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

Alex Figueroa,Simon P Lailvaux,L Lee Grismer,Alexander D Mckelvy,Charles D Bell,Aristeidis Parmakelis

doi:10.1371/journal.pone.0161070

Abstract

BackgroundWith 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).ResultsIncreased 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.ConclusionOur 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.

Highlights

Phylogenies form the cornerstone of our understanding of evolutionary relationships between organisms and provide a historical basis for testing and inferring ecological and evolutionary processes [1,2,3,4]
The supermatrix uses concatenated sequences to estimate large-scale phylogenies with branch lengths [11,12,13,14,15,16,17]. This technique has earned criticism because large amounts of missing data may obscure phylogenetic signal, leading to uncertainty in topology and branch lengths [18,19,20,21], but shortcut coalescence methods are prone to these same shortcomings [10]
The dataset consisted of 9,523 bp from the following 10 genes: three mitochondrial protein-coding genes, cytochrome b, NADH subunit 2 (ND2; 1,042 bp; 334 taxa), and NADH subunit 4 (ND4; 802 bp; 986 taxa); two non-coding ribosomal genes (12S; 790 bp; 1,023 taxa) and (16S; 649 bp; 1,167 taxa); and five nuclear protein-coding genes, brain-derived neurotrophic factor precursor (BDNF; 675 bp; 314 taxa), neurotrophin-3 (NT3; 669 bp; 449 taxa), oocyte maturation factor Mos (c-mos; 753 bp; 957 taxa), and two recombination-activating genes (RAG-1.1; 926 bp; 209 taxa, RAG-1.2; 880 bp; 166 taxa; RAG-1.3; 517 bp; 153 taxa), and (RAG-2; 716 bp; 153 taxa)

Summary

Introduction

Phylogenies form the cornerstone of our understanding of evolutionary relationships between organisms and provide a historical basis for testing and inferring ecological and evolutionary processes [1,2,3,4]. The supermatrix uses concatenated sequences to estimate large-scale phylogenies with branch lengths [11,12,13,14,15,16,17] This technique has earned criticism because large amounts of missing data may obscure phylogenetic signal, leading to uncertainty in topology and branch lengths [18,19,20,21], but shortcut coalescence methods are prone to these same shortcomings [10]. Several studies have shown that concatenated procedures may produce similar results to species-trees [8,22], when there is no agreement among gene trees, and between gene and species trees [7] This is the case for deep divergences because shortcut coalescence has difficulty integrating gene-tree incongruity at this level [10]. 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)

Methods

Results

Conclusion