Input and output files for analyses of divergence times of Gadinae with StarBEAST2 gadinae_starbeast_alignments.tgz gadinae_starbeast.xml gadinae_starbeast.log gadinae_starbeast.trees gadinae_starbeast.tre Input and output files for analyses of divergence times and introgression among Gadus, Arctogadus, and Boreogadus with AIM gadus_arctogadus_boreogadus_aim_alignments.tgz gadus_arctogadus_boreogadus_aim.xml gadus_arctogadus_boreogadus_aim.log gadus_arctogadus_boreogadus_aim.trees gadus_arctogadus_boreogadus_aim_bpp0763.tre gadus_arctogadus_boreogadus_aim_bpp0234.tre Dataset used for analyses of introgression among Gadus, Arctogadus, and Boreogadus with Dsuite gadus_arctogadus_boreogadus_dsuite.vcf.gz Alignments and output trees for analyses of tree-based signals of introgression among Gadus, Arctogadus, and Boreogadus with IQ-TREE gadus_arctogadus_boreogadus_iqtree_alignments.tgz gadus_arctogadus_boreogadus_iqtree_trees.tgz Datasets used for supergene-specific analyses of linkage disequilibrium in Gadus morhua with PLINK gadus_morhua_supergene_lg01_plink.map gadus_morhua_supergene_lg01_plink.ped gadus_morhua_supergene_lg02_plink.map gadus_morhua_supergene_lg02_plink.ped gadus_morhua_supergene_lg07_plink.map gadus_morhua_supergene_lg07_plink.ped gadus_morhua_supergene_lg12_plink.map gadus_morhua_supergene_lg12_plink.ped Input and output files for analyses of divergence times among Gadus morhua populations with SNAPP gadus_morhua_outside_supergenes_snapp.vcf.gz gadus_morhua_outside_supergenes_snapp.xml gadus_morhua_outside_supergenes_snapp.log gadus_morhua_outside_supergenes_snapp.tre gadus_morhua_outside_supergenes_snapp.trees Dataset used for analyses of introgression among Gadus morhua populations with Dsuite gadus_morhua_outside_supergenes_dsuite.vcf.gz Dataset used for analyses of demograpy of Gadus morhua populations with Relate gadus_morhua_outside_supergenes_relate.vcf.gz Input and output files for supergene-specific analyses of divergence times among Gadus morhua populations with SNAPP gadus_morhua_supergene_lg01_snapp.vcf.gz gadus_morhua_supergene_lg01_snapp.xml gadus_morhua_supergene_lg01_snapp.log gadus_morhua_supergene_lg01_snapp.trees gadus_morhua_supergene_lg01_snapp.tre gadus_morhua_supergene_lg02_snapp.vcf.gz gadus_morhua_supergene_lg02_snapp.xml gadus_morhua_supergene_lg02_snapp.log gadus_morhua_supergene_lg02_snapp.trees gadus_morhua_supergene_lg02_snapp.tre gadus_morhua_supergene_lg07_snapp.vcf.gz gadus_morhua_supergene_lg07_snapp.xml gadus_morhua_supergene_lg07_snapp.log gadus_morhua_supergene_lg07_snapp.trees gadus_morhua_supergene_lg07_snapp.tre gadus_morhua_supergene_lg12_snapp.vcf.gz gadus_morhua_supergene_lg12_snapp.xml gadus_morhua_supergene_lg12_snapp.log gadus_morhua_supergene_lg12_snapp.trees gadus_morhua_supergene_lg12_snapp.tre Datasets used for supergene-specific analyses of introgression among Gadus morhua populations with Dsuite gadus_morhua_supergene_lg01_dsuite.vcf.gz gadus_morhua_supergene_lg02_dsuite.vcf.gz gadus_morhua_supergene_lg07_dsuite.vcf.gz gadus_morhua_supergene_lg12_dsuite.vcf.gz Datasets used for supergene-specific analyses of demograpy of Gadus morhua populations with Relate gadus_morhua_supergene_lg01_relate.vcf.gz gadus_morhua_supergene_lg02_relate.vcf.gz gadus_morhua_supergene_lg07_relate.vcf.gz gadus_morhua_supergene_lg12_relate.vcf.gz