Fins, limbs, and tails: outgrowths and axial patterning in vertebrate evolution

The Chromosome-Scale Genome of Chitala ornata Illuminates the Evolution of Early Teleosts

Teleosts are the most prolific vertebrates, occupying the vast majority of aquatic environments, and their pectoral fins have undergone remarkable physiological transformations throughout their evolution. Studying early teleost fishes, such as those belonging to the Osteoglossiformes order, could offer crucial insights into the adaptive evolution of pectoral fins within this group. In this study, we have assembled a chromosomal-level genome for the Clown featherback (Chitala ornata), achieving the highest quality genome assembly for Osteoglossiformes to date, with a contig N50 of 32.78 Mb and a scaffold N50 of 40.73 Mb. By combining phylogenetic analysis, we determined that the Clown featherback diverged approximately 202 to 203 million years ago (Ma), aligning with continental separation events. Our analysis revealed the intriguing discovery that a unique deletion of regulatory elements is adjacent to the Gli3 gene, specifically in teleosts. This deletion might be tied to the specialized adaptation of their pectoral fins. Furthermore, our findings indicate that specific contractions and expansions of transposable elements (TEs) in teleosts, including the Clown featherback, could be connected to their adaptive evolution. In essence, this study not only provides a high-quality genomic resource for Osteoglossiformes but also sheds light on the evolutionary trajectory of early teleosts.

Emergence of a left-right symmetric body plan in vertebrate embryos

External bilateral symmetry is a prevalent feature in vertebrates, which emerges during early embryonic development. To begin with, vertebrate embryos are largely radially symmetric before transitioning to bilaterally symmetry, after which, morphogenesis of various bilateral tissues (e.g somites, otic vesicle, limb bud), and structures (e.g palate, jaw) ensue. While a significant amount of work has probed the mechanisms behind symmetry breaking in the left-right axis leading to asymmetric positioning of internal organs, little is known about how bilateral tissues emerge at the same time with the same shape and size and at the same position on the two sides of the embryo. By discussing emergence of symmetry in many bilateral tissues and structures across vertebrate model systems, we highlight that understanding symmetry establishment is largely an open field, which will provide deep insights into fundamental problems in developmental biology for decades to come.

A developmental perspective of homology and evolutionary novelty

The development and evolution of multicellular body plans is complex. Many distinct organs and body parts must be reproduced at each generation, and those that are traceable over long time scales are considered homologous. Among the most pressing and least understood phenomena in evolutionary biology is the mode by which new homologs, or "novelties" are introduced to the body plan and whether the developmental changes associated with such evolution deserve special treatment. In this chapter, we address the concepts of homology and evolutionary novelty through the lens of development. We present a series of case studies, within insects and vertebrates, from which we propose a developmental model of multicellular organ identity. With this model in hand, we make predictions regarding the developmental evolution of body plans and highlight the need for more integrative analysis of developing systems.

Developing an integrated understanding of the evolution of arthropod segmentation using fossils and evo-devo

Segmentation is fundamental to the arthropod body plan. Understanding the evolutionary steps by which arthropods became segmented is being transformed by the integration of data from evolutionary developmental biology (evo-devo), Cambrian fossils that allow the stepwise acquisition of segmental characters to be traced in the arthropod stem-group, and the incorporation of fossils into an increasingly well-supported phylogenetic framework for extant arthropods based on genomic-scale datasets. Both evo-devo and palaeontology make novel predictions about the evolution of segmentation that serve as testable hypotheses for the other, complementary data source. Fossils underpin such hypotheses as arthropodization originating in a frontal appendage and then being co-opted into other segments, and segmentation of the endodermal midgut in the arthropod stem-group. Insights from development, such as tagmatization being associated with different modes of segment generation in different body regions, and a distinct patterning of the anterior head segments, are complemented by palaeontological evidence for the pattern of tagmatization during ontogeny of exceptionally preserved fossils. Fossil and developmental data together provide evidence for a short head in stem-group arthropods and the mechanism of its formation and retention. Future breakthroughs are expected from identification of molecular signatures of developmental innovations within a phylogenetic framework, and from a focus on later developmental stages to identify the differentiation of repeated units of different systems within segmental precursors.

Anatomical network analysis of the musculoskeletal system reveals integration loss and parcellation boost during the fins-to-limbs transition

Tetrapods evolved from within the lobe-finned fishes around 370 Ma. The evolution of limbs from lobe-fins entailed a major reorganization of the skeletal and muscular anatomy of appendages in early tetrapods. Concurrently, a degree of similarity between pectoral and pelvic appendages also evolved. Here, we compared the anatomy of appendages in extant lobe-finned fishes (Latimeria and Neoceratodus) and anatomically plesiomorphic amphibians (Ambystoma, Salamandra) and amniotes (Sphenodon) to trace and reconstruct the musculoskeletal changes that took place during the fins-to-limbs transition. We quantified the anatomy of appendages using network analysis. First, we built network models-in which nodes represent bones and muscles, and links represent their anatomical connections-and then we measured network parameters related to their anatomical integration, heterogeneity, and modularity. Our results reveal an evolutionary transition toward less integrated, more modular appendages. We interpret this transition as a diversification of muscle functions in tetrapods compared to lobe-finned fishes. Limbs and lobe-fins show also a greater similarity between their pectoral and pelvic appendages than ray-fins do. These findings on extant species provide a basis for future quantitative and comprehensive reconstructions of the anatomy of limbs in early tetrapod fossils, and a way to better understand the fins-to-limbs transition.

Evolutionary parallelisms of pectoral and pelvic network-anatomy from fins to limbs

Lobe-fins transformed into limbs during the Devonian period, facilitating the water-to-land transition in tetrapods. We traced the evolution of well-articulated skeletons across the fins-to-limbs transition, using a network-based approach to quantify and compare topological features of fins and limbs. We show that the topological arrangement of bones in pectoral and pelvic appendages evolved in parallel during the fins-to-limbs transition, occupying overlapping regions of the morphospace, following a directional trend, and decreasing their disparity over time. We identify the presence of digits as the morphological novelty triggering topological changes that discriminated limbs from fins. The origin of digits caused an evolutionary shift toward appendages that were less densely and heterogeneously connected, but more assortative and modular. Disparity likewise decreased for both appendages, more markedly until a time concomitant with the earliest-known tetrapod tracks. Last, we rejected the presence of a pectoral-pelvic similarity bottleneck at the origin of tetrapods.

Expression of meis and hoxa11 in dipnoan and teleost fins provides new insights into the evolution of vertebrate appendages

Background

The concerted activity of Meis and Hoxa11 transcription factors is essential for the subdivision of tetrapod limbs into proximo-distal (PD) domains; however, little is know about the evolution of this patterning mechanism. Here, we aim to study the expression of meis and hoxa11 orthologues in the median and paired rayed fins of zebrafish and in the lobed fins of the Australian lungfish.

Results

First, a late phase of expression of meis1.1 and hoxa11b in zebrafish dorsal and anal fins relates with segmentation of endochondral elements in proximal and distal radials. Second, our zebrafish in situ hybridization results reveal spatial and temporal changes between pectoral and pelvic fins. Third, in situ analysis of meis1, meis3 and hoxa11 genes in Neoceratodus pectoral fins identifies decoupled domains of expression along the PD axis.

Conclusions

Our data raise the possibility that the origin of stylopod and zeugopod lies much deeper in gnathostome evolution and that variation in meis and hoxa11 expression has played a substantial role in the transformation of appendage anatomy. Moreover, these observations provide evidence that the Meis/Hoxa11 profile considered a hallmark of stylopod/zeugopod patterning is present in Neoceratodus.

Electronic supplementary material

The online version of this article (10.1186/s13227-018-0099-9) contains supplementary material, which is available to authorized users.

Comparative anatomy of zebrafish paired and median fin muscles: basis for functional, developmental, and macroevolutionary studies

In the last decades, Danio rerio became one of the most used model organisms in various evo-devo studies devoted to the fin skeletal anatomy and fin-limb transition. Surprisingly, there is not even a single paper about the detailed anatomy of the adult muscles of the five fin types of this species. To facilitate more integrative developmental, functional, genetic, and evolutionary studies of the appendicular musculoskeletal system of the zebrafish and to provide a basis for further comparisons with other fishes and tetrapods, we describe here the identity, overall configuration, and attachments of appendicular muscles in a way that can be easily understood and implemented by non-anatomist researchers. We show that the muscle pattern of the caudal fin is very different from patterns seen in other fins but is very consistent within teleosts. Our observations support the idea of the developmental and evolutionary distinction of the caudal fin and point out that the musculature of the adult zebrafish pectoral and pelvic fins is in general very similar. Both paired fins have superficial and deep layers of abductors and adductors going to all/most rays plus the dorsal and ventral arrectors going only to the first ray. Nevertheless, we noted three major differences between the pelvic and pectoral fins of adult zebrafishes: (i) the pectoral girdle lacks a retractor muscle, which is present in the pelvic girdle - the retractor ischii; (ii) the protractor of the pelvic girdle is an appendicular/trunk muscle, while that of the pectoral girdle is a branchiomeric muscle; (iii) the first ray of the pectoral fin is moved by an additional arrector-3. The anal and dorsal fins consist of serially repeated units, each of which comprises one half-ray and three appendicular muscles (one erector, depressor, and inclinator) on each side of the body. The outermost rays are attachment points for the longitudinal protractor and retractor. Based on our results, we discuss whether the pectoral appendage might evolutionarily be closer to the head than to the pelvic appendage and whether the pelvic appendage might have been derived from the trunk/median fins. We discuss a hypothesis of paired fin origin that is a hybrid of the fin-fold and Gegenbaur's theories. Lastly, our data indicate that D. rerio is indeed an appropriate model organism for the appendicular musculature of teleosts in particular and, at least in the case of the paired fins, also of actinopterygians as a whole.

The role of HoxA11 and HoxA13 in the evolution of novel fin morphologies in a representative batoid (Leucoraja erinacea)

Background

Batoids exhibit unique body plans with derived fin morphologies, such as the anteriorly expanded pectoral fins that fuse to the head, or distally extended anterior pelvic fin lobes used for a modified swimming technique utilized by skates (Rajidae). The little skate (Leucoraja erinacea), exhibits both of these unique fin morphologies. These fin modifications are not present in a typical shark body plan, and little is known regarding the mechanisms underlying their development. A recent study identified a novel apical ectodermal ridge (AER) associated with the development of the anterior pectoral fin in the little skate, but the role of the posterior HoxA genes was not featured during skate fin development.

Results

We present the first evidence for HoxA expression (HoxA11 and HoxA13) in novel AER domains associated with the development of three novel fin morphologies in a representative batoid, L. erinacea. We found HoxA13 expression associated with the recently described novel AER in the anterior pectoral fin, and HoxA11 expression in a novel AER domain in the anterior pelvic fin that we describe here. We find that both HoxA11 and HoxA13 are expressed in claspers, and while HoxA11 is expressed in pelvic fins and claspers, HoxA13 is expressed exclusively in developing claspers of males. Finally, HoxA11 expression is associated with the developing fin rays in paired fins.

Conclusion

Overall, these results indicate that the posterior HoxA genes play an important role in the morphological evolution of paired fins in a representative batoid. These data suggest that the batoids utilize a unique Hox code, where the posterior HoxA genes exhibit distinct expression patterns that are likely associated with specification of novel fin morphologies.

Electronic supplementary material

The online version of this article (10.1186/s13227-017-0088-4) contains supplementary material, which is available to authorized users.

Similarity of morphological composition and developmental patterning in paired fins of the elephant shark

Jawed vertebrates, or gnathostomes, have two sets of paired appendages, pectoral and pelvic fins in fishes and fore- and hindlimbs in tetrapods. As for paired limbs, paired fins are purported serial homologues, and the advent of pelvic fins has been hypothesized to have resulted from a duplication of the developmental mechanisms present in the pectoral fins, but re-iterated at a posterior location. Developmental similarity of gene expression between pectoral and pelvic fins has been documented in chondrichthyans, but a detailed morphological description of the progression of paired fin development for this group is still lacking. We studied paired fin development in an ontogenetic series of a phylogenetically basal chondrichthyan, the elephant shark Callorhinchus milii. A strong similarity in the morphology and progression of chondrification between the pectoral and pelvic fins was found, which could be interpretated as further evidence of serial homology in paired fins, that could have arisen by duplication. Furthermore, this high degree of morphological and developmental similarity suggests the presence of morphological and developmental modules within paired fins, as observed in paired limbs. This is the first time morphological and developmental modules are described for the paired fins of chimaeras.

Muscle development in the shark Scyliorhinus canicula: implications for the evolution of the gnathostome head and paired appendage musculature

BACKGROUND

The origin of jawed vertebrates was marked by profound reconfigurations of the skeleton and muscles of the head and by the acquisition of two sets of paired appendages. Extant cartilaginous fish retained numerous plesiomorphic characters of jawed vertebrates, which include several aspects of their musculature. Therefore, myogenic studies on sharks are essential in yielding clues on the developmental processes involved in the origin of the muscular anatomy.

RESULTS

Here we provide a detailed description of the development of specific muscular units integrating the cephalic and appendicular musculature of the shark model, Scyliorhinus canicula. In addition, we analyze the muscle development across gnathostomes by comparing the developmental onset of muscle groups in distinct taxa. Our data reveal that appendicular myogenesis occurs earlier in the pectoral than in the pelvic appendages. Additionally, the pectoral musculature includes muscles that have their primordial developmental origin in the head. This culminates in a tight muscular connection between the pectoral girdle and the cranium, which founds no parallel in the pelvic fins. Moreover, we identified a lateral to ventral pattern of formation of the cephalic muscles, that has been equally documented in osteichthyans but, in contrast with these gnathostomes, the hyoid muscles develop earlier than mandibular muscle in S. canicula.

CONCLUSION

Our analyses reveal considerable differences in the formation of the pectoral and pelvic musculatures in S. canicula, reinforcing the idea that head tissues have contributed to the formation of the pectoral appendages in the common ancestor of extant gnathostomes. In addition, temporal differences in the formation of some cranial muscles between chondrichthyans and osteichthyans might support the hypothesis that the similarity between the musculature of the mandibular arch and of the other pharyngeal arches represents a derived feature of jawed vertebrates.

Fin modules: an evolutionary perspective on appendage disparity in basal vertebrates

BACKGROUND

Fishes are extremely speciose and also highly disparate in their fin configurations, more specifically in the number of fins present as well as their structure, shape, and size. How they achieved this remarkable disparity is difficult to explain in the absence of any comprehensive overview of the evolutionary history of fish appendages. Fin modularity could provide an explanation for both the observed disparity in fin configurations and the sequential appearance of new fins. Modularity is considered as an important prerequisite for the evolvability of living systems, enabling individual modules to be optimized without interfering with others. Similarities in developmental patterns between some of the fins already suggest that they form developmental modules during ontogeny. At a macroevolutionary scale, these developmental modules could act as evolutionary units of change and contribute to the disparity in fin configurations. This study addresses fin disparity in a phylogenetic perspective, while focusing on the presence/absence and number of each of the median and paired fins.

RESULTS

Patterns of fin morphological disparity were assessed by mapping fin characters on a new phylogenetic supertree of fish orders. Among agnathans, disparity in fin configurations results from the sequential appearance of novel fins forming various combinations. Both median and paired fins would have appeared first as elongated ribbon-like structures, which were the precursors for more constricted appendages. Among chondrichthyans, disparity in fin configurations relates mostly to median fin losses. Among actinopterygians, fin disparity involves fin losses, the addition of novel fins (e.g., the adipose fin), and coordinated duplications of the dorsal and anal fins. Furthermore, some pairs of fins, notably the dorsal/anal and pectoral/pelvic fins, show non-independence in their character distribution, supporting expectations based on developmental and morphological evidence that these fin pairs form evolutionary modules.

CONCLUSIONS

Our results suggest that the pectoral/pelvic fins and the dorsal/anal fins form two distinct evolutionary modules, and that the latter is nested within a more inclusive median fins module. Because the modularity hypotheses that we are testing are also supported by developmental and variational data, this constitutes a striking example linking developmental, variational, and evolutionary modules.

Characteristic tetrapod musculoskeletal limb phenotype emerged more than 400 MYA in basal lobe-finned fishes

Previous accounts of the origin of tetrapod limbs have postulated a relatively sudden change, after the split between extant lobe-finned fish and tetrapods, from a very simple fin phenotype with only two muscles to the highly complex tetrapod condition. The evolutionary changes that led to the muscular anatomy of tetrapod limbs have therefore remained relatively unexplored. We performed dissections, histological sections, and MRI scans of the closest living relatives of tetrapods: coelacanths and lungfish. Combined with previous comparative, developmental and paleontological information, our findings suggest that the characteristic tetrapod musculoskeletal limb phenotype was already present in the Silurian last common ancestor of extant sarcopterygians, with the exception of the autopod (hand/foot) structures, which have no clear correspondence with fish structures. Remarkably, the two major steps in this long process – leading to the ancestral fin anatomy of extant sarcopterygians and limb anatomy of extant tetrapods, respectively – occurred at the same nodes as the two major similarity bottlenecks that led to the striking derived myological similarity between the pectoral and pelvic appendages within each taxon. Our identification of probable homologies between appendicular muscles of sarcopterygian fish and tetrapods will allow more detailed reconstructions of muscle anatomy in early tetrapods and their relatives.

Looking Beyond the Genes: The Interplay Between Signaling Pathways and Mechanics in the Shaping and Diversification of Epithelial Tissues

The core of Evo-Devo lies in the intuition that the way tissues grow during embryonic development, the way they sustain their structure and function throughout lifetime, and the way they evolve are closely linked. Epithelial tissues are ubiquitous in metazoans, covering the gut and internal branched organs, as well as the skin and its derivatives (ie, teeth). Here, we discuss in vitro, in vivo, and in silico studies on epithelial tissues to illustrate the conserved, dynamical, and complex aspects of their development. We then explore the implications of the dynamical and nonlinear nature of development on the evolution of their size and shape at the phenotypic and genetic levels. In rare cases, when the interplay between signaling and mechanics is well understood at the cell level, it is becoming clear that the structure of development leads to covariation of characters, an integration which in turn provides some predictable structure to evolutionary changes. We suggest that such nonlinear systems are prone to genetic drift, cryptic genetic variation, and context-dependent mutational effects. We argue that experimental and theoretical studies at the cell level are critical to our understanding of the phenotypic and genetic evolution of epithelial tissues, including carcinomas.

HoxA and HoxD expression in a variety of vertebrate body plan features reveals an ancient origin for the distal Hox program

Background

Hox genes are master regulatory genes that specify positional identities during axial development in animals. Discoveries regarding their concerted expression patterns have commanded intense interest due to their complex regulation and specification of body plan features in jawed vertebrates. For example, the posterior HoxD genes switch to an inverted collinear expression pattern in the mouse autopod where HoxD13 switches from a more restricted to a less restricted domain relative to its neighboring gene on the cluster. We refer to this program as the ‘distal phase’ (DP) expression pattern because it occurs in distal regions of paired fins and limbs, and is regulated independently by elements in the 5′ region upstream of the HoxD cluster. However, few taxa have been evaluated with respect to this pattern, and most studies have focused on pectoral fin morphogenesis, which occurs relatively early in development.

Results

Here, we demonstrate for the first time that the DP expression pattern occurs with the posterior HoxA genes, and is therefore not solely associated with the HoxD gene cluster. Further, DP Hox expression is not confined to paired fins and limbs, but occurs in a variety of body plan features, including paddlefish barbels - sensory adornments that develop from the first mandibular arch (the former ‘Hox-free zone), and the vent (a medial structure that is analogous to a urethra). We found DP expression of HoxD13 and HoxD12 in the paddlefish barbel; and we present the first evidence for DP expression of the HoxA genes in the hindgut and vent of three ray-finned fishes. The HoxA DP expression pattern is predicted by the recent finding of a shared 5′ regulatory architecture in both the HoxA and HoxD clusters, but has not been previously observed in any body plan feature.

Conclusions

The Hox DP expression pattern appears to be an ancient module that has been co-opted in a variety of structures adorning the vertebrate bauplan. This module provides a shared genetic program that implies deep homology of a variety of distally elongated structures that has played a significant role in the evolution of morphological diversity in vertebrates

Electronic supplementary material

The online version of this article (doi:10.1186/2041-9139-5-44) contains supplementary material, which is available to authorized users.

The origins of adipose fins: an analysis of homoplasy and the serial homology of vertebrate appendages

Adipose fins are appendages found on the dorsal midline between the dorsal and caudal fins in more than 6000 living species of teleost fishes. It has been consistently argued that adipose fins evolved once and have been lost repeatedly across teleosts owing to limited function. Here, we demonstrate that adipose fins originated repeatedly by using phylogenetic and anatomical evidence. This suggests that adipose fins are adaptive, although their function remains undetermined. To test for generalities in the evolution of form in de novo vertebrate fins, we studied the skeletal anatomy of adipose fins across 620 species belonging to 186 genera and 55 families. Adipose fins have repeatedly evolved endoskeletal plates, anterior dermal spines and fin rays. The repeated evolution of fin rays in adipose fins suggests that these fins can evolve new tissue types and increased structural complexity by expressing fin-associated developmental modules in these new territories. Patterns of skeletal elaboration differ between the various occurrences of adipose fins and challenge prevailing hypotheses for vertebrate fin origin. Adipose fins represent a powerful and, thus far, barely studied model for exploring the evolution of vertebrate limbs and the roles of adaptation and generative biases in morphological evolution.

Late development of hagfish vertebral elements

It has been demonstrated recently that hagfishes, one of two groups of extant jawless vertebrates, have cartilaginous vertebral elements. Embryological and gene expression analyses have also shown that this group of animals develops a sclerotome, the potential primordium of the axial skeleton. However, it has not been shown unequivocally that the hagfish sclerotome truly differentiates into cartilage, because access to late-stage embryos and information about the cartilaginous extracellular matrix (ECM) are lacking for these animals. Here we investigated the expression patterns of the biglycan/decorin (BGN/DCN) gene in the inshore hagfish, Eptatretus burgeri. The homologue of this gene encodes the major noncollagenous component of the cartilaginous ECM among gnathostomes. We clearly identified the expression of this gene in adult vertebral tissues and in embryonic mesenchymal cells on the ventral aspect of the notochord. Taking into account that the sclerotome in the gnathostomes expresses BGN/DCN gene during the chondrogenesis, it is highly expected the hagfish BGN/DCN-positive mesenchymal cells are derived from the sclerotomes. We propose that hagfishes and gnathostomes share conserved developmental mechanisms not only in their somite differentiation, but also in chondrogenesis of their vertebral elements.

The evolutionary history of the development of the pelvic fin/hindlimb

The arms and legs of man are evolutionarily derived from the paired fins of primitive jawed fish. Few evolutionary changes have attracted as much attention as the origin of tetrapod limbs from the paired fins of ancestral fish. The hindlimbs of tetrapods are derived from the pelvic fins of ancestral fish. These evolutionary origins can be seen in the examination of shared gene and protein expression patterns during the development of pelvic fins and tetrapod hindlimbs. The pelvic fins of fish express key limb positioning, limb bud induction and limb outgrowth genes in a similar manner to that seen in hindlimb development of higher vertebrates. We are now at a point where many of the key players in the development of pelvic fins and vertebrate hindlimbs have been identified and we can now readily examine and compare mechanisms between species. This is yielding fascinating insights into how the developmental programme has altered during evolution and how that relates to anatomical change. The role of pelvic fins has also drastically changed over evolutionary history, from playing a minor role during swimming to developing into robust weight-bearing limbs. In addition, the pelvic fins/hindlimbs have been lost repeatedly in diverse species over evolutionary time. Here we review the evolution of pelvic fins and hindlimbs within the context of the changes in anatomical structure and the molecular mechanisms involved.

Tetrapod-like axial regionalization in an early ray-finned fish

Tetrapods possess up to five morphologically distinct vertebral series: cervical, thoracic, lumbar, sacral and caudal. The evolution of axial regionalization has been linked to derived Hox expression patterns during development and the demands of weight-bearing and walking on land. These evolutionary and functional explanations are supported by an absence of similar traits in fishes, living and extinct. Here, I show that, Tarrasius problematicus, a marine ray-finned fish from the Mississippian (Early Carboniferous; 359-318 Ma) of Scotland, is the first non-tetrapod known to possess tetrapod-like axial regionalization. Tarrasius exhibits five vertebral regions, including a seven-vertebrae 'cervical' series and a reinforced 'sacrum' over the pelvic area. Most vertebrae possess processes for intervertebral contact similar to tetrapod zygapophyses. The fully aquatic Tarrasius evolved these morphologies alongside other traits convergent with early tetrapods, including a naked trunk, and a single median continuous fin. Regional modifications in Tarrasius probably facilitated pelagic swimming, rather than a terrestrial lifestyle or walking gait, presenting an alternative scenario for the evolution of such traits in tetrapods. Axial regionalization in Tarrasius could indicate tetrapod-like Hox expression patterns, possibly representing the primitive state for jawed vertebrates. Alternately, it could signal a weaker relationship, or even a complete disconnect, between Hox expression domains and vertebrate axial plans.

Evolution of vertebrate appendicular structures: Insight from genetic and palaeontological data

The new body of evidence from fossils and comparative-developmental analysis of subset of appendicular patterning genes has revealed that limb elements seen in tetrapods are assembled in fish fin over evolutionary time. However, despite of deep homology in basic structure and underlying developmental system, there remains a large morphological gap between distal elements of tetrapod limb and distal fin skeleton of tetrapodomorph fish. Understanding the genetic basis of major transformations in distal-limb morphology is the next challenge for evolutionary developmental biologists. Here by integrating data from fossils, comparative-developmental and genetic studies, models are proposed describing the evolution of cis-regulatory elements as a basis for diversification of appendicular architecture. Instead of emphasizing the subset of developmental genes, for instance Hoxd genes, the focus here is on the significance of elucidating cis-regulatory elements for multiple other key molecular players of limb/fin development and genetic/molecular interactions among them, for a better understanding of the developmental and genetic basis of limb evolution.

Pelvic fins in teleosts: structure, function and evolution

The pelvic fins of teleosts are paired appendages that are considered to be homologous to the hind limbs of tetrapods. Because they are less important for swimming, their morphology and function can be flexibly modified, and such modifications have probably facilitated the adaptations of teleosts to various environments. Recently, among these modifications, pelvic-fin loss has gained attention in evolutionary developmental biology. Pelvic-fin loss, however, has only been investigated in a few model species, and various biological aspects of pelvic fins in teleosts in general remain poorly understood. This review summarizes the current state of knowledge regarding pelvic fins, such as their structure, function and evolution, to elucidate their contribution to the considerable diversity of teleosts. This information could be invaluable for future investigations into various aspects of pelvic fins, which will provide clues to understanding the evolution, diversity and adaptations of teleosts.

Tri-phasic expression of posterior Hox genes during development of pectoral fins in zebrafish: implications for the evolution of vertebrate paired appendages

During development of the limbs, Hox genes belonging to the paralogous groups 9-13 are expressed in three distinct phases, which play key roles in the segmental patterning of limb skeletons. In teleost fishes, which have a very different organization in their fin skeletons, it is not clear whether a similar patterning mechanism is at work. To determine whether Hox genes are also expressed in several distinct phases during teleost paired fin development, we re-analyzed the expression patterns of hox9-13 genes during development of pectoral fins in zebrafish. We found that, similar to tetrapod Hox genes, expression of hoxa/d genes in zebrafish pectoral fins occurs in three distinct phases, in which the most distal/third phase is correlated with the development of the most distal structure of the fin, the fin blade. Like in tetrapods, hox gene expression in zebrafish pectoral fins during the distal/third phase is dependent upon sonic hedgehog signaling (hoxa and hoxd genes) and the presence of a long-range enhancer (hoxa genes), which indicates that the regulatory mechanisms underlying tri-phasic expression of Hox genes have remained relatively unchanged during evolution. Our results suggest that, although simpler in organization, teleost fins do have a distal structure that might be considered comparable to the autopod region of limbs.

Gene expression patterns underlying proximal-distal skeletal segmentation in late-stage zebrafish, Danio rerio

Timing and pattern of expression of ten candidate segmentation genes or gene pairs were reviewed or examined in developing median fins of late-stage zebrafish, Danio rerio. We found a general correspondence in timing and pattern of expression between zebrafish fin radial segmentation and tetrapod joint development, suggesting that molecular mechanisms underlying radial segmentation have been conserved over 400 million years of evolution. Gene co-expression during segmentation (5.5-6.5 mm SL) is similar between tetrapods and zebrafish: bmp2b, bmp4, chordin, and gdf5 in interradial mesenchyme and ZS; bapx1, col2a1, noggin3, and sox9a in chondrocytes. Surprisingly, wnt9a is not expressed in the developing median fins, though wnt9b is detected. In contrast to all other candidate segmentation genes we examined, bapx1 is not expressed in the caudal fin, which does not segment. Together, these data suggest a scenario of gene interactions underlying radial segmentation based on the patterns and timing of candidate gene expression.

Insights from sharks: evolutionary and developmental models of fin development

The shark and its embryology have recently returned to the spotlight as a model animal in the quest to determine the origins of paired appendages during vertebrate evolution. As the most basal living gnathostomes, sharks and other extant chondrichthyans are ideal models to elucidate the developmental mechanisms utilised in mesoderm-derived primitive fin morphologies. Chondrichthyans occupy a phylogenetic position and possess morphological structures that can answer major questions on the origin of the body plan of vertebrates. This review will outline the past, present, and future use of shark species as a model system with particular emphasis on the recent studies that have utilised comparative molecular embryology of chondrichthyan species to examine the question of the origin of the paired fins. We will also examine the problems and pitfalls of utilising chondrichthyans and the barriers that remain to their utilisation in the modern era of developmental biology.

Conservation of Pitx1 expression during amphibian limb morphogenesis

In contrast to the pattern of limb emergence in mammals, chicks, and the newt N. viridescens, embryos such as Xenopus laevis and Eleutherodactylus coqui initiate pelvic limb buds before they develop pectoral ones. We studied the expression of Pitx1 in X. laevis and E. coqui to determine if this paired-like homeodomain transcription factor directs differentiation specifically of the hindlimb, or if it directs the second pair of limbs to form, namely the forelimbs. We also undertook to determine if embryonic expression patterns were recapitulated during the regeneration of an amputated limb bud. Pitx1 is expressed in hindlimbs in both X. laevis and E. coqui, and expression is similar in both developing and regenerating limb buds. Expression in hindlimbs is restricted to regions of proliferating mesenchyme.

Importance of SoxE in neural crest development and the evolution of the pharynx

The neural crest, a defining character of vertebrates, is of prime importance to their evolutionary origin. To understand neural crest evolution, we explored molecular mechanisms underlying craniofacial development in the basal jawless vertebrate, sea lamprey (Petromyzon marinus), focusing on the SoxE (Sox8, Sox9 and Sox10) gene family. In jawed vertebrates, these are important transcriptional regulators of the neural crest, and the loss of Sox9 causes abnormal craniofacial development. Here we report that two lamprey SoxE genes are expressed in migrating neural crest and crest-derived prechondrocytes in posterior branchial arches, whereas a third paralogue is expressed later in the perichondrium and mandibular arch. Morpholino knock-down of SoxE1 reveals that it is essential for posterior branchial arch development, although the mandibular arch is unaffected. The results show that chondrogenic function of SoxE regulators can be traced to the lamprey-gnathostome common ancestor and indicate that lamprey SoxE genes might have undergone independent duplication to have distinct functions in mandibular versus caudal branchial arches. This work sheds light on the homology of vertebrate branchial arches and supports their common origin at the base of vertebrates.

The Greatest Step in Vertebrate History: A Paleobiological Review of the Fish‐Tetrapod Transition

Recent discoveries of previously unknown fossil forms have dramatically transformed understanding of many aspects of the fish-tetrapod transition. Newer paleobiological approaches have also contributed to changed views of which animals were involved and when, where, and how the transition occurred. This review summarizes major advances made and reevaluates alternative interpretations of important parts of the evidence. We begin with general issues and concepts, including limitations of the Paleozoic fossil record. We summarize important features of paleoclimates, paleoenvironments, paleobiogeography, and taphonomy. We then review the history of Devonian tetrapods and their closest stem group ancestors within the sarcopterygian fishes. It is now widely accepted that the first tetrapods arose from advanced tetrapodomorph stock (the elpistostegalids) in the Late Devonian, probably in Euramerica. However, truly terrestrial forms did not emerge until much later, in geographically far-flung regions, in the Lower Carboniferous. The complete transition occurred over about 25 million years; definitive emergences onto land took place during the most recent 5 million years. The sequence of character acquisition during the transition can be seen as a five-step process involving: (1) higher osteichthyan (tetrapodomorph) diversification in the Middle Devonian (beginning about 380 million years ago [mya]), (2) the emergence of "prototetrapods" (e.g., Elginerpeton) in the Frasnian stage (about 372 mya), (3) the appearance of aquatic tetrapods (e.g., Acanthostega) sometime in the early to mid-Famennian (about 360 mya), (4) the appearance of "eutetrapods" (e.g., Tulerpeton) at the very end of the Devonian period (about 358 mya), and (5) the first truly terrestrial tetrapods (e.g., Pederpes) in the Lower Carboniferous (about 340 mya). We discuss each of these steps with respect to inferred functional utility of acquired character sets. Dissociated heterochrony is seen as the most likely process for the evolutionarily rapid morphological transformations required. Developmental biological processes, including paedomorphosis, played important roles. We conclude with a discussion of phylogenetic interpretations of the evidence.

Modularity and integration in the hominoid scapula

In this paper, several hypotheses of morphological integration within the hominoid (ape) scapula are tested. In particular, whether the scapula represents a set of developmental tissues sharing tight correlations between constituent parts (i.e., highly integrated) or is more modularly organized (i.e., covariation is greater within regions than between) is tested. Whether the patterns of integration in the scapula have changed over phylogenetic time or in response to selective forces is also examined. Results from two different analyses (matrix correlations and edge deviance) indicate traits comprising the blade and acromion, and to a weaker degree the glenoid, correlate highly with each other. The coracoid exhibits more independence from other parts of the scapula, perhaps reflecting its distinct evolutionary developmental history. Overall, similarity in species-specific patterns of correlation was high between all taxa. Correlation matrix similarity was significantly correlated with functional similarity and morphological distance, but not with phylogenetic distance. These results are congruent with other studies of integration that suggest correlation patterns remain stable over evolutionary time. There are changes associated with phylogeny, but the tight link between functional similarity and phylogenetic distance at this level of comparison presents possible challenges to interpretation. Overall similarities in the pattern of integration in all taxa might be better interpreted as relative strengthening or weakening of trait correlations rather than broadscale changes in the pattern of relationship between developmental regions. Larger sample sizes with greater taxonomic/functional breadth, and finer scale analyses of patterns of correlation are needed to test these hypotheses further.

Expression of anterior Hox genes during larval development of the gastropod Haliotis asinina

We report the spatial expression patterns of five anterior Hox genes during larval development of the gastropod mollusc Haliotis asinina, an unsegmented spiralian lophotrochozoan. Molecular alignments and phylogenetic analysis indicate that these genes are homologues of Drosophila HOM-C genes labial, proboscipedia, zen, Deformed, and Sex combs reduced; the abalone genes are named Has-Hox1, -Hox2, -Hox3, -Hox4, and -Hox5. Has-Hox transcripts are first detected in the free-swimming trochophore larval stage and restricted to the posttrochal ectoderm. Has-Hox2, -Hox3, and -Hox4 are expressed in bilaterally symmetrical and overlapping patterns in presumptive neuroectodermal cells on the ventral side of the trochophore. Has-Hox1 expression is restricted to a ring of cells on the dorsoposterior surface, corresponding to the outer mantle edge where new larval shell is being synthesized. There appears to be little change in the expression domains of these Has-Hox genes in pre- and posttorsional veliger larvae, with expression maintained in ectodermal and neuroectodermal tissues. Has-Hox2, -Hox3, -Hox4, and-Hox5 appear to be expressed in a colinear manner in the ganglia and connectives in the twisted nervous system. This pattern is not evident in older larvae. Has-Hox1 and-Hox4 are expressed in the margin of the mantle in the posttorsional veliger, suggesting that Hox genes play a role in gastropod shell formation.

Early tetrapod relationships revisited

In an attempt to investigate differences between the most widely discussed hypotheses of early tetrapod relationships, we assembled a new data matrix including 90 taxa coded for 319 cranial and postcranial characters. We have incorporated, where possible, original observations of numerous taxa spread throughout the major tetrapod clades. A stem-based (total-group) definition of Tetrapoda is preferred over apomorphy- and node-based (crown-group) definitions. This definition is operational, since it is based on a formal character analysis. A PAUP* search using a recently implemented version of the parsimony ratchet method yields 64 shortest trees. Differences between these trees concern: (1) the internal relationships of aïstopods, the three selected species of which form a trichotomy; (2) the internal relationships of embolomeres, with Archeria crassidisca and Pholiderpeton scut collapsed in a trichotomy with a clade formed by Anthracosaurus russelli and Pholiderpeton attheyi; (3) the internal relationships of derived dissorophoids, with four amphibamid species forming an unresolved node with a clade consisting of micromelerpetontids and branchiosaurids and a clade consisting of albanerpetontids plus basal crown-group lissamphibians; (4) the position of albenerpetontids and Eocaecilia micropoda, which form an unresolved node with a trichotomy subtending Karaurus sharovi, Valdotriton gracilis and Triadobatrachus massinoti; (5) the branching pattern of derived diplocaulid nectrideans, with Batrachiderpeton reticulatum and Diceratosaurus brevirostris collapsed in a trichotomy with a clade formed by Diplocaulus magnicornis and Diploceraspis burkei. The results of the original parsimony run--as well as those retrieved from several other treatments of the data set (e.g. exclusion of postcranial and lower jaw data; character reweighting; reverse weighting)--indicate a deep split of early tetrapods between lissamphibian- and amniote-related taxa. Colosteids, Crassigyrinus, Whatcheeria and baphetids are progressively more crownward stem-tetrapods. Caerorhachis, embolomeres, gephyrostegids, Solenodonsaurus and seymouriamorphs are progressively more crownward stem-amniotes. Eucritta is basal to temnospondyls, with crown-lissamphibians nested within dissorophoids. Westlothiana is basal to Lepospondyli, but evidence for the monophyletic status of the latter is weak. Westlothiana and Lepospondyli form the sister group to diadectomorphs and crown-group amniotes. Tuditanomorph and microbrachomorph microsaurs are successively more closely related to a clade including proximodistally: (1) lysorophids; (2) Acherontiscus as sister taxon to adelospondyls; (3) scincosaurids plus diplocaulids; (4) urocordylids plus aïstopods. A data set employing cranial characters only places microsaurs on the amniote stem, but forces remaining lepospondyls to appear as sister group to colosteids on the tetrapod stem in several trees. This arrangement is not significantly worse than the tree topology obtained from the analysis of the complete data set. The pattern of sister group relationships in the crownward part of the temnospondyl-lissamphibian tree re-emphasizes the important role of dissorophoids in the lissamphibian origin debate. However, no specific dissorophoid can be identified as the immediate sister taxon to crown-group lissamphibians. The branching sequence of various stem-group amniotes reveals a coherent set of internested character-state changes related to the acquisition of progressively more terrestrial habits in several Permo-Carboniferous forms.

Morphological affinities of the Australopithecus afarensis hand on the basis of manual proportions and relative thumb length

The hands of apes and humans differ considerably with regard to proportions between several bones. Of critical significance is the long thumb relative to other fingers, which is the basis for human-like pad-to-pad precision grip capability, and has been considered by some as evidence of tool-making. The nature and timing of the evolutionary transition from ape-like to human-like manual proportions, however, have remained unclear as a result of the lack of appropriate fossil material. In this article, the manual proportions of Australopithecus afarensis from locality AL 333/333w (Hadar, Ethiopia) are investigated by means of bivariate and multivariate morphometric analyses, in order to test the hypothesis that human-like proportions, including an enhanced thumb/hand relationship, originally evolved as an adaptation to stone tool-making. Although some evidence for human-like manual proportions had been previously proposed for this taxon, conclusive evidence was lacking. Our results indicate that A. afarensis possessed overall manual proportions, including an increased thumb/hand relationship that, contrary to previous reports, is fully human and would have permitted pad-to-pad human-like precision grip capability. We show that these human-like proportions in A. afarensis mainly result from hand shortening, as in modern humans, and that these conclusions are robust enough as to be non-dependent on whether the bones belong to a single individual or not. Since A. afarensis predates the appearance of stone tools in the archeological record, the above-mentioned conclusions permit a confident refutation of the null hypothesis that human-like manual proportions are an adaptation to stone tool-making, and thus alternative explanations must be therefore sought. One hypothesis would consider manipulative behaviors (including tool-use and/or non-lithic tool-making) in early hominines exceeding those reported among extant non-human primates. Alternatively, on the basis of the many adaptations to committed bipedalism in A. afarensis, we propose the hypothesis that once arboreal behaviors became adaptively insignificant and forelimb-dominated locomotor selection pressures were relaxed with the adoption of terrestrial bipedalism, human-like manual proportions could have merely evolved as a result of the complex manipulation selection pressures already present in extant non-human primates. Both hypotheses are not mutually exclusive, and even other factors such as pleiotropy cannot be currently discarded.

Origin and early evolution of vertebrate skeletonization

Data from living and extinct faunas of primitive vertebrates imply very different scenarios for the origin and evolution of the dermal and oral skeletal developmental system. A direct reading of the evolutionary relationships of living primitive vertebrates implies that the dermal scales, teeth, and jaws arose synchronously with a cohort of other characters that could be considered unique to jawed vertebrates: the dermoskeleton is primitively composed of numerous scales, each derived from an individual dental papilla; teeth are primitively patterned such that they are replaced in a classical conveyor-belt system. The paleontological record provides a unique but complementary perspective in that: 1) the organisms in which the skeletal system evolved are extinct and we have no recourse but to fossils if we aim to address this problem; 2) extinct organisms can be classified among, and in the same way as, living relatives; 3) a holistic approach to the incorporation of all data provides a more complete perspective on early vertebrate evolution. This combined approach is of no greater significance than in dealing with the origin of the skeleton and, combined with recent discoveries and new phylogenetic analyses, we have been able to test and reject existing hypotheses for the origin of the skeleton and erect a new model in their place.

From fins to limbs to fins: limb evolution in fossil marine reptiles

Limb osteology and ontogenetic patterns of limb ossification are reviewed for extinct lineages of aquatically adapted diapsid reptiles. Phylogenies including these fossil taxa show that paddle-like limbs were independently derived, and that the varied limb morphologies were produced by evolutionary modifications to different aspects of the limb skeleton. Ancient marine reptiles modify the limb by reducing the relative size of the epipodials, modifying the perichondral and periosteal surface of elements distal to the propodials, and evolving extremes of hyperphalangy and hyperdactyly. Developmental genetic models illuminate gene systems that may have controlled limb evolution in these animals.

Fins to limbs: what the fossils say

A broad phylogenetic review of fins, limbs, and girdles throughout the stem and base of the crown group is needed to get a comprehensive idea of transformations unique to the assembly of the tetrapod limb ground plan. In the lower part of the tetrapod stem, character state changes at the pectoral level dominate; comparable pelvic level data are limited. In more crownward taxa, pelvic level changes dominate and repeatedly precede similar changes at pectoral level. Concerted change at both levels appears to be the exception rather than the rule. These patterns of change are explored by using afternative treatments of data in phylogenetic analyses. Results highlight a large data gap in the stem group preceding the first appearance of limbs with digits. It is also noted that the record of morphological diversity among stem tetrapods is somewhat worse than that of basal crown group tetrapods. The pre-limbed evolution of stem tetrapod paired fins is marked by a gradual reduction in axial segment numbers (mesomeres); pectoral fins of the sister group to limbed tetrapods include only three. This reduction in segment number is accompanied by increased regional specialization, and these changes are discussed with reference to the phylogenetic distribution of characteristics of the stylopod, zeugopod, and autopod.

Stomach regional specification requiresHoxa5-driven mesenchymal-epithelial signaling

The genetic control of gut regionalization relies on a hierarchy of molecular events in which the Hox gene family of transcription factors is suspected to be key participant. We have examined the role of Hox genes in gut patterning using the Hoxa5–/– mice as a model. Hoxa5 is expressed in a dynamic fashion in the mesenchymal component of the developing gut. Its loss of function results in gastric enzymatic anomalies in Hoxa5–/– surviving mutants that are due to perturbed cell specification during stomach development. Histological, biochemical and molecular characterization of the mutant stomach phenotype may be compatible with a homeotic transformation of the gastric mucosa. As the loss of mesenchymal Hoxa5 function leads to gastric epithelial defects, Hoxa5 should exert its action by controlling molecules involved in mesenchymal-epithelial signaling. Indeed, in the absence of Hoxa5 function, the expression of genes encoding for signaling molecules such as sonic hedgehog, Indian hedgehog, transforming growth factor β family members and fibroblast growth factor 10, is altered. These findings provide insight into the molecular controls of patterning events of the stomach, supporting the notion that Hoxa5 acts in regionalization and specification of the stomach by setting up the proper domains of expression of signaling molecules.

Evolution of median fin modules in the axial skeleton of fishes

Detailed examples of how hierarchical assemblages of modules change over time are few. We found broadly conserved phylogenetic patterns in the directions of development within the median fins of fishes. From these, we identify four modules involved in their positioning and patterning. The evolutionary sequence of their hierarchical assembly and secondary dissociation is described. The changes in these modules during the evolution of fishes appear to be produced through dissociation, duplication and divergence, and co-option. Although the relationship between identified median fin modules and underlying mechanisms is unclear, Hox addresses may be correlated. Comparing homologous gene expression and function in various fishes may test these predictions.The earliest actinopterygians likely had dorsal and anal fins that were symmetrically positioned via a positioning module. The common patterning (differentiation) of skeletal elements within the dorsal and anal fins may have been set into motion by linkage to this positioning module. Frequent evolutionary changes in dorsal and anal fin position indicate a high level of dissociability of the positioning module from the patterning module. In contrast, the patterning of the dorsal and anal fins remains linked: In nearly all fishes, the endo- and exoskeletal elements of the two fins co-differentiate. In all fishes, the exoskeletal fin rays differentiate in the same directions as the endoskeletal supports, indicating complete developmental integration. In acanthopterygians, a new first dorsal fin module evolved via duplication and divergence. The median fins provide an example of how basic modularity is maintained over 400 million years of evolution.

The last common bilaterian ancestor

Many regulatory genes appear to be utilized in at least superficially similar ways in the development of particular body parts in Drosophila and in chordates. These similarities have been widely interpreted as functional homologies, producing the conventional view of the last common protostome-deuterostome ancestor (PDA) as a complex organism that possessed some of the same body parts as modern bilaterians. Here we discuss an alternative view, in which the last common PDA had a less complex body plan than is frequently conceived. This reconstruction alters expectations for Neoproterozoic fossil remains that could illustrate the pathways of bilaterian evolution.