Molecular Evidence for the Nonmonophyly of the Asian Natricid GenusXenochrophis(Serpentes, Colubroidea) as Inferred from Mitochondrial and Nuclear Genes (original) (raw)
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Systematic Biology, 2003
Phylogenetic relationships among advanced snakes ( Acrochordus + Colubroidea = Caenophidia) and the position of the genus Acrochordus relative to colubroid taxa are contentious. These concerns were investigated by phylogenetic analysis of fragments from four mitochondrial genes representing 62 caenophidian genera and 5 noncaenophidian taxa. Four methods of phylogeny reconstruction were applied: matrix representation with parsimony (MRP) supertree consensus, maximum parsimony, maximum likelihood, and Bayesian analysis. Because of incomplete sampling, extensive missing data were inherent in this study. Analyses of individual genes retrieved roughly the same clades, but branching order varied greatly between gene trees, and nodal support was poor. Trees generated from combined data sets using maximum parsimony, maximum likelihood, and Bayesian analysis had medium to low nodal support but were largely congruent with each other and with MRP supertrees. Conclusions about caenophidian relationships were based on these combined analyses. The Xenoderminae, Viperidae, Pareatinae, Psammophiinae, Pseudoxyrophiinae, Homalopsinae, Natricinae, Xenodontinae, and Colubrinae (redefined) emerged as monophyletic, whereas Lamprophiinae, Atractaspididae, and Elapidae were not in one or more topologies. A clade comprising Acrochordus and Xenoderminae branched closest to the root, and when Acrochordus was assessed in relation to a colubroid subsample and all five noncaenophidians, it remained associated with the Colubroidea. Thus, Acrochordus + Xenoderminae appears to be the sister group to the Colubroidea, and Xenoderminae should be excluded from Colubroidea. Within Colubroidea, Viperidae was the most basal clade. Other relationships appearing in all final topologies were (1) a clade comprising Psammophiinae, Lamprophiinae, Atractaspididae, Pseudoxyrophiinae, and Elapidae, within which the latter four taxa formed a subclade, and (2) a clade comprising Colubrinae, Natricinae, and Xenodontinae, within which the latter two taxa formed a subclade. Pareatinae and Homalopsinae were the most unstable clades.
Phylogeny of the Colubroidea (Serpentes): New evidence from mitochondrial and nuclear genes
Molecular Phylogenetics and Evolution, 2005
The Colubroidea contains over 85% of all the extant species of snakes and is recognized as monophyletic based on morphological and molecular data. Using DNA sequences (cyt b, c-mos) from 100 species we inferred the phylogeny of colubroids with special reference to the largest family, the Colubridae. Tree inference was obtained using Bayesian, likelihood, and parsimony methods. All analyses produced Wve major groups, the Pareatidae, Viperidae, Homalopsidae, the Elapidae, and the Colubridae. The speciWc content of the latter two groups has been altered to accommodate evolutionary history and to yield a more stable taxonomy. We propose an updated classiWcation based on the reallocation of species as indicated by our inferred phylogeny.
Current Herpetology, 2014
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Evolution and phylogeny of the genus Natrix (Serpentes: Colubridae)
2006
Some aspects of the natural history of snakes of the colubrid genus Natrix have been well studied. With their extensive European distribution and relative abundance, their ecology, reproduction and behaviour are well known. Yet other facets of their biology remain poorly understood. These include knowledge of Natrix phylogeny, hypotheses explaining the current distribution of the three extant members of the genus, and their evolution and relationships. In this study we used molecular data, the nucleotide sequences of four protein-coding mitochondrial genes (3806 bp total), to provide a well-supported phylogeny for the genus Natrix. With these molecular data, evidence from the fossil record, and knowledge of palaeogeological events, we used two approaches in designing a time scale which we used to date the major events in Natrix speciation and intraspecific variation. Our data strongly support a phylogeny for the genus in which N. maura is basal with N. natrix and N. tessellata being sister species. The calibrated molecular clock suggests that N. maura diverged from the common ancestor of the three species 18-27 mya and that N. natrix and N. tessellata diverged 13-22 mya. Although the ranges of these estimates are large they support an early Miocene to late Oligocene origin for the three species. Intraspecific divergence is estimated to have commenced 5.3,
CERN European Organization for Nuclear Research - Zenodo, 2022
A new species of the genus Herpetoreas is described from Murlen National Park, Mizoram, northeastern India, based on morphological differences and molecular evidence inferred from the mitochondrial cytochrome b and 16S rRNA genes. The new taxon represents the seventh nominal species in the genus Herpetoreas, out of which three species, i.e., H. pealii, H. platyceps and H. xenura, have been recorded from northeastern India as well. An updated taxonomic key to the species of Herpetoreas is provided. Our phylogenetic reconstructions of selected natricine and colubrine snakes from Mizoram state, northeastern India, also contribute to the systematics and known distribution of the little known species Gongylosoma scriptum, and corroborate its taxonomic placement into the subfamily Colubrinae. Moreover, the first mo lecular based identifications for Liopeltis stoliczkae and Sibynophis collaris from Mizoram are presented.
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.
Biological Journal of the Linnean Society, 2012
We investigated intraspecific phylogenetic relationships in the natricine snake, Rhabdophis tigrinus. A partial sequence of mitochondrial cytochrome b gene (990 bp) was sequenced for 220 individuals from 112 populations. The phylogeny indicated monophyly of the Japanese populations against the continental and Taiwanese populations, sister relationships of the Japanese and continental populations, and monophyly of the whole species. The results strongly suggested substantial genetic divergences among population assemblages from those three regions. We thus consider both lateralis from the continent, which is often synonymized to R. tigrinus, and formosanus from Taiwan, which is usually regarded as a subspecies of the latter, as distinct full species based on the evolutionary species concept. In the Japanese populations, haplotypes were classified to in two major clades (I and II) that were parapatric to each other. Clade I consisted of three distinct subclades (I-A, I-B, and I-C), of which the former two were parapatric with each other, whereas the latter was sympatric with each of the former two subclades. The geographical haplotype structure exhibited by the Japanese populations is likely to have resulted from a series of allopatric differentiations with rapid range extensions of resultant lineages, leading to secondary contact or further admixture of mitochondrial haplotype clades and subclades.
Organisms Diversity & Evolution, 2009
The dice snake, Natrix tessellata (Laurenti, 1768), is a suitable study organism to address questions of Eurasian phylogeography due to its wide Palearctic distribution. We analysed complete mitochondrial cytochrome b sequences and nuclear ISSR-PCR fingerprints of more than 300 specimens representing nearly the entire geographic range. Nine major mitochondrial lineages were discovered based on mtDNA sequences. The three most basal lineages comprised populations from Iran, Jordan-Egypt, and Greece, respectively. Other lineages were associated with samples from the Turkish peninsula, the Caucasus, the Aral Sea, and eastern Kazakhstan. A sister-group relationship was found between two lineages from Crete and the European mainland. Assuming an evolutionary rate of 1.35% sequence divergence per million years, among-lineage p-distances of 1.7-8.4% suggest that intraspecific differentiation might date back as far as the Miocene/Pliocene transition 5-6 million years ago. The pattern of genetic differentiation in mitochondrial phylogeny with regard to Asia Minor and the region of the Aral Sea was not congruent with the results of the nuclear ISSR-PCR analyses, and suggests admixing within some mtDNA clades at contact zones. The taxonomic implications of the high intraspecific variation in the dice snake are discussed.
American Museum Novitates, 2018
We investigate the phylogenetic relationships of two poorly known Natricinae, Parahelicops and Pararhabdophis, for which we obtained nucleotide sequence data from one mitochondrial gene (cytochrome b) and three nuclear genes (CMOS, NT3, and RAG1). Maximum parsimony, maximum likelihood, and combined and partitioned Bayesian analyses suggest that both Parahelicops and Pararhabdophis are embedded within the genus Hebius. To align classification with phylogeny, we synonymize Parahelicops and Pararhabdophis with Hebius.