Figueroa Alex, McKelvy Alexander D, Grismer L Lee, Bell Charles D, Lailvaux Simon P
Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States of America.
Department of Biology, The Graduate School and Center, City University of New York, New York, NY, United States of America.
PLoS One. 2016 Sep 7;11(9):e0161070. doi: 10.1371/journal.pone.0161070. eCollection 2016.
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).
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.
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.
蛇类有超过3500个物种，形态和生态多样，占有鳞目多样性的36%。尽管多次尝试估计蛇类的高级别亲缘关系，以及对属级或种级系统发育进行了大量评估，但尚未完成一个仅专注于蛇类的大规模种级系统发育研究。在此，我们使用最大似然法，基于一个包含1745个分类单元（1652个蛇类物种 + 7个外类群分类单元）和来自10个基因座（5个核基因座、5个线粒体基因座）的9523个碱基对的超级矩阵，提供了迄今为止最大规模的蛇类生命树估计，其中包括先前未测序的属（2个）和物种（61个）。
增加分类单元采样得到了一个具有新的高级别拓扑结构的系统发育树，证实了许多低级别关系，低至种级别的节点支持值较高（> 85%），物种水平的节点支持率为73.69%。尽管大多数科和亚科以> 88%的支持值被强烈支持为单系类群，但一些科和许多属是并系的，主要是由于分类单元和基因座采样有限，导致超级矩阵稀疏，一些近缘分类单元之间的序列重叠最小。去除所有流氓分类单元和分类地位不确定的物种后，除了五个有问题的分支外，高级别关系和支持值相对保持不变。
我们的分析产生了新的高级别和低级别拓扑结构；解决了一些先前的拓扑问题；建立了新的并系关系；为金花蛇属、飞蛇属、锦蛇属和金花蛇属设立了一个新的亚科，金花蛇亚科；并将斑马锦蛇（Coluber）zebrinus归入一个新属，莫潘维尔德蛇属。尽管我们对一些明显有问题的节点提供了见解，但在更深的系统发育尺度上，解决这些节点可能需要对进化较慢的核基因进行采样。
