A large-scale systematic framework of Chinese snakes based on a unified multilocus marker system

Snakes are one of the most diverse groups of terrestrial vertebrates, with
approximately 3500 extant species, some of which are closely related to
human life. A robust phylogeny and taxonomy of snakes is crucial for us to
know, study, protect and make use of them. For a large group such as
snakes, cross-study data utilization is important which can be facilitated
by standardization of the loci used for systematic analyses. In this
study, we combined 5 mitochondrial markers, 19 vertebrate-universal
nuclear protein coding (NPC) markers and 72 snake-specific noncoding
intron markers, and generated a unified multilocus marker system for
studies of snake systematics. This marker system is an addition to the
squamate conserved locus set compiled for large-scale sequence capture
experiments. We applied this marker system to over 440 snake samples and
constructed the currently most comprehensive systematics framework of the
snakes in China. Robust snake phylogenetic relationships were recovered at
both deep and shallow evolutionary depths, demonstrating the usefulness of
this multilocus marker system. Discordance was revealed by a parallel
comparison between the snake tree based on our multilocus marker system
and that based on only the mitochondrial loci, highlighting the necessity
of using multiple marker types to better understand the snake evolutionary
histories. The divergence times of different snake groups were estimated
with the multilocus data set. Our comprehensive snake tree not only
confirms many important nodes inferred in previous studies but also
contributes new insights into the phylogenetic relationships among snakes.
Suggestions are made for the current snake taxonomy.