Dataset_detailsA list of the alignment dataset files included in the Dryad repository, including the filtering thresholds used to generate each dataset.vcf_Ref-aligned_AalcalicaDirectory containing the GATK output .vcf file from reference(O. niloticus)-aligned reads of A. alcalica. Directory contains 1 .vcf file and 1 index file.vcf_Ref-aligned_AgrahamiDirectory containing the GATK output .vcf file from reference-aligned reads of A. grahami. Directory contains 1 .vcf file and 1 index file.vcf_Ref-aligned_AlatilabrisDirectory containing the GATK output .vcf file from reference-aligned reads of A. latilabris. Directory contains 1 .vcf file and 1 index file.vcf_Ref-aligned_AndalalaniDirectory containing the GATK output .vcf file from reference-aligned reads of A. ndalalani. Directory contains 1 .vcf file and 1 index file.vcf_Ref-aligned_OamphimelasDirectory containing the GATK output .vcf file from reference-aligned reads of O. amphimelas. Directory contains 1 .vcf file and 1 index file.vcf_de-novo_AalcalicaDirectory containing the GATK output .vcf file from denovo-assembled reads of A. alcalica. Directory contains 1 .vcf file and 1 index file.vcf_de-novo_AgrahamiDirectory containing the GATK output .vcf file from denovo-assembled reads of A. grahami. Directory contains 1 .vcf file and 1 index file.vcf_de-novo_AlatilabrisDirectory containing the GATK output .vcf file from denovo-assembled reads of A. latilabris. Directory contains 1 .vcf file and 1 index file.vcf_de-novo_AndalalaniDirectory containing the GATK output .vcf file from denovo-assembled reads of A. ndalalani. Directory contains 1 .vcf file and 1 index file.vcf_de-novo_OamphimelasDirectory containing the GATK output .vcf file from denovo-assembled reads of O. amphimelas. Directory contains 1 .vcf file and 1 index file.DatasetA_n92Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'.DatasetB_n25Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetC_n92Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetD_n92Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetE_n92Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetF_n48Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetG_n91Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetH_n91Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetJ_n91Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetK_n91Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetL_n91Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetM_n84Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetN_n84Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetP_n38Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetQ_n38Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetR_n84Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetS_n16Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetT_n16Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetU_n16Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetV_n16Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetW_n14Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'DatasetX_n24Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'Output_tree_filesTree files from ML and SNAPP analysis, including the results presented in the following manuscript figures: 2, S3, S4, S5.

Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.