Phylogenetics of Advanced Snakes (Caenophidia) Based on Four Mitochondrial Genes

Abstract

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.

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

“…Our results for advanced snakes (Caenophidia) are generally similar to those of other recent studies [41,42,169], and will only be briefly described. However, in contrast to most recent studies [20,36,41,42,81,159,160], Acrochordidae is here strongly placed (SHL = 95) as the sister group to Xenodermatidae.…”

“…This clade is then the sister group to the remaining Colubroidea, which form a strongly supported clade (SHL = 100; Figures 1, 22). This relationship has been found in some previous studies [169,170], and was hypothesized by early authors [171]. Further evidence will be required to resolve this conclusively.…”

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

“…The major problems hindering resolution of this clade are 1) placement of Xenodermatidae inside or outside of Colubroidea; 2) placement of Homalopsidae; 3) topology of Lamprophiidae; and 4) topology of Colubridae. Previous studies have placed Xenodermatidae as sister to Acrochordidae [15,37] or as basal in Colubroidea [23,27,40,42,47,87], have placed Homalopsidae as sister to Lamprophiidae + Elapidae [15,27,40] or as sister to (Lamprophiidae + Elapidae) + Colubridae [23,32,39,42,45,47], and have shown conflicting topologies for the subfamilies within Lamprophiidae and Colubridae [15,23,27,28,37,40,45,47]. Pyron et al [22] used seven methods to examine these relationships showing Xenodermatidae as basal in Colubroidea with varying support and Homalopsidae as sister to (Lamprophiidae + Elapidae) + Colubridae with strong support.…”

Morphological integration and adaptation in the snake feeding system: a comparative phylogenetic study

“…, 2000; Lee & Scanlon, 2002; Slowinski & Lawson, 2002; Vidal & Hedges, 2002a,b,2004; Wilcox et al. , 2002; Kelly et al. , 2003; Townsend et al.…”