Estimating F-statistics for the analysis of population structure.
Bruce S. Weir,C. Clark Cockerham +1 more
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TLDR
The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973).Abstract:
This journal frequently contains papers that report values of F-statistics estimated from genetic data collected from several populations. These parameters, FST, FIT, and FIS, were introduced by Wright (1951), and offer a convenient means of summarizing population structure. While there is some disagreement about the interpretation of the quantities, there is considerably more disagreement on the method of evaluating them. Different authors make different assumptions about sample sizes or numbers of populations and handle the difficulties of multiple alleles and unequal sample sizes in different ways. Wright himself, for example, did not consider the effects of finite sample size. The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973). We start with the parameters and construct appropriate estimators for them, rather than beginning the discussion with various data functions. The extension of Cockerham's work to multiple alleles and loci will be made explicit, and the use of jackknife procedures for estimating variances will be advocated. All of this may be regarded as an extension of a recent treatment of estimating the coancestry coefficient to serve as a mea-read more
Citations
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Distribution of SUN, OVATE, LC and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity
Gustavo Rubén Rodríguez,Stéphane Muños,Claire Anderson,Sung-Chur Sim,Andrew P. Michel,Mathilde Causse,Brian B. McSpadden Gardener,David M. Francis,Esther van der Knaap +8 more
TL;DR: The data suggested that the LC, FAS, and SUN mutations arose in the same ancestral population while the OVATE mutation arose in a separate lineage, whereas the SUN mutation appeared to be a postdomestication event arising in Europe.
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Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers
Joseph Lachance,Benjamin Vernot,Clara C. Elbers,Bart Ferwerda,Alain Froment,Jean-Marie Bodo,Godfrey Lema,Wenqing Fu,Thomas B. Nyambo,Timothy R. Rebbeck,Kun Zhang,Joshua M. Akey,Sarah A. Tishkoff +12 more
TL;DR: The whole genomes of five individuals in each of three different hunter-gatherer populations are sequenced and numerous loci that harbor signatures of local adaptation are identified, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing.
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Loci associated with skin pigmentation identified in African populations
Nicholas G. Crawford,Derek E. Kelly,Matthew E. B. Hansen,Marcia Holsbach Beltrame,Shaohua Fan,Shanna L. Bowman,Shanna L. Bowman,Ethan M. Jewett,Alessia Ranciaro,Simon Thompson,Yancy Lo,Susanne P. Pfeifer,Jeffrey D. Jensen,Michael Campbell,Michael Campbell,William Beggs,Farhad Hormozdiari,Farhad Hormozdiari,Sununguko Wata Mpoloka,Gaonyadiwe G. Mokone,Thomas B. Nyambo,Dawit Wolde Meskel,Gurja Belay,Jake Haut,Nisc Comparative Sequencing Program,Harriet Rothschild,Leonard I. Zon,Leonard I. Zon,Yi Zhou,Michael A. Kovacs,Mai Xu,Tongwu Zhang,Kevin Bishop,Jason Sinclair,Cecilia Rivas,Eugene Elliot,Jiyeon Choi,Shengchao A. Li,Shengchao A. Li,Belynda Hicks,Belynda Hicks,Shawn M. Burgess,Christian C. Abnet,Dawn E. Watkins-Chow,Elena Oceana,Yun S. Song,Eleazar Eskin,Kevin M. Brown,Michael S. Marks,Michael S. Marks,Stacie K. Loftus,William J. Pavan,Meredith Yeager,Meredith Yeager,Stephen J. Chanock,Sarah A. Tishkoff +55 more
TL;DR: It is shown that both dark and light pigmentation alleles arose before the origin of modern humans and that both light and dark pigmented skin has continued to evolve throughout hominid history.
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Demography and Genetic Structure of a Recovering Grizzly Bear Population
Katherine C. Kendall,Jeffrey B. Stetz,John Boulanger,Amy C. Macleod,David Paetkau,Gary C. White +5 more
TL;DR: In this paper, the authors used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population.
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A Genome-Wide Search for Signals of High Altitude Adaptation in Tibetans
Shuhua Xu,Shilin Li,Yajun Yang,Jingze Tan,Haiyi Lou,Wenfei Jin,Ling Yang,Xuedong Pan,Jiucun Wang,Yiping Shen,Bai-Lin Wu,Bai-Lin Wu,Hongyan Wang,Li Jin,Li Jin +14 more
TL;DR: In this article, the authors conducted a genome-wide study of 1,000,000 genetic variants in 46 Tibetans and 92 Han Chinese (HAN) for identifying the signals of high-altitude adaptations (HAAs) in Tibetan genomes.
References
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Journal ArticleDOI
Analysis of Gene Diversity in Subdivided Populations
TL;DR: A method is presented by which the gene diversity (heterozygosity) of a subdivided population can be analyzed into its components, i.e., the gene diversities within and between subpopulations.
Book
The jackknife, the bootstrap, and other resampling plans
TL;DR: The Delta Method and the Influence Function Cross-Validation, Jackknife and Bootstrap Balanced Repeated Replication (half-sampling) Random Subsampling Nonparametric Confidence Intervals as mentioned in this paper.
Journal ArticleDOI
The interpretation of population structure by F-statistics with special regard to systems of mating
TL;DR: It was found that there is no equilibrium in either case short of complete fixation locally, in spite of the linear increase in number of different ancestors with increasing number of ancestral generations, in contrast to systems (half first cousin or second cousin) in which this increase is more than linear and a steady state is rapidly attained with respect to heterozygosis.
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