Genomic evidence sheds new light on phylogeny of Rhabdophis nuchalis (sensu lato) complex (Serpentes: Natricidae)

Abstract

Stable taxonomy and robust phylogeny are essential for the evolution and conservation of organisms. The Rhabdophis nuchalis (sensu lato) complex presently contains three species (R. nuchalis, R. chiwen, R. pentasupralabialis). Although several studies have explored the diversity and phylogeography of this group, certain issues related to systematics and taxonomy remain unresolved. Here, based on genome-wide data, including single nucleotide polymorphisms (SNPs) generated from ddRAD-seq and mitochondrial DNA (mtDNA), we re-evaluated the phylogenetic relationships and cryptic diversity of this species group. Our results are generally consistent with previous studies but provide some new insights. Phylogenetic relationship reconstruction based on SNPs and mtDNA revealed that three species in the R. nuchalis (sensu lato) complex did not form a monophyly but each species is well supported as monophyletic lineage in SNP-based analyses. Population structure analyses showed genetic admixture between several species pairs. Additionally, the population in eastern Yunnan, China, was identified as a potential cryptic species and thus described as a new species based on morphological data. From our results and previous studies, we redefined the distribution boundary for each species in the R. nuchalis (sensu lato) species complex.