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.本研究采集了坦噶尼喀湖全域的样本，利用其核DNA（nuclear DNA）与线粒体DNA（mitochondrial DNA, mtDNA）序列，以明确*Lamprologus callipterus*与*Neolamprologus fasciatus*之间的演化关系。核DNA数据支持这两种贝壳繁殖型亮丽鱼亚科慈鲷互为互惠单系群。然而线粒体DNA序列分析结果显示：其一，*Lamprologus callipterus*包含两个分化显著且地理分布间断（南北分隔）的mtDNA谱系；其二，*Neolamprologus fasciatus*的个体聚类于与*Lamprologus callipterus*北部谱系互为姊妹群的分支中。*Lamprologus callipterus*的两个mtDNA谱系的分歧时间约为68.4万年至120万年前，这一时间节点与坦噶尼喀湖经历的主要水位低位期重合——彼时该湖被分割为多个孤立的次级湖盆。这表明*Lamprologus callipterus*的两个mtDNA谱系起源于不同次级湖盆中的种群隔离事件。*Neolamprologus fasciatus*系统发育位置的不一致性，最合理的解释是曾发生一次源自*Lamprologus callipterus*向*Neolamprologus fasciatus*的古老单向基因渐渗。值得注意的是，本研究数据显示该事件导致了*Neolamprologus fasciatus*体内完全的mtDNA替换。进一步分析表明，杂交事件发生于*Lamprologus callipterus*两个mtDNA谱系分化之后不久，大概率仍处于该水位低位期，且随后入侵的mtDNA谱系扩散至整个坦噶尼喀湖范围。