High-throughput sequencing reveals inbreeding depression in a natural population

JI Hoffman, F Simpson, P David, JM (Jolianne) Rijks, Thijs Kuiken, MAS Thorne, RC Lacy, KK Dasmahapatra

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159 Citations (Scopus)

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.
Original languageUndefined/Unknown
Pages (from-to)3775-3780
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of Ame
Volume111
Issue number10
DOIs
Publication statusPublished - 2014

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