An Improved F(st) Estimator

PloS One
Guanjie ChenCharles N Rotimi

Abstract

The fixation index F(st) plays a central role in ecological and evolutionary genetic studies. The estimators of Wright ([Formula: see text]), Weir and Cockerham ([Formula: see text]), and Hudson et al. ([Formula: see text]) are widely used to measure genetic differences among different populations, but all have limitations. We propose a minimum variance estimator [Formula: see text] using [Formula: see text] and [Formula: see text]. We tested [Formula: see text] 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 [Formula: see text] has smaller bias than [Formula: see text] for small sample sizes and smaller bias than [Formula: see text] for large sample sizes. Also, [Formula: see text] has smaller variance than [Formula: see text] for small Fst values and smaller variance than [Formula: see text] for large F(st) values. We demonstrated that approximately 30 subpopulations and 30 individuals per subpopulation are required in order to accurately estimate F(st).

References

Sep 1, 1973·Theoretical Population Biology·C C Cockerham, B S Weir
Nov 25, 2003·American Journal of Human Genetics·Noah A RosenbergJonathan K Pritchard
Jul 1, 1950·British Medical Journal·S WRIGHT
Aug 12, 1950·Nature·S WRIGHT
Mar 30, 2012·The New England Journal of Medicine·Fasil Tekola AyeleGail Davey
Nov 23, 2012·Genetics·Mattias JakobssonNoah A Rosenberg
Jul 19, 2013·Genome Research·Gaurav BhatiaAlkes L Price
Jul 30, 2014·The Pharmacogenomics Journal·Fasil Tekola-AyeleMelanie J Newport
Apr 7, 2016·PLoS Genetics·Fernando RacimoMontgomery Slatkin

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Citations

May 8, 2018·Animals : an Open Access Journal From MDPI·Mei ZhouMingxing Chu
Aug 3, 2017·Human Heredity·Daniel ShrinerCharles N Rotimi

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