title: High-throughput sequencing reveals inbreeding depression in a natural population.
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.
authors.affiliation: Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany.
authors.forename: Joseph I
authors.initials: JI
authors.lastname: Hoffman
authors.forename: Fraser
authors.initials: F
authors.lastname: Simpson
authors.forename: Patrice
authors.initials: P
authors.lastname: David
authors.forename: Jolianne M
authors.initials: JM
authors.lastname: Rijks
authors.forename: Thijs
authors.initials: T
authors.lastname: Kuiken
authors.forename: Michael A S
authors.initials: MA
authors.lastname: Thorne
authors.forename: Robert C
authors.initials: RC
authors.lastname: Lacy
authors.forename: Kanchon K
authors.initials: KK
authors.lastname: Dasmahapatra
mesh_terms: D000818:Animals; D056084:Genetic Fitness / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D007087:Illinois; D007178:Inbreeding; D009659:North Sea; D010542:Peromyscus / Q000235:genetics*; D046049:Phoca / Q000235:genetics* / Q000469:parasitology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D015183:Restriction Mapping
keywords: RAD sequencing; genetic variability; heterozygosity fitness correlation; inbreeding; single nucleotide polymorphism