Data from: Assessing species boundaries and the phylogenetic position of the rare Szechwan Ratsnake, Euprepiophis perlacea (Serpentes: Colubridae), using coalescent-based methods

Delimiting species and clarifying phylogenetic relationships are the main goals of systematics. For species with questionable taxonomic status, species delimitation approaches using multi-species coalescent models with multiple loci are recommended if morphological data are unavailable or unhelpful. Moreover, these methods will also reduce subjectivity based on genetic distance or requirement of monophyletic genetic lineages. We determine the validity and phylogenetic position of a rare and long controversial species of Chinese reptile, the Szechwan ratsnake (Euprepiophis perlacea), using multi-locus data from multiple individuals and coalescent-based approaches. Species were first delimited using Bayesian Phylogenetics & Phylogeography (BP&P), Brownie and Bayes Factor model comparison approaches, while relationships among species were estimated using species tree inference in *BEAST. Results indicate that Euprepiophis perlacea is a distinct species sister to Euprepiophis mandarinus. Despite gene tree discrepancy, the coalescent model-based approaches used here demonstrate the taxonomic validity and the phylogenetic position of Euprepiophis perlacea. These approaches objectively test the validity of questionable species diagnoses based on morphological characters and determine their phylogenetic position.

物种界定与系统发育关系解析是系统分类学（systematics）的核心研究目标。对于分类学地位存疑的类群，若形态学数据无法获取或参考价值有限，推荐采用基于多基因座与多物种溯祖模型（multi-species coalescent models）的物种界定方法。此外，此类方法还可降低基于遗传距离或单系遗传支系（monophyletic genetic lineages）要求所带来的主观性。

本研究针对中国珍稀且长期存在分类争议的爬行动物物种——四川锦蛇（Szechwan ratsnake, *Euprepiophis perlacea*），采用多个体多基因座数据与基于溯祖模型的分析方法，对其分类有效性与系统发育位置进行厘定。研究首先采用贝叶斯系统发育与系统地理学（Bayesian Phylogenetics & Phylogeography, BP&P）、Brownie以及贝叶斯因子模型比较等方法开展物种界定，并借助*BEAST*软件中的物种树推断流程估算物种种间关系。

分析结果显示，*Euprepiophis perlacea*是与*Euprepiophis mandarinus*互为姐妹群的独立有效物种。尽管存在基因树（gene tree）拓扑冲突，但本研究采用的基于溯祖模型的分析方法，证实了四川锦蛇的分类有效性与系统发育位置。此类方法可客观检验基于形态性状所提出的存疑物种界定的合理性，并准确厘定其系统发育位置。