High-throughput sequencing reveals inbreeding depression in a natural population
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 re...
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Online Access: | http://nora.nerc.ac.uk/id/eprint/505236/ https://doi.org/10.1073/pnas.1318945111 |
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ftnerc:oai:nora.nerc.ac.uk:505236 2024-02-11T10:07:57+01:00 High-throughput sequencing reveals inbreeding depression in a natural population Hoffman, Joseph I. Simpson, Fraser David, Patrice Rijks, Jolianne M. Kuiken, Thijs Thorne, Michael A.S. Lacy, Robert C. Dasmahapatra, Kanchon K. 2014-03-11 http://nora.nerc.ac.uk/id/eprint/505236/ https://doi.org/10.1073/pnas.1318945111 unknown Hoffman, Joseph I.; Simpson, Fraser; David, Patrice; Rijks, Jolianne M.; Kuiken, Thijs; Thorne, Michael A.S. orcid:0000-0001-7759-612X Lacy, Robert C.; Dasmahapatra, Kanchon K. 2014 High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences, 111 (10). 3775-3780. https://doi.org/10.1073/pnas.1318945111 <https://doi.org/10.1073/pnas.1318945111> Publication - Article PeerReviewed 2014 ftnerc https://doi.org/10.1073/pnas.1318945111 2024-01-12T00:03:13Z 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 Natural Environment Research Council: NERC Open Research Archive Oldfield ENVELOPE(50.617,50.617,-66.833,-66.833) Proceedings of the National Academy of Sciences 111 10 3775 3780 |
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Open Polar |
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Natural Environment Research Council: NERC Open Research Archive |
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ftnerc |
language |
unknown |
description |
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 I. Simpson, Fraser David, Patrice Rijks, Jolianne M. Kuiken, Thijs Thorne, Michael A.S. Lacy, Robert C. Dasmahapatra, Kanchon K. |
spellingShingle |
Hoffman, Joseph I. Simpson, Fraser David, Patrice Rijks, Jolianne M. Kuiken, Thijs Thorne, Michael A.S. Lacy, Robert C. Dasmahapatra, Kanchon K. High-throughput sequencing reveals inbreeding depression in a natural population |
author_facet |
Hoffman, Joseph I. Simpson, Fraser David, Patrice Rijks, Jolianne M. Kuiken, Thijs Thorne, Michael A.S. Lacy, Robert C. Dasmahapatra, Kanchon K. |
author_sort |
Hoffman, Joseph I. |
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 |
publishDate |
2014 |
url |
http://nora.nerc.ac.uk/id/eprint/505236/ https://doi.org/10.1073/pnas.1318945111 |
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 |
Hoffman, Joseph I.; Simpson, Fraser; David, Patrice; Rijks, Jolianne M.; Kuiken, Thijs; Thorne, Michael A.S. orcid:0000-0001-7759-612X Lacy, Robert C.; Dasmahapatra, Kanchon K. 2014 High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences, 111 (10). 3775-3780. https://doi.org/10.1073/pnas.1318945111 <https://doi.org/10.1073/pnas.1318945111> |
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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1790606824088535040 |