PT - JOURNAL ARTICLE
AU - Rosenberg, Noah A.
AU - Jakobsson, Mattias
TI - The Relationship Between Homozygosity and the Frequency of the Most Frequent Allele
AID - 10.1534/genetics.107.084772
DP - 2008 Aug 01
TA - Genetics
PG - 2027--2036
VI - 179
IP - 4
4099 - http://www.genetics.org/content/179/4/2027.short
4100 - http://www.genetics.org/content/179/4/2027.full
SO - Genetics2008 Aug 01; 179
AB - Homozygosity is a commonly used summary of allele-frequency distributions at polymorphic loci. Because high-frequency alleles contribute disproportionately to the homozygosity of a locus, it often occurs that most homozygotes are homozygous for the most frequent allele. To assess the relationship between homozygosity and the highest allele frequency at a locus, for a given homozygosity value, we determine the lower and upper bounds on the frequency of the most frequent allele. These bounds suggest tight constraints on the frequency of the most frequent allele as a function of homozygosity, differing by at most \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\frac{1}{4}\) \end{document} and having an average difference of \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\frac{2}{3}\) \end{document} − π2/18 ≈ 0.1184. The close connection between homozygosity and the frequency of the most frequent allele—which we illustrate using allele frequencies from human populations—has the consequence that when one of these two quantities is known, considerable information is available about the other quantity. This relationship also explains the similar performance of statistical tests of population-genetic models that rely on homozygosity and those that rely on the frequency of the most frequent allele, and it provides a basis for understanding the utility of extended homozygosity statistics in identifying haplotypes that have been elevated to high frequency as a result of positive selection.