Runs of homozygosity in killer whale genomes provide a global record of demographic histories
Abstract 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,...
Published in: | Molecular Ecology |
---|---|
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Other Authors: | , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Wiley
2021
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1111/mec.16137 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16137 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.16137 |
id |
crwiley:10.1111/mec.16137 |
---|---|
record_format |
openpolar |
spelling |
crwiley:10.1111/mec.16137 2024-09-09T19:50:08+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. Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung H2020 European Research Council H2020 Marie Skłodowska-Curie Actions 2021 http://dx.doi.org/10.1111/mec.16137 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16137 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.16137 en eng Wiley http://creativecommons.org/licenses/by-nc/4.0/ Molecular Ecology volume 30, issue 23, page 6162-6177 ISSN 0962-1083 1365-294X journal-article 2021 crwiley https://doi.org/10.1111/mec.16137 2024-08-01T04:22:25Z Abstract 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 Wiley Online Library Pacific Molecular Ecology 30 23 6162 6177 |
institution |
Open Polar |
collection |
Wiley Online Library |
op_collection_id |
crwiley |
language |
English |
description |
Abstract 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. |
author2 |
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung H2020 European Research Council H2020 Marie Skłodowska-Curie Actions |
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. |
spellingShingle |
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 |
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 |
publisher |
Wiley |
publishDate |
2021 |
url |
http://dx.doi.org/10.1111/mec.16137 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16137 https://onlinelibrary.wiley.com/doi/full-xml/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 volume 30, issue 23, page 6162-6177 ISSN 0962-1083 1365-294X |
op_rights |
http://creativecommons.org/licenses/by-nc/4.0/ |
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 |
_version_ |
1809919490855534592 |