A new subfamily of fossorial colubroid snakes from the Western Ghats of peninsular India

Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies

Formalin preservation of museum specimens has long been considered a barrier to molecular research due to extensive crosslinking and chemical modification. However, recent optimisation of hot alkaline lysis and proteinase K digestion DNA extraction methods have enabled a growing number of studies to overcome these challenges and conduct genome-wide re-sequencing and targeted locus-specific sequencing. The newest, and perhaps most unexpected utility of formalin preservation in archival samples is its ability to preserve in situ DNA-protein interactions at a molecular level. Retrieving this signal provides information about the relative compaction or accessibility of the genome to the transcriptional machinery required for gene expression. Thus, exposure to formalin essentially corresponds to taking a snapshot of organism-wide gene expression at the time of death. While DNA methylation and RNA-Seq analyses of dried tissues have provided glimpses into historical gene regulation, these techniques were previously limited to skeletal or desiccated remains, offering only partial insights. By examining fluid-preserved specimens, molecular tools can now be applied to a broader range of tissues, enabling more detailed tissue-specific gene regulation profiling across vertebrates. In this review, we chronicle the historical use of formaldehyde in collections and discuss how targeted chromatin profiling with assays like MNase-seq and FAIRE-seq are surmounting fixation challenges and unlocking invaluable insights into historical genomes and gene expression profiles. The deeper integration of molecular genetics with museum collections bridges the gap between past and present and provides a vital tool that could help us predict and mitigate some of the impacts of future environmental change, novel pathogens, or invasive species.

Description of a New Species of the Pareas hamptoni Complex from Yunnan, China, with Confirmation of P. hamptoni Sensu Stricto in China (Squamata, Pareidae)

We describe a new species of the genus Pareas, based on three specimens collected from Guanyinshan Provincial Nature Reserve in Yuanyang County, Honghe Prefecture, Yunnan Province, China. The new species is distinguished from its congeners by one preocular, one postocular or postocular fused with subocular, loreal not bordering the orbit, one row enlarged vertebral scales, five rows keeled mid-dorsal scales at the middle of the body, 189-192 ventral scales and 72-89 subcaudal scales. The dorsal surfaces of the head and body are yellowish red or yellowish brown, and the belly and ventral surfaces of the head and tail are pinkish yellow or yellow with more or less small black spots. Phylogenetic analyses of mitochondrial DNA recovered the new species being the sister taxon to P. hamptoni sensu stricto. The genetic divergences between the new species and P. hamptoni sensu stricto were 4.2% in the Cyt b sequences and 5.0% in the ND4 sequences. In addition, based on specimens collected from Honghe and Wenshan prefectures, we confirmed that P. hamptoni sensu stricto is distributed in China.

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.

A New Species of Pareas Wagler, 1830 (Squamata, Pareidae) from Northwestern Yunnan, China

A new species of Pareas Wagler, 1830 is described from Dulongjiang Township, Gongshan County, Yunnan Province, China. Phylogenetically, the new species is most closely related to Pareas kaduri Bhosale, Phansalkar, Sawant, Gowande, Patel and Mirza, 2020; however, the genetic divergence (uncorrected p-distance) of the cyt b gene between the new species and P. kaduri reached 9.4%. Morphologically, the new species can be distinguished from P. kaduri by the absence of preoculars, loreal bordering the orbit, the fusion of subocular and postocular, three rows enlarged vertebral scales, five rows keeled mid-dorsal scales at the middle of the body, having more subcaudals, and having a relatively longer tail. In addition, the new species can be distinguished from all other congeners by a combination of morphological characteristics. Our work brings the total number of recognized species of the genus Pareas to 29, of which 23 occur in China.

An expanded description, natural history, and genetic variation of the recently described cobra species Naja fuxi Shi et al., 2022

The morphological variation, extended distribution, and sequence divergence of a recently described of cobra Naja fuxiShi et al., 2022 captured from mountainous areas in Thailand are evaluated by using molecular and morphological analyses. We investigated the genetic variation and affinities of 72 specimens in the genus Naja by using mitochondrial DNA (cytochrome b and control region) and the nuclear DNA gene, C-mos. Morphological examination was conducted for 33 cobra specimens obtained from the northern, western, and north-eastern regions, and data on their natural history were gathered during field surveys. A high degree of genetic differentiation was shown to exist between the cobras collected from lowlands and those from mountainous areas. N. fuxi occurs in uplands bordering Thailand’s Central Basin, whereas the similar looking N. kaouthia Lesson, 1831 is more or less restricted to the lowlands. All phylogenetic and network analyses supported a distinct clade of N. fuxi from north, west, and, north-east regions. In addition, N. fuxi seems to exhibit a split between the north-eastern population and those from the north and west. The range of N. fuxi probably extends far into the mountainous areas of the neighbouring countries Myanmar, Laos, and Vietnam. Morphologically, N. fuxi in Thailand can be distinguished from all other cobra species in the adjacent Oriental Region. The speciation of cobras in Thailand likely reflects key events in the region’s geographical, climate and environmental history.

Maximizing Molecular Data From Low-Quality Fluid-Preserved Specimens in Natural History Collections

Over the past decade, museum genomics studies have focused on obtaining DNA of sufficient quality and quantity for sequencing from fluid-preserved natural history specimens, primarily to be used in systematic studies. While these studies have opened windows to evolutionary and biodiversity knowledge of many species worldwide, published works often focus on the success of these DNA sequencing efforts, which is undoubtedly less common than obtaining minimal or sometimes no DNA or unusable sequence data from specimens in natural history collections. Here, we attempt to obtain and sequence DNA extracts from 115 fresh and 41 degraded samples of homalopsid snakes, as well as from two degraded samples of a poorly known snake, Hydrablabes periops. Hydrablabes has been suggested to belong to at least two different families (Natricidae and Homalopsidae) and with no fresh tissues known to be available, intractable museum specimens currently provide the only opportunity to determine this snake’s taxonomic affinity. Although our aim was to generate a target-capture dataset for these samples, to be included in a broader phylogenetic study, results were less than ideal due to large amounts of missing data, especially using the same downstream methods as with standard, high-quality samples. However, rather than discount results entirely, we used mapping methods with references and pseudoreferences, along with phylogenetic analyses, to maximize any usable molecular data from our sequencing efforts, identify the taxonomic affinity of H. periops, and compare sequencing success between fresh and degraded tissue samples. This resulted in largely complete mitochondrial genomes for five specimens and hundreds to thousands of nuclear loci (ultra-conserved loci, anchored-hybrid enrichment loci, and a variety of loci frequently used in squamate phylogenetic studies) from fluid-preserved snakes, including a specimen of H. periops from the Field Museum of Natural History collection. We combined our H. periops data with previously published genomic and Sanger-sequenced datasets to confirm the familial designation of this taxon, reject previous taxonomic hypotheses, and make biogeographic inferences for Hydrablabes. A second H. periops specimen, despite being seemingly similar for initial raw sequencing results and after being put through the same protocols, resulted in little usable molecular data. We discuss the successes and failures of using different pipelines and methods to maximize the products from these data and provide expectations for others who are looking to use DNA sequencing efforts on specimens that likely have degraded DNA.

Life Science Identifier (Hydrablabes periops)

urn:lsid:zoobank.org:pub:F2AA44 E2-D2EF-4747-972A-652C34C2C09D.

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.

Phylogenetic relationships of xenodermid snakes (Squamata: Serpentes: Xenodermidae), with the description of a new genus

Xenodermidae is a generally poorly known lineage of caenophidian snakes found in South, East and Southeast Asia. We report molecular phylogenetic analyses for a multilocus data set comprising all five currently recognised genera and including new mitochondrial and nuclear gene sequence data for the recently described Stoliczkia vanhnuailianai. Our phylogenetic results provide very strong support for the non-monophyly of Stoliczkia, as presently constituted, with S. borneensis being more closely related to Xenodermus than to the Northeast Indian S. vanhnuailianai. Based on phylogenetic relationships and morphological distinctiveness, we transfer Stoliczkia borneensis to a new monotypic genus endemic to Borneo, Paraxenodermusgen. nov. We also present new morphological data for P. borneensis.

Range extension of the Common Slug Snake Pareas monticola (Cantor, 1839) (Reptilia: Squamata: Pareidae): a new family record for Nepal

In this paper, we present the first evidence of the snake Pareas monticola in Nepal. An individual snake belonging to the species was recorded in eastern Nepal, about 25 km southwest of Darjeeling in India, where the species is known to occur.  

A new species of Xylophis Beddome, 1878 (Serpentes: Pareidae) from the southern Western Ghats of India

We reassess the taxonomy of the Indian endemic snake Xylophis captaini and describe a new species of Xylophis based on a type series of three specimens from the southernmost part of mainland India. Xylophis deepakisp. nov. is most similar phenotypically to X. captaini, with which it was previously confused. The new species differs from X. captaini by having a broader, more regular and ventrally extensive off-white collar, more ventral scales (117–125 versus 102–113), and by lack of flounces on the body and proximal lobes of the hemipenis. Phylogenetic analysis of mitochondrial 16S DNA sequences strongly indicates that the new species is most closely related to X. captaini, differing from it by an uncorrected pairwise genetic distance of 4.2%. A revised key to the species of Xylophis is provided.

A new species of the genus Pareas (Squamata, Pareidae) from Yunnan, China

A new species of Pareas is described from Yunnan Province, China, based on morphological comparisons and molecular data. Genetically, the new species is most closely related to the recently-described Pareasgeminatus, for which we present new topotypic findings. The genetic divergence (uncorrected p-distance) of the cytb gene between the new species and congeners ranged from 6.14% to 24.68%. Morphologically, the new species can be distinguished from P.geminatus and all other congeners. Our work brings the total number of species within the genus Pareas to 22.

A revised taxonomy of Asian snail-eating snakes Pareas (Squamata, Pareidae): evidence from morphological comparison and molecular phylogeny

The Asian snail-eating snakes Pareas is the largest genus of the family Pareidae (formerly Pareatidae), and widely distributed in Southeast Asia. However, potential diversity remains poorly explored due to their highly conserved morphology and incomplete samples. Here, on basis of more extensive sampling, interspecific phylogenetic relationships of the genus Pareas were reconstructed using two mitochondrial fragments (cyt b and ND4) and two nuclear genes (c-mos and Rag1), and multivariate morphometrics conducted for external morphological data. Both Bayesian Inference and Maximum Likelihood analyses consistently showed that the genus Pareas was comprised of two distinct, monophyletic lineages with moderate to low support values. Based on evidences from molecular phylogeny and morphological data, cryptic diversity of this genus was uncovered and two new species were described. In additional, the validity of P.macularius is confirmed.

Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes)

Caenophidian snakes include the file snake genus Acrochordus and advanced colubroidean snakes that radiated mainly during the Neogene. Although caenophidian snakes are a well-supported clade, their inferred affinities, based either on molecular or morphological data, remain poorly known or controversial. Here, we provide an expanded molecular phylogenetic analysis of Caenophidia and use three non-parametric measures of support-Shimodaira-Hasegawa-Like test (SHL), Felsentein (FBP) and transfer (TBE) bootstrap measures-to evaluate the robustness of each clade in the molecular tree. That very different alternative support values are common suggests that results based on only one support value should be viewed with caution. Using a scheme to combine support values, we find 20.9% of the 1265 clades comprising the inferred caenophidian tree are unambiguously supported by both SHL and FBP values, while almost 37% are unsupported or ambiguously supported, revealing the substantial extent of phylogenetic problems within Caenophidia. Combined FBP/TBE support values show similar results, while SHL/TBE result in slightly higher combined values. We consider key morphological attributes of colubroidean cranial, vertebral and hemipenial anatomy and provide additional morphological evidence supporting the clades Colubroides, Colubriformes, and Endoglyptodonta. We review and revise the relevant caenophidian fossil record and provide a time-calibrated tree derived from our molecular data to discuss the main cladogenetic events that resulted in present-day patterns of caenophidian diversification. Our results suggest that all extant families of Colubroidea and Elapoidea composing the present-day endoglyptodont fauna originated rapidly within the early Oligocene-between approximately 33 and 28 Mya-following the major terrestrial faunal turnover known as the "Grande Coupure" and associated with the overall climate shift at the Eocene-Oligocene boundary. Our results further suggest that the caenophidian radiation originated within the Caenozoic, with the divergence between Colubroides and Acrochordidae occurring in the early Eocene, at ~ 56 Mya.