Data from: Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae)

Species delimitation is a major research focus in evolutionary biology because accurate species boundaries are a prerequisite for the study of speciation. New species delimitation methods (SDMs) can accommodate non-monophyletic species and gene tree discordance as a result of incomplete lineage sorting via the coalescent model, but do not explicitly accommodate gene flow after divergence. Approximate Bayesian Computation (ABC) can incorporate gene flow and estimate other relevant parameters of the speciation process while testing alternative species delimitation hypotheses. We evaluated the accuracy of BPP, SpeDeSTEM, and ABC for delimiting species using simulated data and applied these methods to empirical data from lizards of the Liolaemus darwinii complex. Overall, BPP was the most accurate, ABC showed an intermediate accuracy, and SpeDeSTEM was the least accurate under most simulated conditions. All three SDMs showed lower accuracy when speciation occurred despite gene flow, as found in previous studies, but ABC was the method with the smallest decrease in accuracy. All three SDMs consistently supported the distinctness of southern and northern lineages within L. darwinii. These SDMs based on genetic data should be complemented with novel SDMs based on morphological and ecological data to achieve truly integrative and statistically robust approaches to species discovery.

物种界定（species delimitation）是进化生物学的核心研究议题，精准的物种边界是开展物种形成研究的必要前提。新型物种界定方法（species delimitation methods, SDMs）可通过溯合模型（coalescent model）适配非单系物种以及由不完全谱系分选（incomplete lineage sorting）引发的基因树冲突，但未明确纳入物种分化后的基因流（gene flow）场景。近似贝叶斯计算（Approximate Bayesian Computation, ABC）可在检验不同物种界定假说的同时，纳入基因流并估算物种形成过程中的其他相关参数。我们通过模拟数据评估了BPP、SpeDeSTEM与ABC三种方法的物种界定准确性，并将这些方法应用于达尔文莱欧蜥蜴复合群（Liolaemus darwinii complex）的实证数据。总体而言，在多数模拟实验条件下，BPP的准确性最高，ABC处于中等水平，SpeDeSTEM的准确性最低。当物种形成伴随基因流发生时，三种SDMs的准确性均出现下降，这与既往研究结果一致，其中ABC的准确性降幅最小。三种SDMs均一致支持达尔文莱欧蜥蜴复合群内南部支系与北部支系的分化显著性。这类基于遗传数据的物种界定方法，应当与基于形态学和生态学数据的新型物种界定方法相互补充，以构建真正具备整合性与统计稳健性的物种发现研究范式。