The Relationship Between Haplotype-Based FST and Haplotype Length

F ST is a statistic that is frequently used to analyze population structure. Recent work has shown that FST depends strongly on the underlying genetic diversity of a locus from which it is computed... The population-genetic statistic FST is used widely to describe allele frequency distributions in s...

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Bibliographic Details
Published in:Genetics (Austin) 2019-09, Vol.213 (1), p.281-295
Main Authors: Mehta, Rohan S, Feder, Alison F, Boca, Simina M, Rosenberg, Noah A
Format: Article
Language:English
Subjects:
Alleles
Chromosomes
Deoxyribonucleic acid
Dependence
DNA
Equilibrium
Gene frequency
Genetic diversity
Genetics
Haplotypes
Human populations
Loci
Nucleotide sequence
Population
Population (statistical)
Population genetics
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Summary:F ST is a statistic that is frequently used to analyze population structure. Recent work has shown that FST depends strongly on the underlying genetic diversity of a locus from which it is computed... The population-genetic statistic FST is used widely to describe allele frequency distributions in subdivided populations. The increasing availability of DNA sequence data has recently enabled computations of FST from sequence-based "haplotype loci." At the same time, theoretical work has revealed that FST has a strong dependence on the underlying genetic diversity of a locus from which it is computed, with high diversity constraining values of FST to be low. In the case of haplotype loci, for which two haplotypes that are distinct over a specified length along a chromosome are treated as distinct alleles, genetic diversity is influenced by haplotype length: longer haplotype loci have the potential for greater genetic diversity. Here, we study the dependence of FST on haplotype length. Using a model in which a haplotype locus is sequentially incremented by one biallelic locus at a time, we show that increasing the length of the haplotype locus can either increase or decrease the value of FST, and usually decreases it. We compute FST on haplotype loci in human populations, finding a close correspondence between the observed values and our theoretical predictions. We conclude that effects of haplotype length are valuable to consider when interpreting FST calculated on haplotypic data.
ISSN:0016-6731
1943-2631
DOI:10.1534/genetics.119.302430