Data from: Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes

Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and occasional gene flow between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker data set containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our data set that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.

适应辐射（adaptive radiation）被认为是驱动地球上绝大多数已灭绝与现存生物多样性演化的核心驱动力。以大量物种快速涌现、且源于对不同生态位的适应性演化为特征的适应辐射实例，是进化生物学领域的重要研究体系。然而，由于此类类群的谱系形成速率极快，且参与辐射的物种间偶发基因交流，重建经历适应辐射的物种的系统发育历史往往颇具挑战。
本研究针对已知存在基因渐渗（introgression）的快速分化谱系，提出了一种全新的物种树（species-tree）估算方法，并将其应用于一套多标记数据集（multimarker data set）：该数据集涵盖东非丽鱼科45个物种，每个物种最多包含16号标本，总计522个个体，研究核心聚焦于坦噶尼喀湖（Lake Tanganyika）丽鱼物种群。
我们首先通过分析单个基因树中最近共同祖先（most recent common ancestors）的年龄分布，鉴定出本数据集内带有显著古老基因渐渗信号的谱系。基于此，我们提出了坦噶尼喀湖丽鱼不同谱系间基因渐渗的三项假说：其一，布伦格罗丽鱼族（Boulengerochromini，或布伦格罗丽鱼族与深海丽鱼族（Bathybatini））的祖先曾从衍生的H类群获取基因组遗传物质；其二，亮鲷族（Cyprichromini）与奇鳍丽鱼族（Perissodini）的共同祖先先后从布伦格罗丽鱼族和/或深海丽鱼族获得基因渐渗；其三，坦噶尼喀湖朴丽鱼族（Haplochromini）及其近缘河生谱系从燕尾丽鱼族（Cyphotilapiini）获取了遗传物质。
随后，我们采用多物种溯祖模型（multispecies coalescent model）估算坦噶尼喀湖丽鱼的物种树，但排除了参与上述基因渐渗事件的谱系——因多物种溯祖模型无法纳入基因渐渗过程。由此得到的物种树具有较高稳健性，结果显示隆头丽鱼族（Lamprologini）与H类群（包括咽齿丽鱼族（Eretmodini））互为姊妹谱系，并在H类群基部识别出一系列快速分化事件。
通过多物种溯祖模型估算的分化时间显著晚于基于序列拼接法（concatenation）的年龄估算结果，且与东非大湖（Great Lakes of East Africa）的地质历史相吻合。最后，我们采用似然框架对三项基因渐渗假说进行了严格检验，结果为坦噶尼喀湖部分丽鱼族间的基因渐渗提供了强有力的支持。