Planned intervention: On Wednesday April 3rd 05:30 UTC Zenodo will be unavailable for up to 2-10 minutes to perform a storage cluster upgrade.
Published August 1, 2021 | Version v1
Dataset Open

Origin and fate of supergenes in Atlantic cod

  • 1. Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
  • 2. Zoological Institute, University of Basel, Basel, Switzerland
  • 3. Marine and Freshwater Research Institute, Hafnarfjördur, Iceland
  • 4. Ian
  • 5. Kjetill Sigurd
  • 6. Sissel

Description

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

Files

gadinae_starbeast.xml

Files (5.7 GB)

Name Size Download all
md5:dc8adbed36d0d6c370ee45d88f0876c3
41.3 MB Download
md5:2ca6e46a97ee58d5b1b78c171831ba02
12.6 kB Download
md5:960a6004ae329e56858d704e39786c6c
1.1 MB Download
md5:35aec31815ec862293a8f3f658155163
2.2 MB Preview Download
md5:75ed733816c28cd9bf47d8f4f8c7a3d2
112.1 kB Download
md5:a4cb0a2bdf6d8f704eae17126258a6f4
4.2 MB Download
md5:dad439dade24e0e90645e3df7e6acb9c
2.4 MB Download
md5:574fb5d572dc949827709fb5b7b84d28
4.4 MB Preview Download
md5:5324ed0f240b449b79beddd89800f36d
393.1 kB Download
md5:59873a18834def274b2161ab9cc101e9
6.7 kB Download
md5:379f69418dfde20f9252572e7b6f433c
6.7 kB Download
md5:0ad3279262f3c8c8e8e6b63913dd5082
1.9 GB Download
md5:610f7cd660b6064f374ecbb6fb466295
3.4 MB Download
md5:b6d34bdb94e984104c2566b910b3cb17
105.7 kB Download
md5:d2f29f57aba73cc1352879bf7eddb286
3.4 GB Download
md5:f69dd63eaa54689de015904a6eb89541
65.0 MB Download
md5:87d4d1775a055e4cb6582ff85381a838
159.3 kB Download
md5:356ac4e0456286a291b5eb52c0002234
15.1 kB Download
md5:f33e5ffde447e4b944d1af6f502495c8
1.4 MB Download
md5:89206e64a2ec89e48bcb399b3f1af3fd
71.6 MB Download
md5:4a6c55a748d42717f0b310b36f1a7103
29.0 kB Preview Download
md5:e69f4fa86ab1847beb46269d9b3e7ee0
103.1 MB Download
md5:6350263326de8e5f932f3de587ed3780
74.4 kB Download
md5:bc06ef33e21f483d2c72c747f40d1bad
1.0 MB Download
md5:2e42e202f0ada4aee94d09bb14202784
2.3 MB Download
md5:637cb97d486ed14c2a63399d54147699
159.5 kB Download
md5:87c5a2bac33c4f9b3380f8b0f9939e03
14.9 kB Download
md5:5dcf4132fcca054f8c9f175fa4d7d888
1.4 MB Download
md5:e7fddab6c56f8b0435b89b33496e7f5f
29.0 kB Preview Download
md5:fddcde1dae88b39a2a95576ea87422ba
35.3 MB Download
md5:89f659d4d00a9d16248368be2d11806b
16.5 kB Download
md5:926db2836e43f2dcc6327e634fa36ece
223.0 kB Download
md5:6ef63f54845effa3004a906e1d5c61e5
771.2 kB Download
md5:f163fea19a0c0b57483c0b17ebf07071
159.2 kB Download
md5:5a2c072e9acb3aada0558a5ddbba91aa
15.1 kB Download
md5:2dfad53d2ba71263528ccc9dc8bd19d7
1.4 MB Download
md5:786f83d4bbeb691e98ff181c64f2dac6
29.0 kB Preview Download
md5:366913707e55dce415aa57c24356d0c9
61.2 MB Download
md5:7490e872d6803cb6cbb9b76956233184
79.5 kB Download
md5:76632ae51c0dc65cbc1d01e7f950ba13
1.1 MB Download
md5:0658755859445306b2506df6eafaa9de
1.3 MB Download
md5:2a22655d7dcdb5d97c8dee3679119133
159.7 kB Download
md5:895c8da4900d61c9047f5f355869c852
15.0 kB Download
md5:88555d065d5234f147243f57cb5f3979
1.4 MB Download
md5:c740aaa238a583297073fe8987c52403
29.0 kB Preview Download
md5:6f3736133f33cb2bcb2188f37105098c
78.2 MB Download
md5:a8a643a4f8eee0547688a6c6fc42b7ff
65.4 kB Download
md5:f70301b31b588f618a1a7e2d93d24ef2
927.8 kB Download
md5:7c3a993e090d06a0d092527628aa1897
1.4 MB Download
md5:5b52a9e1f359c3e7b5f0b347c1656890
159.3 kB Download
md5:42f80b3b23f17e21621bd93dd61a4ee2
14.9 kB Download
md5:79f05b2a1fb911b8079bc55ec0486dd2
1.4 MB Download
md5:70e4aa5f8bec33df67b1a2964b64f4ed
29.0 kB Preview Download
md5:ea55dae3ce58ba43f9c438480744c98a
2.1 MB Download
md5:4ec8330c3e45a4b146674a6f191fc503
618.8 kB Download
md5:bc0b1fde1a9354fb40f426e5bb4627bd
1.9 MB Download
md5:631c118198f0d3e994ec537910850d38
1.9 MB Download