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

Despite the wide range of shapes and sizes that accompany a vast variety of functions, the development of tetrapod limbs follows a conservative pattern of de novo condensation, branching, and segmentation. Development of the zeugopodium and digital arch typically occurs in a posterior to anterior sequence, referred to as postaxial dominance, with a digital sequence of 4-3-5-2-1. The only exception to this pattern in all of living Tetrapoda can be found in salamanders, which display a preaxial dominance in limb development, a de novo condensation of a basale commune (distal carpal/tarsal 1+2) and a precoccial development of digits I and II. These divergent patterns have puzzled researchers for over a century leading to various explanatory hypotheses. Despite many advances in research on tetrapod limb development, the divergent evolution of these two pathways and its causes are still not understood. Based on an extensive ontogenetic series we investigated the pattern of limb development of the 300 Ma old branchiosaurid amphibian Apateon. This revealed a preaxial dominance in limb development that was previously believed to be unique and derived for modern salamanders. The Branchiosauridae are favored as close relatives of extant salamanders in most phylogenetic hypotheses of the highly controversial origins and relationships of extant amphibians. The findings provide new insights into the evolution of developmental pathways in tetrapod limb development, the relationships of modern amphibians with possible Paleozoic antecedents, and their initial timing of divergence.     

How body size and development biased the direction of evolution in early amphibians

Evolutionary change does not proceed in every direction with equal probability. Evolutionary biases or constraints are limitations on the mode, direction and tempo of evolution. Early tetrapods provide interesting examples, especially Paleozoic and Mesozoic amphibians. (1) Body size had a strong impact on morphology and development in early amphibians, resulting in manifold convergences imposed by design limitations. Miniaturisation had similar effects in a wide range of Paleozoic tetrapods, which are consistent with observations on extant salamanders. Gigantism was a common feature of Triassic temnospondyls, correlating with slow developmental rates similar to those of gigantic salamanders and the convergent evolution of bone density. (2) Ontogeny imposes constraints on evolution by canalised (buffered) developmental sequences. In Paleozoic temnospondyls, ontogenetic trajectories evolved by several different modes (truncation of the trajectory, shifting of events or condensation of events). Metamorphosis is an extreme example of a condensed developmental sequence, which first evolved in Paleozoic temnospondyls, increased in salamanders and culminated in anurans. It imposes strong biases that may be broken by three conceivable modes: (1) loss of the adult period (neoteny), (2) loss of the larval period (direct development) and (3) ‘unpacking’ of metamorphosis by re-evolving the plesiomorphic trajectory.     

Metamorphosis and neoteny: alternative pathways in an extinct amphibian clade

Abstract The Branchiosauridae was a clade of small amphibians from the Permo-Carboniferous with an overall salamander-like appearance. The clade is distinguished by an extraordinary fossil record that comprises hundreds of well-preserved specimens, representing a wide range of ontogenetic stages. Branchiosaurids had external gills and weakly ossified skeletons, and due to this larval appearance their status as neotenic (perennibranchiate) froms has long been accepted. Despite their extensive fossil record large specimens with an adult morphology appeared to be lacking altogether, but recently two adult specimens were identified in a rich sample of Apateon gracilis collected in the 19th century from a locality near Dresden, Saxony. These specimens are unique among branchiosaurids in showing a high level of ossification, including bones that have never been reported in a branchiosaur. These highlight the successive formation of features believed to indicate terrestrial locomotion, as well as feeding on larger prey items. Moreover, these transformations occurred in a small time window (whereas the degree of size increase is used as a proxy of time) and the degree of concentration of developmental events in branchiosaurids is unique among tetrapods outside the lissamphibians. These specimens are compared with large adults of the neotenic branchiosaurid Apateon caducus from the Saar-Nahe Basin, which despite their largetr body size lack the features found in the adult. A. gracilis specimens. These specimens give new insight into patterns of metamorphosis (morphological transformation) in branchiosaurids that are believed to be correlated to a change of habitat, and clearly show that different life-history pathways comparable to those of modern salamanders were already estabilshed in this Paleozoic clade.     

Microsaurs as possible apodan ancestors

The specific ancestry and nature of the relationships of modern amphibians have not yet been established. Detailed comparisons of the anatomy of the skull roof, palate and braincase of living apodans and the Paleozoic microsaur Goniorhynchus demonstrate greater similarities than between apodans and any other group of amphibians, fossil or recent. Unlike any other amphibians, extensive pleurosphenoid ossifications are developed in the area of the Vth nerve, uniting the otic capsule with the sphenethmoid. Other important features that they share (although not uniquely) include the presence of all the primitive dermal elements of the palate, a solidly roofed temporal region, a row of palatal teeth parallel to the marginal dentition and a row of teeth on the medial surface of the lower jaw. The stapes has a similar configuration and position, totally different from that of frogs and salamanders. Such similarities do not necessarily prove close relationship, but indicate the necessity for considering that apodans may have an ancestry distinct from that of frogs and salamanders.     

Evolution of ossification sequences in salamanders and urodele origins assessed through event-pairing and new methods

SUMMARY Ossification sequences of the skull in extant Urodela and in Permo‐Carboniferous Branchiosauridae have already been used to study the origin of lissamphibians. But most of these studies did not consider some recent methods developed to analyze the developmental sequences within a phylogenetic framework. Here, we analyze the ossification sequences of 24 cranial bones of 23 extant species of salamanders using the event‐pairing method. This reveals new developmental synapomorphies for several extant salamander taxa and ancestral sequences for Urodela under four alternative reference phylogenies. An analysis with the 12 bones for which ossification sequence data are available in urodeles and in the branchiosaurid Apateon is also performed in order to compare the ancestral condition of the crown‐group of Urodela to the sequence of Apateon. This reveals far more incompatibilities than previously suggested. The similarities observed between some extant salamanders and branchiosaurids may result from extensive homoplasy, as the extreme variation observed in extant Urodela suggests, or be plesiomorphic, as the conservation of some ossification patterns observed in other remotely related vertebrates like actinopterygians suggests. We propose a new, simpler method based on squared‐change optimization to estimate the relative timing of ossification of various bones of hypothetical ancestors, and use independent‐contrasts analysis to estimate the confidence intervals around these times. Our results show that the uncertainty of the ancestral ossification sequence of Urodela is much greater than event‐pairing suggests. The developmental data do not allow to conclude that branchiosaurids are closely related to salamanders and their limited taxonomic distribution in Paleozoic taxa precludes testing hypotheses about lissamphibian origins. This is true regardless of the analytical method used (event‐pairing or our new method based on squared‐change parsimony). Simulations show that the new analytical method is generally more powerful to detect evolutionary shifts in developmental timing, and has lower Type I error rate than event‐pairing. It also makes fewer errors in ancestral character value or state assignment than event‐pairing.     

Development and evolution of the tetrapod skull–neck boundary

The origin and evolution of the vertebrate skull have been topics of intense study for more than two centuries. Whereas early theories of skull origin, such as the influential vertebral theory, have been largely refuted with respect to the anterior (pre‐otic) region of the skull, the posterior (post‐otic) region is known to be derived from the anteriormost paraxial segments, i.e. the somites. Here we review the morphology and development of the occiput in both living and extinct tetrapods, taking into account revised knowledge of skull development by augmenting historical accounts with recent data. When occipital composition is evaluated relative to its position along the neural axis, and specifically to the hypoglossal nerve complex, much of the apparent interspecific variation in the location of the skull–neck boundary stabilizes in a phylogenetically informative way. Based on this criterion, three distinct conditions are identified in (i) frogs, (ii) salamanders and caecilians, and (iii) amniotes. The position of the posteriormost occipital segment relative to the hypoglossal nerve is key to understanding the evolution of the posterior limit of the skull. By using cranial foramina as osteological proxies of the hypoglossal nerve, a survey of fossil taxa reveals the amniote condition to be present at the base of Tetrapoda. This result challenges traditional theories of cranial evolution, which posit translocation of the occiput to a more posterior location in amniotes relative to lissamphibians (frogs, salamanders, caecilians), and instead supports the largely overlooked hypothesis that the reduced occiput in lissamphibians is secondarily derived. Recent advances in our understanding of the genetic basis of axial patterning and its regulation in amniotes support the hypothesis that the lissamphibian occipital form may have arisen as the product of a homeotic shift in segment fate from an amniote‐like condition.     

The importance of global parsimony and historical bias in understanding tetrapod evolution. Part I. Systematics,middle ear evolution and jaw suspension

A phylogenetic analysis based on a data matrix of 43 taxa and 155 osteological characters has produced a new hypothesis of tetrapod phylogeny that is drastically different from the established consensus. Among Paleozoic taxa, only diadectomorphs appear to be related to amniotes. In contrast to previous hypotheses, lissamphibians appear to have been derived from lepospondyls. Seymouriamorphs, gephyrostegids, embolomeres, temnospondyls, and loxommatids are stem-tetrapods. The new phylogeny suggests that the absence of a tympanic middle ear in salamanders and gymnophiones is a primitive character.     

The skull and jaw musculature as guides to the ancestry of salamanders

The fossil record provides no evidence supporting a unique common ancestry for frogs, salamanders and apodans. The ancestors of the modern orders may have diverged from one another as recently as 250 million years ago, or as long ago as 400 million years according to current theories of various authors. In order to evaluate the evolutionary patterns of the modern orders it is necessary to determine whether their last common ancestor was a rhipidistian fish, a very primitive amphibian, a labyrimhodom or a ‘lissamphibian’. The broad cranial similarities of frogs and salamanders, especially the dominance of the braincase as a supporting element, can be associated with the small size of the skull in their immediate ancestors. Hynobiids show the most primitive cranial pattern known among the living salamander families and “provide a model for determining the nature of the ancestors of the entire order. Features expected in ancestral salamanders include: (1) Emargination of the cheek; (2) Movable suspensorium formed by the quadrate, squamosal and pterygoid; (3) Occipital condyle posterior to jaw articulation; (4) Distinct prootic and opisthotic; (5) Absence ol otic notch; (6) Stapes forming a structural link between braincase and cheek. In the otic region, cheek and jaw suspension, the primitive salamander pattern (resembles most closely the microsaurs among known Paleozoic amphibians, and shows no significant features in common with either ancestral frogs or the majority of labyrinth odonts. The basic pattern of the adductor jaw musculature is consistent within both frogs and salamanders, but major differences are evident between the two groups. The dominance of the adductor mandibulae externus in salamanders can be associated with the open cheek in all members of that order, and the small size of this muscle in frogs can be associated with the large otic notch. The spread of different muscles over the otic capsule, the longus head ol the adductor mandibulae posterior in frogs and the superficial head of the adductor mandibulae internus in salamanders, indicates that fenestration of the skull posterodorsal to the orbit occurred separately in the ancestors of the two groups. Reconstruction of the probable pattern of the jaw musculature in Paleozoic amphibians indicates that frogs and salamanders might have evolved from a condition hypothesized for primitive labyrinthodonts, but the presence of a large otic notch in dissorophids suggests specialization toward the anuran, not the urodele condition. The presence of either an einarginated cheek or an embayment of the lateral surface of the dentary and the absence of an otic notch in microsaurs indicate a salamander-like distribution of die adductor jaw muscles. The ancestors of frogs and salamanders probably diverged from one another in the early Carboniferous, Frogs later evolved from small labyrinthodonts and salamanders from microsaurs. Features considered typical of lissamphibians evolved separately in the two groups in the late Permian andTriassic.     

Variation in the trophic basis of production and energy flow associated with emergence of larval salamander assemblages from forest ponds

1. Larval amphibians are a dominant consumer in many freshwater systems, yet limited data on energy transfers between aquatic food resources and larvae and between metamorphosed larvae and adjacent habitats preclude an accurate assessment of their roles as links between aquatic and terrestrial food webs.
2. During 2003–04, we derived prey-specific assimilation efficiencies, analysed stomach contents, and intensively sampled ambystomatid salamander assemblages in four ponds to quantify the trophic basis of larval production. Using estimates of the contribution of each prey taxon to larval production, we constructed quantitative food webs and assessed variation in pathways of energy flow associated with emergences.
3. Overall, metamorphosed salamanders exported 3–8% of total prey production, required to account for total salamander production, to adjacent forest. Aquatic insects, zooplankton and amphibian prey were most important to energy flow associated with emergence; amounts of larval production attributed to each of these prey types shifted during development and varied among salamander taxa.
4. The majority of variation in the trophic basis of production among species was attributed to copepods (Cyclopidae) and three families of aquatic insects (Chironomidae, Chaoboridae and Culicidae). Dominant prey types contributing to the production of metamorphosed salamanders varied among ponds, representing different pathways for energy transfers between aquatic resources and forest habitats. These findings further our understanding of the ecological roles of amphibians and thus the consequences of amphibian declines and extinctions.     

The morphology and post-hatching development of the skull of Bolitoglossa nicefori (Caudata: Plethodontidae): developmental implications of recapitulation and repatterning

The cranial morphology of the direct-developing salamander Bolitoglossa nicefori and its post-hatching development are described and compared with that of other urodeles. Four stages of cranial development are defined on the basis of conspicuous events that occur during post-hatching ontogeny. The adult skull morphology of B. nicefori is similar to that of other plethodontids; however, some regions show interspecific variation. The post-hatching ontogeny of the skull and the stage of ossification observed in the hatchlings of B. nicefori show two important ontogenetic features: (1) a mosaic of early larval, metamorphic and post-metamorphic skull features in hatchlings, and (2) absence of characteristic larval elements in skull and hyoid apparatus. The distinctive stage of ossification in the hatchlings of B. nicefori could be caused by heterochronic changes in the ossification sequence, compared to the ontogeny of metamorphic salamanders. The possible heterochronic changes and the absence of larval traits are perhaps due to ontogenetic repatterning, yet without an obvious impact on the adult skull morphology (absence of morphological novelties). This might indicate a compartmentalized development. Further studies should be performed in order to establish the possible occurrence of recapitulatory patterns or ontogenetic repatterning in the skull morphogenesis of B. nicefori during its embryonic development.     

Ossification patterns in the tetrapod limb – conservation and divergence from morphogenetic events

Two different patterns of the condensation and chondrification of the limbs of tetrapods are known from extensive studies on their early skeletal development. These are on the one hand postaxial dominance in the sequential formation of skeletal elements in amniotes and anurans, and on the other, preaxial dominance in urodeles. The present study investigates the relative sequence of ossification in the fore‐ and hindlimbs of selected tetrapod taxa based on a literature survey in comparison to the patterns of early skeletal development, i.e. mesenchymal condensation and chondrification, representing essential steps in the late stages of tetrapod limb development. This reveals the degree of conservation and divergence of the ossification sequence from early morphogenetic events in the tetrapod limb skeleton. A step‐by‐step recapitulation of condensation and chondrification during the ossification of limbs can clearly be refuted. However, some of the deeper aspects of early skeletal patterning in the limbs, i.e. the general direction of development and sequence of digit formation are conserved, particularly in anamniotes. Amniotes show a weaker coupling of the ossification sequence in the limb skeleton with earlier condensation and chondrification events. The stronger correlation between the sequence of condensation/chondrification and ossification in the limbs of anamniotes may represent a plesiomorphic trait of tetrapods. The pattern of limb ossification across tetrapods also shows that some trends in the sequence of ossification of their limb skeleton are shared by major clades possibly representing phylogenetic signals. This review furthermore concerns the ossification sequence of the limbs of the Palaeozoic temnospondyl amphibian Apateon sp. For the first time this is described in detail and its patterns are compared with those observed in extant taxa. Apateon sp. shares preaxial dominance in limb development with extant salamanders and the specific order of ossification events in the fore‐ and hindlimb of this fossil dissorophoid is almost identical to that of some modern urodeles.     

Molecular Evidence for the Early History of Living Amphibians

The evolutionary relationships of the three orders of living amphibians (lissamphibians) has been difficult to resolve, partly because of their specialized morphologies. Traditionally, frogs and salamanders are considered to be closest relatives, and all three orders are thought to have arisen in the Paleozoic (>250 myr). Here, we present evidence from the DNA sequences of four mitochondrial genes (2.7 kilobases) that challenges the conventional hypothesis and supports a salamander–caecilian relationship. This, in light of the fossil record and distribution of the families, suggests a more recent (Mesozoic) origin for salamanders and caecilians directly linked to the initial breakup of the supercontinent Pangaea. We propose that this single geologic event isolated salamanders and archaeobatrachian frogs on the northern continents (Laurasia) and the caecilians and neobatrachian frogs on the southern continents (Gondwana). Among the neobatrachian frog families, molecular evidence supports a South American clade and an African clade, inferred here to be the result of mid-Cretaceous vicariance.     

Molecular phylogeny of swallowtail butterflies of the tribe Papilionini (Papilionidae, Lepidoptera).

Swallowtail butterflies of the tribe Papilionini number about 225 species and are currently used as model organisms in several research areas, including genetics, chemical ecology and phylogenetics of host plant utilization and mimicry, mechanisms of speciation, and conservation. We have inferred phylogenetic relationships for a sample of 18 species of the genus Papilio (sensu lato) and five outgroup taxa by sequencing two stretches of mitochondrial DNA that correspond to segments 12886-13370 and 12083-12545 of Drosophila melanogaster mitochondrial DNA and consist of sections of the genes for the large ribosomal RNA and subunit 1 of NADH-dehydrogenase. Our data support the monophyly of Papilio and, within it, of several traditionally recognized subgroups. Species belonging to groups that utilize primarily Rutaceae as larval foodplants form two clusters, corresponding to Old World and American taxa, respectively, while two previously recognized clades-of American and South Asian-Austronesian origin-whose members were known to feed mostly on Lauraceae and Magnoliaceae, are observed to form a clade. The sister group of Papilio is found to be the South Asian genus Meandrusa, which also happens to feed on Lauraceae. The latter plant family is therefore the probable larval host of the ancestor Papilio and the shift to Rutaceae (which four-fifths of extant Papilio species use as foodplants) is more likely to have occurred only after the initial diversification of the genus.     

Orthodox and unorthodox phylogenetic relationships among tunas revealed by the nucleotide sequence analysis of the mitochondrial DNA control region

A phylogeny of all eight recognized taxa of the genus Thunnus was constructed from approximately 400 base pairs of sequence of the mitochondrial DNA (mtDNA) control region. The PCR-amplified control region I segment studied contained a total of 186 variable sites and 159 phylogenetically informative sites. Diagnostic sequences for every taxon were identified. Neighbour-joining phylogenies supported monophyletic origins of the temperate subgenus Thunnus and of the tropical subgenus Neothunnus . Similar results were obtained by maximum parsimony analyses except that there was no support for a monophyletic origin of the subgenus Thunnus . Bigeye tuna, which have been difficult to place in either subgenus using conventional morphological data, was identified as the sister species of Neothunnus . Within the subgenus Thunnus , the Atlantic bluefin and Southern bluefin tunas were shown to be sister taxa of the highly divergent monophyletic clade formed by the Pacific northern bluefin and the Albacore tunas. The conspecific Atlantic ( T. thynnus thynnus ) and Pacific ( T. t. orientalis ) northern bluefin tunas were more divergent (Tamura-Nei distance 0·145 ± 0·019) from each other than the average distance separating most species-pairs within the genus. Thus, a re-examination of their status as subspecies of T. thunnus is warranted.     

Pecularities of bony skeleton development in Asian clawed salamanders (Onychodactylus, Hynobiidae) related to embryonization

We studied skull, vertebral column, and limb skeleton development in Japanese clawed salamander Onychodactylus japonicus (Hynobiidae). The study is based on the ontogenetic series of embryos and larvae obtained from wild-captured adults by artificial induction of breeding using hormonal stimulation. The first stages of the skeleton formation in O. japonicus are shifted to the late embryonic period and hatching larvae already possess a well-ossified vertebral column, large number of skull ossifications and show signs of ossification in the forelimb skeleton. Compared to the primitive pattern of the skeleton development typical for other hynobiid salamanders, O. japonicus shows a number of heterochronies related to embryonization. In particular, this species is characterized by an earlier ossification of the vertebral column compared to that of the skull and by the delayed development and early reduction of the coronoid. Our results, along with the previously reported data on the skeleton development in the Fischer’s clawed salamander O. fischeri (Smirnov and Vassilieva, 2002), indicate that the genus Onychodactylus is characterized by the loss or reduction of several skeletal features typically found at early larval stages in other Hynobiidae species. In particular, provisional bones (especially the coronoid) and their dentition are underdeveloped. In addition, it is corroborated that the first tooth generation is absent in Onychodactylus, whereas such monocuspid nonpedicellate tooth generation normally develops at the early larval stages of other caudate amphibians. Since similar patterns of skeleton ontogeny are observed in other caudate groups with different extent of embryonization, it is proposed that, in different lineages of Urodela, the evolution of ontogeny followed similar pathways and was accompanied by the same changes in skeletogenesis.     

Skull ontogeny: developmental patterns of fishes conserved across major tetrapod clades

In vertebrates, the ontogeny of the bony skull forms a particularly complex part of embryonic development. Although this area used to be restricted to neontology, recent discoveries of fossil ontogenies provide an additional source of data. One of the most detailed ossification sequences is known from Permo-Carboniferous amphibians, the branchiosaurids. These temnospondyls form a near-perfect link between the piscine osteichthyans and the various clades of extant tetrapods, retaining a full complement of dermal bones in the skull. For the first time, the broader evolutionary significance of these event sequences is analyzed, focusing on the identification of sequence heterochronies. A set of 120 event pairs was analyzed by event pair cracking, which helped identify active movers. A cladistic analysis of the event pair data was also carried out, highlighting some shared patterns between widely divergent clades of tetrapods. The analyses revealed an unexpected degree of similarity between the widely divergent taxa. Most interesting is the apparently modular composition of the cranial sequence: five clusters of bones were discovered in each of which the elements form in the same time window: (1) jaw bones, (2) marginal palatal elements, (3) circumorbital bones, (4) skull roof elements, and (5) neurocranial ossifications. In the studied taxa, these "modules" have in most cases been shifted fore and back on the trajectory relative to the Amia sequence, but did not disintegrate. Such "modules" might indicate a high degree of evolutionary limitation (constraint).     

The evolution of metamorphosis in temnospondyls

Temnospondyls, possible relatives of extant amphibians and crudely similar to recent salamanders, are known from larval, neotenic and metamorphosed stages. Here, ontogenetic data of various temnospondyl taxa are analysed in order to recognize metamorphosis. Here, metamorphosis is strictly defined as a shift from an aquatic to a terrestrial existence. Following a check-list of criteria, the most likely metamorphosis-induced changes are proved in three temnospondyl lineages: eryopids, zatrachydids and dissorophoids. In a few other, unrelated taxa, terrestrial adults are known but no larval or metamorphosing forms. The distribution of metamorphosis among the Temnospondyli does not strictly correlate with phylogeny, which highlights the widespread occurrence of neoteny. In each group, characteristic patterns of metamorphosis are described and compared. Among temnospondyls, dissorophoids had the most intensive type of metamorphosis, characterized by a condensed ontogeny and a relatively small body size. The result was a distinct transformed morphotype with far-reaching terrestrial adaptations.     

Metamorphosis of cranial design in tiger salamanders (Ambystoma tigrinum): A morphometric analysis of ontogenetic change

While ontogenetic analyses of skull development have contributed to our understanding of phylogenetic patterns in vertebrates, there are few studies of taxa that undergo a relatively discrete and rapid change in morphology during development (metamorphosis). Morphological changes occurring in the head at metamorphosis in tiger salamanders (Ambystoma tigrinum) were quantified by a morphometric analysis of cranial osteology and myology to document patterns of change during metamorphosis. We employed a cross-sectional analysis using a sample of larvae just prior to metamorphosis and a sample of transformed individuals just after metamorphosis, as well as larvae undergoing metamorphosis. There were no differences in external size of the head among the larval and transformed samples. The hyobranchial apparatus showed many dramatic changes at metamorphosis, including shortening of ceratobranchial 1 and the basibranchial. The subarcualis rectus muscle increased greatly in length at metamorphosis, as did hypobranchial length and internasal distance. A truss analysis of dorsal skull shape showed that at metamorphosis the snout becomes wider, the maxillary and squamosal triangles rotate posteromedially, and the neurocranium shortens (while maintaining its width), resulting in an overall decrease in skull length at metamorphosis. These morphometric differences are interpreted in light of recent data on the functional morphology of feeding in salamanders. Morphological reorganization of the hyobranchial apparatus and shape changes in the skull are related to the acquisition of a novel terrestrial feeding mode (tongue projection) at metamorphosis. Metamorphic changes (both internal and external) that can be used to judge metamorphic condition are discussed.