High-throughput sequencing reveals inbreeding depression in a natural population

Hoffman J, Simpson F, Patrice D, Rijks J, Kuiken T, Thorne M, Lacy R, Dasmahapatra K (2014)
Proceedings of the National Academy of Sciences of the United States of America 111(10): 3775-3780.

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Abstract
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.
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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.
Hoffman, J., Simpson, F., Patrice, D., Rijks, J., Kuiken, T., Thorne, M., Lacy, R., et al. (2014). High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences of the United States of America, 111(10), 3775-3780.
Hoffman, J., Simpson, F., Patrice, D., Rijks, J., Kuiken, T., Thorne, M., Lacy, R., and Dasmahapatra, K. (2014). High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences of the United States of America 111, 3775-3780.
Hoffman, J., et al., 2014. High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences of the United States of America, 111(10), p 3775-3780.
J. Hoffman, 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, vol. 111, 2014, pp. 3775-3780.
Hoffman, J., Simpson, F., Patrice, D., Rijks, J., Kuiken, T., Thorne, M., Lacy, R., Dasmahapatra, K.: High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences of the United States of America. 111, 3775-3780 (2014).
Hoffman, Joseph, Simpson, Fraser, Patrice, David, Rijks, Jolianne, Kuiken, Thijs, Thorne, Michael, Lacy, Robert, and Dasmahapatra, Kanchon. “High-throughput sequencing reveals inbreeding depression in a natural population”. Proceedings of the National Academy of Sciences of the United States of America 111.10 (2014): 3775-3780.
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