Data from: An empirical comparison of a character-based and a coalescent-based approach to species delimitation in a young avian complex

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.物种发现是分类学的一项基础性核心职责。近年来，基于溯祖（coalescent）的物种界定方法愈发受到关注，这类方法旨在在物种分化早期阶段客观地识别物种。然而，目前鲜有实证研究将这类新兴方法与基于性状（character）的物种发现方法进行对比。本研究中，我们同时采用基于性状法与基于溯祖法，对一个近缘鸟类复合类群——白头鹎（Pycnonotus sinensis）/台湾鹎（Pycnonotus taivanus）进行物种界定。基于羽色、线粒体数据以及13个核内含子性状数据集的种群聚类分析，得出了相互矛盾的物种界定假说：羽色数据支持划分为3个物种，线粒体数据支持2个物种，核内含子数据则仅支持1个物种。这类冲突在新近分化的物种类群中实属常见；通过整合所有数据源，我们最终界定出3个得到多套独立一致性状证据支持的物种，以及1个仅由单个性状支持、支持度相对较弱的第四种。我们尝试使用基于溯祖的物种界定工具贝叶斯系统发育与系统地理学（Bayesian Phylogenetics and Phylogeography, BPP）来验证物种假说，结果发现了若干可能会影响物种识别统计支持度的问题。研究发现，θ先验分布对物种分化概率具有显著影响：较低的θ先验值始终倾向于支持物种拆分，较高的θ先验值则始终倾向于支持物种合并。分辨率更高的指导树同样会整体提升物种分化概率。最后，我们发现有提示性证据表明，BPP对由种内过程（如距离隔离）引发的非随机交配的差异化效应较为敏感；因此，BPP或许并非界定独立演化种群谱系的保守性方法。基于上述顾虑，我们对BPP结果的可靠性提出质疑，并仅基于性状数据得出关于物种界定边界的结论。