Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River

Understanding the drivers of diversification is a central goal in evolutionary biology but can be challenging when lineages radiate quickly and/or hybridize frequently. Cichlids in the tribe Lamprologini, an exceptionally diverse clade found in the Congo basin, exemplify these issues: their evolutionary history has been difficult to untangle with previous data sets, particularly with regard to river-dwelling lineages in the genus Lamprologus. This clade notably includes the only known blind and depigmented cichlid, Lamprologus lethops. Here, we reconstructed the evolutionary, population, and biogeographic history of a Lamprologus clade from the Congo River by leveraging genomic data and sampling over 50 lamprologine species from the entire Lake Tanganyika radiation. This study provides the most comprehensive species-level coverage to date of the riverine taxa within this lacustrine-origin clade. We found that in the mid-late Pliocene, two lineages of Lake Tanganyika lamprologines independently colonized the Congo River, where they subsequently hybridized and diversified, forming the current monophyletic group of riverine Lamprologus. Our estimates for divergence time and introgression align with the region's geological history and suggest rapid speciation in Lamprologus species from the Congo River marked by rapids-driven vicariance and water level fluctuations, and repeated episodes of secondary contact and reticulation. As a result of our analyses, we propose the taxonomic restriction of the genus Lamprologus to Congo River taxa only. The complex evolutionary history of this group-characterized by introgressive hybridization followed by a rapid series of isolation and reconnection-illustrates the multifaceted dynamics of speciation that have shaped the rich biodiversity of this region.