Data from: Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America

We investigate phylogeographic patterns and delimit species boundaries within Amatitlania, a genus of Central American cichlid fishes. Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals spanning the geographical ranges of all three currently recognized Amatitlania species strongly supported one major clade, with a relatively diverged subclade corresponding to A. kanna samples from eastern Costa Rica and Panama. Gene trees and networks revealed marked incongruences between phylogeographic structure and morpho-species taxonomy as a result of species-level polyphyly. Bayes factor comparisons of species delimitation models accounting for incomplete lineage sorting under the multispecies coalescent decisively supported the recognition of two distinct species within Amatitlania corresponding to Amatitlania nigrofasciata and A. kanna lineages. The only clearly genetically and morphologically diagnosable species was A. kanna. These results strongly suggest that incomplete lineage sorting provides the best explanation for the polyphyly of A. kanna, whereas the polyphyly of A. siquia is likely a result of an imperfect taxonomy. Additional insights from coalescent-dating, network, and historical demographic analyses suggested that the two species of Amatitlania diversified only since the early Pleistocene, and that A. nigrofasciata experienced population expansions from approximately 200 000 years ago in the mid-late Pleistocene onward. We discuss implications of our results for the taxonomy and evolutionary history of Amatitlania and, more broadly, of Central American freshwater fishes.

本研究针对中美洲慈鲷鱼类饰带丽体鱼属（Amatitlania）的系统地理学模式展开调查，并对其物种边界进行界定。我们对覆盖当前已正式确认的3个饰带丽体鱼属物种全部分布范围的318份个体的线粒体DNA（mitochondrial DNA）序列开展系统发育分析，结果强力支持存在一个主演化支，其中包含对应哥斯达黎加东部与巴拿马地区A. kanna样本的一个分化程度相对较高的亚演化支。基因树与基因网络分析显示，受物种水平多系性影响，系统地理学结构与形态物种分类体系之间存在显著不一致性。基于多物种溯祖框架下考虑不完全谱系分选的物种界定模型的贝叶斯因子比较，结果明确支持将饰带丽体鱼属划分为两个独立有效物种，分别对应饰带丽体鱼（Amatitlania nigrofasciata）与A. kanna支系。当前唯一可通过遗传与形态特征明确鉴别的物种为A. kanna。上述结果强烈表明，不完全谱系分选是A. kanna多系性的最佳解释，而A. siquia的多系性则很可能源于不完善的分类学界定。通过溯祖测年、基因网络与历史种群动态分析得到的额外结论显示，饰带丽体鱼属的两个物种仅在更新世早期以来发生分化，且A. nigrofasciata的种群扩张自约20万年前的中晚更新世起持续进行。本研究最后讨论了上述结果对饰带丽体鱼属乃至更广范围的中美洲淡水鱼类的分类学与进化历史研究的启示。