Data from: Upstream analyses create problems with DNA-based species delimitation

Genetic-based delimitation of species typically involves a multistep process in which DNA data are analyzed with a series of different programs. Although the performance of the programs associated with each step has been evaluated separately, no analysis has considered how errors in the upstream assignment of individuals to putative species impacts the accuracy of species delimited in downstream analyses, such as those associated with the coalescent-based Bayesian program bpp. Here we show that because the minimal data requirements for accurate performance in each of the separate steps involved in the delimitation process differ, the reliability of inferences about species delimited from DNA sequences can be compromised. Our results provide important insights into the practice of species delimitation. Specifically, even if users exercise the practices advocated for DNA-based delimitation, there may very well be errors in individual-species association, and consequently uncertainty in the guide tree (both derived from upstream analyses that are prerequisites for analyses with bpp), which can lead to under or overestimation of biodiversity, even though the Bayesian program bpp itself may perform very well. These results highlight the usefulness of complementary data (i.e., data in addition to genetic data), especially for the assignment of individuals to putative species, to improve the accuracy of species delimitation.

基于遗传学的物种界定通常包含一套多步骤分析流程，即通过多款不同程序对DNA数据进行解析。尽管学界已针对该流程各环节所使用程序的独立性能开展了评估，但尚无研究考量将个体归类至推定物种的上游分析误差，会如何影响下游分析中所界定物种的准确性——例如基于溯祖理论的贝叶斯程序BPP相关分析。本研究表明，由于物种界定流程各独立环节实现准确性能所需的最低数据要求存在差异，基于DNA序列开展物种界定推断的可靠性或遭削弱。我们的研究结果为物种界定实践提供了重要洞见：具体而言，即便研究者遵循了基于DNA开展物种界定的推荐操作规范，个体与推定物种的关联仍可能存在误差，进而导致指导树（该树源自BPP分析的前置上游分析流程）存在不确定性；即便贝叶斯程序BPP本身的性能表现优异，此类不确定性仍可能引发生物多样性的低估或高估。上述研究结果凸显了互补数据（即除遗传数据外的其他类型数据）的应用价值，尤其是在将个体归类至推定物种的环节中，此类数据可有效提升物种界定的准确性。