CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.
Rutgers, the State University of New Jersey, Piscataway, New Jersey.
Mol Ecol Resour. 2019 Sep;19(5):1164-1180. doi: 10.1111/1755-0998.13027. Epub 2019 Jun 6.
Organisms sampled for population-level research are typically assigned to species by morphological criteria. However, if those criteria are limited to one sex or life stage, or the organisms come from a complex of closely related forms, the species assignments may misdirect analyses. The impact of such sampling can be assessed from the correspondence of genetic clusters, identified only from patterns of genetic variation, to the species identified using only phenotypic criteria. We undertook this protocol with the rock-dwelling mbuna cichlids of Lake Malawi, for which species within genera are usually identified using adult male coloration patterns. Given high local endemism of male colour patterns, and considerable allele sharing among species, there persists considerable taxonomic uncertainty in these fishes. Over 700 individuals from a single transect were photographed, genotyped and separately assigned: (a) to morphospecies using photographs; and (b) to genetic clusters using five widely used methods. Overall, the correspondence between clustering methods was strong for larger clusters, but methods varied widely in estimated number of clusters. The correspondence between morphospecies and genetic clusters was also strong for larger clusters, as well as some smaller clusters for some methods. These analyses generally affirm (a) adult male-limited sampling and (b) the taxonomic status of Lake Malawi mbuna, as the species in our study largely appear to be well-demarcated genetic entities. More generally, our analyses highlight the challenges for clustering methods when the number of populations is unknown, especially in cases of highly uneven sample sizes.
用于群体水平研究的生物通常根据形态标准被分配到物种中。然而，如果这些标准仅限于一个性别或生命阶段，或者生物体来自密切相关的形式复合体，那么物种的分配可能会误导分析。可以通过仅从遗传变异模式识别的遗传聚类与仅使用表型标准识别的物种之间的对应关系来评估这种采样的影响。我们使用马拉维湖的岩石栖息 mbuna 慈鲷进行了这项研究，这些慈鲷通常使用成年雄性的颜色图案来识别属内的物种。鉴于当地雄性颜色模式的高度特有性以及物种之间相当大的等位基因共享，这些鱼类仍然存在相当大的分类学不确定性。从一个单一的横断面上拍摄了超过 700 个个体的照片、进行了基因分型，并分别进行了以下处理：(a) 使用照片对形态种进行分类；(b) 使用五种广泛使用的方法对遗传聚类进行分类。总体而言，较大聚类的聚类方法之间的对应关系较强，但方法在估计聚类数量方面差异很大。形态种和遗传聚类之间的对应关系也很强，对于某些方法的一些较小聚类也是如此。这些分析普遍证实了以下两点：(a) 仅对成年雄性进行采样，以及 (b) 马拉维湖 mbuna 的分类地位，因为我们研究中的物种在很大程度上似乎是很好区分的遗传实体。更普遍地说，我们的分析强调了聚类方法在种群数量未知时面临的挑战，尤其是在样本大小极不均匀的情况下。
