Data from: Repeated trans-watershed hybridisation among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution

The megadiverse haplochromine cichlid radiations of the East African lakes, famous examples of explosive speciation and adaptive radiation, are according to recent studies, introgressed by different riverine lineages. This study is informed by the first comprehensive mitochondrial and nuclear DNA dataset from extensive sampling of riverine haplochromine cichlids. It includes species from the lower Congo and Angolan (River Kwanza) drainages. Reconstruction of phylogenetic hypotheses revealed the paradox of clearly discordant phylogenetic signals. Closely related mtDNA haplotypes are distributed thousands of kilometers apart and across major African watersheds, whereas some neighbouring species carry drastically divergent mtDNA haplotypes. At shallow and deep phylogenetic layers, strong signals of hybridisation are attributed to the complex late Miocene/early Pliocene palaeo-history of African rivers. Hybridisation of multiple lineages across changing watersheds shaped each of the major haplochromine radiations in lakes Tanganyika, Victoria, Malawi and the Kalahari Palaeolakes, as well as a miniature species flock in the Congo basin (River Fwa). Based on our results, introgression occurred not only on a spatially restricted scale, but massively over almost the whole range of the haplochromine distribution. This provides an alternative view on the origin and exceptional high diversity of this enigmatic vertebrate group.

东非湖泊中物种多样性极高的单型丽鱼（haplochromine cichlid）辐射类群，作为爆发式物种形成与适应性辐射的经典范例，根据最新研究显示，其基因组已被不同河流支系所渐渗。本研究依托首个针对河流生境下单型丽鱼的大规模采样所获得的综合性线粒体DNA（mitochondrial DNA, mtDNA）与核DNA数据集展开。该数据集涵盖了刚果河下游与安哥拉宽扎河（River Kwanza）流域的类群。系统发育假说重建结果揭示了一处显著矛盾：存在明显不一致的系统发育信号——亲缘关系极近的mtDNA单倍型会分布在数千公里之外，且跨越非洲主要流域；而部分地理相邻的物种却携带差异极大的线粒体单倍型。无论是系统发育树的浅分支还是深分支层级中，均存在强烈的杂交信号，这可归因于非洲河流在晚中新世-早上新世时期复杂的古地理演化历史。跨不断变化流域的多支系杂交事件，塑造了坦噶尼喀湖、维多利亚湖、马拉维湖以及喀拉哈里古湖的各大单型丽鱼辐射类群，同时也造就了刚果盆地富瓦河（River Fwa）中的小型物种集群。基于本研究结果，单型丽鱼类群的渐渗杂交不仅存在于局部空间尺度，更在其分布范围的绝大多数区域大规模发生。这一发现为解释这一神秘脊椎动物类群的起源与极高多样性提供了全新视角。