An Improved F(st) Estimator.
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,...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0135368 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Guanjie Chen |
| collection | DOAJ |
| description | 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). |
| format | Article |
| id | doaj-art-ad412614e35f4e579d721537af036fc6 |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-ad412614e35f4e579d721537af036fc62025-08-20T03:10:09ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-01108e013536810.1371/journal.pone.0135368An Improved F(st) Estimator.Guanjie ChenAo YuanDaniel ShrinerFasil Tekola-AyeleJie ZhouAmy R BentleyYanxun ZhouChuntao WangMelanie J NewportAdebowale AdeyemoCharles N RotimiThe 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).https://doi.org/10.1371/journal.pone.0135368 |
| spellingShingle | 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 An Improved F(st) Estimator. PLoS ONE |
| title | An Improved F(st) Estimator. |
| title_full | An Improved F(st) Estimator. |
| title_fullStr | An Improved F(st) Estimator. |
| title_full_unstemmed | An Improved F(st) Estimator. |
| title_short | An Improved F(st) Estimator. |
| title_sort | improved f st estimator |
| url | https://doi.org/10.1371/journal.pone.0135368 |
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