Genomics reveals broad hybridization in deeply divergent Palearctic grass and water snakes (Natrix spp.).

Understanding speciation is one of the cornerstones of biological diversity research. Currently, speciation is often understood as a continuous process of divergence that continues until genetic or other incompatibilities minimize or prevent interbreeding. The Palearctic snake genus Natrix is an ideal group to study speciation, as it comprises taxa representing distinct stages of the speciation process, ranging from widely interbreeding parapatric taxa through parapatric species with very limited gene flow in narrow hybrid zones to widely sympatric species. To understand the evolution of reproductive isolation through time, we have sequenced the genomes of all five species within this genus and two additional subspecies. We used both long-read and short-read methods to sequence and de-novo-assemble two high-quality genomes (Natrix h. helvetica, Natrix n. natrix) to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp, respectively, and used these as references to assemble the remaining short-read-based genomes. Our phylogenomic analyses yielded a well-supported dated phylogeny and evidence for a surprisingly complex history of interspecific gene flow, including between widely sympatric species. Furthermore, evidence for gene flow was also found for currently allopatric species pairs. Genetic exchange among these well-defined, distinct, and several million-year-old reptile species emphasizes that speciation and maintenance of species distinctness can occur despite continued genetic exchange.

The phylogenomic and biogeographic history of the gartersnakes, watersnakes, and allies (Natricidae: Thamnophiini).

North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using âˆ¼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.

Molecular phylogenetics of sub-Saharan African natricine snakes, and the biogeographic origins of the Seychelles endemic Lycognathophis seychellensis.

Phylogenetic relationships of sub-Saharan African natricine snakes are understudied and poorly understood, which in turn has precluded analyses of the historical biogeography of the Seychelles endemic Lycognathophis seychellensis. We inferred the phylogenetic relationships of Seychelles and mainland sub-Saharan natricines by analysing a multilocus DNA sequence dataset for three mitochondrial (mt) and four nuclear (nu) genes. The mainland sub-Saharan natricines and L. seychellensis comprise a well-supported clade. Two maximally supported sets of relationships within this clade are (Limnophis,Natriciteres) and (Afronatrix,(Hydraethiops,Helophis)). The relationships of L. seychellensis with respect to these two lineages are not clearly resolved by analysing concatenated mt and nu data. Analysed separately, nu data best support a sister relationship of L. seychellensis with (Afronatrix,(Hydraethiops,Helophis)) and mt data best support a sister relationship with all mainland sub-Saharan natricines. Methods designed to cope with incomplete lineage sorting strongly favour the former hypothesis. Genetic variation among up to 33 L. seychellensis from five Seychelles islands is low. Fossil calibrated divergence time estimates support an overseas dispersal of the L. seychellensis lineage to the Seychelles from mainland Africa ca. 43-25 million years before present (Ma), rather than this taxon being a Gondwanan relic.

Identity of the holotype and type locality of Rhabdophis leonardi (Wall, 1923) (Colubridae: Natricinae), with notes on the morphology and natural history of the species in southwestern China.

The original description of Natrix leonardi (currently Rhabdophis leonardi) by Frank Wall in 1923, based on a specimen from the "Upper Burma Hills," lacked important morphological details that have complicated the assignment of recently collected material. Furthermore, although the holotype was never lost, its location has been misreported in one important taxonomic reference, leading to further confusion. We report the correct repository of the holotype (Natural History Museum, London), together with its current catalog number. We also describe key features of that specimen that were omitted from the original description, and provide new details on the morphology of the species, including sexual dichromatism unusual for the genus, based upon specimens from southern Sichuan, China. Rhabdophis leonardi is distinguished from its congeners by the following characters: 15 or 17 DSR at midbody and 6 supralabials; distinct annulus around the neck, broad and red in males, and narrow and orange with a black border in females; dorsal ground color light green or olive; some lateral and dorsal scales possessing black edges, the frequency of black edges gradually increasing from anterior to posterior, forming irregular and ill-defined transverse black bands; eye with prominent green iris; black ventral spots with a red edge, most numerous at midbody but extending halfway down the length of the tail. In southwestern China, this species is frequently found at 1730-2230 m elevation. It has been documented to prey upon anuran amphibians, including toads. A recently published phylogenetic analysis showed this species to be deeply nested with the genus Rhabdophis, as a member of the R. nuchalis Group. That analysis also revealed the existence of two closely related but geographically distinct subclades in the molecular analysis, one of which may represent an unnamed taxon.

The Endangered Sardinian Grass Snake: Distribution Update, Bioclimatic Niche Modelling, Dorsal Pattern Characterisation, and Literature Review.

The Sardinian grass snake, Natrix helvetica cetti, is an endangered endemic snake subspecies with a restricted and highly fragmented geographic distribution. Information on its ecology and detailed geographic distribution are scarce and may negatively impact on its conservation status. Therefore, a literature review on its taxonomy, morphology, ecology, and conservation is presented here. Moreover, field records from the authors, citizen science and the existing literature provide an updated geographic distribution highlighting its presence within 13 new and 7 historic 10 × 10 km cells. Bioclimatic niche modelling was then applied to explore patterns of habitat suitability and phenotypic variation within N. h. cetti. The geographic distribution of the species was found to be positively correlated with altitude and precipitation values, whereas temperature showed a negative correlation. Taken together, these outcomes may explain the snake's presence, particularly in eastern Sardinia. In addition, analysis of distribution overlap with the competing viperine snake (N. maura) and the urodeles as possible overlooked trophic resources (Speleomantes spp. and Euproctus platycephalus) showed overlaps of 66% and 79%, respectively. Finally, geographical or bioclimatic correlations did not explain phenotypic variation patterns observed in this highly polymorphic taxon. Perspectives on future research to investigate N. h. cetti's decline and support effective conservation measures are discussed.

A new species of fossorial natricid snakes of the genus Trachischium Günther, 1858 (Serpentes: Natricidae) from the Himalayas of northeastern India.

A new species of natricid snakes, Trachischium apteii sp. nov. is described from the northeastern Indian State of Arunachal Pradesh. The new species differs from its congeners in the following suite of characters: dorsal scales in 15:15:15 rows, SVL 293-299mm, higher ventral count 143-150, very faint dorsal longitudinal lines, absence of yellow patch on the neck and the belly being pale yellow. Preliminary discussion on the phylogenetic position of the members of the genus Trachischium is presented. This discovery of a new snake species advocates the need for dedicated surveys to document biodiversity across Arunachal Pradesh and the neighbouring States of northeastern India.

Morphological and molecular review of Jacob's Mountain Stream Keelback Opisthotropis jacobi Angel Bourret, 1933 (Squamata: Natricidae) with description of a sibling species from northern Vietnam.

New morphological data including hemipenis morphology is provided for Opisthotropis jacobi, a poorly known Mountain Stream Keelback from Vietnam and China, based on three newly collected individuals from Sa Pa (Lao Cai Province) and Tam Dao (Vinh Phuc Province) in northern Vietnam. In addition, morphological data from Vietnam is summarized based on the original description (Angel Bourret 1933), on the overview book by Bourret (1936) and on a number of smaller, little-known contributions by the latter author along with re-examination of specimens deposited in the herpetological collection of the Muséum national d'Histoire naturelle, Paris. We also sequenced a fragment of the mitochondrial cytochrome b from the newly collected specimens of the Jacob's Mountain Stream Keelback and performed molecular analyses of new and existing data of the genus. A recently discovered Opisthotropis population from Tay Yen Tu Nature Reserve in Bac Giang Province, northern Vietnam, which at the first glance resembled O. jacobi morphologically, is shown to diverge both genetically and morphologically from the existing species and is herein described as a new species. Opisthotropis voquyi sp. nov. is characterized by the combination of the following characters: internasal not in contact with loreal; one preocular; usually two postoculars; one anterior temporal; one posterior temporal; 7 or 8, rarely 9 supralabials; 25 maxillary teeth; subcaudals 74-86; 15 dorsal scale rows at neck, at midbody and before vent; body scales smooth or only with few faint keels; and dorsal scales being greyish, greyish-brown or brown in preservative, posteriorly more or less edged with pale greyish-brown. Phylogenetically, the new species is supported as a sister taxon to O. jacobi, but the two taxa are approximately 10% divergent based on cytochrome b data.