Data from: High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment|基因组学数据集|鱼类遗传学数据集

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.