We present a molecular phylogenetic analysis of caenophidian (advanced) snakes using sequences from two mitochondrial genes (12S and 16S rRNA) and one nuclear (c-mos) gene (1681 total base pairs), and with 131 terminal taxa sampled from throughout all major caenophidian lineages but focussing on Neotropical xenodontines. Direct optimization parsimony analysis resulted in a well-resolved phylogenetic tree, which corroborates some clades identified in previous analyses and suggests new hypotheses for the composition and relationships of others. The major salient points of our analysis are: (1) placement of Acrochordus, Xenodermatids, and Pareatids as successive outgroups to all remaining caenophidians (including viperids, elapids, atractaspidids, and all other "colubrid" groups); (2) within the latter group, viperids and homalopsids are sucessive sister clades to all remaining snakes; (3) the following monophyletic clades within crown group caenophidians: Afro-Asian psammophiids (including Mimophis from Madagascar), Elapidae (including hydrophiines but excluding Homoroselaps), Pseudoxyrhophiinae, Colubrinae, Natricinae, Dipsadinae, and Xenodontinae. Homoroselaps is associated with atractaspidids. Our analysis suggests some taxonomic changes within xenodontines, including new taxonomy for Alsophis elegans, Liophis amarali, and further taxonomic changes within Xenodontini and the West Indian radiation of xenodontines. Based on our molecular analysis, we present a revised classification for caenophidians and provide morphological diagnoses for many of the included clades; we also highlight groups where much more work is needed. We name as new two higher taxonomic clades within Caenophidia, one new subfamily within Dipsadidae, and, within Xenodontinae five new tribes, six new genera and two resurrected genera. We synonymize Xenoxybelis and Pseudablabes with Philodryas; Erythrolamprus with Liophis; and Lystrophis and Waglerophis with Xenodon.Este trabalho apresenta uma análise filogenética molecular das serpentes avançadas (Caenophidia), realizada com base na análise de seqüências de dois genes mitocondriais (rRNA 12S e 16S) e de um gene nuclear (c-mos; 1681 pares de bases no total) e com 131 táxons terminais, amostrados a partir das principais linhagens de Caenophidia, com ênfase nos xenodontíneos neotropicais. A análise de parcimônia dos dados mediante otimização direta resultou em uma árvore filogenética bem resolvida que, por um lado, corrobora alguns dos clados identificados em análises anteriores e por outro, estabelece novas hipóteses sobre a composição de outros grupos e do relacionamento entre eles. Os principais resultados obtidos salientam: (1) a alocação de Achrochordus, xenodermatídeos e pareatídeos como grupos externos sucessivos de todos os demais cenofídios (incluindo viperídeos, elapídeos, atractaspidídeos e todos os grupos de "colubrídeos"); (2) que, em relação ao último grupo, viperídeos e homalopsídeos podem ser considerados como clados irmãos dos demais; (3) a existência, dentro do grande grupo dos cenofidia, dos seguintes sub-grupos: psamophiídeos afro-asiáticos (incluindo o gênero Mimophis, de Madagascar), Elapidae (incluindo os hidrophiíneos, mas excluindo Homoroselaps, associado aos atractaspidídeos), Pseudoxyrhophiinae, Colubrinae, Natricinae, Dipsadinae e Xenodontinae. A análise sugere algumas alterações de cunho taxonômico dentro dos xenodontíneos, incluindo realocações genéricas para Alsophis elegans, Liophis amarali e modificações substanciais em relação a Xenodontini e à radiação dos xenodontíneos das Antilhas. Também é a aqui apresentada uma revisão da classificação de Caenophidia, baseada inicialmente nas análises moleculares, mas provendo diagnoses morfológicas para muitos dos clados incluídos, realçando os grupos que ainda merecem atenção especial no futuro. São aqui nomeados originalmente dois grandes clados dentro de Caenophidia, uma nova subfamília dentro de Dipsadidae e, dentro de Xenodontinae, cinco novas tribos e seis novos gêneros, sendo ainda dois gêneros revalidados. Os gêneros Xenoxybelis e Pseudablabes são considerados sinônimos de Philodryas; Erythrolamprus, sinônimo de Liophis; Lystrophis e Waglerophis, sinônimos de Xenodon.FAPESPFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) - BIOTAConselho Nacional de Desenvovimento Científico e Tecnológico (CNPq)Natural Sciences and Engineering Research Council (NSERC), Canad

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

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.