RT Journal Article
SR Electronic
T1 Unbiased Estimation of Gene Diversity in Samples Containing Related Individuals: Exact Variance and Arbitrary Ploidy
JF Genetics
JO Genetics
FD Genetics Society of America
SP 1367
OP 1387
DO 10.1534/genetics.110.121756
VO 186
IS 4
A1 DeGiorgio, Michael
A1 Jankovic, Ivana
A1 Rosenberg, Noah A.
YR 2010
UL http://www.genetics.org/content/186/4/1367.abstract
AB Gene diversity, a commonly used measure of genetic variation, evaluates the proportion of heterozygous individuals expected at a locus in a population, under the assumption of Hardyâ€“Weinberg equilibrium. When using the standard estimator of gene diversity, the inclusion of related or inbred individuals in a sample produces a downward bias. Here, we extend a recently developed estimator shown to be unbiased in a diploid autosomal sample that includes known related or inbred individuals to the general case of arbitrary ploidy. We derive an exact formula for the variance of the new estimator, \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\tilde{H}}\) \end{document}, and present an approximation to facilitate evaluation of the variance when each individual is related to at most one other individual in a sample. When examining samples from the human X chromosome, which represent a mixture of haploid and diploid individuals, we find that \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\tilde{H}}\) \end{document} performs favorably compared to the standard estimator, both in theoretical computations of mean squared error and in data analysis. We thus propose that \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\tilde{H}}\) \end{document} is a useful tool in characterizing gene diversity in samples of arbitrary ploidy that contain related or inbred individuals.