Data from: Species Delimitation with Gene Flow

Species are commonly thought to be evolutionarily independent in a way that populations within a species are not. In recent years, studies that seek to identify evolutionarily independent lineages (i.e., to delimit species) using genetic data have typically adopted multispecies coalescent approaches that assume that evolutionary independence is formed by the differential sorting of ancestral alleles due to genetic drift. However, gene flow appears to be common among populations and nascent species, and while this process may inhibit lineage divergence (and thus independence), it is usually not explicitly considered when delimiting species. In this paper, we apply PHRAPL, a recently described method for phylogeographic model selection, to species delimitation. We describe an approach to delimiting species using PHRAPL that attempts to account for both genetic drift and gene flow, and we compare the method’s performance to that of a popular delimitation approach (BPP) using both simulated and empirical datasets. PHRAPL generally infers the correct demographic-delimitation model when the generating model includes gene flow between taxa, given a sufficient amount of data. When the generating model includes only isolation in the recent past, PHRAPL will in some cases fail to differentiate between gene flow and divergence, leading to model misspecification. Nevertheless, the explicit consideration of gene flow by PHRAPL is an important complement to existing delimitation approaches, particularly in systems where gene flow is likely important.

物种通常被认为在演化上具有独立性，而同一物种内的种群则不具备这一特征。近年来，借助遗传数据鉴定演化独立性谱系（即物种界定）的研究，通常采用多物种溯祖（multispecies coalescent）方法，这类方法假设演化独立性由遗传漂变导致的祖先等位基因差异分选所形成。然而，种群与新生物种间的基因流（gene flow）似乎十分普遍；尽管该过程会抑制谱系分化（进而影响演化独立性），但在物种界定研究中，该因素通常未被纳入明确考量范围。本研究将新近提出的系统地理模型选择方法PHRAPL应用于物种界定任务。我们提出了一种依托PHRAPL开展物种界定的分析框架，该框架可同时考量遗传漂变与基因流的影响，并通过模拟数据集与实证数据集，将该方法的性能与主流物种界定方法BPP进行对比。当生成模型包含类群间基因流且数据量充足时，PHRAPL通常可准确推断出人口统计学-物种界定模型。当生成模型仅涉及近期隔离过程时，PHRAPL在部分场景下无法区分基因流与类群分化，进而导致模型误设。尽管如此，PHRAPL对基因流的明确考量仍是对现有物种界定方法的重要补充，尤其适用于基因流作用显著的研究体系。