Genome Analyses Reveal Diverse Riverine Genetic Contributions to the Lake Malawi Cichlid Radiation

This dataset contains several supporting files used in the study "Genome Analyses Reveal Diverse Riverine Genetic Contributions to the Lake Malawi Cichlid Radiation" (Gresham et al. 2025). We collected whole-genome sequencing data for 315 African pseudocrenilabrine cichlid species in order to detect signatures of gene flow between lineages. We provide the following files generated/used in these analyses: Dtrios_malawi_nonmalawi_BBAA.txt - output of Dsuite Dtrios calculating D statistics and f4-ratios for all possible trios of 315 African pseudocrenilabrine cichlid species. Data used was whole-genome resequencing data aligned to the Astatotilapia callitpera reference genome. NJ_tree.nwk - Newick Neighbour-Joining phylogenomic tree - distance matrix calculated using plink and divided by the accessible genome size. the tree was then rooted to a reconstructed ancestral sequence.  ML_tree.tre - Newick Maximum likelihood phylogenomic tree - trees calculated in 100KB non overlapping windows with the GTR+G+I model in IQ-TREE. a consensus tree was then built using ASTRAL-III, and rooted to a reconstructed ancestral sequence.  Supplementary_Table_1.xlsx - Metadata provided for all samples used.  The variant call format (VCF) files produced in this study are available under EVA accession number XXXX. The VCF files contain biallelic SNP data for 612 African Pseudocrenilabrine cichlid samples (from Malawi and non-Malawi species) and also include a reconstructed ancestral state sequence of the common ancestor between the Cyphotilapiini and Pseudocrenilabrini tribes as an additional sample (see Blumer et al. 2025 for ancestral state sequence reconstruction methods). Supplementary_Table_1.xlsx provides information on all samples within the VCF files. Genetic material and sequences are subject to an Access and Benefits Sharing (ABS) agreement with the Government of Malawi. Any person who wishes to use this data for any form of commercial purpose must first enter into a commercial licensing and benefit-sharing arrangement with the Government of Malawi.