Data for: 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 datasets, particularly with regard to river-dwelling lineages in
the genus Lamprologus. This clade notably includes the only known blind
and depigmented cichlid, L. lethops. Here, we reconstructed the
evolutionary, population, and biogeographic history of a clade of
Lamprologus from the Congo River by sampling over 50 species of
lamprologines using genomic data and providing the best species-level
coverage of this fauna to date. 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,
repeated secondary contact, and reticulation. This complex hybrid origin,
followed by a rapid series of isolation and reticulation events,
illustrates the multifaceted dynamics of speciation that have shaped the
rich biodiversity of this region.