The phylogeny and classification of caenophidian snakes inferred from seven nuclear protein-coding genes

Abstract

More than 80% of the approximately 3000 living species of snakes are placed in the taxon Caenophidia (advanced snakes), a group that includes the families Acrochordidae, Viperidae, Elapidae, Atractaspididae, and the paraphyletic 'Colubridae'. Previous studies using DNA sequences have involved few nuclear genes (one or two). Several nodes have therefore proven difficult to resolve with statistical significance. Here, we investigated the higher-level relationships of caenophidian snakes with seven nuclear proteincoding genes and obtained a well-supported topology. Accordingly, some adjustments to the current classification of Caenophidia are made to better reflect the relationships of the groups. The phylogeny also indicates that, ancestrally, caenophidian snakes are Asian and nocturnal in origin, although living species occur on nearly all continents and are ecologically diverse.

Molecular phylogeny of advanced snakes (Serpentes, Caenophidia) with an emphasis on South American Xenodontines: a revised classification and descriptions of new taxa

“…Subsequently, Pinou et al (2004) applied the resurrected name "Elapoidea" to a clade comprising Atractaspis + Elapidae. "Elapoidea" has subsequently been used for "Clade A" of Lawson et al (2005) in several molecular phylogenetic studies (Vidal et al, 2007(Vidal et al, , 2008; Kelly et al, 2009; see also our results below). Clade B of Lawson et al (2005) was referred to as "Colubroidea" by Pinou et al (2004) and subsequent authors.…”

“…These authors made little attempt to analyze the effects of taxon sampling and long branch attraction (Felsenstein, 1978) or repulsion (Siddall & Whiting 1999) in small molecular data matrices, problems that were acknowledged by Kraus & Brown (1998) and Kelly et al (2008), and supported by simulation and other studies (e.g., Goertzen & Theriot, 2003;Salisbury & Kim, 2001). Vidal et al (2007) argued that the problem of long branch attraction (and repulsion) in more basal nodes was better addressed through gene sampling rather than taxon sampling, but this will only partially solve the issue. Increasing gene sampling in a reduced taxon sample can actually reinforce long branch attraction (or repulsion), and increasing the taxon sampling density will at least help reveal unstable clades within a phylogenetic analysis.…”

“…They were the first to recognize the basal rooting of the Xenodermatinae on the basis of molecular data, although various authors (e.g., Boulenger, 1894) had long recognized their relative basal position within caenophidians. Corrections and modifications to Zaher's (1999) generic arrangement followed in several molecular studies, which concentrated on the "boodontine" and psammophiine lineages, and in the placement of the North American xenodontines (Pinou et al, 2004;Lawson et al, 2005;Vidal et al, 2007Vidal et al, , 2008. Most importantly, the paraphyletic family Colubridae was redefined as a much more restrictive group, and most of the subfamilies recognized by Zaher (1999) were rearranged among various families and superfamilies (Pinou et al, 2004;Lawson et al, 2005;Vidal et al 2007Vidal et al , 2008.…”

“…Corrections and modifications to Zaher's (1999) generic arrangement followed in several molecular studies, which concentrated on the "boodontine" and psammophiine lineages, and in the placement of the North American xenodontines (Pinou et al, 2004;Lawson et al, 2005;Vidal et al, 2007Vidal et al, , 2008. Most importantly, the paraphyletic family Colubridae was redefined as a much more restrictive group, and most of the subfamilies recognized by Zaher (1999) were rearranged among various families and superfamilies (Pinou et al, 2004;Lawson et al, 2005;Vidal et al 2007Vidal et al , 2008. Lawson et al (2005) revised the allocation of many genera based on a molecular phylogeny of 100 caenophidians representing all subfamilies recognized by Zaher (1999).…”

“…Clade B of Lawson et al (2005) was referred to as "Colubroidea" by Pinou et al (2004) and subsequent authors. Vidal et al (2007Vidal et al ( , 2008) studied broad patterns of phylogenetic relationships among caenophidians based on an analysis of sequences from approximately 25-30 taxa, primarily from Africa, and revised some of the taxonomy of snakes based on their analyses. However, we feel that some of their formally recognized taxa are only weakly supported by their molecular data, or receive conflicting phylogenetic signals in different data sets.…”