Data from: Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

Amino Acid Alignments For Genes in Fig6aThese are the haplotypes used to build the haplotype trees showing shared depth adaptation of the Diplotaxodon and 'deep benthic' groups. The alignments are in the 'fasta' format. Haplotype phase is based on the BEAGLE output (not shapeit). Both haplotypes are included per species. The fasta headers indicate group assignment (e.g. mbuna), and then the first three letters of the genus name and the first three letters of the species name.AminoAcidAlignmentsForFig6.tar.gzAll whole-genome variant calls (after BEAGLE genotype refinement)The final product of our variant calling pipeline; obtained as described under: "Variant calling, filtering, and genotype refinement" in Supplementary Methods. This file also includes the A. calliptera samples from Indian Ocean Catchment and outgroup genotypes (N. brichardi), based on a whole genome alignment between the N. brichardi reference and the Lake Malawi M. zebra reference (again described in Supplementary methods).Malinsky_et_al_2018_LakeMalawiCichlids.vcf.gzPhylogenetic treesAll trees linked from Fig 2c, also all SNAPP MCMC samples, and all local Maximum Likelihood trees, both without and with the Indian Ocean (IO) catchment A. calliptera. For details see Methods.phylogenies.tar.gzD statisticsThis table gives values of Patterson’s D(h1, h2, h3, h4) for all combinations of samples of the cichlid species given in Supplementary Table S1 of Malinsky et al. 2018, where the outgroup (h4) is fixed as N. brichardi from Lake Tanganyika. Note that the different geographic variants of A. calliptera were treated separately.D_statistics_allSpeciesTrioCombinations.tsv.gzf statisticsThis table gives values of the f4 admixture ratio f(h1, h2, h3, h4) ([see SOM18 in ref. 31, and fG in ref. 48 in Malinsky et al. 2018] for all combinations of species for which D(h1,h2,h3,h4)>0. The outgroup (h4) is fixed as N. brichardi from Lake Tanganyika. Note that the different geographic variants of A. calliptera were treated separately.f-stats.tsv.gz