Jackson Nathan D, Carstens Bryan C, Morales Ariadna E, O'Meara Brian C
Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 442 Hesler Biology Building, Knoxville, TN 37996, USA.
Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA.
Syst Biol. 2017 Sep 1;66(5):799-812. doi: 10.1093/sysbio/syw117.
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 article, we apply Phylogeographic Inference using Approximate Likelihoods (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. [approximate likelihoods; coalescent simulations; genealogical divergence index; Homo sapiens; isolation-with-migration; multispecies coalescent; Sarracenia; Scincella.].
通常认为物种在进化上是独立的，而同一物种内的种群则并非如此。近年来，利用遗传数据来识别进化上独立的谱系（即界定物种）的研究通常采用多物种溯祖方法，该方法假定进化独立性是由遗传漂变导致的祖先等位基因的差异分选形成的。然而，基因流在种群和新物种中似乎很常见，虽然这个过程可能会抑制谱系分化（进而抑制独立性），但在界定物种时通常没有明确考虑这一点。在本文中，我们将使用近似似然法的系统发育地理学推断法（PHRAPL），一种最近描述的用于系统发育地理学模型选择的方法，应用于物种界定。我们描述了一种使用PHRAPL来界定物种的方法，该方法试图同时考虑遗传漂变和基因流，并使用模拟数据集和实证数据集将该方法的性能与一种流行的界定方法（BPP）进行比较。在有足够数据的情况下，如果生成模型包括类群之间的基因流，PHRAPL通常能推断出正确的种群统计学界定模型。当生成模型仅包括近期的隔离时，在某些情况下PHRAPL无法区分基因流和分化，从而导致模型误设。尽管如此，PHRAPL对基因流的明确考虑是对现有界定方法的重要补充, 特别是在基因流可能很重要的系统中。[近似似然法；溯祖模拟；谱系分化指数；智人；迁移隔离模型；多物种溯祖；瓶子草属；蜓蜥属。]
