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. ORCID: https://orcid.org/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. 10.1073/pnas.1318945111

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Abstract/Summary

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

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.1073/pnas.1318945111
Programmes:	BAS Programmes > Polar Science for Planet Earth (2009 - ) > Ecosystems
ISSN:	0027-8424
Additional Keywords:	inbreeding, genetic variability, heterozygosity fitness correlation, single nucleotide polymorphism
Date made live:	04 Mar 2014 12:02 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/505236

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