DOI: 10.5061/dryad.p9s04
title: Data from: Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population

description: 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.
description: Data used in the
 analysis of Lifespan.Data file with one row
 per individual song sparrow used in the analysis of Lifespan, with the
 following columns. Age: Relative lifespan, i.e. lifespan (in years)
 divided by mean lifespan of all individuals in this dataset. Sex: Sex of
 the individual, i.e. Male or Female. F: Pedigree-based inbreeding
 coefficient. MLH: Mean heterozygosity across 160 microsatellite markers.
 hi_*: 160 columns with heterozygosity data at each of 160 microsatellite
 markers, with 0=homozygous, 1=heterozygous, NA=unknown.LifespanData.csvData used in the analysis of Lifetime number of banded offspring.Data file with one row per individual song sparrow used in the analysis of Lifetime number of banded offspring, with the following columns. Banded: Relative lifetime number of banded offspring, i.e. number of banded offspring produced by the focal individual across its lifetime divided by the mean number of banded offspring of all individuals in this dataset. Sex: Sex of the individual, i.e. Male or Female. F: Pedigree-based inbreeding coefficient. MLH: Mean heterozygosity across 160 microsatellite markers. hi_*: 160 columns with heterozygosity data at each of 160 microsatellite markers, with 0=homozygous, 1=heterozygous, NA=unknown.BandedOffspringData.csvData used in the analysis of Lifetime number of adult offspring.Data file with one row per individual song sparrow used in the analysis of Lifetime number of adult offspring, with the following columns. Recruits: Relative lifetime number of adult offspring, i.e. number of offspring reaching adulthood (i.e. one year old) produced by the focal individual across its lifetime divided by the mean number of adult offspring of all individuals in this dataset. Sex: Sex of the individual, i.e. Male or Female. F: Pedigree-based inbreeding coefficient. MLH: Mean heterozygosity across 160 microsatellite markers. hi_*: 160 columns with heterozygosity data at each of 160 microsatellite markers, with 0=homozygous, 1=heterozygous, NA=unknown.AdultOffspringData.csvData used in the analysis of Lifetime number of adult offspring produced by adult individuals.Data file with one row per individual song sparrow used in the analysis of Lifetime number of adult offspring produced by adult individuals, with the following columns. Fecundity: Relative lifetime number of adult offspring produced by adult individuals, i.e. number of offspring reaching adulthood (i.e. one year old) produced by the focal individual across its lifetime divided by the mean number of adult offspring of all individuals in this dataset (all focal individuals in this dataset are adults). Sex: Sex of the individual, i.e. Male or Female. F: Pedigree-based inbreeding coefficient. MLH: Mean heterozygosity across 160 microsatellite markers. hi_*: 160 columns with heterozygosity data at each of 160 microsatellite markers, with 0=homozygous, 1=heterozygous, NA=unknown.AdultOffspringOfAdultsData.csvFunction used to perform gene-dropping simulations across a pedigree.This function performs gene-dropping simulations of genotypes across a pedigree and outputs heterozygosity and genotype information. See description in file for details.GeneDroppingSimulationFunction.R