Data from: Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish

We used nuclear and mitochondrial DNA sequences from specimens collected throughout Lake Tanganyika to clarify the evolutionary relationship between Lamprologus callipterus and Neolamprologus fasciatus. The nuclear data supports the reciprocal monophyly of these two shell breeding lamprologine cichlids. However, mitochondrial DNA (mtDNA) sequences show that 1) L. callipterus includes two divergent and geographically disjunct (North-South) mtDNA lineages; and that 2) N. fasciatus individuals cluster in a lineage sister group to the northern lineage of L. callipterus. The two mtDNA lineages of L. callipterus diverged c. 684 Kya to 1.2 Mya, coinciding with a major water level low stand in Lake Tanganyika, which divided the lake into isolated sub-lakes. This suggests that the two mtDNA lineages originated as the result of the separation of L. callipterus populations in different sub-basins. The incongruent phylogenetic position of N. fasciatus can best be explained by an ancient unidirectional introgression from L. callipterus into N. fasciatus. Remarkably, our data indicate that this event resulted in the complete mtDNA replacement in N. fasciatus. Our data suggest that hybridization occurred soon after the divergence of the two L. callipterus mtDNA lineages, probably still during the water level low stand, and that subsequently the invading mtDNA lineage spread throughout the lake.本研究采集坦噶尼喀湖全域的标本，获取其核DNA与线粒体DNA序列，旨在阐明隆头丽鱼（Lamprologus callipterus）与新亮丽鲷（Neolamprologus fasciatus）之间的演化关系。核DNA数据支持这两种螺壳繁殖型隆头丽鱼亚科慈鲷互为单系群。然而线粒体DNA（mtDNA）序列结果显示：其一，隆头丽鱼包含两个分化显著且地理分布隔绝的南北分支线粒体谱系；其二，新亮丽鲷的个体聚类于与隆头丽鱼北部线粒体谱系互为姐妹群的演化分支中。 隆头丽鱼的两个线粒体DNA谱系的分化时间约为68.4万年至120万年前，这与坦噶尼喀湖经历的一次大规模低水位停滞期高度吻合——此次事件将该湖分割为多个孤立的次级湖盆。这表明隆头丽鱼的两个线粒体谱系起源于不同次级湖盆中种群的地理隔离分化事件。 新亮丽鲷演化位置与核DNA系统发育结果的不一致性，最适宜用一次发生于隆头丽鱼向新亮丽鲷的古老单向基因渐渗事件来解释。值得注意的是，本研究数据显示该事件导致新亮丽鲷的线粒体DNA发生了完全替换。 本研究数据提示，杂交事件发生于隆头丽鱼两个线粒体谱系分化之后不久，大概率仍处于该低水位停滞期，且后续入侵的线粒体谱系扩散至整个坦噶尼喀湖。