High-throughput sequencing reveals inbreeding depression in a natural population
Hoffman J, Simpson F, Patrice D, et al. High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences of the United States of America . 2014;111(10):3775-3780. Proxy measures of genome-wide heterozygosity based on approximately 10 m...
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ftubbiepub:oai:pub.uni-bielefeld.de:2663373 2023-05-15T17:58:56+02:00 High-throughput sequencing reveals inbreeding depression in a natural population Hoffman, Joseph Simpson, Fraser Patrice, David Rijks, Jolianne Kuiken, Thijs Thorne, Michael Lacy, Robert Dasmahapatra, Kanchon 2014 https://pub.uni-bielefeld.de/record/2663373 eng eng Proceedings of the National Academy of Sciences info:eu-repo/semantics/altIdentifier/doi/10.1073/pnas.1318945111 info:eu-repo/semantics/altIdentifier/issn/0027-8424 info:eu-repo/semantics/altIdentifier/issn/1091-6490 info:eu-repo/semantics/altIdentifier/wos/000332564800039 info:eu-repo/semantics/altIdentifier/pmid/24586051 https://pub.uni-bielefeld.de/record/2663373 info:eu-repo/semantics/closedAccess single nucleotide polymorphism RAD sequencing heterozygosity fitness correlation genetic variability inbreeding http://purl.org/coar/resource_type/c_6501 info:eu-repo/semantics/article doc-type:article text 2014 ftubbiepub https://doi.org/10.1073/pnas.1318945111 2022-02-08T22:32:49Z Hoffman J, Simpson F, Patrice D, et al. High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences of the United States of America . 2014;111(10):3775-3780. Proxy measures of genome-wide heterozygosity based on approximately 10 microsatellites have been used to uncover heterozygosity fitness correlations (HFCs) for a wealth of important fitness traits in natural populations. However, effect sizes are typically very small and the underlying mechanisms remain contentious, as a handful of markers usually provides little power to detect inbreeding. We therefore used restriction site associated DNA (RAD) sequencing to accurately estimate genome-wide heterozygosity, an approach transferrable to any organism. As a proof of concept, we first RAD sequenced oldfield mice (Peromyscus polionotus) from a known pedigree, finding strong concordance between the inbreeding coefficient and heterozygosity measured at 13,198 single-nucleotide polymorphisms (SNPs). When applied to a natural population of harbor seals (Phoca vitulina), a weak HFC for parasite infection based on 27 microsatellites strengthened considerably with 14,585 SNPs, the deviance explained by heterozygosity increasing almost fivefold to a remarkable 49%. These findings arguably provide the strongest evidence to date of an HFC being due to inbreeding depression in a natural population lacking a pedigree. They also suggest that under some circumstances heterozygosity may explain far more variation in fitness than previously envisaged. Article in Journal/Newspaper Phoca vitulina PUB - Publications at Bielefeld University Oldfield ENVELOPE(50.617,50.617,-66.833,-66.833) Proceedings of the National Academy of Sciences 111 10 3775 3780 |
institution |
Open Polar |
collection |
PUB - Publications at Bielefeld University |
op_collection_id |
ftubbiepub |
language |
English |
topic |
single nucleotide polymorphism RAD sequencing heterozygosity fitness correlation genetic variability inbreeding |
spellingShingle |
single nucleotide polymorphism RAD sequencing heterozygosity fitness correlation genetic variability inbreeding Hoffman, Joseph Simpson, Fraser Patrice, David Rijks, Jolianne Kuiken, Thijs Thorne, Michael Lacy, Robert Dasmahapatra, Kanchon High-throughput sequencing reveals inbreeding depression in a natural population |
topic_facet |
single nucleotide polymorphism RAD sequencing heterozygosity fitness correlation genetic variability inbreeding |
description |
Hoffman J, Simpson F, Patrice D, et al. High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences of the United States of America . 2014;111(10):3775-3780. Proxy measures of genome-wide heterozygosity based on approximately 10 microsatellites have been used to uncover heterozygosity fitness correlations (HFCs) for a wealth of important fitness traits in natural populations. However, effect sizes are typically very small and the underlying mechanisms remain contentious, as a handful of markers usually provides little power to detect inbreeding. We therefore used restriction site associated DNA (RAD) sequencing to accurately estimate genome-wide heterozygosity, an approach transferrable to any organism. As a proof of concept, we first RAD sequenced oldfield mice (Peromyscus polionotus) from a known pedigree, finding strong concordance between the inbreeding coefficient and heterozygosity measured at 13,198 single-nucleotide polymorphisms (SNPs). When applied to a natural population of harbor seals (Phoca vitulina), a weak HFC for parasite infection based on 27 microsatellites strengthened considerably with 14,585 SNPs, the deviance explained by heterozygosity increasing almost fivefold to a remarkable 49%. These findings arguably provide the strongest evidence to date of an HFC being due to inbreeding depression in a natural population lacking a pedigree. They also suggest that under some circumstances heterozygosity may explain far more variation in fitness than previously envisaged. |
format |
Article in Journal/Newspaper |
author |
Hoffman, Joseph Simpson, Fraser Patrice, David Rijks, Jolianne Kuiken, Thijs Thorne, Michael Lacy, Robert Dasmahapatra, Kanchon |
author_facet |
Hoffman, Joseph Simpson, Fraser Patrice, David Rijks, Jolianne Kuiken, Thijs Thorne, Michael Lacy, Robert Dasmahapatra, Kanchon |
author_sort |
Hoffman, Joseph |
title |
High-throughput sequencing reveals inbreeding depression in a natural population |
title_short |
High-throughput sequencing reveals inbreeding depression in a natural population |
title_full |
High-throughput sequencing reveals inbreeding depression in a natural population |
title_fullStr |
High-throughput sequencing reveals inbreeding depression in a natural population |
title_full_unstemmed |
High-throughput sequencing reveals inbreeding depression in a natural population |
title_sort |
high-throughput sequencing reveals inbreeding depression in a natural population |
publisher |
Proceedings of the National Academy of Sciences |
publishDate |
2014 |
url |
https://pub.uni-bielefeld.de/record/2663373 |
long_lat |
ENVELOPE(50.617,50.617,-66.833,-66.833) |
geographic |
Oldfield |
geographic_facet |
Oldfield |
genre |
Phoca vitulina |
genre_facet |
Phoca vitulina |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1073/pnas.1318945111 info:eu-repo/semantics/altIdentifier/issn/0027-8424 info:eu-repo/semantics/altIdentifier/issn/1091-6490 info:eu-repo/semantics/altIdentifier/wos/000332564800039 info:eu-repo/semantics/altIdentifier/pmid/24586051 https://pub.uni-bielefeld.de/record/2663373 |
op_rights |
info:eu-repo/semantics/closedAccess |
op_doi |
https://doi.org/10.1073/pnas.1318945111 |
container_title |
Proceedings of the National Academy of Sciences |
container_volume |
111 |
container_issue |
10 |
container_start_page |
3775 |
op_container_end_page |
3780 |
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1766167659653627904 |