Limb ossification in the Paleozoic branchiosaurid Apateon (Temnospondyli) and the early evolution of preaxial dominance in tetrapod limb development

The evolutionary consequences of epigenesis and neutral change: A conceptual approach at the organismal level

Living beings are autopoietic systems with highly context-dependent structural dynamics and interactions, that determine whether a disturbance in the genotype or environment will lead or not to phenotypic change. The concept of epigenesis entails how a change in the phenotype may not correspond to a change in the structure of an earlier developmental stage, including the genome. Disturbances of embryonic structure may fail to change the phenotype, as in regulated development, or when different genotypes are associated to a single phenotype. Likewise, the same genotype or early embryonic structure may develop different phenotypes, as in phenotypic plasticity. Disturbances that fail to trigger phenotypic change are considered neutral, but even so, they can alter unexpressed developmental potential. Here, we present conceptual diagrams of the "epigenic field": similar to Waddington's epigenetic landscapes, but including the ontogenic niche (organism/environment interactional dynamics during ontogeny) as a factor in defining epigenic fields, rather than just selecting among possible pathways. Our diagrams illustrate transgenerational changes of genotype, ontogenic niche, and their correspondence (or lack thereof) with changes of phenotype. Epigenic fields provide a simple way to understand developmental constraints on evolution, for instance: how constraints evolve as a result of developmental system drift; how neutral changes can be involved in genetic assimilation and de-assimilation; and how constraints can evolve as a result of neutral changes in the ontogenic niche (not only the genotype). We argue that evolutionary thinking can benefit from a framework for evolution with conceptual foundations at the organismal level.

Morphology and ontogeny of carpus and tarsus in stereospondylomorph temnospondyls

Skeletal development is well known in temnospondyls, the most diverse group of Paleozoic and Mesozoic amphibians. However, the elements of carpus and tarsus (i.e., the mesopodium) were always the last bones to ossify relative to the other limb bones and with regard to the rest of the skeleton, and are preserved only in rare cases. Thus, in contrast to the other parts of the limb skeleton, little is known about the ontogeny and sequence of ossification of the temnospondyl carpus and tarsus. We intended to close this gap by studying the ontogenies of a number of Permo/Carboniferous stereospondylomorphs, the only temnospondyls with preserved growth series in which the successive ossification of carpals and tarsals can be traced. Studying the degree of mesopodial ossification within the same species show that it is not necessarily correlated with body size. This indicates that individual age rather than size determined the degree of mesopodial ossification in stereospondylomorphs and that the largest individuals are not necessarily the oldest ones. In the stereospondylomorph tarsus, the distal tarsals show preaxial development in accordance with most early tetrapods and salamanders. However, the more proximal mesopodials exhibit postaxial dominance, i.e., the preaxial column (tibiale, centrale 1) consistently started to ossify after the central column (centralia 2-4, intermedium) and the postaxial column (fibulare). Likewise, we observed preaxial development of the distal carpals in the stereospondylomorph carpus, as in most early tetrapods for which a statement can be made. However, in contrast to the tarsus, the more proximal carpals were formed by preaxial development, i.e., the preaxial column (radiale, centrale 1) ossified after the central column (centralia 2-4, intermedium) and before the postaxial column (ulnare). This pattern is unique among known early tetrapods and occurs only in certain extant salamanders. Furthermore, ossification proceeded from distal to proximal in the central column of the stereospondylomorph carpus, whereas the ossification advanced from proximal to distal in the central column of the tarsus. Despite these differences, a general ossification pattern that started from proximolateral (intermedium or centrale 4) to mediodistal (distal tarsal and carpal 1) roughly in a diagonal line is common to all stereospondylomorph mesopodials investigated. This pattern might basically reflect the alignment of stress within the mesopodium during locomotion. Our observations might point to a greater variability in the development of the mesopodium in stereospondylomorphs and probably other early tetrapods than in most extant tetrapods, possibly mirroring a similar variation as seen in the early phases of skeletogenesis in salamander carpus and tarsus.

Regionalization, constraints, and the ancestral ossification patterns in the vertebral column of amniotes

The development of the vertebral column has been studied extensively in modern amniotes, yet many aspects of its evolutionary history remain enigmatic. Here we expand the existing data on four major vertebral developmental patterns in amniotes based on exceptionally well-preserved specimens of the early Permian mesosaurid reptile Mesosaurus tenuidens: (i) centrum ossification, (ii) neural arch ossification, (iii) neural arch fusion, and (iv) neurocentral fusion. We retrace the evolutionary history of each pattern and reconstruct the ancestral condition in amniotes. Despite 300 million years of evolutionary history, vertebral development patterns show a surprisingly stability in amniotes since their common ancestor. We propose that this stability may be linked to conservatism in the constraints posed by underlying developmental processes across amniotes. We also point out that birds, mammals, and squamates each show specific trends deviating from the ancestral condition in amniotes, and that they remain rather unchanged within these lineages. The stability of their unique patterns demonstrates a certain homogeneity of vertebral developmental constraints within these lineages, which we suggest might be linked to their specific modes of regionalization. Our research provides a framework for the evolution of axial development in amniotes and a foundation for future studies.

Ossification patterns of the carpus and tarsus in salamanders and impacts of preaxial dominance on the fin-to-limb transition

Early limb skeletogenesis in salamanders is characterized by preaxial elements, digits I and II forming earlier than their postaxial counterparts (digits III to V), a phenomenon known as preaxial dominance, whereas in amniotes and anurans, these developmental sequences are reversed. This pattern characterizes the late skeletogenesis of digits and zeugopodium of anamniote tetrapods but remains unknown in carpals/tarsals. To correct this gap in knowledge, we investigate the ossification patterns of the carpals/tarsals in six salamander families/clades based on micro-computed tomography scans. We found that preaxial dominance is seen in the distal carpals/tarsals of several salamander clades and diverse early tetrapods, such as temnospondyls and amniotes. This distribution suggests that preaxial dominance is a primitive developmental pattern in tetrapods. Our results demonstrate that the distal carpals/tarsals are developmentally and evolutionarily independent in the autopodium, and preaxial dominance facilitates stabilization of the number of distal carpals/tarsals during fin-to-limb transition and digit reduction in early tetrapods.

THE FORELIMBS OF ALVAREZSAUROIDEA (DINOSAURIA: THEROPODA): INSIGHT FROM EVOLUTIONARY TERATOLOGY

Alvarezsauroidea (Tetanurae) are non-avian theropod dinosaurs whose forelimb evolution is characterised by overdevelopment of digit I, at the expense of the other two digits, complemented by a drastic forelimb shortening in derived species (Parvicursorinae). These variations are recognised as evolutionary developmental anomalies. Evolutionary teratology hence leads to a double diagnosis with 1) macrodactyly of digit I and microdactyly of digits II and III, plus 2) anterior micromelia. The teratological macrodactyly/microdactyly coupling evolved first. Developmental mechanisms disturbing limb proportion are thought to be convergent with those of other Tetanurae (Tyrannosauridae, Carcharodontosauridae). As for the manual anomalies, both are specific to Alvarezsauroidea (macrodactyly/microdactyly) and inherited (digit loss/reduction). While considering the frame-shift theory, posterior digits develop before the most anterior one. There would therefore be a decrease in the area devoted to digits II (condensation 3) and III (condensation 4), in connection with the Shh signalling pathway, interacting with other molecular players such as the GLI 3 protein and the Hox system. Developmental independence of digit I (condensation 2) would contribute to generate a particular morphology. Macrodactyly would be linked to a variation in Hoxd-13, impacting Gli3 activity, increasing cell proliferation. The loss/reduction of digital ray/phalanges (digits II and III), would be associated to Shh activity, a mechanism inherited from the theropodan ancestry. The macrodactyly/macrodactyly coupling, and then anterior micromelia, fundamentally changed the forelimb mechanical function, compared to the 'classical' grasping structure of basal representatives and other theropods. The distal ossification of the macrodactylian digit has been identified as physiological, implying the use of the structure. However, the debate of a particular 'adaptive' use is pointless since the ecology of an organism is interactively complex, being both at the scale of the individual and dependent on circumstances. Other anatomical features also allow for compensation and a different predation (cursorial hindlimbs). This article is protected by copyright. All rights reserved.

Towards comparative analyses of salamander limb regeneration

Among tetrapods, only salamanders can regenerate their limbs and tails throughout life. This amazing regenerative ability has attracted the attention of scientists for hundreds of years. Now that large, salamander genomes are beginning to be sequenced for the first time, omics tools and approaches can be used to integrate new perspectives into the study of tissue regeneration. Here we argue the need to move beyond the primary salamander models to investigate regeneration in other species. Salamanders at first glance come across as a phylogenetically conservative group that has not diverged greatly from their ancestors. While salamanders do present ancestral characteristics of basal tetrapods, including the ability to regenerate limbs, data from fossils and data from studies that have tested for species differences suggest there may be considerable variation in how salamanders develop and regenerate their limbs. We review the case for expanded studies of salamander tissue regeneration and identify questions and approaches that are most likely to reveal commonalities and differences in regeneration among species. We also address challenges that confront such an initiative, some of which are regulatory and not scientific. The time is right to gain evolutionary perspective about mechanisms of tissue regeneration from comparative studies of salamander species.

Sesamoids in Caudata and Gymnophiona (Lissamphibia): absences and evidence

An integrative definition of sesamoid bones has been recently proposed, highlighting their relationship with tendons and ligaments, their genetic origin, the influence of epigenetic stimuli on their development, and their variable tissue composition. Sesamoid bones occur mainly associated with a large number of mobile joints in vertebrates, most commonly in the postcranium. Here, we present a survey of the distribution pattern of sesamoids in 256 taxa of Caudata and Gymnophiona and 24 taxa of temnospondyls and lepospondyls, based on dissections, high-resolution X-ray computed tomography from digital databases and literature data. These groups have a pivotal role in the interpretation of the evolution of sesamoids in Lissamphibia and tetrapods in general. Our main goals were: (1) to contribute to the knowledge of the comparative anatomy of sesamoids in Lissamphibia; (2) to assess the evolutionary history of selected sesamoids. We formally studied the evolution of the observed sesamoids by optimizing them in the most accepted phylogeny of the group. We identified only three bony or cartilaginous sesamoids in Caudata: the mandibular sesamoid, which is adjacent to the jaw articulation; one located on the mandibular symphysis; and one located in the posterior end of the maxilla. We did not observe any cartilaginous or osseous sesamoid in Gymnophiona. Mapping analyses of the sesamoid dataset of urodeles onto the phylogeny revealed that the very conspicuous sesamoid in the mandibular symphysis of Necturus beyeri and Amphiuma tridactylum is an independent acquisition of these taxa. On the contrary, the sesamoid located between the maxilla and the lower jaw is a new synapomorphy that supports the node of Hydromantes platycephalus and Karsenia coreana. The absence of a mandibular sesamoid is plesiomorphic to Caudata, whereas it is convergent in seven different families. The absence of postcranial sesamoids in salamanders might reveal a paedomorphic pattern that would be visible in their limb joints.

Pentadactyl manus of the Metoposaurus krasiejowensis from the Late Triassic of Poland, the first record of pentadactyly among Temnospondyli

Temnospondyli are commonly believed to have possessed four digits in the manus and five in the pes. However, actual finds of articulated autopodia are extremely rare. Therefore, an articulated, slightly incomplete forelimb skeleton with preserved manus of Metoposaurus krasiejowensis from the Late Triassic of Poland is important in providing new details about the structure and ossification sequence in the temnospondyl limb. The most important observation is the presence of five metacarpals in this specimen. This allows reconstructing the manus as pentadactyl. The number of phalanges and the distribution of distal articulation facets allow reconstruction of the digit formula as (2?)-3-3-(3?)-(2?). The well-developed fifth digit suggests that the Metoposaurus manus shows a unique ossification sequence: the reduction or late ossification of the first digit conforms to the amniote-frog pattern, and the early development of the second and third digit makes Metoposaurus similar to salamanders. Based on the distribution of pentadactyly vs. tetradactyly in the temnospondyl manus, the number of digits was not phylogenetically constrained in temnospondyls, similar to today's amphibians.

Can We Reliably Calibrate Deep Nodes in the Tetrapod Tree? Case Studies in Deep Tetrapod Divergences

Recent efforts have led to the development of extremely sophisticated methods for incorporating tree-wide data and accommodating uncertainty when estimating the temporal patterns of phylogenetic trees, but assignment of prior constraints on node age remains the most important factor. This depends largely on understanding substantive disagreements between specialists (paleontologists, geologists, and comparative anatomists), which are often opaque to phylogeneticists and molecular biologists who rely on these data as downstream users. This often leads to misunderstandings of how the uncertainty associated with node age minima arises, leading to inappropriate treatments of that uncertainty by phylogeneticists. In order to promote dialogue on this subject, we here review factors (phylogeny, preservational megabiases, spatial and temporal patterns in the tetrapod fossil record) that complicate assignment of prior node age constraints for deep divergences in the tetrapod tree, focusing on the origin of crown-group Amniota, crown-group Amphibia, and crown-group Tetrapoda. We find that node priors for amphibians and tetrapods show high phylogenetic lability and different phylogenetic treatments identifying disparate taxa as the earliest representatives of these crown groups. This corresponds partially to the well-known problem of lissamphibian origins but increasingly reflects deeper instabilities in early tetrapod phylogeny. Conversely, differences in phylogenetic treatment do not affect our ability to recognize the earliest crown-group amniotes but do affect how diverse we understand the earliest amniote faunas to be. Preservational megabiases and spatiotemporal heterogeneity of the early tetrapod fossil record present unrecognized challenges in reliably estimating the ages of tetrapod nodes; the tetrapod record throughout the relevant interval is spatially restricted and disrupted by several major intervals of minimal sampling coincident with the emergence of all three crown groups. Going forward, researchers attempting to calibrate the ages for these nodes, and other similar deep nodes in the metazoan fossil record, should consciously consider major phylogenetic uncertainty, preservational megabias, and spatiotemporal heterogeneity, preferably examining the impact of working hypotheses from multiple research groups. We emphasize a need for major tetrapod collection effort outside of classic European and North American sections, particularly from the southern hemisphere, and suggest that such sampling may dramatically change our timelines of tetrapod evolution.

The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13

In the tetrapod limb, the digits (fingers or toes) are the elements most subject to morphological diversification in response to functional adaptations. However, despite their functional importance, the mechanisms controlling digit morphology remain poorly understood. Here we have focused on understanding the special morphology of the thumb (digit 1), the acquisition of which was an important adaptation of the human hand. To this end, we have studied the limbs of the Hoxa13 mouse mutant that specifically fail to form digit 1. We show that, consistent with the role of Hoxa13 in Hoxd transcriptional regulation, the expression of Hoxd13 in Hoxa13 mutant limbs does not extend into the presumptive digit 1 territory, which is therefore devoid of distal Hox transcripts, a circumstance that can explain its agenesis. The loss of Hoxd13 expression, exclusively in digit 1 territory, correlates with increased Gli3 repressor activity, a Hoxd negative regulator, resulting from increased Gli3 transcription that, in turn, is due to the release from the negative modulation exerted by Hox13 paralogs on Gli3 regulatory sequences. Our results indicate that Hoxa13 acts hierarchically to initiate the formation of digit 1 by reducing Gli3 transcription and by enabling expansion of the 5'Hoxd second expression phase, thereby establishing anterior-posterior asymmetry in the handplate. Our work uncovers a mutual antagonism between Gli3 and Hox13 paralogs that has important implications for Hox and Gli3 gene regulation in the context of development and evolution.

Congenital thumb differences- current concepts

Anomalies of the thumb development are not uncommon and may be associated with a number of syndromes also. These anomalies range from total absence to duplication. Reconstructive surgery for the creation of an opposable thumb is the most rewarding aspect of Hand Surgery and also the most challenging. Classification systems have been modified for better description. A number of procedures have been introduced to improve the functionality of the hand in anomalies and age old concepts are undergoing a metamorphosis to further this. A brief description of the common conditions and their treatment are discussed here and highlighted by selected clinical cases.

Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix

The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69-122) recovered, for example, Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the "temnospondyl hypothesis" on the origin of Lissamphibia (TH) to be more parsimonious than the "lepospondyl hypothesis" (LH)-though only, as we show, by one step. We report 4,200 misscored cells, over half of them due to typographic and similar accidental errors. Further, some characters were duplicated; some had only one described state; for one, most taxa were scored after presumed relatives. Even potentially continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved-we document and justify all changes to the matrix-but no characters are added, we find (Analysis R1) much longer trees with, for example, monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; and Anthracosauria either crownward or rootward of Temnospondyli. The LH is nine steps shorter than the TH (R2; constrained) and 12 steps shorter than the "polyphyly hypothesis" (PH-R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, a large clade that includes the adelogyrinids, urocordylid "nectrideans" and aïstopods occupies that position. As expected from the taxon/character ratio, most bootstrap values are low. Adding 56 terminal taxa to the original 102 increases the resolution (and decreases most bootstrap values). The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4; unconstrained) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH. Casineria, in which we tentatively identify a postbranchial lamina, emerges rather far from amniote origins in a gephyrostegid-chroniosuchian grade. Bayesian inference (Analysis EB, settings as in R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample. We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes (e.g. preaxial/postaxial polarity in limb development), and prospects for further improvement of this matrix. Even in its revised state, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates. Sufficient improvement will be laborious-but not difficult.

Evolution of the muscular system in tetrapod limbs

While skeletal evolution has been extensively studied, the evolution of limb muscles and brachial plexus has received less attention. In this review, we focus on the tempo and mode of evolution of forelimb muscles in the vertebrate history, and on the developmental mechanisms that have affected the evolution of their morphology. Tetrapod limb muscles develop from diffuse migrating cells derived from dermomyotomes, and the limb-innervating nerves lose their segmental patterns to form the brachial plexus distally. Despite such seemingly disorganized developmental processes, limb muscle homology has been highly conserved in tetrapod evolution, with the apparent exception of the mammalian diaphragm. The limb mesenchyme of lateral plate mesoderm likely plays a pivotal role in the subdivision of the myogenic cell population into individual muscles through the formation of interstitial muscle connective tissues. Interactions with tendons and motoneuron axons are involved in the early and late phases of limb muscle morphogenesis, respectively. The mechanism underlying the recurrent generation of limb muscle homology likely resides in these developmental processes, which should be studied from an evolutionary perspective in the future.

Ontogeny of the Appendicular Skeleton in Melanosuchus niger (Crocodylia: Alligatoridae)

The objective of the present study was to analyze chondrogenesis and the ossification pattern of the limbs of Melanosuchus niger in order to contribute with possible discussions on homology and the fusion pattern of autopodial elements and phylogeny. In the Reserva Extrativista do Lago Cuniã, Rondônia, Brazil, six nests were marked and two eggs removed from each nest at 24-hour intervals until hatching. Embryos were cleared using KOH; bone tissue was stained with alizarin red S and cartilage with Alcian blue. Routine staining with HE was also performed. In the pectoral girdle, the scapula showed ossification centers before the coracoid process. In the pelvic girdle, the ilium and the ischium were condensed as a single cartilage, although ossification took place through two separate centers, forming distinct elements in the adult. The pubis developed from an independent cartilaginous center with free end, which reflects its function in breathing. In the initial stages, the stylopodium and the zeugopodium developed from the condensation of a Y-shaped cartilage in the limbs, and differentiation of the primary axis and digital arch were observed. The greatest changes were observed in the mesopodia. In their evolution, Crocodylia underwent a vast reduction in the number of autopodial elements as a consequence of fusions and ossification of some elements. This study shows that the chondrogenesis and ossification sequences are dissociated. Moreover, the differences between M. niger and other species show clear variation in the patterns for these events in Alligatoridae.

A new hynobiid-like salamander (Amphibia, Urodela) from Inner Mongolia, China, provides a rare case study of developmental features in an Early Cretaceous fossil urodele

A new fossil salamander, Nuominerpeton aquilonaris (gen. et sp. nov.), is named and described based on specimens from the Lower Cretaceous Guanghua Formation of Inner Mongolia, China. The new discovery documents a far northern occurrence of Early Cretaceous salamanders in China, extending the geographic distribution for the Mesozoic fossil record of the group from the Jehol area (40th-45th parallel north) to near the 49th parallel north. The new salamander is characterized by having the orbitosphenoid semicircular in shape; coracoid plate of the scapulocoracoid greatly expanded with a convex ventral and posterior border; ossification of two centralia in carpus and tarsus; and first digit being about half the length of the second digit in both manus and pes. The new salamander appears to be closely related to hynobiids, although this inferred relationship awaits confirmation by research in progress by us on a morphological and molecular combined analysis of cryptobranchoid relationships. Comparison of adult with larval and postmetamorphic juvenile specimens provides insights into developmental patterns of cranial and postcranial skeletons in this fossil species, especially resorption of the palatine and anterior portions of the palatopterygoid in the palate and the coronoid in the mandible during metamorphosis, and postmetamorphic ossification of the mesopodium in both manus and pes. Thus, this study provides a rare case study of developmental features in a Mesozoic salamander.

Cranial Morphology of the Carboniferous-Permian Tetrapod Brachydectes newberryi (Lepospondyli, Lysorophia): New Data from µCT

Lysorophians are a group of early tetrapods with extremely elongate trunks, reduced limbs, and highly reduced skulls. Since the first discovery of this group, general similarities in outward appearance between lysorophians and some modern lissamphibian orders (specifically Urodela and Gymnophiona) have been recognized, and sometimes been the basis for hypotheses of lissamphibian origins. We studied the morphology of the skull, with particular emphasis on the neurocranium, of a partial growth series of the lysorophian Brachydectes newberryi using x-ray micro-computed tomography (μCT). Our study reveals similarities between the braincase of Brachydectes and brachystelechid recumbirostrans, corroborating prior work suggesting a close relationship between these taxa. We also describe the morphology of the epipterygoid, stapes, and quadrate in this taxon for the first time. Contra the proposals of some workers, we find no evidence of expected lissamphibian synapomorphies in the skull morphology in Brachydectes newberryi, and instead recognize a number of derived amniote characteristics within the braincase and suspensorium. Morphology previously considered indicative of taxonomic diversity within Lysorophia may reflect ontogenetic rather than taxonomic variation. The highly divergent morphology of lysorophians represents a refinement of morphological and functional trends within recumbirostrans, and is analogous to morphology observed in many modern fossorial reptiles.

An orphan gene is necessary for preaxial digit formation during salamander limb development

Limb development in salamanders differs from other tetrapods in that the first digits to form are the two most anterior (preaxial dominance). This has been proposed as a salamander novelty and its mechanistic basis is unknown. Salamanders are the only adult tetrapods able to regenerate the limb, and the contribution of preaxial dominance to limb regeneration is unclear. Here we show that during early outgrowth of the limb bud, a small cohort of cells express the orphan gene Prod1 together with Bmp2, a critical player in digit condensation in amniotes. Disruption of Prod1 with a gene-editing nuclease abrogates these cells, and blocks formation of the radius and ulna, and outgrowth of the anterior digits. Preaxial dominance is a notable feature of limb regeneration in the larval newt, but this changes abruptly after metamorphosis so that the formation of anterior and posterior digits occurs together within the autopodium resembling an amniote-like pattern.

Early evolution of limb regeneration in tetrapods: evidence from a 300-million-year-old amphibian

Salamanders are the only tetrapods capable of fully regenerating their limbs throughout their entire lives. Much data on the underlying molecular mechanisms of limb regeneration have been gathered in recent years allowing for new comparative studies between salamanders and other tetrapods that lack this unique regenerative potential. By contrast, the evolution of animal regeneration just recently shifted back into focus, despite being highly relevant for research designs aiming to unravel the factors allowing for limb regeneration. We show that the 300-million-year-old temnospondyl amphibian Micromelerpeton, a distant relative of modern amphibians, was already capable of regenerating its limbs. A number of exceptionally well-preserved specimens from fossil deposits show a unique pattern and combination of abnormalities in their limbs that is distinctive of irregular regenerative activity in modern salamanders and does not occur as variants of normal limb development. This demonstrates that the capacity to regenerate limbs is not a derived feature of modern salamanders, but may be an ancient feature of non-amniote tetrapods and possibly even shared by all bony fish. The finding provides a new framework for understanding the evolution of regenerative capacity of paired appendages in vertebrates in the search for conserved versus derived molecular mechanisms of limb regeneration.

Skeletal Morphogenesis of Microbrachis and Hyloplesion (Tetrapoda: Lepospondyli), and Implications for the Developmental Patterns of Extinct, Early Tetrapods

The ontogeny of extant amphibians often is used as a model for that of extinct early tetrapods, despite evidence for a spectrum of developmental modes in temnospondyls and a paucity of ontogenetic data for lepospondyls. I describe the skeletal morphogenesis of the extinct lepospondyls Microbrachis pelikani and Hyloplesion longicostatum using the largest samples examined for either taxon. Nearly all known specimens were re-examined, allowing for substantial anatomical revisions that affect the scoring of characters commonly used in phylogenetic analyses of early tetrapods. The palate of H. longicostatum is re-interpreted and suggested to be more similar to that of M. pelikani, especially in the nature of the contact between the pterygoids. Both taxa possess lateral lines, and M. pelikani additionally exhibits branchial plates. However, early and rapid ossification of the postcranial skeleton, including a well-developed pubis and ossified epipodials, suggests that neither taxon metamorphosed nor were they neotenic in the sense of branchiosaurids and salamanders. Morphogenetic patterns in the foot suggest that digit 5 was developmentally delayed and the final digit to ossify in M. pelikani and H. longicostatum. Overall patterns of postcranial ossification may indicate postaxial dominance in limb and digit formation, but also more developmental variation in early tetrapods than has been appreciated. The phylogenetic position and developmental patterns of M. pelikani and H. longicostatum are congruent with the hypothesis that early tetrapods lacked metamorphosis ancestrally and that stem-amniotes exhibited derived features of development, such as rapid and complete ossification of the skeleton, potentially prior to the evolution of the amniotic egg.

Identification of the orphan gene Prod 1 in basal and other salamander families

BACKGROUND

The urodele amphibians (salamanders) are the only adult tetrapods able to regenerate the limb. It is unclear if this is an ancestral property that is retained in salamanders but lost in other tetrapods or if it evolved in salamanders. The three-finger protein Prod 1 is implicated in the mechanism of newt limb regeneration, and no orthologs have been found in other vertebrates, thus providing evidence for the second viewpoint. It has also been suggested that this protein could play a role in salamander-specific aspects of limb development. There are ten families of extant salamanders, and Prod 1 has only been identified in two of them to date. It is important to determine if it is present in other families and, particularly, the basal group of two families which diverged approximately 200 MYA.

FINDINGS

We have used polymerase chain reaction (PCR) to identify Prod 1 in a Chinese hynobiid species Batrachuperus longdongensis. We obtained an intestinal transcriptome of the plethodontid Aneides lugubris and, from this, identified a primer which allowed PCR of two Prod 1 genes from this species. All known Prod 1 sequences from nine species in four families have been aligned, and a phylogenetic tree has been derived.

CONCLUSIONS

Prod 1 is found in basal salamanders of the family Hynobiidae, and in at least three other families, so it may be present in all extant salamanders. It remains a plausible candidate to have been involved in the origins of limb regeneration, as well as the apomorphic aspects of limb development.

Variation in salamanders: an essay on genomes, development, and evolution

Regeneration is studied in a few model species of salamanders, but the ten families of salamanders show considerable variation, and this has implications for our understanding of salamander biology. The most recent classification of the families identifies the cryptobranchoidea as the basal group which diverged in the early Jurassic. Variation in the sizes of genomes is particularly obvious, and reflects a major contribution from transposable elements which is already present in the basal group.Limb development has been a focus for evodevo studies, in part because of the variable property of pre-axial dominance which distinguishes salamanders from other tetrapods. This is thought to reflect the selective pressures that operate on a free-living aquatic larva, and might also be relevant for the evolution of limb regeneration. Recent fossil evidence suggests that both pre-axial dominance and limb regeneration were present 300 million years ago in larval temnospondyl amphibians that lived in mountain lakes. A satisfying account of regeneration in salamanders may need to address all these different aspects in the future.

Review of the molecular development of the thumb: digit primera

The thumb, or digit 1, is not a typical digit. In addition to its unusual mobility and function, its formation is also unusual. It is the last digit to form and the most commonly targeted when limb development is disrupted. The thumb domain is defined by the overlapping expression of HOXA13, TBX5, GLI3R, and HOXD13 and, importantly, by an absence of other distal HOXD transcription factors. This brief review, combining developmental biology and clinical genetics, discusses the current understanding of how the thumb domain is established.

Salamander limb development: integrating genes, morphology, and fossils

The development of the tetrapod limb during skeletogenesis follows a highly conservative pattern characterized by a general proximo-distal progression in the establishment of skeletal elements and a postaxial polarity in digit development. Salamanders represent the only exception to this pattern and display an early establishment of distal autopodial structures, specifically the basale commune, an amalgamation of distal carpal and tarsal 1 and 2, and a distinct preaxial polarity in digit development. This deviance from the conserved tetrapod pattern has resulted in a number of hypotheses to explain its developmental basis and evolutionary history. Here we summarize the current knowledge of salamander limb development under consideration of the fossil record to provide a deep time perspective of this evolutionary pathway and highlight what data will be needed in the future to gain a better understanding of salamander limb development specifically and tetrapod limb development and evolution more broadly.

Palaeoecological and palaeoenvironmental influences revealed by long-bone palaeohistology: the example of the Permian branchiosaurid Apateon

Apateon, a small temnospondyl from the Permian freshwater-lake deposits of the Saar-Nahe Basin (SW Germany), is known by exceptionally well-preserved material. Here we report the first palaeohistological analysis of Apateon that focuses on its life-history traits and palaeoenvironments. Different samples (different localities and horizons) of Apateon caducus and Apateon pedestris have been analysed. Their stylopod histology shows different growth rhythms that might be correlated to changes in palaeoecosystems: food availability and/or presence of predators. Palaeoenvironmental influences are also recognized during the limb-bone osteogenesis by the expression of simple and/or double patterns of Lines of Arrested Growth (LAG). A double-LAG pattern expresses hibernating and aestivating arrests of growth in extant newts. The fossil samples from the two stratigraphically oldest horizons preserved a similar double-LAG pattern, suggesting that they may have hibernated and aestivated every year because of harsh climatic conditions. The Saar-Nahe lake system probably passed from a higher altitude zone into a lower one, possibly because of subsidence and/or erosion. It could also be correlated to the size of the lakes that differs from one locality to another, inducing different responses of the organisms to the climatic variations.

The lissamphibian humerus and elbow joint, and the origins of modern amphibians

The origins and evolution of the three major clades of modern amphibians are still a source of controversy, and no general consensus exists as to their relationship to the various known Paleozoic taxa. This may indicate that additional character complexes should be studied to resolve their phylogenetic relationship. The salamander elbow joint has been fundamentally misinterpreted in previous morphological descriptions. In caudates and anurans, both the radius and ulna (fused in anurans) articulate with the characteristically large capitulum (radial condyle), although part of the ulnar articulating surface fits into to the smooth trochlear region. The salamander "ulnar condyle" of previous descriptions is in fact the entepicondyle. The condition seen in batrachians (i.e., salamanders and frogs) may be a lissamphibian synapomorphy because the elbow region of the primitive fossil caecilian Eocaecilia resembles those of frogs and salamanders. In addition to the large and bulbous capitulum, all lissamphibian humeri lack an entepicondylar foramen, and possess a distally pointing entepicondyle, a low and rounded ectepicondyle, and an elongated shaft. These characters are identified in key fossil forms to assess the support for the different hypotheses proposed for the evolutionary origins of lissamphibians. Temnospondyli is the only group of early tetrapods that shows a progressive evolution of lissamphibian traits in the humerus and elbow joint. Furthermore, among Paleozoic taxa, the dissorophoid temnospondyl Doleserpeton annectens is the only taxon that has the full set of humeral features shared by all lissamphibians. These results add support for the theory of a monophyletic origin of lissamphibians from dissorophoidtemnospondyls.

Amphibian development in the fossil record

Ontogenetic series of extinct taxa are extremely rare and when preserved often incomplete and difficult to interpret. However, the fossil record of amphibians includes a number of well-preserved ontogenetic sequences for temnospondyl and lepospondyl taxa, which have provided valuable information about the development of these extinct groups. Here we summarize the current knowledge on fossil ontogenies of amphibians, their potential and limitations for relationship assessments, and discuss the insights they have provided for our understanding of the anatomy, life history, and ecology of extinct amphibians.

Fish fingers: digit homologues in sarcopterygian fish fins

A defining feature of tetrapod evolutionary origins is the transition from fish fins to tetrapod limbs. A major change during this transition is the appearance of the autopod (hands, feet), which comprises two distinct regions, the wrist/ankle and the digits. When the autopod first appeared in Late Devonian fossil tetrapods, it was incomplete: digits evolved before the full complement of wrist/ankle bones. Early tetrapod wrists/ankles, including those with a full complement of bones, also show a sharp pattern discontinuity between proximal elements and distal elements. This suggests the presence of a discontinuity in the proximal-distal sequence of development. Such a discontinuity occurs in living urodeles, where digits form before completion of the wrist/ankle, implying developmental independence of the digits from wrist/ankle elements. We have observed comparable independent development of pectoral fin radials in the lungfish Neoceratodus (Osteichthyes: Sarcopterygii), relative to homologues of the tetrapod limb and proximal wrist elements in the main fin axis. Moreover, in the Neoceratodus fin, expression of Hoxd13 closely matches late expression patterns observed in the tetrapod autopod. This evidence suggests that Neoceratodus fin radials and tetrapod digits may be patterned by shared mechanisms distinct from those patterning the proximal fin/limb elements, and in that sense are homologous. The presence of independently developing radials in the distal part of the pectoral (and pelvic) fin may be a general feature of the Sarcopterygii.