Runs of homozygosity in killer whale genomes provide a global record of demographic histories
| Type | Article | ||||||||||||
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| Date | 2021-12 | ||||||||||||
| Language | English | ||||||||||||
| Author(s) | Foote Andrew D. 1, 2, 3, Hooper Rebecca4, Alexander Alana5, Baird Robin W.6, Baker Charles Scott7, 8, Ballance Lisa7, 9, Barlow Jay9, Brownlow Andrew10, Collins Tim11, Constantine Rochelle8, Dalla Rosa Luciano12, Davison Nicholas J.10, Durban John W.7, 9, Esteban Ruth13, Excoffier Laurent3, Fordyce Martin Sarah L.1, Forney Karin A.14, 15, Gerrodette Tim9, Gilbert M. Thomas P.1, 16, Guinet Christophe17, Hanson M. Bradley18, Li Songhai19, Martin Michael D.1, Robertson Kelly M.9, Samarra Filipa I. P.20, Stephanis Renaud13, Tavares Sara B.21, 22, Tixier Paul17, 23, Totterdell John A.24, Wade Paul25, Wolf Jochen B. W.26, Fan Guangyi27, 28, 29, Zhang Yaolei27, 30, Morin Philiip A9 |
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| Affiliation(s) | 1 : Department of Natural History NTNU University Museum Norwegian University of Science and Technology (NTNU Trondheim ,Norway 2 : Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor Gwynedd, UK 3 : CMPG Institute of Ecology and Evolution University of Bern Bern, Switzerland 4 : University of Exete, rPenryn Campus Penryn Cornwall,UK 5 : Department of Anatomy School of Biomedical Sciences University of Otago Dunedin, New Zealand 6 : Cascadia Research Olympia Washington, USA 7 : Marine Mammal Institute Oregon State University Newport Oregon, USA 8 : School of Biological Sciences University of Auckland Auckland,New Zealand 9 : Marine Mammal and Turtle Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanographic and Atmospheric Administration La Jolla California ,USA 10 : Scottish Marine Animal Stranding Scheme Institute of Biodiversity Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow, UK 11 : Ocean Giants Program Wildlife Conservation Society New York City, New York, USA 12 : Laboratório de Ecologia e Conservação da Megafauna Marinha Instituto de Oceanografia Universidade Federal do Rio Grande Rio Grande ,Brazil 13 : CIRCE, Conservation, Information and Research on Cetaceans Algeciras, Spain 14 : Marine Mammal and Turtle Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Moss Landing California, USA 15 : Moss Landing Marine Laboratories San Jose State University Moss Landing California ,USA 16 : Section for Evolutionary Genomics The GLOBE Institute University of Copenhagen Copenhagen ,Denmark 17 : UMR 7372 La Rochelle Université – CNRS Centre d’Etudes Biologiques de Chizé (CEBC) Villiers‐en‐Bois ,France 18 : National Marine Fisheries Service National Oceanic and Atmospheric Administration Northwest Fisheries Science Center Seattle Washington, USA 19 : Marine Mammal and Marine Bioacoustics Laboratory Institute of Deep‐Sea Science and Engineering Chinese Academy of Science Sanya ,China 20 : University of Iceland's Institute of Research Centres Vestmannaeyjar, Iceland 21 : Scottish Oceans Institute East Sands University of St. Andrews St. Andrews, UK 22 : Cetacean Research Program Pacific Biological Station, Fisheries and Oceans Canada Nanaimo ,Canada 23 : MARBEC, Université de Montpellier‐CNRS‐IFREMER‐IRD Sète ,France 24 : Cetacean Research Centre (CETREC WA Esperance Western ,Australia 25 : National Marine Mammal Laboratory National Marine Fisheries Service National Oceanic and Atmospheric AdministrationAlaska Fisheries Science Center Seattle Washington, USA 26 : Section of Evolutionary Biology Department of Biology II Ludwig Maximilian University of Munich Planegg‐Martinsried, Germany 27 : BGI‐QingdaoBGI‐Shenzhen Qingdao ,China 28 : BGI‐Shenzhen Shenzhen, China 29 : China National GeneBankBGI‐Shenzhen Shenzhen ,China 30 : Translational Immunology group Department of Biotechnology and Biomedicine Technical University of Denmark Lyngby ,Denmark |
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| Source | Molecular Ecology (0962-1083) (Wiley), 2021-12 , Vol. 30 , N. 23 , P. 6162-6177 | ||||||||||||
| DOI | 10.1111/mec.16137 | ||||||||||||
| WOS© Times Cited | 29 | ||||||||||||
| Note | Special Issue: WHOLE GENOME SEQUENCING IN MOLECULAR ECOLOGY | ||||||||||||
| Keyword(s) | Runs of Homozygosity, Demography, killer whale, Orcinus orca, whole genome sequencing, inbreeding | ||||||||||||
| 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. |
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