Runs of homozygosity in killer whale genomes provide a global record of demographic histories
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Runs of homozygosity in killer whale genomes provide a global record of demographic histories. / 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; Martin, Sarah L. Fordyce; 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.; de Stephanis, Renaud; Tavares, Sara B.; Tixier, Paul; Totterdell, John A.; Wade, Paul; Wolf, Jochen B. W.; Fan, Guangyi; Zhang, Yaolei; Morin, Phillip A.
In: Molecular Ecology, Vol. 30, No. 23, 2021, p. 6162-6177.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Runs of homozygosity in killer whale genomes provide a global record of demographic histories
AU - Foote, Andrew D.
AU - Hooper, Rebecca
AU - Alexander, Alana
AU - Baird, Robin W.
AU - Baker, Charles Scott
AU - Ballance, Lisa
AU - Barlow, Jay
AU - Brownlow, Andrew
AU - Collins, Tim
AU - Constantine, Rochelle
AU - Dalla Rosa, Luciano
AU - Davison, Nicholas J.
AU - Durban, John W.
AU - Esteban, Ruth
AU - Excoffier, Laurent
AU - Martin, Sarah L. Fordyce
AU - Forney, Karin A.
AU - Gerrodette, Tim
AU - Gilbert, M. Thomas P.
AU - Guinet, Christophe
AU - Hanson, M. Bradley
AU - Li, Songhai
AU - Martin, Michael D.
AU - Robertson, Kelly M.
AU - Samarra, Filipa I. P.
AU - de Stephanis, Renaud
AU - Tavares, Sara B.
AU - Tixier, Paul
AU - Totterdell, John A.
AU - Wade, Paul
AU - Wolf, Jochen B. W.
AU - Fan, Guangyi
AU - Zhang, Yaolei
AU - Morin, Phillip A.
N1 - Publisher Copyright: © 2021 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.
PY - 2021
Y1 - 2021
N2 - 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.
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.
KW - Demography
KW - inbreeding
KW - killer whale
KW - Orcinus orca
KW - Runs of Homozygosity
KW - whole genome sequencing
U2 - 10.1111/mec.16137
DO - 10.1111/mec.16137
M3 - Journal article
C2 - 34416064
AN - SCOPUS:85114054886
VL - 30
SP - 6162
EP - 6177
JO - Molecular Ecology
JF - Molecular Ecology
SN - 0962-1083
IS - 23
ER -
ID: 281702480