FN Archimer Export Format PT J TI Runs of homozygosity in killer whale genomes provide a global record of demographic histories BT AF 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 Fordyce Martin, Sarah L. 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. Stephanis, Renaud Tavares, Sara B. Tixier, Paul Totterdell, John A. Wade, Paul Wolf, Jochen B. W. Fan, Guangyi Zhang, Yaolei Morin, Philiip A AS 1:1,2,3;2:4;3:5;4:6;5:7,8;6:7,9;7:9;8:10;9:11;10:8;11:12;12:10;13:7,9;14:13;15:3;16:1;17:14,15;18:9;19:1,16;20:17;21:18;22:19;23:1;24:9;25:20;26:13;27:21,22;28:17,23;29:24;30:25;31:26;32:27,28,29;33:27,30;34:9; FF 1:;2:;3:;4:;5:;6:;7:;8:;9:;10:;11:;12:;13:;14:;15:;16:;17:;18:;19:;20:;21:;22:;23:;24:;25:;26:;27:;28:;29:;30:;31:;32:;33:;34:; C1 Department of Natural History NTNU University Museum Norwegian University of Science and Technology (NTNU Trondheim ,Norway Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor Gwynedd, UK CMPG Institute of Ecology and Evolution University of Bern Bern, Switzerland University of Exete, rPenryn Campus Penryn Cornwall,UK Department of Anatomy School of Biomedical Sciences University of Otago Dunedin, New Zealand Cascadia Research Olympia Washington, USA Marine Mammal Institute Oregon State University Newport Oregon, USA School of Biological Sciences University of Auckland Auckland,New Zealand Marine Mammal and Turtle Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanographic and Atmospheric Administration La Jolla California ,USA Scottish Marine Animal Stranding Scheme Institute of Biodiversity Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow, UK Ocean Giants Program Wildlife Conservation Society New York City, New York, USA Laboratório de Ecologia e Conservação da Megafauna Marinha Instituto de Oceanografia Universidade Federal do Rio Grande Rio Grande ,Brazil CIRCE, Conservation, Information and Research on Cetaceans Algeciras, Spain Marine Mammal and Turtle Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Moss Landing California, USA Moss Landing Marine Laboratories San Jose State University Moss Landing California ,USA Section for Evolutionary Genomics The GLOBE Institute University of Copenhagen Copenhagen ,Denmark UMR 7372 La Rochelle Université – CNRS Centre d’Etudes Biologiques de Chizé (CEBC) Villiers‐en‐Bois ,France National Marine Fisheries Service National Oceanic and Atmospheric Administration Northwest Fisheries Science Center Seattle Washington, USA Marine Mammal and Marine Bioacoustics Laboratory Institute of Deep‐Sea Science and Engineering Chinese Academy of Science Sanya ,China University of Iceland's Institute of Research Centres Vestmannaeyjar, Iceland Scottish Oceans Institute East Sands University of St. Andrews St. Andrews, UK Cetacean Research Program Pacific Biological Station, Fisheries and Oceans Canada Nanaimo ,Canada MARBEC, Université de Montpellier‐CNRS‐IFREMER‐IRD Sète ,France Cetacean Research Centre (CETREC WA Esperance Western ,Australia National Marine Mammal Laboratory National Marine Fisheries Service National Oceanic and Atmospheric AdministrationAlaska Fisheries Science Center Seattle Washington, USA Section of Evolutionary Biology Department of Biology II Ludwig Maximilian University of Munich Planegg‐Martinsried, Germany BGI‐QingdaoBGI‐Shenzhen Qingdao ,China BGI‐Shenzhen Shenzhen, China China National GeneBankBGI‐Shenzhen Shenzhen ,China Translational Immunology group Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby ,Denmark C2 UNIV NORWEGIAN, NORWAY UNIV BANGOR, UK UNIV BERN, SWITZERLAND UNIV EXETER, UK UNIV OTAGO, NEW ZEALAND CASCADIA RESEARCH OLYMPIA, USA UNIV OREGON STATE, USA UNIV AUCKLAND, NEW ZEALAND NOAA, USA UNIV GLASGOW, UK WILDLIFE CONSERVAT SOC, USA UNIV FED RIO GRANDE, BRAZIL CIRCE, SPAIN NOAA, USA UNIV SAN JOSE STATE, USA UNIV COPENHAGEN, DENMARK UNIV LA ROCHELLE, FRANCE NOAA, USA CHINESE ACAD SCI, CHINA UNIV ICELAND, ICELAND UNIV ST ANDREWS, UK MPO, CANADA IRD, FRANCE CETREC WA, AUSTRALIA NOAA, USA UNIV MUNICH, GERMANY BGI, CHINA BGI, CHINA CNGB, CHINA UNIV TECH DENMARK, DENMARK UM MARBEC IN WOS Cotutelle UMR copubli-france copubli-europe copubli-univ-france copubli-int-hors-europe copubli-sud IF 6.622 TC 30 UR https://archimer.ifremer.fr/doc/00720/83218/88211.pdf https://archimer.ifremer.fr/doc/00720/83218/88212.docx LA English DT Article DE ;Runs of Homozygosity;Demography;killer whale;Orcinus orca;whole genome sequencing;inbreeding AB 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. PY 2021 PD DEC SO Molecular Ecology SN 0962-1083 PU Wiley VL 30 IS 23 UT 000695314500001 BP 6162 EP 6177 DI 10.1111/mec.16137 ID 83218 ER EF