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（systematics）的核心使命之一。近年来，旨在于物种分化早期客观界定物种的基于溯祖（coalescent）的物种界定方法愈发受到学界关注。然而，鲜有实证研究将这类新兴方法与基于性状的物种发现路径进行对比。本研究针对亲缘关系密切的鸟类复合群——淡喉鹎/台湾鹎（Pycnonotus sinensis/Pycnonotus taivanus），分别采用基于性状的方法与基于溯祖的方法开展物种界定工作。对羽色、线粒体基因组以及13个核内含子的性状数据集开展种群聚集分析后，得到了相互矛盾的物种假说：羽色数据支持划分为3个物种，线粒体数据支持划分为2个物种，而核内含子数据则支持仅为1个物种。这类冲突在新近分化的类群中实属常见；本研究整合所有来源的数据后，界定出3个得到独立一致性状证据验证的物种，以及1个仅由单一性状识别、支持度较弱的第四物种。借助贝叶斯系统发育与系统地理学（BPP）——一种基于溯祖的物种界定方法——对物种假说进行验证的过程中，我们发现了若干可能影响物种识别统计支持度的问题。研究发现，θ先验对物种形成概率具有显著影响：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。分辨率更高的引导树也会整体提升物种形成概率。最后，我们得到了提示性证据：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或许并非界定独立进化种群谱系的保守方法。基于上述顾虑，我们对BPP结果的可靠性提出质疑，并将物种界限的相关结论完全建立在性状数据之上。