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...
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Online Access: | https://hdl.handle.net/11250/2778770 https://doi.org/10.1111/mec.16137 |
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ftntnutrondheimi:oai:ntnuopen.ntnu.no:11250/2778770 2023-05-15T17:03:27+02:00 Runs of homozygosity in killer whale genomes provide a global record of demographic histories Foote, Andrew Hooper, Rebecca Alexander, Alana Baird, Robin Baker, Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Rosa, Luciano Dalla Davison, Nicholas J. Durban, John Esteban, Ruth Excoffier, Laurent Forney, Karin A. Gerrodette, Tim Gilbert, Marcus Thomas Pius Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Sarah Martin, Michael David 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://hdl.handle.net/11250/2778770 https://doi.org/10.1111/mec.16137 eng eng Wiley urn:issn:0962-1083 https://hdl.handle.net/11250/2778770 https://doi.org/10.1111/mec.16137 cristin:1927812 Navngivelse-Ikkekommersiell 4.0 Internasjonal http://creativecommons.org/licenses/by-nc/4.0/deed.no CC-BY-NC Molecular Ecology Peer reviewed Journal article 2021 ftntnutrondheimi https://doi.org/10.1111/mec.16137 2021-09-22T22:35:40Z 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. publishedVersion Article in Journal/Newspaper Killer Whale Orca Orcinus orca Killer whale NTNU Open Archive (Norwegian University of Science and Technology) Pacific Molecular Ecology |
institution |
Open Polar |
collection |
NTNU Open Archive (Norwegian University of Science and Technology) |
op_collection_id |
ftntnutrondheimi |
language |
English |
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. publishedVersion |
format |
Article in Journal/Newspaper |
author |
Foote, Andrew Hooper, Rebecca Alexander, Alana Baird, Robin Baker, Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Rosa, Luciano Dalla Davison, Nicholas J. Durban, John Esteban, Ruth Excoffier, Laurent Forney, Karin A. Gerrodette, Tim Gilbert, Marcus Thomas Pius Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Sarah Martin, Michael David 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. |
spellingShingle |
Foote, Andrew Hooper, Rebecca Alexander, Alana Baird, Robin Baker, Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Rosa, Luciano Dalla Davison, Nicholas J. Durban, John Esteban, Ruth Excoffier, Laurent Forney, Karin A. Gerrodette, Tim Gilbert, Marcus Thomas Pius Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Sarah Martin, Michael David 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 |
author_facet |
Foote, Andrew Hooper, Rebecca Alexander, Alana Baird, Robin Baker, Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Rosa, Luciano Dalla Davison, Nicholas J. Durban, John Esteban, Ruth Excoffier, Laurent Forney, Karin A. Gerrodette, Tim Gilbert, Marcus Thomas Pius Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Sarah Martin, Michael David 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 |
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 |
publisher |
Wiley |
publishDate |
2021 |
url |
https://hdl.handle.net/11250/2778770 https://doi.org/10.1111/mec.16137 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Killer Whale Orca Orcinus orca Killer whale |
genre_facet |
Killer Whale Orca Orcinus orca Killer whale |
op_source |
Molecular Ecology |
op_relation |
urn:issn:0962-1083 https://hdl.handle.net/11250/2778770 https://doi.org/10.1111/mec.16137 cristin:1927812 |
op_rights |
Navngivelse-Ikkekommersiell 4.0 Internasjonal http://creativecommons.org/licenses/by-nc/4.0/deed.no |
op_rightsnorm |
CC-BY-NC |
op_doi |
https://doi.org/10.1111/mec.16137 |
container_title |
Molecular Ecology |
_version_ |
1766057315418505216 |