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

  • Pirmin Nietlisbach (Creator)
  • Lukas F. Keller (Creator)
  • Glauco Camenisch (Creator)
  • Frédéric Guillaume (Creator)
  • Peter Arcese (Creator)
  • Jane Reid (Creator)
  • Erik Postma (Creator)

Dataset

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.

Data type

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.csv

Data 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.csv

Data 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.csv

Data 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.csv

Function 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

Copyright and Open Data Licencing

This work is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.
Date made available7 Feb 2017
PublisherDryad Digital Repository
Geographical coverageCanada, Mandarte Island, British Columbia. [48° 38' N 123° 17' W]

Keywords

  • Heterozygosity-fitness correlation
  • Holocene
  • identity disequilibrium
  • Melospiza melodia
  • short tandem repeats
  • song sparrow

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