DOI: 10.5061/dryad.s01kf
title: Data from: High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment

description: 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.
description: 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.