%0 Journal Article
%A Mehta, Rohan S.
%A Feder, Alison F.
%A Boca, Simina M.
%A Rosenberg, Noah A.
%T The Relationship Between Haplotype-Based *F*_{ST} and Haplotype Length
%D 2019
%R 10.1534/genetics.119.302430
%J Genetics
%P genetics.302430.2019
%X 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 specied length along a chromosome are treated as distinct alleles, genetic diversity is in uenced 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, nding 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.
%U https://www.genetics.org/content/genetics/early/2019/07/08/genetics.119.302430.full.pdf