Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.
Syst Biol. 2012 Jan;61(1):63-79. doi: 10.1093/sysbio/syr077. Epub 2011 Aug 9.
The rapid accumulation of multilocus data sets has led to dramatic advances in methodologies for estimating evolutionary relationships among closely related species, but relatively less advancement has been made in methods for discriminating between competing species delimitation hypotheses. Multilocus data sets provide an advantage in testing species delimitation scenarios because they offer a direct test of species monophyly and aid in the biological interpretation of such phenomena as allele-sharing and deep coalescent events. Most species tree estimation methods that are designed to analyze multilocus data sets require the a priori assignment of individuals to species categories and therefore do not provide a strategy to directly test competing species delimitation scenarios. An approach was recently proposed that utilizes a coalescent-based species tree estimation method to inform species delimitation decisions by comparing likelihood scores that measure the fit of gene trees within a given species tree. We use a multilocus nuclear and mitochondrial DNA sequence data set to both reexamine a recently proposed species delimitation scenario in the Etheostoma simoterum species complex and test the utility of species tree estimation methods in testing species delimitation hypotheses. Descriptions of species in the E. simoterum species complex of snubnose darters, a group of six teleost freshwater fish species, are based largely on male nuptial coloration. Most of the putative species are nonmonophyletic at every examined locus. Using a novel combination of Bayesian-estimated gene tree topologies, Bayesian phylogenetic species tree inferences, coalescent simulations, and examination of phenotypic variation, we assess the occurrence of shared alleles among species, and we propose that results from our analyses support a three-species rather than a six-species delimitation scenario in the E. simoterum complex. We found that comparing likelihood scores from the species tree estimation approach used across many potential delimitation scenarios resulted in a systematic bias toward over-splitting in the E. simoterum complex and failed to support a species delimitation scenario that was consistent with geography, phenotype, or any previous species delimitation hypothesis. Despite common expectations, we demonstrate that application of molecular approaches to species delimitation can result in the recognition of fewer, instead of a larger number of species. In addition, our analyses highlight the importance of phenotypic character information in providing an independent assessment of alternative species delimitation hypotheses in the E. simoterum species complex.
多基因数据集的快速积累使得估计密切相关物种之间进化关系的方法取得了显著进展，但在区分竞争物种界限假说的方法方面相对进展较少。多基因数据集在检验物种界限情景方面具有优势，因为它们提供了物种单系性的直接检验，并有助于解释等位基因共享和深合并事件等现象。大多数旨在分析多基因数据集的种系树估计方法都需要先验地将个体分配到物种类别，因此不能提供直接检验竞争物种界限情景的策略。最近提出了一种方法，该方法利用基于合并的种系树估计方法，通过比较衡量给定种系树内基因树拟合度的似然评分来告知物种界限决策。我们使用多基因核和线粒体 DNA 序列数据集来重新检验最近提出的 Etheostoma simoterum 物种复合体的物种界限情景，并测试种系树估计方法在检验物种界限假说中的效用。Etheostoma simoterum 物种复合体的 snubnose darters 是一组六种淡水鱼类，其物种描述主要基于雄性婚色。在每个检查的基因座上，大多数假定的物种都不是单系的。使用贝叶斯估计的基因树拓扑结构、贝叶斯系统发育物种树推断、合并模拟和表型变异的检查的新颖组合，我们评估了物种之间共享等位基因的出现情况，并提出我们的分析结果支持在 E. simoterum 复合体中采用三物种而不是六物种的界限情景。我们发现，比较在许多潜在的界限情景中使用的种系树估计方法的似然评分会导致 E. simoterum 复合体中过度分裂的系统偏差，并且无法支持与地理、表型或任何先前的物种界限假设一致的物种界限情景。尽管有共同的期望，但我们证明，将分子方法应用于物种界限划分可能会导致识别的物种数量减少，而不是增加。此外，我们的分析强调了表型特征信息在为 E. simoterum 物种复合体中的替代物种界限假说提供独立评估方面的重要性。
