Bell Museum of Natural History, Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, 55108, USA.
Mol Ecol. 2013 Oct;22(19):4943-57. doi: 10.1111/mec.12446.
The process of discovering species is a fundamental responsibility of systematics. Recently, there has been a growing interest in coalescent-based methods of species delimitation aimed at objectively identifying species early in the divergence process. However, few empirical studies have compared these new methods with character-based approaches for discovering species. In this study, we applied both a character-based and a coalescent-based approaches to delimit species in a closely related avian complex, the light-vented/Taiwan bulbul (Pycnonotus sinensis/Pycnonotus taivanus). Population aggregation analyses of plumage, mitochondrial and 13 nuclear intron character data sets produced conflicting species hypotheses with plumage data suggesting three species, mitochondrial data suggesting two species, and nuclear intron data suggesting one species. Such conflict is expected among recently diverged species, and by integrating all sources of data, we delimited three species verified with independently congruent character evidence as well as a more weakly supported fourth species identified by a single character. Attempts to validate species hypothesis using Bayesian Phylogenetics and Phylogeography (BPP), a coalescent-based method of species delimitation, revealed several issues that can seemingly affect statistical support for species recognition. We found that θ priors had a dramatic impact on speciation probabilities, with lower values consistently favouring splitting and higher values consistently favouring lumping. More resolved guide trees also resulted in overall higher speciation probabilities. Finally, we found suggestive evidence that BPP is sensitive to the divergent effects of nonrandom mating caused by intraspecific processes such as isolation-with-distance, and therefore, BPP may not be a conservative method for delimiting independently evolving population lineages. Based on these concerns, we questioned the reliability of BPP results and based our conclusions about species limits exclusively on character data.
物种发现的过程是系统学的基本职责。最近，人们对基于合并的物种界定方法越来越感兴趣，这些方法旨在在分化过程的早期客观地识别物种。然而，很少有经验研究将这些新方法与基于特征的方法进行比较，以发现物种。在这项研究中，我们应用了基于特征和基于合并的方法来划定亲缘关系密切的鸟类复合体——亮喉/台湾画眉（Pycnonotus sinensis/Pycnonotus taivanus）中的物种。羽毛、线粒体和 13 个核内含子特征数据集的种群聚集分析产生了相互矛盾的物种假说，其中羽毛数据表明有三个物种，线粒体数据表明有两个物种，核内含子数据表明有一个物种。这种冲突在最近分化的物种中是预期的，通过整合所有来源的数据，我们划定了三个物种，这些物种的特征证据独立一致，还有一个支持较弱的第四个物种，仅由一个特征确定。使用基于合并的物种界定方法——贝叶斯系统发生和系统地理学（BPP）来验证物种假说，我们发现了一些似乎会影响物种识别统计支持的问题。我们发现θ先验值对物种形成概率有显著影响，较低的值一直有利于分裂，而较高的值一直有利于合并。更解析的引导树也导致了整体更高的物种形成概率。最后，我们发现了一些有说服力的证据表明，BPP 对由种内过程（如隔离距离）引起的非随机交配的分歧效应敏感，因此，BPP 可能不是一种保守的方法，无法用于划定独立进化的种群谱系。基于这些担忧，我们对 BPP 结果的可靠性提出了质疑，并完全基于特征数据得出了关于物种界限的结论。
