavity of gnathostomes). During the transition to gnamostomes, the premandibular cheeks and lips of the old mouth remained in place, and are represented in ammocoete lampreys, chimaeroids, and sharks. The stages in the evolution of gnathostomes, driven by selection for increasing activity, are modelled as: ancestral vertebrate (with unjointed branchial arches) to early pre-gnathostome (jointed internal arches and stronger ventilation) to late pre-gnadiostome (with mouth-closing, ventilatory 'jaws') to early gnathostome (feeding jaws).     

The phyllolepid placoderm Cowralepis mclachlani: Insights into the evolution of feeding mechanisms in jawed vertebrates

Remarkably preserved specimens of Cowralepis mclachlani Ritchie, 2005 (Proc Linn Soc NSW 126:215–259) (Phyllolepida, Placodermi) represent a unique ontogenetic sequence adding to our understanding of anatomy, function, and phylogeny among basal jawed vertebrates (gnathostomes). A systematic review demonstrates that the Phyllolepida are a subgroup of the Arthrodira. Consideration of visceral and neurocranial characters supports the hypothesis that placoderms are the sister group to remaining gnathostomes. Placoderms possess, as adult plesiomorphic features, a number of characters that are only seen in the development of extant gnathostomes—a peramorphic shift relative to placoderms. Developmental evidence in vertebrates leads to a revised polarity of character transitions. These include 1) hyomandibula‐neurocranium and ventral parachordal‐palatoquadrate articulations (vertebrate synapomorphies); 2) jointed pharynx, paired basibranchials, anterior ethmoidal‐palatoquadrate articulation, short trabeculae cranii, and anterior and posterior neurocranial fissures (gnathostome synapomorphies); and 3) fused basibranchials, dorsal palatoquadrate‐neurocranium articulation, loss of the anterior neurocranial fissure, elongated trabeculae cranii, and transfer of the ventral parachordal‐palatoquadrate articulation to the trabeculae (crown group gnathostomes). The level of preservation in C. mclachlani provides the basis for a reinterpretation of phyllolepid anatomy and function. Cowralepis mclachlani possesses paired basibranchials allowing the reinterpretation of the visceral skeleton in other placoderms. Mandible depression in C. mclachlani follows an osteichthyan pattern and the ventral visceral skeleton acts as a functional unit. Evidence for hypobranchial musculature demonstrates the neural crest origin of the basibranchials and that Cowralepis was a suction feeder. Finally, the position of the visceral skeleton relative to the neurocranium in placoderms parallels the condition in selachians and osteichthyans, but differs in the elongation of the occiput. The cucullaris fossa of placoderms (interpreted as a site of muscle attachment) is shown to represent, in part, the parabranchial chamber. J. Morphol., 2009. © 2009 Wiley‐Liss, Inc.     

The characters of Palaeozoic jawed vertebrates

Newly discovered fossils from the Silurian and Devonian periods are beginning to challenge embedded perceptions about the origin and early diversification of jawed vertebrates (gnathostomes). Nevertheless, an explicit cladistic framework for the relationships of these fossils relative to the principal crown lineages of the jawed vertebrates (osteichthyans: bony fishes and tetrapods; chondrichthyans: sharks, batoids, and chimaeras) remains elusive. We critically review the systematics and character distributions of early gnathostomes and provide a clearly stated hierarchy of synapomorphies covering the jaw‐bearing stem gnathostomes and osteichthyan and chondrichthyan stem groups. We show that character lists, designed to support the monophyly of putative groups, tend to overstate their strength and lack cladistic corroboration. By contrast, synapomorphic hierarchies are more open to refutation and must explicitly confront conflicting evidence. Our proposed synapomorphy scheme is used to evaluate the status of the problematic fossil groups Acanthodii and Placodermi, and suggest profitable avenues for future research. We interpret placoderms as a paraphyletic array of stem‐group gnathostomes, and suggest what we regard as two equally plausible placements of acanthodians: exclusively on the chondrichthyan stem, or distributed on both the chondrichthyan and osteichthyan stems. © 2014 The Authors. Zoological Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of The Linnean Society of London     

Evolution of electrosensory ampullary organs: conservation of Eya4 expression during lateral line development in jawed vertebrates

The lateral line system of fishes and amphibians comprises two ancient sensory systems: mechanoreception and electroreception. Electroreception is found in all major vertebrate groups (i.e. jawless fishes, cartilaginous fishes, and bony fishes); however, it was lost in several groups including anuran amphibians (frogs) and amniotes (reptiles, birds, and mammals), as well as in the lineage leading to the neopterygian clade of bony fishes (bowfins, gars, and teleosts). Electroreception is mediated by modified “hair cells,” which are collected in ampullary organs that flank lines of mechanosensory hair cell containing neuromasts. In the axolotl (a urodele amphibian), grafting and ablation studies have shown a lateral line placode origin for both mechanosensory neuromasts and electrosensory ampullary organs (and the neurons that innervate them). However, little is known at the molecular level about the development of the amphibian lateral line system in general and electrosensory ampullary organs in particular. Previously, we identified Eya4 as a marker for lateral line (and otic) placodes, neuromasts, and ampullary organs in a shark (a cartilaginous fish) and a paddlefish (a basal ray‐finned fish). Here, we show that Eya4 is similarly expressed during otic and lateral line placode development in the axolotl (a representative of the lobe‐finned fish clade). Furthermore, Eya4 expression is specifically restricted to hair cells in both neuromasts and ampullary organs, as identified by coexpression with the calcium‐buffering protein Parvalbumin3. As well as identifying new molecular markers for amphibian mechanosensory and electrosensory hair cells, these data demonstrate that Eya4 is a conserved marker for lateral line placodes and their derivatives in all jawed vertebrates.     

An automated algorithm for extracting functional immunologic V-genes from genomes in jawed vertebrates

Variable (V) domains of immunoglobulins (Ig) and T cell receptors (TCR) are generated from genomic V gene segments (V-genes). At present, such V-genes have been annotated only within the genome of a few species. We have developed a bioinformatics tool that accelerates the task of identifying functional V-genes from genome datasets. Automated recognition is accomplished by recognizing key V-gene signatures, such as recombination signal sequences, size of the exon region, and position of amino acid motifs within the translated exon. This algorithm also classifies extracted V-genes into either TCR or Ig loci. We describe the implementation of the algorithm and validate its accuracy by comparing V-genes identified from the human and mouse genomes with known V-gene annotations documented and available in public repositories. The advantages and utility of the algorithm are illustrated by using it to identify functional V-genes in the rat genome, where V-gene annotation is still incomplete. This allowed us to perform a comparative human–rodent phylogenetic analysis based on V-genes that supports the hypothesis that distinct evolutionary pressures shape the TCRs and Igs V-gene repertoires. Our program, together with a user graphical interface, is available as open-source software, downloadable at http://code.google.com/p/vgenextract/.     

Agnathans recent and fossil,and the origin of jawed vertebrates

Summary During the last 15 years we have gained considerably more knowledge about the anatomy, physiology and molecular sequences of the modern agnathans. This knowledge has been analysed with modern systematic techniques which provide clear, unambiguous statements of relationships. At present there is a conflict between the results obtained using morphological/physiological data and that using molecular data. During the next few years it is likely that more molecular sequences will become available for analysis. Whether this will fuel the conflict or resolve the issue remains to be seen.The great increase in our knowledge of the diversity of fossil agnathans is continuing to provide much new anatomical information and this allows more firmly based phylogenies to be constructed. From these we may be able to delimit more precisely the course of evolutionary changes of functional systems in the early history of vertebrates.Many of our decisions concerning primitiveness or degeneracy of the modern agnathans can be gained through study of the ontogenetic development and the variation between the ontogenies from species to species. Lampreys are relatively well known in this respect. However, we lack comparable detailed studies of the development of hagfishes. A major research field is here waiting to be reaped.     

Reproductive costs in terrestrial male vertebrates: insights from bird studies

Reproduction requires resources that cannot be allocated to other functions resulting in direct reproductive costs (i.e. trade-offs between current reproduction and subsequent survival/reproduction). In wild vertebrates, direct reproductive costs have been widely described in females, but their occurrence in males remains to be explored. To fill this gap, we gathered 53 studies on 48 species testing direct reproductive costs in male vertebrates. We found a trade-off between current reproduction and subsequent performances in 29% of the species and in every clade. As 73% of the studied species are birds, we focused on that clade to investigate whether such trade-offs are associated with (i) levels of paternal care, (ii) polygyny or (iii) pace of life. More precisely for this third question, it is expected that fast species (i.e. short lifespan, early maturity, high fecundity) pay a cost in terms of survival, whereas slow species (with opposite characteristics) do so in terms of fecundity. Our findings tend to support this hypothesis. Finally, we pointed out the potential confounding effects that should be accounted for when investigating reproductive costs in males and strongly encourage the investigation of such costs in more clades to understand to what extent our results are relevant for other vertebrates.     

Evolution in parallel: new insights from a classic system

Neo-darwinists have long argued that parallel evolution, the repeated evolution of similar phenotypes in closely related lineages, is caused by the action of similar environments on alleles at many loci of small effect. A more controversial possibility is that the genetic architecture of traits initiates parallelism, sometimes through fixation of alleles of large effect. Recent research (by Cole et al., Colosimo et al., Cresko et al., and Shapiro et al.) offers the surprising insight that reduction in two armor traits of threespine stickleback is governed by independently segregating major loci as well as additional quantitative trait loci (QTL), and that alleles at the same major loci are associated with parallel phenotypes in globally distributed populations. This research suggests the emergence of a new and exciting vertebrate model system for evolutionary genetics.     

Distinct mechanisms for mRNA localization during embryonic axis specification in the wasp Nasonia

mRNA localization is a powerful mechanism for targeting factors to different regions of the cell and is used in Drosophila to pattern the early embryo. During oogenesis of the wasp Nasonia, mRNA localization is used extensively to replace the function of the Drosophila bicoid gene for the initiation of patterning along the antero-posterior axis. Nasonia localizes both caudal and nanos to the posterior pole, whereas giant mRNA is localized to the anterior pole of the oocyte; orthodenticle1 (otd1) is localized to both the anterior and posterior poles. The abundance of differentially localized mRNAs during Nasonia oogenesis provided a unique opportunity to study the different mechanisms involved in mRNA localization. Through pharmacological disruption of the microtubule network, we found that both anterior otd1 and giant, as well as posterior caudal mRNA localization was microtubule-dependent. Conversely, posterior otd1 and nanos mRNA localized correctly to the posterior upon microtubule disruption. However, actin is important in anchoring these two posteriorly localized mRNAs to the oosome, the structure containing the pole plasm. Moreover, we find that knocking down the functions of the genes tudor and Bicaudal-D mimics disruption of microtubules, suggesting that tudor's function in Nasonia is different from flies, where it is involved in formation of the pole plasm.     

Evolution of the bilaterian germ line: lineage origin and modulation of specification mechanisms

A key focus of evolutionary developmental biology (evo–devo)in recent years has been to elucidate the evolution of developmentalmechanisms as a means of reconstructing the hypothetical lastcommon ancestors of various clades. Prominent among such reconstructionshave been proposals as to the nature of the mysterious "Urbilateria,"originally defined as the last common ancestor of the extantBilateria (protostomes and deuterostomes). Indeed, drawingsof this animal can now be found, as well as detailed informationon the genetics and morphological processes that it used toconstruct its gut, heart, eyes, appendages, segments, and bodyregions. Perhaps surprisingly, however, no explanations haveyet been offered as to how this animal might have achieved thesuccessful reproduction that must have been necessary for itto give rise to those lineages that are ancestral to today'sdiverse clades. The present article examines the comparativedata available to date on the specification of the only cellscontaining the genetic hereditary material, the germ cells,and speculates on the possible evolutionary and developmentalorigin of the Urbilaterian germ line.