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

Autor: Kelly M. Robertson, Rebecca Hooper, Rochelle Constantine, Renaud de Stephanis, Sara Tavares, Alana Alexander, Guangyi Fan, John A. Totterdell, Ruth Esteban, Nicholas J. Davison, Tim Gerrodette, Lisa T. Ballance, John W. Durban, Songhai Li, Paul Tixier, Phillip A. Morin, Michael D. Martin, C. S. Baker, Sarah L. Fordyce Martin, Robin W. Baird, Jay Barlow, Luciano Dalla Rosa, Filipa I. P. Samarra, Andrew Brownlow, Tim Collins, Laurent Excoffier, Andrew D. Foote, M. Bradley Hanson, Jochen B. W. Wolf, M. Thomas P. Gilbert, Karin A. Forney, Christophe Guinet, Paul R. Wade, Yaolei Zhang
Přispěvatelé: 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), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)
Rok vydání: 2021
Předmět:
Zdroj: Molecular Ecology (0962-1083) (Wiley), 2021-12, Vol. 30, N. 23, P. 6162-6177
Foote, A D, Hooper, R, Alexander, A, Baird, R W, Baker, C S, Ballance, L, Barlow, J, Brownlow, A, Collins, T, Constantine, R, Dalla Rosa, L, Davison, N J, Durban, J W, Esteban, R, Excoffier, L, Fordyce Martin, S L, Forney, K A, Gerrodette, T, Gilbert, M T P, Guinet, C, Hanson, M B, Li, S, Martin, M D, Robertson, K M, Samarra, F I P, de Stephanis, R, Tavares, S B, Tixier, P, Totterdell, J A, Wade, P, Wolf, J B W, Fan, G, Zhang, Y & Morin, P A 2021, ' Runs of homozygosity in killer whale genomes provide a global record of demographic histories ', Molecular Ecology, vol. 30, no. 23, pp. 6162-6177 . https://doi.org/10.1111/mec.16137
Molecular Ecology
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; ... (2021). Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Molecular Ecology, 30(23), pp. 6162-6177. Wiley-Blackwell 10.1111/mec.16137
Molecular Ecology, 2021, 30, pp.6162-6177. ⟨10.1111/mec.16137⟩
Molecular Ecology, Wiley, 2021, ⟨10.1111/mec.16137⟩
Foote, A D, Hooper, R, Alexander, A, Baird, R W, Baker, C S, Ballance, L, Barlow, J, Brownlow, A, Collins, T, Constantine, R, Dalla Rosa, L, Davison, N J, Durban, J W, Esteban, R, Excoffier, L, Martin, S L F, Forney, K A, Gerrodette, T, Gilbert, M T P, Guinet, C, Hanson, M B, Li, S, Martin, M D, Robertson, K M, Samarra, F I P, de Stephanis, R, Tavares, S B, Tixier, P, Totterdell, J A, Wade, P, Wolf, J B W, Fan, G, Zhang, Y & Morin, P A 2021, ' Runs of homozygosity in killer whale genomes provide a global record of demographic histories ', Molecular Ecology, vol. 30, no. 23, pp. 6162-6177 . https://doi.org/10.1111/mec.16137
ISSN: 1365-294X
0962-1083
Popis: 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 (1.5 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.
Databáze: OpenAIRE
Externí odkaz: