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An Improved Fst Estimator

Author

Listed:
  • Guanjie Chen
  • Ao Yuan
  • Daniel Shriner
  • Fasil Tekola-Ayele
  • Jie Zhou
  • Amy R Bentley
  • Yanxun Zhou
  • Chuntao Wang
  • Melanie J Newport
  • Adebowale Adeyemo
  • Charles N Rotimi

Abstract

The fixation index Fst plays a central role in ecological and evolutionary genetic studies. The estimators of Wright (F ^ s t 1), Weir and Cockerham (F ^ s t 2), and Hudson et al. (F ^ s t 3) are widely used to measure genetic differences among different populations, but all have limitations. We propose a minimum variance estimator F ^ s t m using F ^ s t 1 and F ^ s t 2. We tested F ^ s t m 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 F ^ s t m has smaller bias than F ^ s t 2 for small sample sizes and smaller bias than F ^ s t 1 for large sample sizes. Also, F ^ s t m has smaller variance than F ^ s t 2 for small Fst values and smaller variance than F ^ s t 1 for large Fst values. We demonstrated that approximately 30 subpopulations and 30 individuals per subpopulation are required in order to accurately estimate Fst.

Suggested Citation

  • Guanjie Chen & Ao Yuan & Daniel Shriner & Fasil Tekola-Ayele & Jie Zhou & Amy R Bentley & Yanxun Zhou & Chuntao Wang & Melanie J Newport & Adebowale Adeyemo & Charles N Rotimi, 2015. "An Improved Fst Estimator," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-15, August.
    • Handle: RePEc:plo:pone00:0135368
    DOI: 10.1371/journal.pone.0135368
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