DOI: 10.5281/zenodo.4560275
title: Origin and fate of supergenes in Atlantic cod

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