Runs of homozygosity in killer whale genomes provide a global record of demographic histories
Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we invest...
Published in: | Molecular Ecology |
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Format: | Article in Journal/Newspaper |
Language: | English |
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2021
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Online Access: | https://curis.ku.dk/portal/da/publications/runs-of-homozygosity-in-killer-whale-genomes-provide-a-global-record-of-demographic-histories(249be6ee-dbe9-4885-8cc7-72fc016055a5).html https://doi.org/10.1111/mec.16137 https://curis.ku.dk/ws/files/287618620/Runs_of_homozygosity_in_killer_whale_genomes_provide_a_global_record_of_demographic_histories.pdf |
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ftcopenhagenunip:oai:pure.atira.dk:publications/249be6ee-dbe9-4885-8cc7-72fc016055a5 2024-06-09T07:47:28+00:00 Runs of homozygosity in killer whale genomes provide a global record of demographic histories Foote, Andrew D. Hooper, Rebecca Alexander, Alana Baird, Robin W. Baker, Charles Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Dalla Rosa, Luciano Davison, Nicholas J. Durban, John W. Esteban, Ruth Excoffier, Laurent Martin, Sarah L. Fordyce Forney, Karin A. Gerrodette, Tim Gilbert, M. Thomas P. Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Michael D. Robertson, Kelly M. Samarra, Filipa I. P. de Stephanis, Renaud Tavares, Sara B. Tixier, Paul Totterdell, John A. Wade, Paul Wolf, Jochen B. W. Fan, Guangyi Zhang, Yaolei Morin, Phillip A. 2021 application/pdf https://curis.ku.dk/portal/da/publications/runs-of-homozygosity-in-killer-whale-genomes-provide-a-global-record-of-demographic-histories(249be6ee-dbe9-4885-8cc7-72fc016055a5).html https://doi.org/10.1111/mec.16137 https://curis.ku.dk/ws/files/287618620/Runs_of_homozygosity_in_killer_whale_genomes_provide_a_global_record_of_demographic_histories.pdf eng eng info:eu-repo/semantics/openAccess Foote , A D , Hooper , R , Alexander , A , Baird , R W , Baker , C S , Ballance , L , Barlow , J , Brownlow , A , Collins , T , Constantine , R , Dalla Rosa , L , Davison , N J , Durban , J W , Esteban , R , Excoffier , L , Martin , S L F , Forney , K A , Gerrodette , T , Gilbert , M T P , Guinet , C , Hanson , M B , Li , S , Martin , M D , Robertson , K M , Samarra , F I P , de Stephanis , R , Tavares , S B , Tixier , P , Totterdell , J A , Wade , P , Wolf , J B W , Fan , G , Zhang , Y & Morin , P A 2021 , ' Runs of homozygosity in killer whale genomes provide a global record of demographic histories ' , Molecular Ecology , vol. 30 , no. 23 , pp. 6162-6177 . https://doi.org/10.1111/mec.16137 Demography inbreeding killer whale Orcinus orca Runs of Homozygosity whole genome sequencing article 2021 ftcopenhagenunip https://doi.org/10.1111/mec.16137 2024-05-16T11:29:21Z Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression. Article in Journal/Newspaper Killer Whale Orca Orcinus orca Killer whale University of Copenhagen: Research Pacific Molecular Ecology 30 23 6162 6177 |
institution |
Open Polar |
collection |
University of Copenhagen: Research |
op_collection_id |
ftcopenhagenunip |
language |
English |
topic |
Demography inbreeding killer whale Orcinus orca Runs of Homozygosity whole genome sequencing |
spellingShingle |
Demography inbreeding killer whale Orcinus orca Runs of Homozygosity whole genome sequencing Foote, Andrew D. Hooper, Rebecca Alexander, Alana Baird, Robin W. Baker, Charles Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Dalla Rosa, Luciano Davison, Nicholas J. Durban, John W. Esteban, Ruth Excoffier, Laurent Martin, Sarah L. Fordyce Forney, Karin A. Gerrodette, Tim Gilbert, M. Thomas P. Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Michael D. Robertson, Kelly M. Samarra, Filipa I. P. de Stephanis, Renaud Tavares, Sara B. Tixier, Paul Totterdell, John A. Wade, Paul Wolf, Jochen B. W. Fan, Guangyi Zhang, Yaolei Morin, Phillip A. Runs of homozygosity in killer whale genomes provide a global record of demographic histories |
topic_facet |
Demography inbreeding killer whale Orcinus orca Runs of Homozygosity whole genome sequencing |
description |
Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression. |
format |
Article in Journal/Newspaper |
author |
Foote, Andrew D. Hooper, Rebecca Alexander, Alana Baird, Robin W. Baker, Charles Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Dalla Rosa, Luciano Davison, Nicholas J. Durban, John W. Esteban, Ruth Excoffier, Laurent Martin, Sarah L. Fordyce Forney, Karin A. Gerrodette, Tim Gilbert, M. Thomas P. Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Michael D. Robertson, Kelly M. Samarra, Filipa I. P. de Stephanis, Renaud Tavares, Sara B. Tixier, Paul Totterdell, John A. Wade, Paul Wolf, Jochen B. W. Fan, Guangyi Zhang, Yaolei Morin, Phillip A. |
author_facet |
Foote, Andrew D. Hooper, Rebecca Alexander, Alana Baird, Robin W. Baker, Charles Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Dalla Rosa, Luciano Davison, Nicholas J. Durban, John W. Esteban, Ruth Excoffier, Laurent Martin, Sarah L. Fordyce Forney, Karin A. Gerrodette, Tim Gilbert, M. Thomas P. Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Michael D. Robertson, Kelly M. Samarra, Filipa I. P. de Stephanis, Renaud Tavares, Sara B. Tixier, Paul Totterdell, John A. Wade, Paul Wolf, Jochen B. W. Fan, Guangyi Zhang, Yaolei Morin, Phillip A. |
author_sort |
Foote, Andrew D. |
title |
Runs of homozygosity in killer whale genomes provide a global record of demographic histories |
title_short |
Runs of homozygosity in killer whale genomes provide a global record of demographic histories |
title_full |
Runs of homozygosity in killer whale genomes provide a global record of demographic histories |
title_fullStr |
Runs of homozygosity in killer whale genomes provide a global record of demographic histories |
title_full_unstemmed |
Runs of homozygosity in killer whale genomes provide a global record of demographic histories |
title_sort |
runs of homozygosity in killer whale genomes provide a global record of demographic histories |
publishDate |
2021 |
url |
https://curis.ku.dk/portal/da/publications/runs-of-homozygosity-in-killer-whale-genomes-provide-a-global-record-of-demographic-histories(249be6ee-dbe9-4885-8cc7-72fc016055a5).html https://doi.org/10.1111/mec.16137 https://curis.ku.dk/ws/files/287618620/Runs_of_homozygosity_in_killer_whale_genomes_provide_a_global_record_of_demographic_histories.pdf |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Killer Whale Orca Orcinus orca Killer whale |
genre_facet |
Killer Whale Orca Orcinus orca Killer whale |
op_source |
Foote , A D , Hooper , R , Alexander , A , Baird , R W , Baker , C S , Ballance , L , Barlow , J , Brownlow , A , Collins , T , Constantine , R , Dalla Rosa , L , Davison , N J , Durban , J W , Esteban , R , Excoffier , L , Martin , S L F , Forney , K A , Gerrodette , T , Gilbert , M T P , Guinet , C , Hanson , M B , Li , S , Martin , M D , Robertson , K M , Samarra , F I P , de Stephanis , R , Tavares , S B , Tixier , P , Totterdell , J A , Wade , P , Wolf , J B W , Fan , G , Zhang , Y & Morin , P A 2021 , ' Runs of homozygosity in killer whale genomes provide a global record of demographic histories ' , Molecular Ecology , vol. 30 , no. 23 , pp. 6162-6177 . https://doi.org/10.1111/mec.16137 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1111/mec.16137 |
container_title |
Molecular Ecology |
container_volume |
30 |
container_issue |
23 |
container_start_page |
6162 |
op_container_end_page |
6177 |
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1801378558873960448 |