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MBE Advance Access published online on November 6, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn254
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Research Article

An Unbiased Estimator of Gene Diversity in Samples Containing Related Individuals

Michael DeGiorgio1,* and Noah A. Rosenberg1,2

1 Center for Computational Medicine and Biology, University of Michigan
2 Department of Human Genetics and the Life Sciences Institute, University of Michigan

* Corresponding author Michael DeGiorgio, Center for Computational Medicine and Biology, University of Michigan, 2017 Palmer Commons, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA, Phone +1 734 615 9551, Fax +1 734 615 6553, email: degiormi{at}umich.edu

Received for publication July 28, 2008. Revision received September 29, 2008. Accepted for publication October 23, 2008.

Gene diversity is sometimes estimated from samples that contain inbred or related individuals. If inbred or related individuals are included in a sample, then the standard estimator for gene diversity produces a downward bias, caused by an inflation of the variance of estimated allele frequencies. We develop an unbiased estimator for gene diversity that relies on kinship coefficients for pairs of individuals with known relationship, and that reduces to the standard estimator when all individuals are non-inbred and unrelated. Applying our estimator to data simulated based on allele frequencies observed for microsatellite loci in human populations, we find that the new estimator performs favorably compared to the standard estimator in terms of bias and similarly in terms of mean squared error. For human population-genetic data, we find that a close linear relationship previously seen between gene diversity and distance from East Africa is preserved when adjusting for the inclusion of close relatives.

Key Words: Heterozygosity • identity by descent • kinship coefficient


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 Proc. Natl. Acad. Sci. USAHome page
M. DeGiorgio, M. Jakobsson, and N. A. Rosenberg
Out of Africa: Modern Human Origins Special Feature: Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa
PNAS, September 22, 2009; 106(38): 16057 - 16062.
[Abstract] [Full Text] [PDF]


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