Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family.

The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/subfamily level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological synapomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.

Novel phylogenomic inference and 'Out of Asia' biogeography of cobras, coral snakes and their allies.

Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling the biogeographic origin of elapoid snakes, which includes numerous dangerously venomous species as well as species not known to be dangerous to humans. The worldwide distribution of this lineage makes it an ideal group for testing hypotheses related to historical faunal exchanges among the many continents and other landmasses occupied by contemporary elapoid species. We developed a novel suite of genomic resources, included worldwide sampling, and inferred a robust estimate of evolutionary relationships, which we leveraged to quantitatively estimate geographical range evolution through the deep-time history of this remarkable radiation. Our phylogenetic and biogeographical estimates of historical ranges definitively reject a lingering former 'Out of Africa' hypothesis and support an 'Out of Asia' scenario involving multiple faunal exchanges between Asia, Africa, Australasia, the Americas and Europe.

Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family.

Asian mock vipers of the genus Psammodynastes and African forest snakes of the genus Buhoma are two genera belonging to the snake superfamily Elapoidea. The phylogenetic placements of Psammodynastes and Buhoma within Elapoidea has been extremely unstable which has resulted in their uncertain and debated taxonomy. We used ultraconserved elements and traditional nuclear and mitochondrial markers to infer the phylogenetic relationships of these two genera with other elapoids. Psammodynastes, for which a reference genome has been sequenced, were found, with strong branch support, to be a relatively early diverging split within Elapoidea that is sister to a clade consisting of Elapidae, Micrelapidae and Lamprophiidae. Hence, we allocate Psammodynastes to its own family, Psammodynastidae new family. However, the phylogenetic position of Buhoma could not be resolved with a high degree of confidence. Attempts to identify the possible sources of conflict in the rapid radiation of elapoid snakes suggest that both hybridisation/introgression during the rapid diversification, including possible ghost introgression, as well as incomplete lineage sorting likely have had a confounding role. The usual practice of combining mitochondrial loci with nuclear genomic data appears to mislead phylogeny reconstructions in rapid radiation scenarios, especially in the absence of genome scale data.

Rediscovery, range extension, phylogenetic relationships and updated diagnosis of the Ornate Long-tailed Lizard Latastia ornata Monard, 1940 (Squamata: Lacertidae).

The lacertid Latastia ornata was known to date only by its holotype collected in 1938 in Bafatá, central Guinea-Bissau. We report new specimens and localities from Guinea-Conakry, a new country record and major range extension of 700 km SE of the type-locality. We provide an updated diagnosis of the species, including the first genetic and osteological data, and confirm that Latastia ornata is closely related to, but distinct from, L. longicaudata based on external morphology, cranial osteology, DNA data and zoogeography.

Cranial osteology of Hypoptophis (Aparallactinae: Atractaspididae: Caenophidia), with a discussion on the evolution of its fossorial adaptations.

Fossoriality evolved early in snakes, and has left its signature on the cranial morphology of many extinct Mesozoic and early Caenozoic forms. Knowledge of the cranial osteology of extant snakes is indispensable for associating the crania of extinct lineages with a particular mode of life; this applies to fossorial taxa as well. In the present work, we provide a detailed description of the cranium of Hypoptophis wilsonii, a member of the subfamily Aparallactinae, using micro-computed tomography (CT). This is also the first thorough micro-CT-based description of any snake assigned to this African subfamily of predominantly mildly venomous, fossorial, and elusive snakes. The cranium of Hypoptophis is adapted for a fossorial lifestyle, with increased consolidation of skull bones. Aparallactines show a tendency toward reduction of maxillary length by bringing the rear fangs forward. This development attains its pinnacle in the sister subfamily Atractaspidinae, in which the rear fang has become the "front fang" by a loss of the part of the maxilla lying ahead of the fang. These dentitional changes likely reflect adaptation to subdue prey in snug burrows. An endocast of the inner ear of Hypoptophis shows that this genus has the inner ear typical of fossorial snakes, with a large, globular sacculus. A phylogenetic analysis based on morphology recovers Hypoptophis as a sister taxon to Aparallactus. We also discuss the implications of our observations on the burrowing origin hypothesis of snakes.

A contribution to the systematics of Salea anamallayana (Beddome, 1878) and S. horsfieldii Gray, 1845 (Squamata: Agamidae: Draconinae).

Salea anamallayana (Beddome, 1878) and S. horsfieldii Gray, 1845 are two endemic montane forest dwelling draconine agamid lizards from the Western Ghats (India). The original descriptions of these two species were brief and apart from their inclusion in general faunal works, they have never been the focus of a rigorous taxonomic study. In this paper we provide a detailed redescription of the types of those two species. We also reconfirm the status of the subjective synonyms of those two species. We conducted a test of niche conservatism and on the basis of the results of this analysis, we demonstrate that in spite of occurring in apparently analogous habitats, the niche of the two species have diverged significantly. We also provide notes on the distribution and natural history of S. anamallayana and S. horsfieldii.

A study on Ptyas doriae (Boulenger, 1888) with comments on the status of Ptyas hamptoni (Boulenger, 1900) (Squamata: Colubridae: Colubrinae).

Ptyas doriae is a rare snake in northeastern India, Myanmar and southern China. The original description and subsequent accounts of this species were all very brief. We studied most of the available specimens of this species and on this basis we provide a detailed redescription of the species. We give an account of intrapopulational variation in scalation characters and colouration and we also report on a previously undescribed colour morph from Manipur, India. We have examined the holotype of Ptyas hamptoni and found that characters used to distinguish it from P. doriae are inadequate and therefore we herein synonymize the former with the latter species. We also predict the potential distribution of P. doriae by using Maximum Entropy modeling.

Description of a new species of genus Trachischium with a redescription of Trachischium fuscum (Serpentes: Colubridae: Natricinae).

We describe a new species, Trachischium sushantai sp. nov., from Jammu, India. The new species can be distinguished from its congeners by a combination of the following characters: -a single nasal, a singleprefrontal, a single post-ocular, 13 rows of dorsal scales at mid-body, 152 ventrals, 23 pairs of subcaudals and those on anterior half of tail as long as wide and regular hexagon or rhomboid shaped, uniformly dark brown dorsum and brown subcaudals, edged incream or yellow posteriorly. The new species closely resembles T. fuscum. We also provide a redescription of T. fuscum and comments on its subjective synonyms.