“Type D” killer whale genomes reveal long-term small population size and low genetic diversity
Genome sequences can reveal the extent of inbreeding in small populations. Here, we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale...
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Language: | English |
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Oxford University Press (OUP)
2023
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Online Access: | https://archimer.ifremer.fr/doc/00830/94213/101593.pdf https://archimer.ifremer.fr/doc/00830/94213/101594.pdf https://doi.org/10.1093/jhered/esac070 https://archimer.ifremer.fr/doc/00830/94213/ |
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ftarchimer:oai:archimer.ifremer.fr:94213 2024-01-07T09:44:37+01:00 “Type D” killer whale genomes reveal long-term small population size and low genetic diversity Foote, Andrew D Alexander, Alana Ballance, Lisa T Constantine, Rochelle Galletti Vernazzani Muñoz, Bárbara Guinet, Christophe Robertson, Kelly M Sinding, Mikkel-holger S Sironi, Mariano Tixier, Paul Totterdell, John Towers, Jared R Wellard, Rebecca Pitman, Robert L Morin, Phillip A 2023-04 application/pdf https://archimer.ifremer.fr/doc/00830/94213/101593.pdf https://archimer.ifremer.fr/doc/00830/94213/101594.pdf https://doi.org/10.1093/jhered/esac070 https://archimer.ifremer.fr/doc/00830/94213/ eng eng Oxford University Press (OUP) info:eu-repo/grantAgreement/EC/H2020/663830/EU//SIRCIW https://archimer.ifremer.fr/doc/00830/94213/101593.pdf https://archimer.ifremer.fr/doc/00830/94213/101594.pdf doi:10.1093/jhered/esac070 https://archimer.ifremer.fr/doc/00830/94213/ info:eu-repo/semantics/openAccess restricted use Journal Of Heredity (0022-1503) (Oxford University Press (OUP)), 2023-04 , Vol. 114 , N. 2 , P. 94-109 effective population size inbreeding killer whale morphotype runs of homozygosity text Article info:eu-repo/semantics/article 2023 ftarchimer https://doi.org/10.1093/jhered/esac070 2023-12-12T23:51:11Z Genome sequences can reveal the extent of inbreeding in small populations. Here, we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale genome and indicates a severe population bottleneck. Consequently, type D genomes show among the highest level of inbreeding reported for any mammalian species (FROH ≥ 0.65). Detected recombination cross-over events of different haplotypes are up to an order of magnitude rarer than in other killer whale genomes studied to date. Comparison of genomic data from a museum specimen of a type D killer whale that stranded in New Zealand in 1955, with 3 modern genomes from the Cape Horn area, reveals high covariance and identity-by-state of alleles, suggesting these genomic characteristics and demographic history are shared among geographically dispersed social groups within this morphotype. Limitations to the insights gained in this study stem from the nonindependence of the 3 closely related modern genomes, the recent coalescence time of most variation within the genomes, and the nonequilibrium population history which violates the assumptions of many model-based methods. Long-range linkage disequilibrium and extensive runs of homozygosity found in type D genomes provide the potential basis for both the distinctive morphology, and the coupling of genetic barriers to gene flow with other killer whale populations. Article in Journal/Newspaper Killer Whale Killer whale Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) Cape Horn ENVELOPE(-135.021,-135.021,61.583,61.583) New Zealand Journal of Heredity 114 2 94 109 |
institution |
Open Polar |
collection |
Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) |
op_collection_id |
ftarchimer |
language |
English |
topic |
effective population size inbreeding killer whale morphotype runs of homozygosity |
spellingShingle |
effective population size inbreeding killer whale morphotype runs of homozygosity Foote, Andrew D Alexander, Alana Ballance, Lisa T Constantine, Rochelle Galletti Vernazzani Muñoz, Bárbara Guinet, Christophe Robertson, Kelly M Sinding, Mikkel-holger S Sironi, Mariano Tixier, Paul Totterdell, John Towers, Jared R Wellard, Rebecca Pitman, Robert L Morin, Phillip A “Type D” killer whale genomes reveal long-term small population size and low genetic diversity |
topic_facet |
effective population size inbreeding killer whale morphotype runs of homozygosity |
description |
Genome sequences can reveal the extent of inbreeding in small populations. Here, we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale genome and indicates a severe population bottleneck. Consequently, type D genomes show among the highest level of inbreeding reported for any mammalian species (FROH ≥ 0.65). Detected recombination cross-over events of different haplotypes are up to an order of magnitude rarer than in other killer whale genomes studied to date. Comparison of genomic data from a museum specimen of a type D killer whale that stranded in New Zealand in 1955, with 3 modern genomes from the Cape Horn area, reveals high covariance and identity-by-state of alleles, suggesting these genomic characteristics and demographic history are shared among geographically dispersed social groups within this morphotype. Limitations to the insights gained in this study stem from the nonindependence of the 3 closely related modern genomes, the recent coalescence time of most variation within the genomes, and the nonequilibrium population history which violates the assumptions of many model-based methods. Long-range linkage disequilibrium and extensive runs of homozygosity found in type D genomes provide the potential basis for both the distinctive morphology, and the coupling of genetic barriers to gene flow with other killer whale populations. |
format |
Article in Journal/Newspaper |
author |
Foote, Andrew D Alexander, Alana Ballance, Lisa T Constantine, Rochelle Galletti Vernazzani Muñoz, Bárbara Guinet, Christophe Robertson, Kelly M Sinding, Mikkel-holger S Sironi, Mariano Tixier, Paul Totterdell, John Towers, Jared R Wellard, Rebecca Pitman, Robert L Morin, Phillip A |
author_facet |
Foote, Andrew D Alexander, Alana Ballance, Lisa T Constantine, Rochelle Galletti Vernazzani Muñoz, Bárbara Guinet, Christophe Robertson, Kelly M Sinding, Mikkel-holger S Sironi, Mariano Tixier, Paul Totterdell, John Towers, Jared R Wellard, Rebecca Pitman, Robert L Morin, Phillip A |
author_sort |
Foote, Andrew D |
title |
“Type D” killer whale genomes reveal long-term small population size and low genetic diversity |
title_short |
“Type D” killer whale genomes reveal long-term small population size and low genetic diversity |
title_full |
“Type D” killer whale genomes reveal long-term small population size and low genetic diversity |
title_fullStr |
“Type D” killer whale genomes reveal long-term small population size and low genetic diversity |
title_full_unstemmed |
“Type D” killer whale genomes reveal long-term small population size and low genetic diversity |
title_sort |
“type d” killer whale genomes reveal long-term small population size and low genetic diversity |
publisher |
Oxford University Press (OUP) |
publishDate |
2023 |
url |
https://archimer.ifremer.fr/doc/00830/94213/101593.pdf https://archimer.ifremer.fr/doc/00830/94213/101594.pdf https://doi.org/10.1093/jhered/esac070 https://archimer.ifremer.fr/doc/00830/94213/ |
long_lat |
ENVELOPE(-135.021,-135.021,61.583,61.583) |
geographic |
Cape Horn New Zealand |
geographic_facet |
Cape Horn New Zealand |
genre |
Killer Whale Killer whale |
genre_facet |
Killer Whale Killer whale |
op_source |
Journal Of Heredity (0022-1503) (Oxford University Press (OUP)), 2023-04 , Vol. 114 , N. 2 , P. 94-109 |
op_relation |
info:eu-repo/grantAgreement/EC/H2020/663830/EU//SIRCIW https://archimer.ifremer.fr/doc/00830/94213/101593.pdf https://archimer.ifremer.fr/doc/00830/94213/101594.pdf doi:10.1093/jhered/esac070 https://archimer.ifremer.fr/doc/00830/94213/ |
op_rights |
info:eu-repo/semantics/openAccess restricted use |
op_doi |
https://doi.org/10.1093/jhered/esac070 |
container_title |
Journal of Heredity |
container_volume |
114 |
container_issue |
2 |
container_start_page |
94 |
op_container_end_page |
109 |
_version_ |
1787426017142374400 |