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 monophylet..., , , # 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

Dryad DOI: [https://doi.org/10.5061/dryad.8931zcs13](https://doi.org/10.5061/dryad.8931zcs13)

## Data Files

1. `1_assembled_contigs`
* Assembled contigs of the samples analyzed in this study

`/*.contigs.fasta`.
2. `2_UCE_p75_loci_nexus`
* Alignments of individual UCE loci in Nexus format

`/uce-*.nexus`
3. `3_UCE_p75_concatenated`
* Concatenated alignment of UCE loci analyzed in this study

`/lamprologus_dataset10_min75_mafft_gblocks-IQTree.charsets`
`/lamprologus_dataset10_min75_mafft_gblocks-PF.phy`
`/lamprologus_dataset10_min75_mafft_gblocks-raxml.charsets`
`/lamprologus_dataset10_min75_mafft_gblocks.phy`
4. `4_UCE_p75_pruned_random_nexus`
* Alignments of 100 random UCE loci for the pruned data set used in the timetree analysis

`/lamp...,