Estimating F-statistics for the analysis of population structure.
Bruce S. Weir,C. Clark Cockerham +1 more
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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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Effects of human TRIM5α polymorphisms on antiretroviral function and susceptibility to human immunodeficiency virus infection
Hassan Javanbakht,Ping An,Bert Gold,Desiree C. Petersen,Colm O'hUigin,George W. Nelson,Stephen J. O'Brien,Gregory D. Kirk,Roger Detels,Susan Buchbinder,Sharyne Donfield,Sergey Shulenin,Byeongwoon Song,Michel Perron,Matthew Stremlau,Joseph Sodroski,Michael Dean,Cheryl A. Winkler +17 more
TL;DR: Polymorphism in human TRIM5 may influence susceptibility to HIV-1 infection, a possibility that merits additional evaluation in independent cohorts.
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Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids
TL;DR: A novel genome sequencing strategy is presented, useful when evolutionary diversity is the question of interest, and the unique structure of Lake Malawi cichlid genomes should facilitate conceptually new experiments, employing SNPs to identity genotype-phenotype association, using the entire species flock as a mapping panel.
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Mapping migration in a songbird using high‐resolution genetic markers
Kristen C. Ruegg,Kristen C. Ruegg,Eric C. Anderson,Eric C. Anderson,Kristina L. Paxton,Kristina L. Paxton,Vanessa Apkenas,Sirena Lao,Rodney B. Siegel,David F. DeSante,Frank R. Moore,Thomas B. Smith,Thomas B. Smith +12 more
TL;DR: It is shown how high‐resolution genetic markers can be used to identify genetically distinct groups of a migratory bird, the Wilson's warbler (Cardellina pusilla), at fine enough spatial scales to facilitate assessing regional drivers of demographic trends.
Journal ArticleDOI
Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces
TL;DR: The first study of patterns of genetic diversity of sorghum landraces at the local scale in Northern Cameroon is presented, showing how historical factors, variation in breeding systems, and farmers’ practices all affected patterns of Genetic variation.
Journal ArticleDOI
Genetic Differentiation Between American and European Drosophila melanogaster Populations Could Be Attributed to Admixture of African Alleles
G. Caracristi,C. Schlötterer +1 more
TL;DR: Interestingly, genetic distances based on the proportion of shared alleles as well as FST values suggested that the American D. melanogaster populations are more closely related to the African populations than European ones are.
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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