Estimating genome-wide heterozygosity: effects of demographic history and marker type

Heterozygosity-fitness correlations (HFCs) are often used to link individual genetic variation to differences in fitness. However, most studies examining HFCs find weak or no correlations. Here, we derive broad theoretical predictions about how many loci are needed to adequately measure genomic hete...

Full description

Saved in:
Bibliographic Details
Published in:Heredity 2014-03, Vol.112 (3), p.240-247
Main Authors: Miller, J M, Malenfant, R M, David, P, Davis, C S, Poissant, J, Hogg, J T, Festa-Bianchet, M, Coltman, D W
Format: Article
Language:English
Subjects:
Alberta
Animals
Genetic diversity
Genetic Fitness
Genetics, Population
Genome
Genomics
Heterozygote
Inbreeding
Microsatellite Repeats
Models, Genetic
Montana
Original
Ovis canadensis
Polymorphism, Single Nucleotide
Population genetics
Sheep
Sheep, Bighorn - genetics
Translocation
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Heterozygosity-fitness correlations (HFCs) are often used to link individual genetic variation to differences in fitness. However, most studies examining HFCs find weak or no correlations. Here, we derive broad theoretical predictions about how many loci are needed to adequately measure genomic heterozygosity assuming different levels of identity disequilibrium (ID), a proxy for inbreeding. We then evaluate the expected ability to detect HFCs using an empirical data set of 200 microsatellites and 412 single nucleotide polymorphisms (SNPs) genotyped in two populations of bighorn sheep (Ovis canadensis), with different demographic histories. In both populations, heterozygosity was significantly correlated across marker types, although the strength of the correlation was weaker in a native population compared with one founded via translocation and later supplemented with additional individuals. Despite being bi-allelic, SNPs had similar correlations to genome-wide heterozygosity as microsatellites in both populations. For both marker types, this association became stronger and less variable as more markers were considered. Both populations had significant levels of ID; however, estimates were an order of magnitude lower in the native population. As with heterozygosity, SNPs performed similarly to microsatellites, and precision and accuracy of the estimates of ID increased as more loci were considered. Although dependent on the demographic history of the population considered, these results illustrate that genome-wide heterozygosity, and therefore HFCs, are best measured by a large number of markers, a feat now more realistically accomplished with SNPs than microsatellites.
ISSN:0018-067X
1365-2540
DOI:10.1038/hdy.2013.99