Largest snake phylogeny study to date, recovers a new colubrid subfamily

The new subfamily Ahaetuliinae contains Ahaetulla (left) and  Dryophiops (right). JCM

In a recently published paper in PLoS One Figueroa et al. (2016) provide a species level phylogeny for 1652 snake species and describe a new colubrid subfamily and genus based upon 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera and species.The increase of taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic.  With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Some of the highlights include the following:

Similar to many prior examinations, the authors find relationships within Scolecophidia are unresolved with studies showing either Scolecophidia , Anomalepididae or Leptotyphlopidae + Typhlopoidea as sister to all snakes. They found weak support for the placement of Asiatyphlopinae, Afrotyphlopinae, and Madatyphlopinae within Typhlopidae as in previous studies.

They found Cylindrophiidae is paraphyletic with Anomochilidae and recommend retaining the current classification until more species are sampled.

They recovered for Xenophidiidae + Bolyeridae (SHL = 91). Earlier studies considered these sister to various clades within Henophidia but this study found very strong support (SHL = 100) for them as sister to the Caenophidia (SHL = 100), as shown in other studies. These snakes possess morphological characters, particularly within the palate, bolstering their close relationship with Caenophidia and not to Henophidia. If this placement is retained, then Caenophidia should be redefined to include Xenophidiidae and Bolyeridae, or they should be given their own taxonomic grouping.

The study confirmed previous studies finding that Xenodermatidae is sister to the rest of Colubroidea (SHL = 100) and that relationships within Lamprophiidae and Colubridae remain unresolved, but this study found the placement of Homalopsidae contradicted previous work, and they recovered strong support (SHL = 91) for Homalopsidae + Lamprophiidae, and found Elapidae to be nested within Lamprophiidae. Typically, Lamprophiidae and Elapidae are recovered as distinct clades. Pareatidae is consistently placed as sister to Viperidae, which is sister to Colubridae, Elapidae, Homalopsidae, and Lamprophiidae. 

For Colubridae, the study recovered the following four subclades: i) Sibynophiinae + Natricinae (SHL = 80); ii) Pseudoxenodontinae + Dipsadinae (SHL = 82); iii) Grayiinae + Calamariinae (SHL = 70); and iv) Ahaetuliinae subfam. nov. + Colubrinae (SHL = 95). The nodes between these subclades all received very strong support (SHL > 97). The only consistently recovered clade among these is subclade ii; although other studies did not recover this subclade. Several studies also regularly recovered the subclade Natricinae + (Pseudoxenodontinae + Dipsadinae).  Until now, the basal node of Colubrinae has remained ambiguous. Previous authors suggested that monophyly of Ahaetulla, Chrysopelea, and Dendrelaphis at the base of Colubrinae, may warrant recognition as a distinct subfamily, but support for division of these taxa in their study was low. Due to increased sampling, and the inclusion of Dryophiops, we established strong support for recognizing these taxa as a new subfamily, using the name proposed by Pyron et al, Ahaetuliinae subfam. nov.

Citation
Figueroa A, McKelvy AD, Grismer LL, Bell CD, Lailvaux SP (2016) A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus. PLoS ONE 11(9): e0161070. doi:10.1371/journal.pone.0161070