A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus.
BACKGROUND
With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61).


RESULTS
Increased 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, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades.


CONCLUSIONS
Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.
Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America.
Alex
http://orcid.org/0000-0002-5083-9993
A
Figueroa
Department of Biology, The Graduate School and Center, City University of New York, New York, NY, United States of America.|Department of Biology, 6S-143, College of Staten Island, 2800 Victory Boulevard, Staten Island, NY, United States of America.
Alexander D
AD
McKelvy
Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA, United States of America.
L Lee
LL
Grismer
Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America.
Charles D
CD
Bell
Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America.
Simon P
SP
Lailvaux
D000818:Animals; D001499:Bayes Theorem; D004272:DNA, Mitochondrial / Q000235:genetics; D014644:Genetic Variation; D016013:Likelihood Functions; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012911:Snakes / Q000145:classification / Q000235:genetics*; D013045:Species Specificity
D004272:DNA, Mitochondrial