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, Martin, Sarah, Forney, Karin, Gerrodette, Tim, Gilbert, M. Thomas P., Guinet, Christophe, Hanson, M. Bradley, Li, Songhai, Martin, Michael, Robertson, Kelly, Samarra, Filipa, Stephanis, Renaud, Tavares, Sara, Tixier, Paul, Totterdell, John, Wade, Paul, Wolf, Jochen, Fan, Guangyi, Zhang, Yaolei, Morin, Phillip
• Other Authors: Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), 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), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), 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)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2021
• Subjects: Runs of Homozygosity; Demography; killer whale; 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://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.