Osteology of Batrachuperus yenyuanensis (Urodela, Hynobiidae), a high-altitude mountain stream salamander from western China

A comparative atlas of selected skeletal elements of European urodeles (Amphibia: Urodela) for palaeontological investigations

The osteology of European urodeles was studied extensively in the past, but comparative analyses of isolated bones are rare, despite being the most useful tool for the identification of fossil remains. The present work is focused on the most robust skeletal elements (therefore, common in the fossil record: otic–occipitum complexes and vertebrae) and provides taxonomically significant diagnostic characters at the genus level for European genera of urodeles, including some taxa whose osteology was poorly known (e.g. Euproctus and Calotriton). Characters subject to wide variability are identified, and their use is discouraged for diagnoses of extinct species. A selection of diagnostic characters is used herein to build an identification key for each studied skeletal element and for a phylogenetic analysis to understand whether these osteological elements can convey a genuine signal. The analysis under Bayesian inference resulted in a well-supported Salamandridae clade and Pleurodelinae tribe. Salamandrina was recovered as part of the Pleurodelinae, in agreement with previous morphological phylogenetic analyses, but in contrast to the conclusion of molecular studies.

Palatal morphology predicts the paleobiology of early salamanders

Ecological preferences and life history strategies have enormous impacts on the evolution and phenotypic diversity of salamanders, but the yet established reliable ecological indicators from bony skeletons hinder investigations into the paleobiology of early salamanders. Here, we statistically demonstrate by using time-calibrated cladograms and geometric morphometric analysis on 71 specimens in 36 species, that both the shape of the palate and many non-shape covariates particularly associated with vomerine teeth are ecologically informative in early stem- and basal crown-group salamanders. Disparity patterns within the morphospace of the palate in ecological preferences, life history strategies, and taxonomic affiliations were analyzed in detail, and evolutionary rates and ancestral states of the palate were reconstructed. Our results show that the palate is heavily impacted by convergence constrained by feeding mechanisms and also exhibits clear stepwise evolutionary patterns with alternative phenotypic configurations to cope with similar functional demand. Salamanders are diversified ecologically before the Middle Jurassic and achieved all their present ecological preferences in the Early Cretaceous. Our results reveal that the last common ancestor of all salamanders share with other modern amphibians a unified biphasic ecological preference, and metamorphosis is significant in the expansion of ecomorphospace of the palate in early salamanders.

Osteological characteristics of the Setouchi salamander Hynobius setouchi (Urodela, Hynobiidae)

This study described the detailed osteological features of the Setouchi salamander Hynobius setouchi. H. setouchi, which is endemic to central Japan, was recently delineated from the wide range of H. nebulosus species based on molecular and external morphological characteristics. However, the osteological features of the species belonging to the genus Hynobius have not been examined, which has hindered the detailed understanding of morphological diversity in the genus. To address this problem, this study elucidated the osteological features of the salamander using micro-computed tomography scanning and whole-mount double staining methods. The articular, a part of the hypobranchial I, a part of coracoid, pubis, carpus, and tarsus were cartilaginous in small-sized individuals and were partially or completely ossified in large-sized individuals. The degree of ossification varied in the operculum, basibranchial II, and ascending process of the palatoquadrate. However, ossification was not associated with body size. The lacrimal, ossified manus, and ossified pes exhibited varying degrees of articulation or fusion irrespective of body size. Moreover, the cranium and tarsus of H. setouchi exhibited several unique characteristics. These osteological characteristics will aid in revising the taxonomy and phylogeny of the Hynobius species.

Middle Jurassic stem hynobiids from China shed light on the evolution of basal salamanders

The Hynobiidae are an early-diverging clade of crown-group salamanders (urodeles) with an important bearing on the evolution of urodeles. Paleobiology and early-branching patterns of the Hynobiidae remain unclear owing to a poorly documented fossil record. We reported a newly referred specimen to the stem hynobiid, originally named as "Liaoxitriton daohugouensis," but here as Neimengtriton daohugouensis comb. nov., and predates the previously estimated origination time of Hynobiidae for at least 8 Myr. We interpret N. daohugouensis as semiaquatic at the adult stage, a previously unknown paleoecological preference among Mesozoic salamanders. Phenotypic variations of N. daohugouensis enlighten an unrecognized association between caudosacral vertebrae and fertilization modes in the early evolution of urodeles. Our cladistic analyses based on morphological characters not only recognize several stem hynobiids and establish Panhynobia nomen cladinovum for the total-group hynobiids but also shed light on the sequential evolution of morphological features in this primitive urodele clade.

UCE Phylogenomics, detection of a putative hybrid population, and one older mitogenomic node age of Batrachuperus salamanders

The prevalence of incomplete lineage sorting complicates the examination of hybridization and species-level paraphyly with gene trees of a small number of loci. In Asian mountain salamanders of the genus Batrachuperus, possible hybridization and species paraphyly had been identified by utilizing mitochondrial genealogy and fixed allozyme differences. Here we sampled 2909 UCEs in 44 local populations from all six Batrachuperus species, inferred gene and species trees, compared them with mitochondrial and allozyme results, and examined the potential hybridization and species paraphyly. The clustering pattern of single-locus trees, increased proportion of heterozygous SNPs, allele frequency-based migration edge estimation, and intrapopulation long branches (as expected from an increase of genetic lineage and nucleotide diversity) support that an eastern B. karlschmidti population has experienced admixture with B. tibetanus. On the 2909-UCE concatenated and species trees, lower nodal supports were observed when similar proportions of loci agreed with alternative topologies, i.e., a reciprocal monophyly between a Pengxian lineage and the remainder of B. pinchonii (0.379) or a paraphyly of the latter with respect to Pengxian (0.362). The UCE phylogenomics agreed with the relatively recent groupings in the allozyme dendrogram. Despite incomplete lineage sorting, the mitochondrial trees were similar to the UCE trees for deeper relationships of the genus. However, one significant branch-length level discordance was identified. The branch between the common ancestor of B. daochengensis and B. yenyuanensis and common ancestor of the genus was approximately three times shorter on the mitochondrial tree than on the UCE tree, suggesting that the split of the mitochondrial lineages was likely a few million years earlier than the split of species. This finding supports considering possible ancestral polymorphism when interpreting different divergence dates estimated from mitochondrial and genome-wide data.

Comparative osteology of the hynobiid complex Liua-Protohynobius-Pseudohynobius (Amphibia, Urodela): Ⅰ. Cranial anatomy of Pseudohynobius

Hynobiidae are a clade of salamanders that diverged early within the crown radiation and that retain a considerable number of features plesiomorphic for the group. Their evolutionary history is informed by a fossil record that extends to the Middle Jurassic Bathonian time. Our understanding of the evolution within the total group of Hynobiidae has benefited considerably from recent discoveries of stem hynobiids but is constrained by inadequate anatomical knowledge of some extant forms. Pseudohynobius is a derived hynobiid clade consisting of five to seven extant species living endemic to southwestern China. Although this clade has been recognized for over 37 years, osteological details of these extant hynobiids remain elusive, which undoubtedly has contributed to taxonomic controversies over the hynobiid complex Liua-Protohynobius-Pseudohynobius. Here we provide a bone-by-bone study of the cranium in the five extant species of Pseudohynobius (Ps. flavomaculatus, Ps. guizhouensis, Ps. jinfo, Ps. kuankuoshuiensis and Ps. shuichengensis) based on x-ray computer tomography data for 18 specimens. Our results indicate that the cranium in each of these species has a combination of differences in morphology, proportions and articulation patterns in both dermal and endochondral bones. Our study establishes a range of intraspecific differences that will serve as organizing hypotheses for future studies as more extensive collections of these species become available. Morphological features in the cranium for terrestrial ecological adaptation in Hynobiidae are summarized. Based on the results, we also discuss the evolution and development of several potential synapomorphies of Hynobiidae, including features of the orbitosphenoid and articular.

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.

Synchrotron microtomography applied to the volumetric analysis of internal structures of Thoropa miliaris tadpoles

Amphibians are models for studying applied ecological issues such as habitat loss, pollution, disease, and global climate change due to their sensitivity and vulnerability to changes in the environment. Developmental series of amphibians are informative about their biology, and X-ray based 3D reconstruction holds promise for quantifying morphological changes during growth—some with a direct impact on the possibility of an experimental investigation on several of the ecological topics listed above. However, 3D resolution and discrimination of their soft tissues have been difficult with traditional X-ray computed tomography, without time-consuming contrast staining. Tomographic data were initially performed (pre-processing and reconstruction) using the open-source software tool SYRMEP Tomo Project. Data processing and analysis of the reconstructed tomography volumes were conducted using the segmentation semi-automatic settings of the software Avizo Fire 8, which provide information about each investigated tissues, organs or bone elements. Hence, volumetric analyses were carried out to quantify the development of structures in different tadpole developmental stages. Our work shows that synchrotron X-ray microtomography using phase-contrast mode resolves the edges of the internal tissues (as well as overall tadpole morphology), facilitating the segmentation of the investigated tissues. Reconstruction algorithms and segmentation software played an important role in the qualitative and quantitative analysis of each target structure of the Thoropa miliaris tadpole at different stages of development, providing information on volume, shape and length. The use of the synchrotron X-ray microtomography setup of the SYRMEP beamline of Elettra Synchrotron, in phase-contrast mode, allows access to volumetric data for bone formation, eye development, nervous system and notochordal changes during the development (ontogeny) of tadpoles of a cycloramphid frog Thoropa miliaris. As key elements in the normal development of these and any other frog tadpole, the application of such a comparative ontogenetic study, may hold interest to researchers in experimental and environmental disciplines.