Data from: Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic "islands" of high differentiation and demonstrated the association of genotypes across these islands with divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight-vision–associated genes), hormone signaling, and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.SNP chip (Sequenom MassARRAY) primersPrimers for the SNP chip used in the mate-choice experiments (Figure 4; Table S10).I1150_cichlid_design_PCR_primers_sorted_used.txtAll 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 includes both SNPs and indels. High coverage (15x) Massoko littoral and benthic samples are denoted by "HC" in sample names.Massoko_Dryad_VCF_final.vcf.gzMain whole genome phylogenetic treeFigure 2AMassoko_mainWGtree_forDryad.nexusBootstrap replicates for whole genome phylogenetic treeBootstrap replicates for Figure 2AMassoko_bootstrapReplicates_forDryad.nexu