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.

Underground cryptic speciation within the Maghreb: Multilocus phylogeography sheds light on the diversification of the checkerboard worm lizard Trogonophis wiegmanni.

Biogeographic and evolutionary patterns in the North African portion of the Western Palaearctic are poorly known. A high fraction of undescribed diversity is expected in this region, especially in groups such as reptiles. Here we used mitochondrial (12S, 16S, cytb) and nuclear (pomc, rag2, cmos) markers and morphological data to investigate phyletic diversification and phylogeographical structure in the amphisbaenian Trogonophis wiegmanni endemic to the Maghreb. Phylogenetic and molecular dating analyses based on gene trees and species trees support three deeply divergent lineages of Pliocene origin, two in Morocco and one in central Algeria and Tunisia. Parapatry, reciprocal monophyly, high genetic divergence and limited morphological differentiation between them suggest that these lineages represent independent cryptic taxonomic units. Emerging lines of evidence from this study and from available literature on Maghreb taxa support (i) a major biogeographic break between western and eastern Maghreb and (ii) a role of the Atlas as a biogeographic divide within the western Maghreb (Morocco). The origin of these biogeographic units is probably associated with the evolutionary events prompted by the Late Miocene palaeogeographic setting and later by Plio-Pleistocene climatic changes and their interplay with prominent orographic barriers within North Africa.

Visual Pigments, Ocular Filters and the Evolution of Snake Vision.

Much of what is known about the molecular evolution of vertebrate vision comes from studies of mammals, birds and fish. Reptiles (especially snakes) have barely been sampled in previous studies despite their exceptional diversity of retinal photoreceptor complements. Here, we analyze opsin gene sequences and ocular media transmission for up to 69 species to investigate snake visual evolution. Most snakes express three visual opsin genes (rh1, sws1, and lws). These opsin genes (especially rh1 and sws1) have undergone much evolutionary change, including modifications of amino acid residues at sites of known importance for spectral tuning, with several tuning site combinations unknown elsewhere among vertebrates. These changes are particularly common among dipsadine and colubrine "higher" snakes. All three opsin genes are inferred to be under purifying selection, though dN/dS varies with respect to some lineages, ecologies, and retinal anatomy. Positive selection was inferred at multiple sites in all three opsins, these being concentrated in transmembrane domains and thus likely to have a substantial effect on spectral tuning and other aspects of opsin function. Snake lenses vary substantially in their spectral transmission. Snakes active at night and some of those active by day have very transmissive lenses, whereas some primarily diurnal species cut out shorter wavelengths (including UVA). In terms of retinal anatomy, lens transmission, visual pigment spectral tuning and opsin gene evolution the visual system of snakes is exceptionally diverse compared with all other extant tetrapod orders.

Multiple rod-cone and cone-rod photoreceptor transmutations in snakes: evidence from visual opsin gene expression.

In 1934, Gordon Walls forwarded his radical theory of retinal photoreceptor 'transmutation'. This proposed that rods and cones used for scotopic and photopic vision, respectively, were not fixed but could evolve into each other via a series of morphologically distinguishable intermediates. Walls' prime evidence came from series of diurnal and nocturnal geckos and snakes that appeared to have pure-cone or pure-rod retinas (in forms that Walls believed evolved from ancestors with the reverse complement) or which possessed intermediate photoreceptor cells. Walls was limited in testing his theory because the precise identity of visual pigments present in photoreceptors was then unknown. Subsequent molecular research has hitherto neglected this topic but presents new opportunities. We identify three visual opsin genes, rh1, sws1 and lws, in retinal mRNA of an ecologically and taxonomically diverse sample of snakes central to Walls' theory. We conclude that photoreceptors with superficially rod- or cone-like morphology are not limited to containing scotopic or photopic opsins, respectively. Walls' theory is essentially correct, and more research is needed to identify the patterns, processes and functional implications of transmutation. Future research will help to clarify the fundamental properties and physiology of photoreceptors adapted to function in different light levels.

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.

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.

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.

A new species of Uropeltis Cuvier, 1829 (Serpentes: Uropeltidae) from the Anaikatty Hills of the Western Ghats of India.

A new species of Uropeltis is described from a series of six type specimens from the Anaikatty Hills of the Western Ghats of Tamil Nadu, peninsular India. Uropeltis bhupathyi sp. nov. is distinguished from congeners by having more than 200 ventral scales, 17 dorsal scale rows at midbody and by the size and shape of the rostral and frontal shields. Although tens of specimens have been seen in the vicinity of the type locality (and previously reported as U. ellioti), the new species is known only from this locality and faces threats from road traffic, habitat loss and change, and possibly a condition that deforms heads and head shields which is at least superficially similar to snake fungal disease reported from wild snakes in North America and Europe.