The changing views on the evolutionary relationships of extant Salamandridae (Amphibia: Urodela)

Characterization, Comparison of Two New Mitogenomes of Crocodile Newts Tylototriton (Caudata: Salamandridae), and Phylogenetic Implications

Mitochondrial genomes (mitogenomes) are valuable resources in molecular and evolutionary studies, such as phylogeny and population genetics. The complete mitogenomes of two crocodile newts, Tylototriton broadoridgus and Tylototriton gaowangjienensis, were sequenced, assembled, and annotated for the first time using next-generation sequencing. The complete mitogenomes of T. broadoridgus and T. gaowangjienensis were 16,265 bp and 16,259 bp in lengths, which both composed of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 1 control region. The two mitogenomes had high A + T content with positive AT-skew and negative GC-skew patterns. The ratio of non-synonymous and synonymous substitutions showed that, relatively, the ATP8 gene evolved the fastest and COI evolved the slowest among the 13 PCGs. Phylogenetic trees from BI and ML analyses resulted in identical topologies, where the Tylototriton split into two groups corresponding to two subgenera. Both T. broadoridgus and T. gaowangjienensis sequenced here belonged to the subgenus Yaotriton, and these two species shared a tentative sister group relationship. The two mitogenomes reported in this study provided valuable data for future molecular and evolutionary studies of the genus Tylotoriton and other salamanders.

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.

Karyological Diversification in the Genus Lyciasalamandra (Urodela: Salamandridae)

Simple Summary

The Lycian salamanders of the genus Lyciasalamandra are characterized by a debated taxonomy and phylogenetic relationships. They have been the subject of various molecular and phylogenetic analyses, but their chromosomal diversity is completely unknown. We here present a comparative cytogenetic analysis on five out of the seven described species and seven subspecies of Lyciasalamandra, providing the first karyological assessment on the genus and comparing them to closely related representatives of the genus Salamandra. We analyzed the occurrence and distribution of different conserved (chromosome number and morphology) and highly variable karyological features. We found an impressive diversity in the configuration of nucleolus organizing regions (NORs), which alternatively occur either as heteromorphic or homomorphic loci on distinct regions of different chromosome pairs. We highlight that the observed peculiar taxon-specific pattern of chromosome markers supports the taxonomic validity of the different studied evolutionary lineages and is consistent with a scenario of synchronous evolution in the Lycian salamanders.

Abstract

We performed the first cytogenetic analysis on five out of the seven species of the genus Lyciasalamandra, including seven subspecies, and representatives of its sister genus Salamandra. All the studied species have a similar karyotype of 2n = 24, mostly composed of biarmed elements. C-bands were observed on all chromosomes, at centromeric, telomeric and interstitial position. We found a peculiar taxon-specific NOR configuration, including either heteromorphic and homomorphic NORs on distinct regions of different chromosomes. Lyciasalamandra a.antalyana and L. helverseni showed two homomorphic NORs (pairs 8 and 2, respectively), while heteromorphic NORs were found in L. billae (pairs 6, 12), L. flavimembris (pairs 2, 12), L. l. luschani (pairs 2, 12), L. l. basoglui (pairs 6, 12), L. l. finikensis (pairs 2, 6) and S. lanzai (pairs 8, 10). Homomorphic NORs with an additional supernumerary site were shown by S. s. salamandra (pairs 2, 8) and S. s. gigliolii (pairs 2, 10). This unexpected highly variable NOR configuration is probably derived from multiple independent NOR translocations and paracentric inversions and correlated to lineage divergence in Lyciasalamandra. These results support the taxonomic validity of the studied taxa and are consistent with a hypothesized scenario of synchronous evolution in the genus.

Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders

Hybridization can leave genealogical signatures in an organism's genome, originating from the parental lineages and persisting over time. This potentially confounds phylogenetic inference methods that aim to represent evolution as a strictly bifurcating tree. We apply a phylotranscriptomic approach to study the evolutionary history of, and test for inter-lineage introgression in the Salamandridae, a Holarctic salamanders group of interest in studies of toxicity and aposematism, courtship behavior, and molecular evolution. Although the relationships between the 21 currently recognized salamandrid genera have been the subject of numerous molecular phylogenetic studies, some branches have remained controversial and sometimes affected by discordances between mitochondrial vs. nuclear trees. To resolve the phylogeny of this family, and understand the source of mito-nuclear discordance, we generated new transcriptomic (RNAseq) data for 20 salamandrids and used these along with published data, including 28 mitochondrial genomes, to obtain a comprehensive nuclear and mitochondrial perspective on salamandrid evolution. Our final phylotranscriptomic data set included 5455 gene alignments for 40 species representing 17 of the 21 salamandrid genera. Using concatenation and species-tree phylogenetic methods, we find (1) Salamandrina sister to the clade of the "True Salamanders" (consisting of Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), (2) Ichthyosaura sister to the Near Eastern genera Neurergus and Ommatotriton, (3) Triturus sister to Lissotriton, and (4) Cynops paraphyletic with respect to Paramesotriton and Pachytriton. Combining introgression tests and phylogenetic networks, we find evidence for introgression among taxa within the clades of "Modern Asian Newts" and "Modern European Newts". However, we could not unambiguously identify the number, position, and direction of introgressive events. Combining evidence from nuclear gene analysis with the observed mito-nuclear phylogenetic discordances, we hypothesize a scenario with hybridization and mitochondrial capture among ancestral lineages of (1) Lissotriton into Ichthyosaura and (2) Triturus into Calotriton, plus introgression of nuclear genes from Triturus into Lissotriton. Furthermore, both mitochondrial capture and nuclear introgression may have occurred among lineages assigned to Cynops. More comprehensive genomic data will, in the future, allow testing this against alternative scenarios involving hybridization with other, extinct lineages of newts.

Cranial shape evolution of extant and fossil crocodile newts and its relation to reproduction and ecology

The diversity of the vertebrate cranial shape of phylogenetically related taxa allows conclusions on ecology and life history. As pleurodeline newts (the genera Echinotriton, Pleurodeles and Tylototriton) have polymorphic reproductive modes, they are highly suitable for following cranial shape evolution in relation to reproduction and environment. We investigated interspecific differences externally and differences in the cranial shape of pleurodeline newts via two‐dimensional geometric morphometrics. Our analyses also included the closely related but extinct genus Chelotriton to better follow the evolutionary history of cranial shape. Pleurodeles was morphologically distinct in relation to other phylogenetically basal salamanders. The subgenera within Tylototriton (Tylototriton and Yaotriton) were well separated in morphospace, whereas Echinotriton resembled the subgenus Yaotriton more than Tylototriton. Oviposition site choice correlated with phylogeny and morphology. Only the mating mode, with a random distribution along the phylogenetic tree, separated crocodile newts into two morphologically distinct groups. Extinct Chelotriton likely represented several species and were morphologically and ecologically more similar to Echinotriton and Yaotriton than to Tylototriton subgenera. Our data also provide the first comprehensive morphological support for the molecular phylogeny of pleurodeline newts.

Characterization of glycoconjugates and sialic acid modification in the olfactory bulb of the Chinese fire-bellied newt (Cynops orientalis)

Diverse glycoconjugates are expressed in the vertebrate olfactory bulb and serve as guidance cues for axons of nasal receptor neurons. Although the involvement of glycoconjugates in the segregation of the olfactory pathway has been suggested, it is poorly understood in salamanders. In this study, lectin histochemistry was used to determine glycoconjugate distribution in the olfactory bulb of the Chinese fire-bellied newt (Cynops orientalis). Succinylated wheat germ agglutinin (sWGA), Ricinus communis agglutinin-I and Lens culinaris agglutinin showed different bindings in the nerve fibre layer or glomerular layer, or both, between the main and accessory olfactory bulbs. We then investigated the lectin-binding pattern after the removal of terminal sialic acids using neuraminidase. Desialylation resulted in a change in the binding reactivities with seven lectins. Wheat germ agglutinin, sWGA, soybean agglutinin (SBA) and peanut agglutinin showed different degrees of binding between the main and accessory olfactory bulbs. In addition, SBA showed a heterogeneous labelling of glomeruli in the rostral region of the main olfactory bulb. Our results suggest that terminal sialic acids mask the heterogeneity of glycoconjugates in the olfactory bulb of C. orientalis.

Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis

We reconstruct the molecular phylogeny of Near Eastern mountain brook newts of the genus Neurergus (family Salamandridae) based on newly determined RADseq data, and compare the outcomes of concatenation-based phylogenetic reconstruction with species-tree inference. Furthermore, we test the current taxonomy of Neurergus (with four species: Neurergus strauchii, N. crocatus, N. kaiseri, and N. derjugini) against coalescent-based species-delimitation approaches of our genome-wide genetic data set. While the position of N. strauchii as sister species to all other Neurergus species was consistent in all of our analyses, the phylogenetic relationships between the three remaining species changed depending on the applied method. The concatenation approach, as well as quartet-based species-tree inference, supported a topology with N. kaiseri as the closest relative to N. derjugini, while full-coalescent species-tree inference approaches supported N. crocatus as sister species of N. derjugini. Investigating the individual signal of gene trees highlighted an extensive variation among gene histories, most likely resulting from incomplete lineage sorting. Coalescent-based species-delimitation models suggest that the current taxonomy might underestimate the species richness within Neurergus and supports seven species. Based on the current sampling, our analysis suggests that N. strauchii, N. derjugini and N. kaiseri might each be subdivided into further species. However, as amphibian species are known to be composed of deep conspecific lineages that do not always warrant species status, these results need to be cautiously interpreted in an integrative taxonomic framework. We hypothesize that the rather shallow divergences detected within N. kaiseri and N. derjugini likely reflect an ongoing speciation process and thus require further investigation. On the contrary, the much deeper genetic divergence found between the two morphologically and geographically differentiated subspecies of N. strauchii leads us to propose that N. s. barani should be considered a distinct species, Neurergus barani Öz, 1994.