Phylogeography of the smooth greensnake, Opheodrys vernalis (Squamata: Colubridae): divergent lineages and variable demographics in a widely distributed yet enigmatic species (original) (raw)
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In this paper we resolve the taxonomic confusion related to Ahaetulla nasuta anomala (Annandale, 1906). On the basis of molecular and morphological data, we remove it from the synonymy of Ahaetulla nasuta (Lacépède, 1789) and reinstate it as a valid species—Ahaetulla anomala. This species is sexually dichromatic, males are green and females are brown in colour. Though the brown morph morphologically resembles Ahaetulla pulverulenta (Duméril, Bibron & Du-méril, 1854) there are significant morphological and genetic differences between these two species. Additional information on taxonomy, natural history and distribution of the species is provided.
Molecular Phylogenetics and Evolution, 2011
The superfamily Colubroidea (>2500 species) includes the majority of snake species and is one of the most conspicuous and well-known radiations of terrestrial vertebrates. However, many aspects of the phylogeny of the group remain contentious, and dozens of genera have yet to be included in molecular phylogenetic analyses. We present a new, large-scale, likelihood-based phylogeny for the colubroids, including 761 species sampled for up to five genes: cytochrome b (93% of 761 species sampled), ND4 (69%), ND2 (28%), c-mos (54%), and RAG-1 (13%), totaling up to 5814 bp per species. We also compare likelihood bootstrapping and a recently proposed ultra-fast measure of branch support (Shimodaira-Hasegawa-like [SHL] approximate likelihood ratio), and find that the SHL test shows strong support for several clades that were weakly-supported by bootstrapping in this or previous analyses (e.g., Dipsadinae, Lamprophiidae). We find that SHL values are positively related to branch lengths, but show stronger support for shorter branches than bootstrapping. Despite extensive missing data for many taxa (mean = 67% per species), neither bootstrap nor SHL support values for terminal species are related to their incompleteness, and that most highly incomplete taxa are placed in the expected families from previous taxonomy, typically with very strong support. The phylogeny indicates that the Neotropical colubrine genus Scaphiodontophis represents an unexpectedly ancient lineage within Colubridae. We present a revised higher-level classification of Colubroidea, which includes a new subfamily for Scaphiodontophis (Scaphiodontophiinae). Our study provides the most comprehensive phylogeny of Colubroidea to date, and suggests that SHL values may provide a useful complement to bootstrapping for estimating support on likelihood-based trees.
In this paper we present morphometric data recorded on 11 specimens of Lycodon jara (shaw, 1802) and compare them with those of the recently described species Lycodon odishii Mallik, Parida, Mohanty, Mallik, Purohit, Mohanty, Nanda, sindura, Purohit, Mishra & sahoo, 2014. Multivariate comparison of the two species revealed that variation in L. odishii falls well within the range of the L. jara. Lycodon odishii should, therefore, be treated as a junior synonym of L. jara.
Molecular systematics of the genus Sonora (Squamata: Colubridae) in central and western Mexico
Systematics and Biodiversity, 2012
Mexico possesses high levels of endemic biodiversity, especially for squamate reptiles. However, the evolutionary relationships among many reptiles in this region are not well known. The closely related genera of Sonora Baird and Girard 1853 and Procinura Cope 1879 are coralsnake mimics found from the central and western United States to southwestern Mexico and Baja California. Although species delimitation in this group has historically relied upon colour pattern and other morphological characters, many populations of these species display colour pattern polymorphism, which may confound taxonomy. We used molecular phylogenetics to assess the evolutionary relationships and delimit species within Sonora, focusing on the phylogenetic position of Procinura and the validity of S. mutabilis and aequalis. We sequenced two mitochondrial (ND4 and cytb) and two nuclear (c-mos and RAG-1) genes for the single species of Procinura and each of the four species of Sonora. We analysed these sequences using maximum parsimony, maximum likelihood and Bayesian phylogenetic analyses on separately concatenated mitochondrial and nuclear datasets. Additionally, we used Bayesian coalescent methods to build a species tree (Bayesian species tree analysis) and delimit species boundaries (Bayesian species delimitation). All methods indicated that Procinura is deeply nested within Sonora, and most individual species are well supported. However, we found that one taxon (S. aequalis) is paraphyletic with regard to another (S. mutabilis). We recommend that the genus Procinura be synonymised with Sonora and that S. aequalis be synonymised with S. mutabilis. Additionally, the phylogenetic patterns that we document are broadly congruent with a Miocene or Pliocene divergence between S. michoacanensis and S. mutabilis along the Trans-Mexican Volcanic Belt. Finally, our data are consistent with the early evolution of coralsnake mimicry and colour pattern polymorphism within the genus Sonora.
2012
Mexico possesses high levels of endemic biodiversity, especially for squamate reptiles. However, the evolutionary relationships among many reptiles in this region are not well known. The closely related genera of Sonora Baird and Girard 1853 and Procinura Cope 1879 are coralsnake mimics found from the central and western United States to southwestern Mexico and Baja California. Although species delimitation in this group has historically relied upon colour pattern and other morphological characters, many populations of these species display colour pattern polymorphism, which may confound taxonomy. We used molecular phylogenetics to assess the evolutionary relationships and delimit species within Sonora, focusing on the phylogenetic position of Procinura and the validity of S. mutabilis and aequalis. We sequenced two mitochondrial (ND4 and cytb) and two nuclear (c-mos and RAG-1) genes for the single species of Procinura and each of the four species of Sonora. We analysed these sequences using maximum parsimony, maximum likelihood and Bayesian phylogenetic analyses on separately concatenated mitochondrial and nuclear datasets. Additionally, we used Bayesian coalescent methods to build a species tree (Bayesian species tree analysis) and delimit species boundaries (Bayesian species delimitation). All methods indicated that Procinura is deeply nested within Sonora, and most individual species are well supported. However, we found that one taxon (S. aequalis) is paraphyletic with regard to another (S. mutabilis). We recommend that the genus Procinura be synonymised with Sonora and that S. aequalis be synonymised with S. mutabilis. Additionally, the phylogenetic patterns that we document are broadly congruent with a Miocene or Pliocene divergence between S. michoacanensis and S. mutabilis along the Trans-Mexican Volcanic Belt. Finally, our data are consistent with the early evolution of coralsnake mimicry and colour pattern polymorphism within the genus Sonora.