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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

Alda, Fernando12; Alter, S. Elizabeth34; Kurata, Naoko35; Chakrabarty, Prosanta23; Stiassny, Melanie3

Published May 02, 2025 on Dryad. https://doi.org/10.5061/dryad.8931zcs13

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May 02, 2025 version files 3.43 GB

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Abstract

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.