A large-scale systematic framework of Chinese snakes based on a unified multilocus marker system

First report of albinism for Achalinussheni (Serpentes, Xenodermidae), with extended diagnosis of the species

Albinism is an uncommon phenomenon and inherited condition in animals characterized by a partial or complete lack of melanin. The family Xenodermidae Gray, 1849, is a group of caenophidian snakes widely distributed in South, East, and Southeast Asia, including five recognized genera and 36 species. However, there are currently no reports of albinism in any species in Xenodermidae. Achalinussheni Ma, Xu, Qi, Wang, Tang, Huang & Jiang, 2023 was first described based on five male specimens from Loudi City and Nanyue District, Hunan Province, China. At the time, there were no descriptions on female individuals. In this study, we report in detail a collected albinistic specimen of A.sheni, which is the first discovery of wild albinism in the family Xenodermidae. We also provide photographs and descriptions of the first three female specimens of A.sheni and extend the diagnosis of this species.

Comparative genomics sheds new light on the convergent evolution of infrared vision in snakes

Infrared vision is a highly specialized sensory system that evolved independently in three clades of snakes. Apparently, convergent evolution occurred in the transient receptor potential ankyrin 1 (TRPA1) proteins of infrared-sensing snakes. However, this gene can only explain how infrared signals are received, and not the transduction and processing of those signals. We sequenced the genome of Xenopeltis unicolor, a key outgroup species of pythons, and performed a genome-wide analysis of convergence between two clades of infrared-sensing snakes. Our results revealed pervasive molecular adaptation in pathways associated with neural development and other functions, with parallel selection on loci associated with trigeminal nerve structural organization. In addition, we found evidence of convergent amino acid substitutions in a set of genes, including TRPA1 and TRPM2. The analysis also identified convergent accelerated evolution in non-coding elements near 12 genes involved in facial nerve structural organization and optic nerve development. Thus, convergent evolution occurred across multiple dimensions of infrared vision in vipers and pythons, as well as amino acid substitutions, non-coding elements, genes and functions. These changes enabled independent groups of snakes to develop and use infrared vision.

Integrative methods reveal multiple drivers of diversification in rice paddy snakes

Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.

Molecular phylogeny reveals cryptic diversity in Sibynophis from China (Serpentes: Sibynophiidae)

The elucidation of species diversity and distribution is critical within the fields of evolution, genetics, and conservation. The genus Sibynophis contains rare snakes that have historically received little attention. In this study, we conducted comprehensive sampling and use both mitochondrial and nuclear genetic markers to explore Sibynophis species diversity within China. Our findings revealed that S. c. miyiensis should be considered synonymous with S. c. grahami, and S. c. grahami should be gave a specific rank as S. grahami. In addition, we discovered S. triangularis was new to China and Myanmar. Based on the specimens and molecular phylogeny results, we redefined the species distribution boundaries of each Chinese species.

A New Species of Pareas (Squamata, Pareidae) from Guangxi Province, China

We described a new species of genus Pareas from Baise City, Guangxi Zhuang Autonomous Region, China, based on morphological and molecular evidence. Pareas baiseensis sp. nov. is distinguished from its congeners by the combination of (1) Yellowish-brown body colouration; (2) Frontal subhexagonal to diamond-shaped with its lateral sides converging posteriorly; (3) The anterior pair of chin shields is longer than it is broad; (4) Loreal not in contact with the eye, prefrontal in contact with the eye, two or three suboculars; (5) Rows of 15-15-15 dorsal scales, five rows of mid-dorsal scales keeled at the middle of the body, one vertebral scale row enlarged; (6) 187-191 ventrals, 89-97 subcaudals, all divided, cloacal plate single; (7) Two postocular stripes, the nuchal area forming a dark black four-pointed fork collar with the middle tines shorter than the outside tines. The genetic divergence (uncorrected p-distance) between the new species and other representatives of Pareas ranged from 13.9% to 24.4% for Cytochrome b (Cyt b) and 12.1% to 25.5% for NADH dehydrogenase subunit 4 (ND4). Phylogenetic analyses of mitochondrial DNA gene data recovered the new species from being the sister taxon to (P. boulengeri + P. chinensis) from China.

Phylogeny-Related Variations in Venomics: A Test in a Subset of Habu Snakes (Protobothrops)

We conducted a comparative analysis to unveil the divergence among venoms from a subset of Old World habu snakes (Protobothrops) in terms of venomic profiles and toxicological and enzymatic activities. A total of 14 protein families were identified in the venoms from these habu snakes, and 11 of them were shared among these venoms. The venoms of five adult habu snakes were overwhelmingly dominated by SVMP (32.56 ± 13.94%), PLA₂ (22.93 ± 9.26%), and SVSP (16.27 ± 4.79%), with a total abundance of over 65%, while the subadult P. mangshanensis had an extremely low abundance of PLA₂ (1.23%) but a high abundance of CTL (51.47%), followed by SVMP (22.06%) and SVSP (10.90%). Apparent interspecific variations in lethality and enzymatic activities were also explored in habu snake venoms, but no variations in myotoxicity were found. Except for SVSP, the resemblance of the relatives within Protobothrops in other venom traits was estimated to deviate from Brownian motion evolution based on phylogenetic signals. A comparative analysis further validated that the degree of covariation between phylogeny and venom variation is evolutionarily labile and varies among clades of closely related snakes. Our findings indicate a high level of interspecific variation in the venom proteomes of habu snakes, both in the presence or absence and the relative abundance of venom protein families, and that these venoms might have evolved under a combination of adaptive and neutral mechanisms.

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.

T. Lalremsanga EO, Bhosale H, Gowande G, Patel H, Idiatullina SS, Poyarkov NA. Systematics of Trimeresurus popeiorum Smith, 1937 with a revised molecular phylogeny of Asian pitvipers of the genus Trimeresurus Lacépède, 1804 sensu lato

The pit viper snake genus Trimeresurus Lacépède, 1804 sensu lato, is a diverse group of nocturnal serpents comprising over 61 species. The genus is morphologically heterogeneous and has been divided into several subgenera. We present an updated phylogeny of Asian pitvipers and propose a revised classification. Additionally, we revise the taxonomy of T. popeiorum Smith, 1937 and propose taxonomic changes with support from molecular and morphological data. We restrict T. popeiorumsensu stricto to northeastern India, Bangladesh, southern China, and northern Myanmar; populations beyond these areas require further assessment. We also synonymize T. yingjiangensisChen et al., 2019 with T. popeiorum based on overlapping morphological characters, molecular data, and distribution. The findings shed new light on the taxonomy of T. popeiorum, warranting the need for assessing the population of T. popeiorum from southeast Asia.

A New Species of the Genus Achalinus (Squamata: Xenodermidae) from the Dabie Mountains, Anhui, China

A new species of Xenodermid snake, Achalinus dabieshanensissp. nov., was described based on three specimens (two female and one male) collected from the Dabie Mountains of western Anhui Province. It can be distinguished from known congeners by a significant genetic divergence in the mitochondrial gene fragment COI (p-distance ≥ 9.4%) and the following combination of characteristics: (1) length of the suture between the internasals being distinctly shorter than between the prefrontals; (2) a single loreal; (3) dorsal scales strongly keeled, in 23 rows throughout the body; (4) two pairs of prefrontals; (5) six supralabials; (6) five infralabials; (7) temporals 2 + 2 + 3 (or 2 + 2 + 4); (8) 141-155 ventrals; (9) 45-55 subcaudals, unpaired; (10) anal entire; (11) weakly iridescent tinged, uniform, brown to black dorsum with vertebral scales and about three adjacent dorsal scales dark brown forming a longitudinal vertebral line from posterior margin of parietals to tail tip; (12) light brown venter, ventral shields wide, visible on both sides, light brown flanks, giving the appearance of a black subcaudal streak. The recognition of the new species increases the number of described Achalinus species to 22.

NA. The taxonomic status of the kukri snake Oligodon arenarius Vassilieva, 2015 with a redescription of Oligodon macrurus (Angel, 1927) (Squamata, Serpentes, Colubridae)

We investigated the taxonomic status of the recently described kukri snake Oligodon arenarius Vassilieva, 2015 and the morphologically similar Oligodon macrurus (Angel, 1927), two species endemic to the southern coast of Vietnam. Based on phylogenetic analyses using three mitochondrial genes (12S–16S rRNA, cytochrome b), we recovered O. arenarius and O. macrurus in a clade within the O. cyclurus-taeniatus species group, agreeing with previous intrageneric classifications. Genetic distances between O. arenarius and O. macrurus are extremely low (less than 0.5% based on 12S–16S) and render O. arenarius paraphyletic. All preserved specimens of O. arenarius and O. macrurus convey little to no differences in color pattern, hemipenial morphology and osteological features; the latter of which is based on three dimensional micro computer tomography (µCT) scans of one specimen per species. Contrasting these results, univariate and multivariate analyses revealed significant differences in relative tail length, and the number of ventral and subcaudal scales between both species. Although the molecular and morphological datasets present conflicting results, integrating the evidence leads us to synonymize O. arenarius with O. macrurus. We provide a formal redescription of O. macrurus, designate a neotype specimen to avoid future taxonomic confusion, and provide the first detailed osteological description of this species. Oligodon macrurus sensu stricto is endemic to coastal dunefields and adjacent forest habitats in southern Vietnam, where ongoing human development, tourism and road mortality pose significant threats to its conservation. Consequently, we suggest that O. macrurus should be listed as “Vulnerable” based on the assessment criteria of the International Union for Conservation of Nature (IUCN).

A taxonomic re-assessment of Oligodon cinereus (Günther, 1864) (Squamata, Serpentes, Colubridae) populations from southern Indochina

The ashy kukri snake Oligodon cinereus (Günther, 1864) is a widely distributed and morphologically variable species found throughout mainland Southeast Asia. In this paper, we re-assessed the taxonomic status of O. cinereus populations found in southern Indochina (southern Vietnam, Cambodia, and southern Laos), including the recently described Cat Tien kukri snake Oligodon cattienensisVassilieva et al., 2013, which was previously confused with this species. Phylogenetic analyses using mitochondrial DNA from the 12S–16S ribosomal subunit and cytochrome b gene revealed that O. cattienensis is embedded in a mixed clade containing samples of the subspecies O. cinereus pallidocinctus, which bears a dorsal color pattern with white crossbars and black edges. This clade forms a strongly supported sister group with a topotypic sample of O. cinereus cinereus, representing populations bearing a uniform dorsal color pattern and slight reticulate markings, however the genetic divergence between the two clades is very low. The morphological characters used to distinguish O. cattienensis from O. cinereus sensu lato broadly overlap and supposed differences in hemipenial morphology between the two taxa are due to outdated terminologies used to describe the organ. We relegate both O. cattienensis and O. cinereus pallidocinctus to the junior synonymy of O. cinereus and consider all color patterns of this species found near the type locality in Cambodia, southern Laos, and southern Vietnam to represent O. cinereus sensu stricto. Future integrative investigations across the range of O. cinereus sensu lato are needed to resolve the status of the remaining subspecies and synonyms associated with this taxon. Problems associated with hemipenial morphology and Oligodon systematics are also discussed.

On the validity of Hebius sauteri maximus (Malnate, 1962) (Squamata, Natricidae), with the redescription of H. maximus comb. nov. and H. sauteri (Boulenger, 1909)

Hebius sauteri (Boulenger, 1909) has been long recognized as a widely distributed species with three subspecies, namely Hebius sauteri sauteri from Taiwan Island and southeastern China, Hebius sauteri bourreti (Malnate, 1962) from northern Vietnam, and Hebius sauteri maximus (Malnate, 1962) from Sichuan, southwestern China. However, the validity of these subspecies of the H. sauteri complex has not been evaluated. In the current study, we re-evaluate the taxonomic status of H. s. maximus based on morphological and molecular evidence. Molecular phylogenetic results indicate that H. s. maximus is a distantly diverged clade with respect to H. s. sauteri, and that H. s. maximus is morphologically distinguishable from the nominative subspecies. Therefore, our results support the validity of H. s. maximus and we elevate it to full species status, namely Hebius maximuscomb. nov. The distribution range of H. sauteri is revised according to our proposed taxonomic change. Furthermore, detailed redescription, natural history, and coloration of both H. sauteri and H. maximus and comments on the validity of H. s. bourreti are also provided.

Description of a New Cobra (Naja Laurenti, 1768; Squamata, Elapidae) from China with Designation of a Neotype for Naja atra

Taxonomic frameworks for medically important species such as cobras (genus Naja Laurenti, 1768; Squamata, Elapidae) are essential for the medical treatment of snake bites and accurate antivenin development. In this paper, we described the former N. kaouthia populations recorded from China as a new species and designated a neotype for N. atra-based morphological and mitochondrial phylogenetic analysis. The new species N. fuxisp. nov. was morphologically diagnosed from N. kaouthia by (1) regular single narrow crossband present on the middle and posterior parts of the dorsum (3-15, 7.9 ± 2.7, n = 32) and the dorsal surface of the tail (1-6, 4.2 ± 1.1, n = 32) of both adults and juveniles, buff-colored with dark fringes on both edges, vs. South Asian populations (n = 39) and Southeast Asian populations (n = 35) without cross bands, with irregular cross bands or multiple light-colored crossbands pairs, or densely woven lines; (2) small scales between the posterior chin shields, usually three (40%) or two (37%), rarely four (13%), or one (10%) (n = 30) vs. mostly one (81%) and rarely two (19%) (n = 28); (3) ventrals 179-205 (195.4 ± 6.7, n = 33) vs. South Asian populations 179-199 (188.7 ± 5.9, n = 12); Southeast Asian populations 168-186 (177.8 ± 4.9, n = 18). Phylogenetically, the new species forms an independent sister clade to the clade including N. atra, N. kaouthia, N. oxiana and N. sagittifera. Furthermore, the subspecies N. naja polyocellata should be resurrected and recognized as a full species, N. polyocellatacomb. nov., and the subspecies N. sumatrana miolepis should be resurrected.

Complete mitochondrial genomes of Boigakraepelini and Hebiuscraspedogaster (Reptilia, Squamata, Colubridae) and their phylogenetic implications

The complete sequence of the mitochondrial genome is a powerful tool for studying phylogenetic relationships and molecular evolution in various species. In this work, the mitogenomes of Boigakraepelini and Hebiuscraspedogaster were sequenced and characterized for the first time. The lengths of the B.kraepelini and H.craspedogaster mitogenomes were 17,124 bp and 17,120 bp, respectively, and both included 13 protein-coding genes, 22 tRNAs, two rRNAs and two control regions. The arrangements of these mitochondrial genes were the same in B.kraepelini and H.craspedogaster. In addition, both genome compositions showed A+T bias (59.03%, 60.93%) and had positive AT skews (0.179, 0.117) and negative GC skews (-0.397, -0.348). The phylogenetic results illustrated a close relationship between B.kraepelini and the genus Lycodon. Moreover, H.craspedogaster was clustered with other Hebius snakes and closely related to other Natricinae species. These results will provide references for further research on the phylogeny of Colubridae.

A new species of the genus Achalinus (Squamata: Xenodermidae) from Ningshan County, Shaanxi Province, China

A new species of odd-scaled snake in the genus Achalinus is described from Ningshan County, Shaanxi Province, China, based on seven female specimens. Morphologically, the new species can be distinguished from its congeners by the following combination of characters: (1) dorsum iridescent and uniformly dark brown in preservative, longitudinal vertebral line absent; (2) light brown beneath; (3) dotted black streak in the middle of the subcaudals absent; (4) tail length relatively short, TaL/ToL 12–16%, in females; (5) fewer subcaudals, 41–46 in females; (6) dorsal scales 23 rows throughout, strongly keeled; the outer-most rows on both sides are also keeled and slightly enlarged; (7) one loreal; (8) internasal not fused to prefrontal; (9) suture between internasals is similar in size when compared to the suture between prefrontals; (10) preocular and postocular absent; (11) 6 supralabials; (12) 5 infralabials, the first 3 (rarely 2) touching the first pair of chin shields; (13) 3 pairs of chin shields. A phylogenetic analysis using mitochondrial gene, cytochrome c oxidase subunit 1 (CO1), showed that this new species forms a monophyletic group with strong support. In addition, the uncorrected p-distances between the new species and other known congeners ranged from 3.4% to 13.0%. The recognition of the new species increases the number of described Achalinus species to 21.  

Complete Mitogenomes of Polypedates Tree Frogs Unveil Gene Rearrangement and Concerted Evolution within Rhacophoridae

New developments in sequencing technology and nucleotide analysis have allowed us to make great advances in reconstructing anuran phylogeny. As a clade of representative amphibians that have radiated from aquatic to arboreal habitats, our understanding of the systematic status and molecular biology of rhacophorid tree frogs is still limited. We determined two new mitogenomes for the genus Polypedates (Rhacophoridae): P. impresus and P. mutus. We conducted comparative and phylogenetic analyses using our data and seven other rhacophorid mitogenomes. The mitogenomes of the genera Polypedates, Buergeria, and Zhangixalus were almost identical, except that the ATP8 gene in Polypedates had become a non-coding region; Buergeria maintained the legacy "LTPF" tRNA gene cluster compared to the novel "TLPF" order in the other two genera; and B. buergeri and Z. dennysi had no control region (CR) duplication. The resulting phylogenetic relationship supporting the above gene rearrangement pathway suggested parallel evolution of ATP8 gene loss of function (LoF) in Polypedates and CR duplication with concerted evolution of paralogous CRs in rhacophorids. Finally, conflicting topologies in the phylograms of 185 species reflected the advantages of phylogenetic analyses using multiple loci.

Simultaneously collecting coding and non-coding phylogenomic data using homemade full-length cDNA probes, tested by resolving the high-level relationships of Colubridae

Resolving intractable phylogenetic relationships often requires simultaneously analyzing a large number of coding and non-coding orthologous loci. To gather both coding and non-coding data, traditional sequence capture methods require custom-designed commercial probes. Here, we present a cost-effective sequence capture method based on homemade probes, to capture thousands of coding and non-coding orthologous loci simultaneously, suitable for all organisms. This approach, called “FLc-Capture,” synthesizes biotinylated full-length cDNAs from mRNA as capture probes, eliminates the need for costly commercial probe design and synthesis. To demonstrate the utility of FLc-Capture, we prepared full-length cDNA probes from mRNA extracted from a common colubrid snake. We performed capture experiments with these homemade cDNA probes and successfully obtained thousands of coding and non-coding genomic loci from 24 Colubridae species and 12 distantly related snake species of other families. The average capture specificity of FLc-Capture across all tested snake species is 35%, similar to the previously published EecSeq method. We constructed two phylogenomic data sets, one including 1,075 coding loci (∼817,000 bp) and the other including 1,948 non-coding loci (∼1,114,000 bp), to study the phylogeny of Colubridae. Both data sets yielded highly similar and well-resolved trees, with 85% of nodes having >95% bootstrap support. Our experimental tests show that FLc-Capture is a flexible, fast, and cost-effective sequence capture approach for simultaneously gathering coding and non-coding phylogenomic data sets to study intractable phylogenetic questions. We hope that this method will serve as a new data collection tool for evolutionary biologists working in the era of phylogenomics.

Differences between Two Groups of Burmese Vipers (Viperidae: Azemiops) in the Proteomic Profiles, Immunoreactivity and Biochemical Functions of Their Venoms

Two recently revised Azemiops snakes with apparent differences in their external appearances and skeletal morphologies but unclear genetic boundaries have been proposed. Some researchers have refrained from using the newly proposed taxonomy because these two “species” might be two clades corresponding to different geographical populations of Azemiops feae. To improve the understanding of the kinship of these two Burmese viper groups, more of their characteristics should be explored in depth. We performed a comparative analysis of the proteomic profiles and biochemical activities of snake venoms from these two groups (Sichuan A. feae and Zhejiang A. feae) and evaluated the immunorecognition capacity of commercial antivenoms toward them. Eight protein families were identified in venoms from these two groups, while phospholipase B was only detected in venom from Sichuan A. feae. These protein families displayed varying degrees of differences in relative abundance between venoms, and phospholipase A₂ (Sichuan A. feae: 57.15%; Zhejiang A. feae: 65.94%) was the predominated component. Gloydius brevicaudus antivenom exhibited the strongest capacity to immunologically recognize these two venoms, but this was mainly limited to components with high molecular masses, some of which differed between venoms. Additionally, Zhejiang A. feae venom was more toxic than Sichuan A. feae venom, and the venoms expressed remarkable differences in enzymatic activities, probably resulting from the variation in the relative abundance of specific protein families. Our findings unveil differences between the two Burmese viper groups in terms of proteomic profiles, immunoreactivity, and the biochemical functions of their venoms. This information will facilitate the management of snakebites caused by these snakes.

De Novo Genome Assembly Highlights the Role of Lineage-Specific Duplications in the Evolution of Venom in Fea’s Viper

Despite the medical significance to humans and important ecological roles filled by vipers, few high-quality genomic resources exist for these snakes outside of a few genera of pitvipers. Here we sequence, assemble, and annotate the genome of Fea’s Viper (Azemiops feae). This taxon is distributed in East Asia and belongs to a monotypic subfamily, sister to the pitvipers. The newly sequenced genome resulted in a 1.56 Gb assembly, a contig N50 of 1.59 Mb, with 97.6% of the genome assembly in contigs >50 Kb, and a BUSCO completeness of 92.4%. We found that A. feae venom is primarily composed of phospholipase A₂ (PLA₂) proteins expressed by genes that likely arose from lineage-specific PLA₂ gene duplications. Additionally, we show that renin, an enzyme associated with blood pressure regulation in mammals and known from the venoms of two viper species including A. feae, is expressed in the venom gland at comparative levels to known toxins and is present in the venom proteome. The cooption of this gene as a toxin may be more widespread in viperids than currently known. To investigate the historical population demographics of A. feae, we performed coalescent-based analyses and determined that the effective population size has remained stable over the last 100 kyr. This suggests Quaternary glacial cycles likely had minimal influence on the demographic history of A. feae. This newly assembled genome will be an important resource for studying the genomic basis of phenotypic evolution and understanding the diversification of venom toxin gene families.

An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina

Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the "upstream" colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.

Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China

Modern accumulations of genetic data offer unprecedented opportunities for understanding the systematic classification and origins of specific groups of organisms. The genus Sinocyclocheilus is among the most cave abundant genera in Cyprinidae, with 76 recognized species, belonging to four species groups. Recent phylogenetic studies have shown that the classification of species groups within the genus Sinocyclocheilus remains controversial. In this study, we constructed a sequence supermatrix of 26 species from four species groups of the genus Sinocyclocheilus using the mitochondrial genome to reveal phylogenetic relationships, historical biogeography and patterns of species diversification in the genus Sinocyclocheilus. Phylogenetic analysis strongly supports the monophyletic groups of the three species groups (S. jii, S. cyphotergous, and S. tingi groups) except the S. angularis group. Phylogenetic analysis showed that S. anshuiensis and S. microphthalmus, which were recognized as numbers of S. angularis group, formed a strongly supported independent clade. Therefore, we propose a new species group, the S. microphthalmus group, which contains S. anshuiensis and S. microphthalmus. Biogeographic reconstruction suggests that the living Sinocyclocheilus may have originated in north-central Guangxi at the late Eocene and dispersed outward after a vicariance at 32.31 Million years ago (Ma). Early diversification is focused on the late Oligocene (ca. 25 Ma), which is related to the second uplift of the Qinghai-Tibetan Plateau and the lateral extrusion of the Indochina at the Oligocene/Miocene boundary. Our results suggest that two uplifts of the Qinghai-Tibetan Plateau and climate change in the Miocene may have influenced the diversification of the Sinocyclocheilus lineage. This article is protected by copyright. All rights reserved.

A new species of the Achalinus rufescens complex (Xenodermidae: Achalinus) from Fujian Province, China

A new species of the xenodermid snake genus Achalinus Peters, 1869 is described from Fujian Province, China, based on six specimens. Bayesian inference and maximum likelihood analyses based on a mitochondrial DNA fragment (CO1) indicated the new taxon is different from its congeners (pdistance ≥ 18.5%). Morphologically, the new species can be diagnosed from the other species by a combination of following characters: (1) dorsal scales 23 rows throughout, strongly keeled, the most outer rows on both sides also keeled and slightly enlarged; (2) tail relatively longer, TaL/TL ratio 0.260.29 in males, 0.210.22 in females; (3) maxillary teeth 3033; (4) length of suture between internasals significantly longer than that between prefrontals; (5) nasal divided into two sections by nasal cleft; (6) a single loreal; (7) SPO 1, seldom 2; (8) SPL 6, the fourth and fifth contacting eye; (9) IFL5, rarely 6, the first three touching the first pair of chin shields; (10) TMP 79, arranged in three rows; (11) VS 142149 in males, VS 152154 in females; (12) SC 7481 in males, SC 6365 in females, arranged in a single row; (13) cloacal entire; (14) greyish brown above, pale yellow beneath; (15) dorsum with an indistinct longitudinal vertebral stripe. The description of the new species brings the total species of Achalinus to 19.

A new snake species of the genus Gonyosoma Wagler, 1828 (Serpentes: Colubridae) from Hainan Island, China

A new species of the genus Gonyosoma Wagler, 1828 is described herein based on six specimens from the Diaoluoshan Mountains, Hainan Island, Hainan Province, China. The new species, Gonyosoma hainanensesp. nov., is most similar to its continental sister species, Gonyosoma boulengeri (Mocquard, 1897). Both taxa have a scaled protrusion on the anterior portion of the rostrum, distinct from other congeners. However, Gonyosoma hainanensesp. nov. can be distinguished from G. boulengeri by two significant morphological characters: (1) black orbital stripe absent in adults (vs. present in G. boulengeri); and (2) two loreals (vs. one loreal in G. boulengeri). The new species is also genetically divergent and forms a unique clade from its sister species and all other congeners based on sequences of the mitochondrial gene cytochrome b (cyt b).

A new record of odd-scaled snake (Serpentes, Xenodermidae) from Vietnam: expanded description of Parafimbrios vietnamensis based on integrative taxonomy

Based on the combination of molecular and morphological data, we herein report the second known finding of the xenodermid snake species Parafimbriosvietnamensis Ziegler, Ngo, Pham, Nguyen, Le & Nguyen, 2018. The male individual was found in the Yen Bai Province of northwestern Vietnam, more than 200 km from the type locality in Lai Chau Province. Genetic divergence between the newly-collected male and the holotype was low (1.7%), and is in agreement with morphological data that supports that they are conspecific. We give a detailed description of the morphological characters and coloration of the new record and provide an expanded diagnosis of P.vietnamensis. Parafimbrios is a poorly-understood genus, and our recent discovery brings the total number of known specimens of the genus to nine, 1/3 of them having been found in Vietnam (one specimen of P.lao and now two specimens of P.vietnamensis).

A sheep in wolf's clothing: Elaphe xiphodonta sp. nov. (Squamata, Colubridae) and its possible mimicry to Protobothrops jerdonii

Based on combined morphological and osteological characters and molecular phylogenetics, we describe a new species of the genus Elaphe that was discovered from the south slope of the Qinling Mountains, Shaanxi, China, namely Elaphe xiphodonta sp. nov. It is distinguished from the other congeners by a combination of the following characters: dorsal scales in 21-21-17 rows, the medial 11 rows keeled; 202-204 ventral scales, 67-68 subcaudals; two preoculars (including one subpreocular); two postoculars; two anterior temporals, three posterior temporals; reduced numbers of maxillary teeth (9+2) and dentary teeth (12); sharp cutting edges on the posterior or posterolateral surface of the rear maxillary teeth and dentary teeth; dorsal head yellow, three distinct markings on the head and neck; a distinct black labial spot present in supralabials; dorsum yellow, 46-49 complete (or incomplete) large black-edged reddish brown blotches on the body and 12-19 on the tail, two rows of smaller blotches on each ventrolateral side; ventral scales yellow with mottled irregular black blotches, a few irregular small red spots dispersed on the middle of the ventral. Based on molecular phylogenetic analyses, the new species forms the sister taxon to E. zoigeensis. The discovery of this new species increases the number of the recognized species in the genus Elaphe to 17.

Structural and bioinformatic analyses of Azemiops venom serine proteases reveal close phylogeographic relationships to pitvipers from eastern China and the New World

The semi-fossil and pit-less Azemiops feae is possibly the most primitive crotalid species. Here, we have cloned and sequenced cDNAs encoding four serine proteases (vSPs) from the venom glands of Chinese A. feae. Full amino-acid sequences of the major vSP (designated as AzKNa) and three minor vSPs (designated as AzKNb, AzKNc and Az-PA) were deduced. Using Protein-BLAST search, the ten most-similar vSPs for each Azemiops vSP have been selected for multiple sequence alignment, and all the homologs are crotalid vSPs. The results suggest that the A. feae vSPs are structurally most like those of eastern-Chinese Gloydius, Viridovipera, Protobothrops and North American pitvipers, and quite different from more-specialized vSPs such as Agkistrodon venom Protein-C activators. The vSPs from Chinese A. feae and those from Vietnamese A. feae show significant sequence variations. AzKNa is acidic and contains six potential N-glycosylation sites and its surface-charge distribution differs greatly from that of AzKNb, as revealed by 3D-modeling. AzKNb and AzKNc do not contain N-glycosylation sites although most of their close homologs contain one or two. Az-PA belongs to the plasminogen-activator subtype with a conserved N²⁰-glycosylation site. The evolution of this subtype of vSPs in Azemiops and related pitvipers has been traced by phylogenetic analysis.

Contribution to the taxonomy of the genus Lycodon H. Boie in Fitzinger, 1827 (Reptilia: Squamata: Colubridae) in China, with description of two new species and resurrection and elevation of Dinodon septentrionale chapaense Angel, Bourret, 1933

While considerable progress has been made in the taxonomic studies of the genus Lycodon in Asia, questions remain to be clarified regarding the taxonomy of certain groups, particularly those containing species in China. Not only do many regions in China remain overlooked by herpetologists, resulting in the possibility of undiscovered new species, but the surveyed areas also have suspicious records of recognized congeners that require taxonomic confirmations. Combining both morphological and genetic data, we tackle these outstanding issues in the taxonomy of Lycodon in China. In particular, we discover two new species of Lycodon: one from the previously neglected hot-dry valley in the northern Hengduan Mountain Region close to Tibet, and another recluse and cryptic species from the L. fasciatus complex in the downtown park of a major city in southern Sichuan Province. Additionally, we clarify the distribution of L. septentrionalis in China and resurrect and elevate its junior synonym subspecies, Dinodon septentrionale chapaense, as a full, valid species, and we synonymize the recently described L. namdongensis to the resurrected L. chapaensiscomb. nov.. Lycodon chapaensiscomb. nov. thus represents a new national record of reptilian fauna of China. Lastly, based on literature review, we also correct some of the erroneous records of L. fasciatus and L. ruhstrati in China, point out remaining taxonomic issues of the genus for future research, and update the dichotomous key and distribution of the 20 species of Lycodon currently recorded from China.

Out of the Hengduan Mountains: Molecular phylogeny and historical biogeography of the Asian water snake genus Trimerodytes (Squamata: Colubridae)

The Asian water snake genus Trimerodytes (formerly Sinonatrix) is endemic to East and Southeast Asia. Although several species have been included in various phylogenetic studies previously, the evolution and relationships among members of this genus as a whole remain unexplored. In this study, we report the sequencing two protein-coding mitochondrial gene fragments (MTCYB and ND2) and three nuclear genes (c-mos, NT3, and Rag1), reconstruct interspecific phylogeny, and explore biogeography for the genus Trimerodytes. Both Bayesian inference and maximum likelihood analyses consistently recover the monophyly of Trimerodytes with strong support, with T. yapingi the sister-group to the remaining species. The divergence date and ancestral area estimation suggest that Trimerodytes likely originated in Hengduan Mountains (eastern Tibetan Plateau) in western China at 23.93 Ma (95% HPD: 17.09-31.30), and intraspecific divergence began at about 4.23 Ma (95% HPD: 2.74-6.10). Analyses support the validity of T. yunnanensis.

Novel Bradykinin-Potentiating Peptides and Three-Finger Toxins from Viper Venom: Combined NGS Venom Gland Transcriptomics and Quantitative Venom Proteomics of the Azemiops feae Viper

Feae's viper Azemipos feae belongs to the Azemiopinae subfamily of the Viperidae family. The effects of Viperidae venoms are mostly coagulopathic with limited neurotoxicity manifested by phospholipases A2. From A. feae venom, we have earlier isolated azemiopsin, a novel neurotoxin inhibiting the nicotinic acetylcholine receptor. To characterize other A. feae toxins, we applied label-free quantitative proteomics, which revealed 120 unique proteins, the most abundant being serine proteinases and phospholipases A2. In total, toxins representing 14 families were identified, among which bradykinin-potentiating peptides with unique amino acid sequences possessed biological activity in vivo. The proteomic analysis revealed also basal (commonly known as non-conventional) three-finger toxins belonging to the group of those possessing neurotoxic activity. This is the first indication of the presence of three-finger neurotoxins in viper venom. In parallel, the transcriptomic analysis of venom gland performed by Illumina next-generation sequencing further revealed 206 putative venom transcripts. Together, the study unveiled the venom proteome and venom gland transciptome of A. feae, which in general resemble those of other snakes from the Viperidae family. However, new toxins not found earlier in viper venom and including three-finger toxins and unusual bradykinin-potentiating peptides were discovered.