Data from: What have been and what can be delimited as species using molecular data under the multi-species coalescent model? A case study using Hercules beetles (Dynastes; Dynastidae)

Molecular species delimitation using the multi-species coalescent model has become common for statistically and objectively determining species limits. Empirical examples of how consistently different molecular data sets delimit the same level of divergence as species using coalescent-based methods are still lacking. I applied the method of molecular species delimitation in the Bayesian Phylogenetics and Phylogeography (BPP) program to study species delimitation in the divergence between populations and between putative species across four species of Hercules beetles. The quantity and variability of the molecular data affected species delimitation. A divergence that represented a late stage along the speciation continuum, e.g. between sympatric biological species, could be delimited by BPP by fewer and less variable loci than a recent divergence, e.g. between geographic populations. My results further indicated that the use of genomic data could even over-split geographically continuously distributed populations into species. I compared my results with those from other empirical studies and argue for the need of a thorough review of the kind of evolutionary entities, e.g. geographic populations versus morphologically distinct taxa, that have been designated as species and whether such designations are consistent among studies.

基于多物种溯祖模型（multi-species coalescent model）的分子物种界定方法，现已成为统计学上客观厘定物种界限的通用研究手段。然而，目前仍缺乏相关实证案例，能够证实不同分子数据集可通过溯祖类方法，将同等分化程度的类群一致地界定为物种。本研究借助贝叶斯系统发育与系统地理学（Bayesian Phylogenetics and Phylogeography, BPP）程序中的分子物种界定方法，针对4种赫拉克勒斯甲虫（Hercules beetles）的种群间分化以及假定物种间的分化开展物种界定研究。研究结果显示，分子数据的规模与变异程度会对物种界定结果产生显著影响：相较于近期分化的类群（如地理种群间的分化），处于物种形成连续体（speciation continuum）晚期的分化（如同域生物物种（sympatric biological species）间的分化），仅需更少且变异度更低的基因座即可通过BPP程序完成界定。本研究结果还表明，使用基因组数据甚至可能将地理分布连续的种群过度划分为独立物种。最后，本研究将所得结果与其他实证研究进行了对比，并提出亟需全面审视两类被界定为物种的进化实体——即地理种群与形态独特的类群——同时还需核查不同研究间的物种界定标准是否具备一致性。