Gratton Paolo, Trucchi Emiliano, Trasatti Alessandra, Riccarducci Giorgio, Marta Silvio, Allegrucci Giuliana, Cesaroni Donatella, Sbordoni Valerio
Dipartimento di Biologia, Università di Roma "Tor Vergata", Via della Ricerca Scientifica, 00133 Roma Italy; Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, 6, 04103 Leipzig Germany;
Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO Box 1066, Blindern, Oslo 0316 Norway; and Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
Syst Biol. 2016 Mar;65(2):292-303. doi: 10.1093/sysbio/syv087. Epub 2015 Nov 14.
All species concepts are rooted in reproductive, and ultimately genealogical, relations. Genetic data are thus the most important source of information for species delimitation. Current ease of access to genomic data and recent computational advances are blooming a plethora of coalescent-based species delimitation methods. Despite their utility as objective approaches to identify species boundaries, coalescent-based methods (1) rely on simplified demographic models that may fail to capture some attributes of biological species, (2) do not make explicit use of the geographic information contained in the data, and (3) are often computationally intensive. In this article, we present a case of species delimitation in the Erebia tyndarus species complex, a taxon regarded as a classic example of problematic taxonomic resolution. Our approach to species delimitation used genomic data to test predictions rooted in the biological species concept and in the criterion of coexistence in sympatry. We (1) obtained restriction-site associated DNA (RAD) sequencing data from a carefully designed sample, (2) applied two genotype clustering algorithms to identify genetic clusters, and (3) performed within-clusters and between-clusters analyses of isolation by distance as a test for intrinsic reproductive barriers. Comparison of our results with those from a Bayes factor delimitation coalescent-based analysis, showed that coalescent-based approaches may lead to overconfident splitting of allopatric populations, and indicated that incorrect species delimitation is likely to be inferred when an incomplete geographic sample is analyzed. While we acknowledge the theoretical justification and practical usefulness of coalescent-based species delimitation methods, our results stress that, even in the phylogenomic era, the toolkit for species delimitation should not dismiss more traditional, biologically grounded, approaches coupling genomic data with geographic information.
所有物种概念都植根于生殖关系，最终是谱系关系。因此，遗传数据是物种界定最重要的信息来源。当前获取基因组数据的便捷性以及近期的计算进展催生了大量基于溯祖理论的物种界定方法。尽管这些方法作为识别物种边界的客观途径具有实用性，但基于溯祖理论的方法存在以下问题：（1）依赖简化的种群统计模型，可能无法捕捉生物物种的某些特征；（2）没有明确利用数据中包含的地理信息；（3）计算量通常很大。在本文中，我们展示了在Erebia tyndarus物种复合体中的一个物种界定案例，该分类单元被视为分类学分辨率存在问题的经典例子。我们的物种界定方法利用基因组数据来检验基于生物物种概念和同域共存标准的预测。我们（1）从精心设计的样本中获取限制性位点相关DNA（RAD）测序数据，（2）应用两种基因型聚类算法来识别遗传簇，（3）对遗传簇内部和之间进行距离隔离分析，作为对内在生殖障碍的检验。将我们的结果与基于贝叶斯因子界定的溯祖理论分析结果进行比较，结果表明基于溯祖理论的方法可能导致对异域种群过度自信的划分，并且表明当分析不完整的地理样本时，可能会推断出错误的物种界定。虽然我们承认基于溯祖理论的物种界定方法的理论依据和实际用途，但我们的结果强调，即使在系统发育基因组学时代，物种界定的工具包也不应摒弃将基因组数据与地理信息相结合的更传统、基于生物学的方法。
