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.
Dataset_details
A list of the alignment dataset files included in the Dryad repository, including the filtering thresholds used to generate each dataset.
vcf_Ref-aligned_Aalcalica
Directory 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_Agrahami
Directory 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_Alatilabris
Directory 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_Andalalani
Directory 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_Oamphimelas
Directory 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_Aalcalica
Directory 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_Agrahami
Directory 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_Alatilabris
Directory 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_Andalalani
Directory 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_Oamphimelas
Directory containing the GATK output .vcf file from denovo-assembled reads of O. amphimelas. Directory contains 1 .vcf file and 1 index file.
DatasetA_n92
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'.
DatasetB_n25
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetC_n92
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetD_n92
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetE_n92
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetF_n48
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetG_n91
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetH_n91
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetJ_n91
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetK_n91
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetL_n91
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetM_n84
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetN_n84
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetP_n38
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetQ_n38
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetR_n84
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetS_n16
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetT_n16
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetU_n16
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetV_n16
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetW_n14
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
DatasetX_n24
Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
Output_tree_files
Tree files from ML and SNAPP analysis, including the results presented in the following manuscript figures: 2, S3, S4, S5.