A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery, but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question and a subject of vigorous debate. Here we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed.

中文翻译：

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基于模型的物种定界：聚结物种是生殖隔离的吗？

越来越多的系统主义者将物种定义为独立进化的谱系，可以通过分析从属于这些物种的个体中采样的等位基因的种群遗传历史来识别这些谱系。这推动了根植于多物种聚结过程的日益复杂的统计模型的发展。具体而言，这些模型允许仅使用来自独立基因座的 DNA 序列数据同时估计个体样本中存在的物种数量和这些物种的系统发育历史。这些方法在提高物种发现效率方面有着非凡的前景，但需要广泛的验证以确保它们的准确性和精确性。通过这些方法识别的物种是否与替代物种识别标准（例如生殖隔离的测量）所识别的物种相对应，目前是一个悬而未决的问题，也是一个激烈争论的主题。在这里，我们利用物种形成研究史上的经典模型系统，果蝇属的果蝇，对这些方法进行了实证检验。具体来说，我们使用该系统可用的关于生殖隔离的独特综合数据以及 DNA 序列数据，来询问在多物种聚结模型下推断出的果蝇物种是否与数十年的物种形成研究所认可的物种相对应。我们发现基于聚结和基于生殖隔离的推断物种边界的方法对于 77% 的物种对是一致的。我们探索和讨论这些差异的潜在解释。我们还发现，无论物种对是同域分布还是异域分布，两个物种之间的合子前隔离量是基于 DNA 序列数据的物种边界后验概率的强预测因子。