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Runs of homozygosity in killer whale genomes provide a global record of demographic histories
  • +31
  • Andy Foote,
  • Rebecca Hooper,
  • Alana Alexander,
  • Robin Baird,
  • Charles Baker,
  • Lisa Ballance,
  • Jay Barlow,
  • Andrew Brownlow,
  • T. Collins,
  • Rochelle Constantine,
  • Luciano Dalla Rosa,
  • Nicholas Davison,
  • John Durban,
  • Ruth Esteban,
  • Laurent Excoffier,
  • Sarah Fordyce,
  • Karin Forney,
  • Tim Gerrodette,
  • M. Thomas P. Gilbert,
  • Christophe Guinet,
  • Brad Hanson,
  • Songhai Li,
  • Michael Martin,
  • Kelly Robertson,
  • Filipa Samarra,
  • Renaud De Stefanis,
  • Sara Tavares,
  • Paul Tixier,
  • John Totterdell,
  • Paul Wade,
  • Jochen Wolf,
  • Guangyi Fan,
  • Yaolei Zhang,
  • Phillip Morin
Andy Foote
Bangor University

Corresponding Author:andrew.foote@ntnu.no

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Rebecca Hooper
University of Exeter
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Alana Alexander
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Robin Baird
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Charles Baker
Oregon State University
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Lisa Ballance
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Jay Barlow
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Andrew Brownlow
University of Glasgow College of Medical Veterinary and Life Sciences
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T. Collins
Wildlife Conservation Society
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Rochelle Constantine
University of Auckland
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Luciano Dalla Rosa
Universidade Federal do Rio Grande
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Nicholas Davison
Scottish Marine Animal Stranding Scheme
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John Durban
NOAA Fisheries Southwest Fisheries Science Center
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Ruth Esteban
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Laurent Excoffier
University of Bern
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Sarah Fordyce
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Karin Forney
Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA
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Tim Gerrodette
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M. Thomas P. Gilbert
University of Copenhagen
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Christophe Guinet
Centre d'Etudes Biologiques de Chizé
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Brad Hanson
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Songhai Li
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Michael Martin
Norwegian University of Science and Technology
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Kelly Robertson
Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA
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Filipa Samarra
University of St Andrews
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Renaud De Stefanis
CIRCE
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Sara Tavares
University of St Andrews
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Paul Tixier
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John Totterdell
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Paul Wade
Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA
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Jochen Wolf
Ludwig Maximilian University of Munich
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Guangyi Fan
BGI
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Yaolei Zhang
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Phillip Morin
Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA
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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 investigate whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global dataset of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstruct demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We find 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 (<1Mb), 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, including a Scottish population, for which 37.8% of the autosomes comprised of ROH >1.5 Mb in length.
28 Jun 2021Submitted to Molecular Ecology
29 Jun 2021Reviewer(s) Assigned
27 Jul 2021Review(s) Completed, Editorial Evaluation Pending
09 Aug 2021Editorial Decision: Revise Minor
10 Aug 2021Review(s) Completed, Editorial Evaluation Pending
10 Aug 20211st Revision Received
18 Aug 2021Editorial Decision: Accept
Dec 2021Published in Molecular Ecology volume 30 issue 23 on pages 6162-6177. 10.1111/mec.16137