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This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication: https://creativecommons.org/publicdomain/zero/1.0/ (the “License”) Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

The fixation index Fst plays a central role in ecological and evolutionary genetic studies. The estimators of Wright (), Weir and Cockerham (), and Hudson et al. () are widely used to measure genetic differences among different populations, but all have limitations. We propose a minimum variance estimator using and . We tested in simulations and applied it to 120 unrelated East African individuals from Ethiopia and 11 subpopulations in HapMap 3 with 464,642 SNPs. Our simulation study showed that has smaller bias than for small sample sizes and smaller bias than for large sample sizes. Also, has smaller variance than for small Fst values and smaller variance than for large Fst values. We demonstrated that approximately 30 subpopulations and 30 individuals per subpopulation are required in order to accurately estimate Fst.

Details

Title
An Improved Fst Estimator
Author
Chen, Guanjie; Ao Yuan; Shriner, Daniel; Tekola-Ayele, Fasil; Zhou, Jie; Bentley, Amy R; Zhou, Yanxun; Wang, Chuntao; Newport, Melanie J; Adeyemo, Adebowale; Rotimi, Charles N
First page
e0135368
Section
Research Article
Publication year
2015
Publication date
Aug 2015
Publisher
Public Library of Science
e-ISSN
19326203
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
1719268957
Copyright
This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication: https://creativecommons.org/publicdomain/zero/1.0/ (the “License”) Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.