Comparative morphology of oral glands in snakes of the family Homalopsidae reveals substantial variation and additional independent origins of salt glands within Serpentes

Using diffusible iodine-based contrast-enhanced computed tomography (diceCT), we examined the morphology of the oral glands of 12 species of the family Homalopsidae. Snakes of this family exhibit substantial interspecific morphological variation in their oral glands. Particular variables are the venom glands, ranging from large (e.g., Subsessor bocourti) to small (e.g., Erpeton tentaculatum). The supra- and infralabial glands are more uniform in morphology, being the second most developed in almost all the sampled species. Premaxillary glands distinct from the supralabial glands were observed in five species (Myron richardsonii, Bitia hydroides, Cantoria violacea, Fordonia leucobalia, and Gerarda prevostiana), in addition to Cerberus rynchops, the only species in which this condition was previously documented associated with the excretion of salt. In the three species of the saltwater group of homalopsids (C. violacea, F. leucobalia, and G. prevostiana), the premaxillary glands also extend posteriorly, occupying a large area above the supralabial gland, a condition not observed in any other species of snake studied thus far. Character evolution analyses indicate that premaxillary glands differentiated from the supralabial gland and evolved independently three or four times in the family, always in lineages that invaded marine habitats. Our results suggest that the differentiated premaxillary glands are likely salt glands, as is the case in C. rynchops. If corroborated, this increases to six or seven the number of independent evolutionary origins of salt glands in snakes that have undergone an evolutionary transition to marine life.

Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments

Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpression, and sequence evolution. Frogs provide an excellent, yet understudied, system for visual evolution research due to their diversity of ecologies (including biphasic aquatic-terrestrial life cycles) that we hypothesize imposed different selective pressures leading to adaptive evolution of the visual system, notably the opsins that encode the protein component of the visual pigments responsible for the first step in visual perception. Here, we analyze the diversity and evolution of visual opsin genes from 93 new eye transcriptomes plus published data for a combined dataset spanning 122 frog species and 34 families. We find that most species express the four visual opsins previously identified in frogs but show evidence for gene loss in two lineages. Further, we present evidence of positive selection in three opsins and shifts in selective pressures associated with differences in habitat and life history, but not activity pattern. We identify substantial novel variation in the visual opsins and, using microspectrophotometry, find highly variable spectral sensitivities, expanding known ranges for all frog visual pigments. Mutations at spectral-tuning sites only partially account for this variation, suggesting that frogs have used tuning pathways that are unique among vertebrates. These results support the hypothesis of adaptive evolution in photoreceptor physiology across the frog tree of life in response to varying environmental and ecological factors and further our growing understanding of vertebrate visual evolution.

Rediscovery and systematics of Rhinophis fergusonianus Boulenger, 1896 (Serpentes: Uropeltidae) from Indias Western Ghats

The shieldtail snake Rhinophis fergusonianus Boulenger, 1896 was previously known only from the holotype specimen collected approximately 130 years ago from an imprecise Indian locality (Cardamom Hills). We report the rediscovery of this species from four localities, from low-elevation hills on both sides of the Palghat Gap in the southern part of the Western Ghats of peninsular India. We document new specimens of R. fergusonianus and provide a reassessment of the systematics of the species based on external morphology and DNA-sequence data. We also provide a revised key to the identification of Indian species of Rhinophis.

Ongoing declines for the world's amphibians in the face of emerging threats

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

On the taxonomy of Uropeltis petersi (Beddome, 1878) (Serpentes: Uropeltidae) and description of a new, closely related species from the Western Ghats of India

A new species of the uropeltid snake genus Uropeltis Cuvier, 1829 is described from the environs of Munnar in the Anamalai hils of the Western Ghats of peninsular India. Uropeltis tricuspida sp. nov. superficially resembles the poorly known and closely related U. petersi, but differs from that species in having more ventral and subcaudal scales, and a tri- rather than bicuspid posterior tip to the terminal scute.

High-Density Geometric Morphometric Analysis of Intraspecific Cranial Integration in the Barred Grass Snake (Natrix helvetica) and Green Anole (Anolis carolinensis)

How do phenotypic associations intrinsic to an organism, such as developmental and mechanical processes, direct morphological evolution? Comparisons of intraspecific and clade-wide patterns of phenotypic covariation could inform how population-level trends ultimately dictate macroevolutionary changes. However, most studies have focused on analyzing integration and modularity either at macroevolutionary or intraspecific levels, without a shared analytical framework unifying these temporal scales. In this study, we investigate the intraspecific patterns of cranial integration in two squamate species: Natrix helvetica and Anolis carolinensis. We analyze their cranial integration patterns using the same high-density three-dimensional geometric morphometric approach used in a prior squamate-wide evolutionary study. Our results indicate that Natrix and Anolis exhibit shared intraspecific cranial integration patterns, with some differences, including a more integrated rostrum in the latter. Notably, these differences in intraspecific patterns correspond to their respective interspecific patterns in snakes and lizards, with few exceptions. These results suggest that interspecific patterns of cranial integration reflect intraspecific patterns. Hence, our study suggests that the phenotypic associations that direct morphological variation within species extend across micro- and macroevolutionary levels, bridging these two scales.

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 systematics and evolution of the Sri Lankan rainforest land snail Corilla: New insights from RADseq-based phylogenetics

The stylommatophoran land-snail genus Corilla is endemic to Sri Lanka and India's Western Ghats. On the basis of habitat distribution and shell morphology, the 10 extant Sri Lankan species fall into two distinct groups, lowland and montane. Here, we use phylogenetic analyses of restriction-site-associated DNA sequencing (RADseq) data and ancestral-state reconstructions of habitat association and shell morphology to clarify the systematics and evolution of Sri Lankan Corilla. Our dataset consists of 9 species of Corilla. Phylogenetic analyses were based on 88 assemblies (9,604-4,132,850 bp) generated by the RADseq assembler ipyrad, using four parameter combinations and different levels of missing data. Trees were inferred using a maximum likelihood (ML) approach. Ancestral states were reconstructed using maximum parsimony (MP) and ML approaches, with 1 binary state character analysed for habitat association (lowland vs montane) and 6 binary state characters analysed for shell morphology (shape, colour, lip width, length of upper palatal folds, orientation of upper palatal folds and collabral sculpture). Over a wide range of missing data (40-87 % missing individuals per locus) and assembly sizes (62,279-4,132,850 bp), nearly all trees conformed to one of two topologies (A and B), most relationships were strongly supported and total branch support approached the maximal value. Apart from the position of Corilla odontophora 'south', topologies A and B showed similar, well-resolved relationships at and above the species level. Our study agrees with the shell-based taxonomy of C. adamsi, C. beddomeae, C. carabinata, C. colletti and C. humberti (all maximally supported as monophyletic species). It shows that C. erronea and C. fryae constitute a single relatively widespread species (for which the valid name is C. erronea) and that the names C. gudei and C. odontophora each apply to at least two distinct, yet conchologically-cryptic species. The MP and ML ancestral-state reconstructions yielded broadly similar results and provide firm evidence that diversification in Sri Lankan Corilla has involved evolutionary convergence in the shell morphology of lowland lineages, with a pale shell and wide lip having evolved on at least two separate occasions (in C. carabinata and C. colletti) from montane ancestors having a dark, narrow-lipped shell.

Diet and habit explain head-shape convergences in natricine snakes

The concept of ecomorphs, whereby species with similar ecologies have similar phenotypes regardless of their phylogenetic relatedness, is often central to discussions regarding the relationship between ecology and phenotype. However, some aspects of the concept have been questioned, and sometimes species have been grouped as ecomorphs based on phenotypic similarity without demonstrating ecological similarity. Within snakes, similar head shapes have convergently evolved in species living in comparable environments and/or with similar diets. Therefore, ecomorphs could exist in some snake lineages, but this assertion has rarely been tested for a wide-ranging group within a single framework. Natricine snakes (Natricinae) are ecomorphologically diverse and currently distributed in Asia, Africa, Europe and north-central America. They are primarily semiaquatic or ground-dwelling terrestrial snakes, but some are aquatic, burrowing or aquatic and burrowing in habit and may be generalist or specialist in diet. Thus, natricines present an interesting system to test whether snakes from different major habit categories represent ecomorphs. We quantify morphological similarity and disparity in head shape among 191 of the ca. 250 currently recognized natricine species and apply phylogenetic comparative methods to test for convergence. Natricine head shape is largely correlated with habit, but in some burrowers is better explained by dietary specialism. Convergence in head shape is especially strong for aquatic burrowing, semiaquatic and terrestrial ecomorphs and less strong for aquatic and burrowing ecomorphs. The ecomorph concept is useful for understanding natricine diversity and evolution, though would benefit from further refinement, especially for aquatic and burrowing taxa.

On the taxonomic validity of Boiga whitakeri Ganesh et al., 2021 with new insights on Boiga dightoni (Boulenger, 1894) (Reptilia: Squamata: Colubridae)

Colour polymorphism has been previously reported in several colubrid snakes including Boiga spp. In this paper, we report colour variations within the poorly known southern Indian Boiga dightoni, provide the first molecular data for this species, from two localities (including the type locality) and compare them with data from other congeners. Additionally, we provide detailed dentition and hemipenis descriptions for B. dightoni. Molecular data for B. dightoni show very little difference (0.2–0.4% 16S; 0.9–1.2% cyt b) to the recently described Boiga whitakeri, also from southern India. We have re-examined and present new information on the pholidosis of the type specimens of B. whitakeri and reconsider its taxonomic status. On the basis of molecular data and overlapping morphological characteristics, we argue that Boiga whitakeri and Boiga dightoni are conspecific, and place B. whitakeri under the subjective synonymy of the latter. Furthermore, we show that colour polymorphism in B. dightoni is a gender-independent character and that both colour morphs are found in high as well as low elevations and partly in sympatry. A revised key to the Boiga ceylonensis complex is provided.

A near-complete species-level phylogeny of uropeltid snakes harnessing historical museum collections as a DNA source

Uropeltidae is a clade of small fossorial snakes (ca. 64 extant species) endemic to peninsular India and Sri Lanka. Uropeltid taxonomy has been confusing, and the status of some species has not been revised for over a century. Attempts to revise uropeltid systematics and undertake evolutionary studies have been hampered by incompletely sampled and incompletely resolved phylogenies. To address this issue, we take advantage of historical museum collections, including type specimens, and apply genome-wide shotgun (GWS) sequencing, along with recent field sampling (using Sanger sequencing) to establish a near-complete multilocus species-level phylogeny (ca. 87% complete at species level). This results in a phylogeny that supports the monophyly of all genera (if Brachyophidium is considered a junior synonym of Teretrurus), and provides a firm platform for future taxonomic revision. Sri Lankan uropeltids are probably monophyletic, indicating a single colonisation event of this island from Indian ancestors. However, the position of Rhinophis goweri (endemic to Eastern Ghats, southern India) is unclear and warrants further investigation, and evidence that it may nest within the Sri Lankan radiation indicates a possible recolonisation event. DNA sequence data and morphology suggest that currently recognised uropeltid species diversity is substantially underestimated. Our study highlights the benefits of integrating museum collections in molecular genetic analyses and their role in understanding the systematics and evolutionary history of understudied organismal groups.

Ocular lens morphology is influenced by ecology and metamorphosis in frogs and toads

The shape and relative size of an ocular lens affect the focal length of the eye, with consequences for visual acuity and sensitivity. Lenses are typically spherical in aquatic animals with camera-type eyes and axially flattened in terrestrial species to facilitate vision in optical media with different refractive indices. Frogs and toads (Amphibia: Anura) are ecologically diverse, with many species shifting from aquatic to terrestrial ecologies during metamorphosis. We quantified lens shape and relative size using 179 micro X-ray computed tomography scans of 126 biphasic anuran species and tested for correlations with life stage, environmental transitions, adult habits and adult activity patterns. Across broad phylogenetic diversity, tadpole lenses are more spherical than those of adults. Biphasic species with aquatic larvae and terrestrial adults typically undergo ontogenetic changes in lens shape, whereas species that remain aquatic as adults tend to retain more spherical lenses after metamorphosis. Further, adult lens shape is influenced by adult habit; notably, fossorial adults tend to retain spherical lenses following metamorphosis. Finally, lens size relative to eye size is smaller in aquatic and semiaquatic species than other adult ecologies. Our study demonstrates how ecology shapes visual systems, and the power of non-invasive imaging of museum specimens for studying sensory evolution.

Taxonomy and natural history of the poorly known Dindigul shieldtail Uropeltis dindigalensis (Beddome, 1877) (Serpentes: Uropeltidae)

Uropeltis dindigalensis (Beddome, 1877) is a poorly known uropeltid (shieldtail) snake from peninsular India. Here we report morphological data for 14 preserved and nine uncollected specimens, most of which have not been previously reported. We designate a lectotype from the type series, describe it, and present the first published photographs of some of the type material. Recharacterization of U. dindigalensis clarifies its taxonomic distinctiveness and its geographical distribution. We report new natural-history observations from museum specimens and of individuals in life, including viviparity and feeding behaviour. The species is known only from the higher elevations of Sirumalai hills, in the southern end of the Eastern Ghats. Uropeltis dindigalensis appears somewhat capable of tolerating low-intensity agriculture. The main immediate conservation threats are probably greater intensity human activities, including road traffic, and possibly climate change given that the species is restricted to the uppermost elevations of a small hill range. The very small extent of occurrence within a single threat-defined location (none of which lies within a protected area), combined with decreasing quality and quantity of habitat, likely qualifies U. dindigalensis as Critically Endangered (or, at best, Endangered) under IUCN Red List criteria.

Diversity and evolution of amphibian pupil shapes

Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and to test for potential correlations to ecology based on functional hypotheses. Using photographs, we surveyed pupil shape across adults of 1294 amphibian species, 74 families and three orders, and additionally for larval stages for all families of frogs and salamanders with a biphasic ontogeny. For amphibians with a biphasic life history, pupil shape changed in many species that occupy distinct habitats before and after metamorphosis. In addition, non-elongated (circular or diamond) constricted pupils were associated with species inhabiting aquatic or underground environments, and elongated pupils (with vertical or horizontal long axes) were more common in species with larger absolute eye sizes. We propose that amphibians provide a valuable group within which to explore the anatomical, physiological, optical and ecological mechanisms underlying the evolution of pupil shape.

Transcriptomic evidence for visual adaptation during the aquatic to terrestrial metamorphosis in leopard frogs

BACKGROUND

Differences in morphology, ecology, and behavior through ontogeny can result in opposing selective pressures at different life stages. Most animals, however, transition through two or more distinct phenotypic phases, which is hypothesized to allow each life stage to adapt more freely to its ecological niche. How this applies to sensory systems, and in particular how sensory systems adapt across life stages at the molecular level, is not well understood. Here, we used whole-eye transcriptomes to investigate differences in gene expression between tadpole and juvenile southern leopard frogs (Lithobates sphenocephalus), which rely on vision in aquatic and terrestrial light environments, respectively. Because visual physiology changes with light levels, we also tested the effect of light and dark exposure.

RESULTS

We found 42% of genes were differentially expressed in the eyes of tadpoles versus juveniles and 5% for light/dark exposure. Analyses targeting a curated subset of visual genes revealed significant differential expression of genes that control aspects of visual function and development, including spectral sensitivity and lens composition. Finally, microspectrophotometry of photoreceptors confirmed shifts in spectral sensitivity predicted by the expression results, consistent with adaptation to distinct light environments.

CONCLUSIONS

Overall, we identified extensive expression-level differences in the eyes of tadpoles and juveniles related to observed morphological and physiological changes through metamorphosis and corresponding adaptive shifts to improve vision in the distinct aquatic and terrestrial light environments these frogs inhabit during their life cycle. More broadly, these results suggest that decoupling of gene expression can mediate the opposing selection pressures experienced by organisms with complex life cycles that inhabit different environmental conditions throughout ontogeny.

A new pseudosuchian archosaur, Mambawakale ruhuhu gen. et sp. nov., from the Middle Triassic Manda Beds of Tanzania

The Manda Beds of southwest Tanzania have yielded key insights into the early evolutionary radiation of archosaurian reptiles. Many key archosaur specimens were collected from the Manda Beds in the 1930s and 1960s, but until recently, few of these had been formally published. Here, we describe an archosaur specimen collected in 1963 which has previously been referred to informally as Pallisteria angustimentum. We recognize this specimen as the type of a new taxon, Mambawakale ruhuhu gen. et sp. nov. The holotype and only known specimen of M. ruhuhu comprises a partial skull of large size (greater than 75 cm inferred length), lower jaws and fragments of the postcranium, including three anterior cervical vertebrae and a nearly complete left manus. Mambawakale ruhuhu is characterized by several cranial autapomorphies that allow it to be distinguished with confidence from all other Manda Beds archosaurs, with the possible exception of Stagonosuchus nyassicus for which comparisons are highly constrained due to very limited overlapping material. Phylogenetic analysis suggests that M. ruhuhu is an early diverging pseudosuchian, but more precise resolution is hampered by missing data. Mambawakale ruhuhu is one of the largest known pseudosuchians recovered to date from the Middle Triassic.

Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake

Molecular genetic data have recently been incorporated in attempts to reconstruct the ecology of the ancestral snake, though this has been limited by a paucity of data for one of the two main extant snake taxa, the highly fossorial Scolecophidia. Here we present and analyze vision genes from the first eye-transcriptomic and genome-wide data for Scolecophidia, for Anilios bicolor, and A. bituberculatus, respectively. We also present immunohistochemistry data for retinal anatomy and visual opsin-gene expression in Anilios. Analyzed in the context of 19 lepidosaurian genomes and 12 eye transcriptomes, the new genome-wide and transcriptomic data provide evidence for a much more reduced visual system in Anilios than in non-scolecophidian (=alethinophidian) snakes and in lizards. In Anilios, there is no evidence of the presence of 7 of the 12 genes associated with alethinophidian photopic (cone) phototransduction. This indicates extensive gene loss and many of these candidate gene losses occur also in highly fossorial mammals with reduced vision. Although recent phylogenetic studies have found evidence for scolecophidian paraphyly, the loss in Anilios of visual genes that are present in alethinophidians implies that the ancestral snake had a better-developed visual system than is known for any extant scolecophidian.

Multilocus phylogeny, natural history traits and classification of natricine snakes (Serpentes: Natricinae)

Natricine snakes are geographically widespread, species rich (with ~250 extant species) and both morphologically and ecologically diverse. We present a multilocus DNA sequence phylogeny for 249 natricine specimens representing 189 named species, including 69 specimens and 21 species not previously sampled. Our inferred Bayesian and maximum likelihood trees form the basis for evaluations of genus-level classification, historical biogeography, lineage diversification, and dietary, habit and reproductive-mode diversity and evolution, although several, mostly deeper, relationships remain poorly resolved. The optimal trees support natricine origins in Asia, with dispersals to Australo-Melanesia, sub-Saharan Africa (including Seychelles Archipelago, excluding Aldabra), Europe and North Africa and into North and Central America. Viviparity appears to have evolved independently three times in Natricinae but was not significantly associated with an aquatic habit. We found limited associations between habit and diet categories. We propose generic reallocations for four natricine species and highlight other points of uncertainty in natricine classification.

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.

New digital braincase endocasts of two species of Desmatosuchus and neurocranial diversity within Aetosauria (Archosauria: Pseudosuchia)

In the present contribution we revise, figure, and redescribe several isolated braincases of the iconic aetosaur Desmatosuchus from the Placerias Quarry locality, Chinle Formation, Arizona, United States. The detailed study of the isolated braincases from the UCMP collection allowed us to assign them at the species-level and recognize two species of Desmatosuchus for the Placerias Quarry: D. spurensis and D. smalli. The former can be distinguished from the latter by the presence of a transverse sulcus on the parietals, deep median pharyngeal recess on the basisphenoid, almost no gap between the basal tubera and the basipterygoid processes, and the exoccipitals meeting at the midline. The presence of D. smalli at the Placerias Quarry has not been previously reported. Based on the braincases UCMP 27408, 27410, 27407, three new brain endocasts were developed through CT scan images, reconstructing the most complete endocranial casts known for an aetosaur, including the encephalon, cranial nerves, inner ear, and endocranial vasculature. The cranial endocasts also exhibited some differences between both species of Desmatosuchus, with D. spurensis having a distinguishable dural expansion and markedly asymmetric anterior and posterior semicircular canals of the labyrinth. Additionally, the combination of osteological features and the endocranial casts allowed us to identify and discuss the presence of an ossified orbitosphenoid on the anteriormost region of the braincase among aetosaurs. Furthermore, we were able to reinterpret some of the observations made by previous authors on the endocast of the holotype of Desmatosuchus spurensis (UMMP VP 7476) and provide some insight into their neurosensory capabilities.

A new species of Stoliczkia Jerdon, 1870 (Serpentes: Xenodermidae) from Mizoram, India

We describe a new species of Stoliczkia from Mizoram, India. Stoliczkia vanhnuailianai sp. nov. is identified as a member of the genus Stoliczkia by distinct scale arrangements on the posterior of the head, and by scales on the body being separated by scaleless skin, and it differs from the two known congeners in body and head scalation. This is only the third specimen of Stoliczkia collected from India, and the sixth reported specimen for the genus. A revised key to the identification of the species of Stoliczkia is provided.

Contributions to ophiology in Zootaxa 20012020: patterns and trends

There are currently 3,900 recognized, extant snake species belonging to 529 genera globally (Uetz et al. 2021; this study), making snakes one of the most diverse major groups of squamates. Of the 665 currently recognized species that were described between 2001 and 2020 (a ~17% increase in total species), ~34% of these (226 species) were described in Zootaxa. This number does not include species resurrected from synonymy. The other ~66% (439) species were described in 105 other journals, bulletins or books (Fig.1a). Overall, the number of new snake species described every year is gradually increasing, and 40% of the new species described since 2011 were published in Zootaxa. Following Zootaxa, the second ranked journal, with 37 described species since 2001, is Herpetologica (Fig. 2). Anecdotally, the choice of Zootaxa as a publication outlet for new species descriptions by most authors is based on speed of publication post-acceptance, publication free of charge, relatively unconstrained number of papers published per year, relatively unconstrained manuscript length, expert section editors and reviewers, and consolidated scientometric parameters.

Amphibians in Zootaxa: 20 years documenting the global diversity of frogs, salamanders, and caecilians

Zootaxa is a mega-journal that since its inception, 20 years ago, has contributed to the documentation of the planet's biodiversity. Its role concerning terrestrial vertebrates has been crucial especially for amphibians, which are the most threatened class of vertebrates. As current editors of the Amphibia section, we reviewed the state of knowledge of taxonomic publications on amphibians over the last two decades (from 2001 to 2020). Our review reveals that 2,533 frogs, 259 salamanders, and 55 caecilians have been named in these 20 years, mainly in the tropical regions of South America, Asia, and Africa. More than half (57%) of these species descriptions were published in only 10 journals. At least 827 species of the new amphibians (29% of the total) were described in Zootaxa. This mega-journal has served also as a place of publication for monographs and systematic reviews, in addition to short articles documenting the vocalizations of anurans and the morphology of embryos and larvae. Its efficient evaluation process, the freedom of manuscript length, including full-color figures, and free of cost for the authors, has made Zootaxa a favorite for amphibian researchers. In an era of accelerating rates of biodiversity loss, documenting, describing, naming, and proposing evolutionary scenarios for species is, more than ever, an urgent task.

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.

Correction to: Eye‐body allometry across biphasic ontogeny in anuran amphibians

A correction to this paper has been published: https://doi.org/10.1007/s10682-021-10109-w

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.

Eye‐body allometry across biphasic ontogeny in anuran amphibians

Animals with biphasic lifecycles often inhabit different visual environments across ontogeny. Many frogs and toads (Amphibia: Anura) have free-living aquatic larvae (tadpoles) that metamorphose into adults that inhabit a range of aquatic and terrestrial environments. Ecological differences influence eye size across species, but these relationships have not yet been explored across life stages in an ontogenetic allometric context. We examined eye-body size scaling in a species with aquatic larvae and terrestrial adults, the common frog Rana temporaria, using a well-sampled developmental series. We found a shift in ontogenetic allometric trajectory near metamorphosis indicating prioritized growth in tadpole eyes. To explore the effects of different tadpole and adult ecologies on eye-body scaling, we expanded our taxonomic sampling to include developmental series of eleven additional anuran species. Intraspecific eye-body scaling was variable among species, with 8/12 species exhibiting a significant change in allometric slope between tadpoles and adults. Traits categorizing both tadpole ecology (microhabitat, eye position, mouth position) and adult ecology (habitat, activity pattern) across species had significant effects on allometric slopes among tadpoles, but only tadpole eye position had a significant effect among adults. Our study suggests that relative eye growth in the preliminary stages of biphasic anuran ontogenies is somewhat decoupled and may be shaped by both immediate ecological need (i.e. tadpole visual requirements) and what will be advantageous during later adult stages.

The postcranial skeleton of the erythrosuchid archosauriform Garjainia prima from the Early Triassic of European Russia

Erythrosuchidae were large-bodied, quadrupedal, predatory archosauriforms that dominated the hypercarnivorous niche in the aftermath of the Permo-Triassic mass extinction. Garjainia, one of the oldest members of the clade, is known from the late Olenekian of European Russia. The holotype of Garjainia prima comprises a well-preserved skull, but highly incomplete postcranium. Recent taxonomic reappraisal demonstrates that material from a bone bed found close to the type locality, previously referred to as 'Vjushkovia triplicostata', is referable to G. prima. At least, seven individuals comprising cranial remains and virtually the entire postcranium are represented, and we describe this material in detail for the first time. An updated phylogenetic analysis confirms previous results that a monophyletic Garjainia is the sister taxon to a clade containing Erythrosuchus, Shansisuchus and Chalishevia. Muscle scars on many limb elements are clear, allowing reconstruction of the proximal locomotor musculature. We calculate the body mass of G. prima to have been 147-248 kg, similar to that of an adult male lion. Large body size in erythrosuchids may have been attained as part of a trend of increasing body size after the Permo-Triassic mass extinction and allowed erythrosuchids to become the dominant carnivores of the Early and Middle Triassic.

A new Indian species of Rhinophis Hemprich, 1820 closely related to R. sanguineus Beddome, 1863 (Serpentes: Uropeltidae)

A new species of the uropeltid (shieldtail snake) genus Rhinophis is described based on a type series of seven specimens from the Wayanad region of the Western Ghats of peninsular India. The holotype was collected before 1880 but had been misidentified as the phenotypically similar and parapatric (possibly partly sympatric) R. sanguineus. Rhinophis karinthandani sp. nov. is diagnosed by a combination of 15 dorsal scale rows at midbody, 4-8 pairs of subcaudal scales, colour pattern (uniformly dark above, whitish below with extensive dark mottling), and by its distinct mitochondrial DNA sequences (e.g. 7.6% uncorrected p-distance for nd4). Phylogenetic analysis of mitochondrial DNA sequence data indicates that the new species is most closely related to R. sanguineus among currently recognised species, with this pair most closely related to the partly sympatric R. melanoleucus. The new species description brings the number of currently recognised species in the genus to 24, six of which are endemic to India and 18 endemic to Sri Lanka. A new key to the identification of Indian species of Rhinophis is provided.

Description of a new species of Smithophis Giri et al. 2019 (Serpentes: Colubridae: Natricinae) from Arunachal Pradesh, India

A new species of the natricine snake genus Smithophis Giri et al. 2019 is described based on three specimens collected from Arunachal Pradesh, India. An additional three referred specimens are documented. Smithophis arunachalensis sp. nov. differs from all known congeners by a combination of 4-5 (rarely 6) small scales around the eye (excluding labial scales), presence of temporal scales, and a distinctive colour pattern of a blackish dorsum and bright yellow venter that form a sharply-defined zigzag border. The new species is known only from ca. 100 km2 in Lower Dibang Valley and Changlang Districts in eastern Arunachal Pradesh. A revised key to the identification of the species of Smithophis is presented.

Eye size and investment in frogs and toads correlate with adult habitat, activity pattern and breeding ecology

Frogs and toads (Amphibia: Anura) display diverse ecologies and behaviours, which are often correlated with visual capacity in other vertebrates. Additionally, anurans exhibit a broad range of relative eye sizes, which have not previously been linked to ecological factors in this group. We measured relative investment in eye size and corneal size for 220 species of anurans representing all 55 currently recognized families and tested whether they were correlated with six natural history traits hypothesized to be associated with the evolution of eye size. Anuran eye size was significantly correlated with habitat, with notable decreases in eye investment among fossorial, subfossorial and aquatic species. Relative eye size was also associated with mating habitat and activity pattern. Compared to other vertebrates, anurans have relatively large eyes for their body size, indicating that vision is probably of high importance. Our study reveals the role that ecology and behaviour may have played in the evolution of anuran visual systems and highlights the usefulness of museum specimens, and importance of broad taxonomic sampling, for interpreting macroecological patterns.

Insights into the skin of caecilian amphibians from gene expression profiles

Background

Gene expression profiles can provide insights into the molecular machinery behind tissue functions and, in turn, can further our understanding of environmental responses, and developmental and evolutionary processes. During vertebrate evolution, the skin has played a crucial role, displaying a wide diversity of essential functions. To unravel the molecular basis of skin specialisations and adaptations, we compared gene expression in the skin with eight other tissues in a phylogenetically and ecologically diverse species sample of one of the most neglected vertebrate groups, the caecilian amphibians (order Gymnophiona).

Results

The skin of the five studied caecilian species showed a distinct gene expression profile reflecting its developmental origin and showing similarities to other epithelial tissues. We identified 59 sequences with conserved enhanced expression in the skin that might be associated with caecilian dermal specialisations. Some of the up-regulated genes shared expression patterns with human skin and potentially are involved in skin functions across vertebrates. Variation trends in gene expression were detected between mid and posterior body skin suggesting different functions between body regions. Several candidate biologically active peptides were also annotated.

Conclusions

Our study provides the first atlas of differentially expressed sequences in caecilian tissues and a baseline to explore the molecular basis of the skin functions in caecilian amphibians, and more broadly in vertebrates.

A new species of Rhinophis Hemprich, 1820 (Serpentes: Uropeltidae) from southwestern Sri Lanka

A new species of the uropeltid snake genus Rhinophis Hemprich, 1820 is described from near Balangoda, southwestern Sri Lanka. Rhinophis mendisi sp. nov. superficially resembles R. homolepis (Hemprich, 1820) in colour pattern and in its prominent, conical tail shield, but differs from that species in having far fewer ventrals (159-177, n = 13 versus > 195 in the types of R. homolepis and its subjective junior synonym R. gerrardi). The five type specimens and one of the referred specimens of the new species were collected probably between 1894 and 1925, and the only known additional, referred specimens (n = 8) were collected from within ca. 30 km of the type locality in 1972. A lectotype is designated for Mitylia gerrardi Gray, 1858, a subjective junior synonym of R. homolepis.

A new species of Rhinophis Hemprich, 1820 (Reptilia: Uropeltidae), from cloud forest of the Knuckles massif of Sri Lanka

A new species of uropeltid snake is described from the Knuckles Conservation Forest, Matale District, Sri Lanka. Rhinophis gunasekarai sp. nov. is superficially most similar to Rhinophis phillipsi in having yellow lines on the dorsum, blotches on the lateral body, and a relatively small tail shield, but it differs from that species in having substantially fewer ventrals, and a unique number and disposition of the dorsal yellow lines and lateral blotches. The new description brings the uropeltid fauna of Sri Lanka to 17 currently recognized species, all Rhinophis.

Spectral Diversification and Trans-Species Allelic Polymorphism during the Land-to-Sea Transition in Snakes

Snakes are descended from highly visual lizards [1] but have limited (probably dichromatic) color vision attributed to a dim-light lifestyle of early snakes [2-4]. The living species of front-fanged elapids, however, are ecologically very diverse, with ∼300 terrestrial species (cobras, taipans, etc.) and ∼60 fully marine sea snakes, plus eight independently marine, amphibious sea kraits [1]. Here, we investigate the evolution of spectral sensitivity in elapids by analyzing their opsin genes (which are responsible for sensitivity to UV and visible light), retinal photoreceptors, and ocular lenses. We found that sea snakes underwent rapid adaptive diversification of their visual pigments when compared with their terrestrial and amphibious relatives. The three opsins present in snakes (SWS1, LWS, and RH1) have evolved under positive selection in elapids, and in sea snakes they have undergone multiple shifts in spectral sensitivity toward the longer wavelengths that dominate below the sea surface. Several relatively distantly related Hydrophis sea snakes are polymorphic for shortwave sensitive visual pigment encoded by alleles of SWS1. This spectral site polymorphism is expected to confer expanded "UV-blue" spectral sensitivity and is estimated to have persisted twice as long as the predicted survival time for selectively neutral nuclear alleles. We suggest that this polymorphism is adaptively maintained across Hydrophis species via balancing selection, similarly to the LWS polymorphism that confers allelic trichromacy in some primates. Diving sea snakes thus appear to share parallel mechanisms of color vision diversification with fruit-eating primates.

A new species of Rhinophis Hemprich, 1820 (Serpentes: Uropeltidae) from the Wayanad region of peninsular India

A new species of the shieldtail snake genus Rhinophis is described based on a type series of seven recently collected specimens from the Wayanad region of the Western Ghats of peninsular India. Rhinophis melanoleucus sp. nov. is diagnosed based on a combination of 15 dorsal scale rows at (or just behind) midbody, more than 215 ventral scales and a long rostral. The new species also has a distinctive (mostly black and white) colouration. A new key to the identification of Indian species of Rhinophis is provided.

Description of a new species of Xylophis Beddome, 1878 (Serpentes: Pareidae: Xylophiinae) from the Western Ghats, India

We reassessed the systematics of the Indian (semi)fossorial snake Xylophis perroteti (Duméril, Bibron Duméril, 1854) based on morphological and DNA sequence data for type, historical, and new specimens. A population from the Anamalai Hills is distinct from broadly topotypic X. perroteti from the Nilgiri Hills (from which they are separated geographically by the lowland Palghat Gap) on the basis of both external morphology and DNA sequence data. We describe the Anamalai form as a new species, Xylophis mosaicus sp. nov. The new species is more closely related to X. perroteti than to X. stenorhynchus and X. captaini. A new key to identify the species of Xylophis is presented.

Cranial anatomy and taxonomy of the erythrosuchid archosauriform 'Vjushkovia triplicostata' Huene, 1960, from the Early Triassic of European Russia

Erythrosuchidae are a globally distributed and important group of apex predators that occupied Early and Middle Triassic terrestrial ecosystems following the Permo-Triassic mass extinction. The stratigraphically oldest known genus of Erythrosuchidae is Garjainia Ochev, 1958, which is known from the late Early Triassic (late Olenekian) of European Russia and South Africa. Two species of Garjainia have been reported from Russia: the type species, Garjainia prima Ochev, 1958, and 'Vjushkovia triplicostata' von Huene, 1960, which has been referred to Garjainia as either congeneric (Garjainia triplicostata) or conspecific (G. prima). The holotype of G. prima has received relatively extensive study, but little work has been conducted on type or referred material attributed to 'V. triplicostata'. However, this material includes well-preserved fossils representing all parts of the skeleton and comprises seven individuals. Here, we provide a comprehensive description and review of the cranial anatomy of material attributed to 'V. triplicostata', and draw comparisons with G. prima. We conclude that the two Russian taxa are indeed conspecific, and that minor differences between them result from a combination of preservation or intraspecific variation. Our reassessment therefore provides additional information on the cranial anatomy of G. prima. Moreover, we quantify relative head size in erythrosuchids and other early archosauromorphs in an explicit phylogenetic context for the first time. Our results show that erythrosuchids do indeed appear to have disproportionately large skulls, but that this is also true for other early archosauriforms (i.e. proterosuchids), and may reflect the invasion of hypercarnivorous niches by these groups following the Permo-Triassic extinction.

A new genus and species of natricine snake from northeast India

Based on the first molecular phylogenetic analyses of samples from northeast India, specimens referred to Rhabdops from this region are more closely related to the southeast and east Asian natricine genera Opisthotropis Günther, 1872 and Sinonatrix Rossman Eberle, 1977 (as well as to New World and western Palearctic natricines) than to peninsular Indian (true) Rhabdops. Morphologically, these northeast Indian populations differ from other natricines by having a single ('fused' or unpaired) internasal shield and a single prefrontal shield. Given the morphological and phylogenetic distinctiveness of these northeast Indian populations, we refer them to a new genus, Smithophis gen. nov., and transfer Rhabdops bicolor (Blyth, 1854) to Smithophis bicolor comb. nov. Based on morphological and molecular variation within our northeast Indian sample, we additionally describe Smithophis atemporalis sp. nov. from the state of Mizoram.

What lies beneath? Molecular evolution during the radiation of caecilian amphibians

Background

Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians.

Results

A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata.

Conclusions

The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5694-1) contains supplementary material, which is available to authorized users.

Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families

RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation and diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order. We identified vertebrate homologous elements of caecilian functional genes of varying tissue specificity that reveal a great number of unclassified gene families, especially for the skin. We annotated several protein domains for those unknown candidate gene families to investigate their function. We also conducted supertree analyses of a phylogenomic dataset of 1,955 candidate orthologous genes among five caecilian species and other major lineages of vertebrates, with the inferred tree being in agreement with current views of vertebrate evolution and systematics. Our study provides insights into the evolution of vertebrate protein-coding genes, and a basis for future research on the molecular elements underlying the particular biology and adaptations of caecilian amphibians.

Phototactic tails: Evolution and molecular basis of a novel sensory trait in sea snakes

Dermal phototaxis has been reported in a few aquatic vertebrate lineages spanning fish, amphibians and reptiles. These taxa respond to light on the skin of their elongate hind-bodies and tails by withdrawing under cover to avoid detection by predators. Here, we investigated tail phototaxis in sea snakes (Hydrophiinae), the only reptiles reported to exhibit this sensory behaviour. We conducted behavioural tests in 17 wild-caught sea snakes of eight species by illuminating the dorsal surface of the tail and midbody skin using cold white, violet, blue, green and red light. Our results confirmed phototactic tail withdrawal in the previously studied Aipysurus laevis, revealed this trait for the first time in A. duboisii and A. tenuis, and suggested that tail photoreceptors have peak spectral sensitivities between blue and green light (457-514 nm). Based on these results, and an absence of photoresponses in five Aipysurus and Hydrophis species, we tentatively infer that tail phototaxis evolved in the ancestor of a clade of six Aipysurus species (comprising 10% of all sea snakes). Quantifying tail damage, we found that the probability of sustaining tail injuries was not influenced by tail phototactic ability in snakes. Gene profiling showed that transcriptomes of both tail skin and body skin lacked visual opsins but contained melanopsin (opn4x) in addition to key genes of the retinal regeneration and phototransduction cascades. This work suggests that a nonvisual photoreceptor (e.g., Gq rhabdomeric) signalling pathway underlies tail phototaxis, and provides candidate gene targets for future studies of this unusual sensory innovation in reptiles.