Runs of homozygosity in killer whale genomes provide a global record of demographic histories
International audience 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 demo...
Published in: | Molecular Ecology |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2021
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Subjects: | |
Online Access: | https://hal.archives-ouvertes.fr/hal-03346188 https://hal.archives-ouvertes.fr/hal-03346188/document https://hal.archives-ouvertes.fr/hal-03346188/file/Molecular%20Ecology%20-%202021%20-%20Foote%20-%20Runs%20of%20homozygosity%20in%20killer%20whale%20genomes%20provide%20a%20global%20record%20of%20demographic.pdf https://doi.org/10.1111/mec.16137 |
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ftunivnantes:oai:HAL:hal-03346188v1 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
Université de Nantes: HAL-UNIV-NANTES |
op_collection_id |
ftunivnantes |
language |
English |
topic |
Runs of Homozygosity Demography Killer whales Orcinus orca Whole genome sequencing Inbreeding [SDE]Environmental Sciences |
spellingShingle |
Runs of Homozygosity Demography Killer whales Orcinus orca Whole genome sequencing Inbreeding [SDE]Environmental Sciences Foote, Andrew Hooper, Rebecca Alexander, Alana Baird, Robin Baker, Charles Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Dalla Rosa, Luciano Davison, Nicholas Durban, John Esteban, Ruth Excoffier, Laurent Fordyce Martin, Sarah L. Forney, Karin A. Gerrodette, Tim Gilbert, M. Thomas P. Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Michael Robertson, Kelly 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 |
Runs of Homozygosity Demography Killer whales Orcinus orca Whole genome sequencing Inbreeding [SDE]Environmental Sciences |
description |
International audience 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 |
NTNU University Museum Trondheim Norwegian University of Science and Technology Trondheim (NTNU) Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU) School of Biological Sciences Bangor Bangor University Institute of Ecology and Evolution Bern, Switzerland University of Bern University of Exeter University of Otago Dunedin, Nouvelle-Zélande Cascadia Research Washington, USA Marine Mammal Institute Oregon State University (OSU) School of Biological Sciences Auckland University of Auckland Auckland Marine Mammal and Turtle Division (MMTD) Southwest Fisheries Science Center (SWFSC) NOAA National Marine Fisheries Service (NMFS) National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS) National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA) Scottish Marine Animal Stranding Scheme, SRUC Veterinary Service Scotland's Rural College (SRUC) Wildlife Conservation Society (WCS) Laboratório de Ecologia e Conservação da Megafauna Marinha Rio Grande, Brazil Universidade Federal do Rio Grande do Sul Porto Alegre (UFRGS) CIRCE (Conservation, Information and Research on Cetaceans) Moss Landing Marine Laboratories CA, USA (San José State University) San Jose State University San Jose (SJSU) Section for Evolutionary Genomics IT University of Copenhagen (ITU)-GLOBE Institute Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC) La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Northwest Fisheries Science Center (NWFSC) Sanya Key Laboratory of Marine Mammal and Marine Bioacoustics Institute of Deep-sea Science and Engineering Vestmannaeyjar Research and Study Center Scottish Oceans Institute University of St Andrews (SOI) School of Biology University of St Andrews University of St Andrews Scotland -University of St Andrews Scotland Fisheries and Oceans Canada (DFO) MARine Biodiversity Exploitation and Conservation (UMR MARBEC) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS) James Cook University (JCU) Alaska Fisheries Science Center (AFSC) Ludwig Maximilian University Munich (LMU) BGI Qingdao Partenaires INRAE Beijing Genomics Institute Shenzhen (BGI) China National GeneBank Danmarks Tekniske Universitet = Technical University of Denmark (DTU) |
format |
Article in Journal/Newspaper |
author |
Foote, Andrew Hooper, Rebecca Alexander, Alana Baird, Robin Baker, Charles Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Dalla Rosa, Luciano Davison, Nicholas Durban, John Esteban, Ruth Excoffier, Laurent Fordyce Martin, Sarah L. Forney, Karin A. Gerrodette, Tim Gilbert, M. Thomas P. Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Michael Robertson, Kelly 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 Hooper, Rebecca Alexander, Alana Baird, Robin Baker, Charles Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Dalla Rosa, Luciano Davison, Nicholas Durban, John Esteban, Ruth Excoffier, Laurent Fordyce Martin, Sarah L. Forney, Karin A. Gerrodette, Tim Gilbert, M. Thomas P. Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Michael Robertson, Kelly 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 |
HAL CCSD |
publishDate |
2021 |
url |
https://hal.archives-ouvertes.fr/hal-03346188 https://hal.archives-ouvertes.fr/hal-03346188/document https://hal.archives-ouvertes.fr/hal-03346188/file/Molecular%20Ecology%20-%202021%20-%20Foote%20-%20Runs%20of%20homozygosity%20in%20killer%20whale%20genomes%20provide%20a%20global%20record%20of%20demographic.pdf 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 |
ISSN: 0962-1083 EISSN: 1365-294X Molecular Ecology https://hal.archives-ouvertes.fr/hal-03346188 Molecular Ecology, 2021, 30, pp.6162-6177. ⟨10.1111/mec.16137⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1111/mec.16137 hal-03346188 https://hal.archives-ouvertes.fr/hal-03346188 https://hal.archives-ouvertes.fr/hal-03346188/document https://hal.archives-ouvertes.fr/hal-03346188/file/Molecular%20Ecology%20-%202021%20-%20Foote%20-%20Runs%20of%20homozygosity%20in%20killer%20whale%20genomes%20provide%20a%20global%20record%20of%20demographic.pdf doi:10.1111/mec.16137 |
op_rights |
http://creativecommons.org/licenses/by-nc/ info:eu-repo/semantics/OpenAccess |
op_rightsnorm |
CC-BY-NC |
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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1766057322493247488 |
spelling |
ftunivnantes:oai:HAL:hal-03346188v1 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, Charles Scott Ballance, Lisa Barlow, Jay Brownlow, Andrew Collins, Tim Constantine, Rochelle Dalla Rosa, Luciano Davison, Nicholas Durban, John Esteban, Ruth Excoffier, Laurent Fordyce Martin, Sarah L. Forney, Karin A. Gerrodette, Tim Gilbert, M. Thomas P. Guinet, Christophe Hanson, M. Bradley Li, Songhai Martin, Michael Robertson, Kelly 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. NTNU University Museum Trondheim Norwegian University of Science and Technology Trondheim (NTNU) Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU) School of Biological Sciences Bangor Bangor University Institute of Ecology and Evolution Bern, Switzerland University of Bern University of Exeter University of Otago Dunedin, Nouvelle-Zélande Cascadia Research Washington, USA Marine Mammal Institute Oregon State University (OSU) School of Biological Sciences Auckland University of Auckland Auckland Marine Mammal and Turtle Division (MMTD) Southwest Fisheries Science Center (SWFSC) NOAA National Marine Fisheries Service (NMFS) National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS) National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA) Scottish Marine Animal Stranding Scheme, SRUC Veterinary Service Scotland's Rural College (SRUC) Wildlife Conservation Society (WCS) Laboratório de Ecologia e Conservação da Megafauna Marinha Rio Grande, Brazil Universidade Federal do Rio Grande do Sul Porto Alegre (UFRGS) CIRCE (Conservation, Information and Research on Cetaceans) Moss Landing Marine Laboratories CA, USA (San José State University) San Jose State University San Jose (SJSU) Section for Evolutionary Genomics IT University of Copenhagen (ITU)-GLOBE Institute Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC) La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Northwest Fisheries Science Center (NWFSC) Sanya Key Laboratory of Marine Mammal and Marine Bioacoustics Institute of Deep-sea Science and Engineering Vestmannaeyjar Research and Study Center Scottish Oceans Institute University of St Andrews (SOI) School of Biology University of St Andrews University of St Andrews Scotland -University of St Andrews Scotland Fisheries and Oceans Canada (DFO) MARine Biodiversity Exploitation and Conservation (UMR MARBEC) Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS) James Cook University (JCU) Alaska Fisheries Science Center (AFSC) Ludwig Maximilian University Munich (LMU) BGI Qingdao Partenaires INRAE Beijing Genomics Institute Shenzhen (BGI) China National GeneBank Danmarks Tekniske Universitet = Technical University of Denmark (DTU) 2021-08-20 https://hal.archives-ouvertes.fr/hal-03346188 https://hal.archives-ouvertes.fr/hal-03346188/document https://hal.archives-ouvertes.fr/hal-03346188/file/Molecular%20Ecology%20-%202021%20-%20Foote%20-%20Runs%20of%20homozygosity%20in%20killer%20whale%20genomes%20provide%20a%20global%20record%20of%20demographic.pdf https://doi.org/10.1111/mec.16137 en eng HAL CCSD Wiley info:eu-repo/semantics/altIdentifier/doi/10.1111/mec.16137 hal-03346188 https://hal.archives-ouvertes.fr/hal-03346188 https://hal.archives-ouvertes.fr/hal-03346188/document https://hal.archives-ouvertes.fr/hal-03346188/file/Molecular%20Ecology%20-%202021%20-%20Foote%20-%20Runs%20of%20homozygosity%20in%20killer%20whale%20genomes%20provide%20a%20global%20record%20of%20demographic.pdf doi:10.1111/mec.16137 http://creativecommons.org/licenses/by-nc/ info:eu-repo/semantics/OpenAccess CC-BY-NC ISSN: 0962-1083 EISSN: 1365-294X Molecular Ecology https://hal.archives-ouvertes.fr/hal-03346188 Molecular Ecology, 2021, 30, pp.6162-6177. ⟨10.1111/mec.16137⟩ Runs of Homozygosity Demography Killer whales Orcinus orca Whole genome sequencing Inbreeding [SDE]Environmental Sciences info:eu-repo/semantics/article Journal articles 2021 ftunivnantes https://doi.org/10.1111/mec.16137 2023-01-03T23:52:47Z International audience 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 Université de Nantes: HAL-UNIV-NANTES Pacific Molecular Ecology 30 23 6162 6177 |