Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population

• Published in: Proceedings of the Royal Society. B, Biological sciences Vol. 284; no. 1850; p. 20162763
• Main Authors: Nietlisbach, Pirmin, Keller, Lukas F., Camenisch, Glauco, Guillaume, Frédéric, Arcese, Peter, Reid, Jane M., Postma, Erik
• Format: Journal Article
• Language: English
• Published: England The Royal Society 15.03.2017; The Royal Society Publishing
• Edition: Royal Society (Great Britain)
• Subjects: Animals; Bird populations; Coefficient of variation; Evolution; Fitness; Genetic Fitness; Genetic Markers; Genomes; Genotype; Genotyping; Heterozygosity; Heterozygosity–fitness Correlation; Identity Disequilibrium; Inbreeding; Inbreeding Depression; Life history; Markers; Melospiza melodia; Microsatellite Repeats; Microsatellites; Pedigree; Phenotype; Recombination; Reproductive fitness; Short Tandem Repeats; Sparrows - genetics; Melospiza melodia; heterozygosity–fitness correlation; inbreeding depression; short tandem repeats; identity disequilibrium
• ISSN: 0962-8452; 1471-2954; 1471-2954
• DOI: 10.1098/rspb.2016.2763

Although the pedigree-based inbreeding coefficient F predicts the expected proportion of an individual's genome that is identical-by-descent (IBD), heterozygosity at genetic markers captures Mendelian sampling variation and thereby provides an estimate of realized IBD. Realized IBD should hence explain more variation in fitness than their pedigree-based expectations, but how many markers are required to achieve this in practice remains poorly understood. We use extensive pedigree and life-history data from an island population of song sparrows (Melospiza melodia) to show that the number of genetic markers and pedigree depth affected the explanatory power of heterozygosity and F, respectively, but that heterozygosity measured at 160 microsatellites did not explain more variation in fitness than F. This is in contrast with other studies that found heterozygosity based on far fewer markers to explain more variation in fitness than F. Thus, the relative performance of marker- and pedigree-based estimates of IBD depends on the quality of the pedigree, the number, variability and location of the markers employed, and the species-specific recombination landscape, and expectations based on detailed and deep pedigrees remain valuable until we can routinely afford genotyping hundreds of phenotyped wild individuals of genetic non-model species for thousands of genetic markers.