Applying integrative multispecies coalescent models to tackle the long-standing problem of species delimitation in allopatrically distributed populations

提出了多物种聚结模型（MSC）作为解决物种划界这一关键问题的方法。但最近的研究表明，这些模型往往过度分裂异域种群，因为它们受到种群结构的影响，而不仅仅是物种分歧。我们建议解决的问题，物种划界使用异地种群的新热带鱼类家族，Anablepidae，在分类学和系统学一直在流动，在过去的几年里，最近已经描述了几个新的物种，也由我们。这个科提供了一个有趣的系统来研究一般的物种划界问题，因为它包含了两个描述的物种，其种群出现在已经隔离了几百万年的排水沟中（即，可忽略的基因流），而一些物种对在排水系统内是parapatric的（即，基因流的潜力）。此外，这些鱼很容易在受控条件下繁殖，允许进行特定的杂交以测试生殖隔离是否确实在单独的结合谱系之间进化，生殖隔离是根据生物物种概念完成物种形成的主要要求。我们的目标是整合全基因组重测序数据（脊椎动物基因组计划将很快发布该家族的参考基因组）和表型数据（> 70个形态特征和几何形态测量学），以应用新开发的基于聚结器的整合分类方法，将这些数据集结合起来，并使用基因组数据进行贝叶斯参数估计结合启发式系谱分歧指数。然后，我们将验证输出的MSC为基础的物种界定，通过对比它的经验确定的程度之间的物种对生殖隔离。最后，我们将划分我们的分子数据，研究基因座选择对基于MSC的物种界定的影响。该家族Anablepidae构成了一个相对较小的家庭，只有大约20个类群的鱼，并提供了一个可管理的，但进化非常有趣的测试案例，其中一个可以比较，并详尽测试，这些新方法，以帮助识别，分类和描述新的物种，可以以后扩大到其他物种丰富的谱系。

Multispecies coalescent-based models (MSC) were proposed as a solution for the crucial problem of species delimitation. But recent work suggested that these models tend to over-split allopatric populations as they are affected by population structure rather than species divergence alone. We propose to address the problem of species delimitation using allopatric populations of a Neotropical fish family, the Anablepidae, in which taxonomy and systematics have been in flux in the last years and several new species have been recently described, also by us. This family provides an interesting system to study general species delimitation problems as it contains both described species whose populations occur in drainages that have been isolated for several million years (i.e., negligible gene flow), whereas some pairs of species are parapatric within drainages (i.e., potential for gene flow). Additionally, these fish are easy to breed under controlled conditions, allowing to do specific crosses to test if reproductive isolation, the major requirement for the completion of speciation according to the Biological Species Concept, has indeed evolved between separate coalescent lineages. We aim to integrate whole-genome resequencing data (the Vertebrate Genome Project will soon release a reference genome for the family) and phenotypic data (> 70 morphological characters and geometric morphometrics) to apply newly developed coalescent-based integrative taxonomic approaches that combine these data sets, as well as use genomic data to conduct Bayesian parameter estimation combined with heuristic genealogical divergence index. Then, we will validate the output of the MSC-based species delimitations by contrasting it to the empirically determined degree of reproductive isolation among species pairs. Finally, we will partition our molecular data to study the impact of locus selection on MSC-based species delimitation. The familiy Anablepidae constitutes a relatively small family of fish with only about 20 taxa and provides a manageable, but evolutionary highly interesting test case in which one can compare, and exhaustively test, these new methods to aid in the identification, classification and description of new species that can be later scaled up to other more species-rich lineages.