Runs of homozygosity in killer whale genomes provide a global record of demographic histories

• Published in: Molecular Ecology
• Main Authors: 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.
• Other Authors: 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
• Language: English
• Published: HAL CCSD 2021
• Subjects: Runs of Homozygosity; Demography; Killer whales; Orcinus orca; Whole genome sequencing; Inbreeding; [SDE]Environmental Sciences; Pacific; Killer Whale; Orca; Killer whale
• 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

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.