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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Microsatellite genetic variation between and within farmed and wild Atlantic salmon (Salmo salar) populations
TL;DR: Phylogenetic analysis using either populations or individuals as nodes show a clustering of populations into two groups, farmed and wild, which suggests that founder effects and subsequent selection have had more effect on the genetic differentiation between these strains than geographical separation.
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The relative influence of natural selection and geography on gene flow in guppies
TL;DR: In this paper, the relative influence of divergent selection and geographic features on gene flow among populations of Trinidadian guppies (Poecilia reticulata) was determined.
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Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers.
TL;DR: It is argued that the estimators developed should find major applications, notably for conservation biology, and that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size.
Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations : [W633]
Stéphane De Mita,Anne-Céline Thuillet,Nourollah Ahmadi,Stéphanie Manel,Joëlle Ronfort,Yves Vigouroux +5 more
TL;DR: In this article, the authors provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection, and investigate the power and robustness of eight methods to identify loci potentially under selection.
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Microsatellite variability in grapevine cultivars from different European regions and evaluation of assignment testing to assess the geographic origin of cultivars
Kristina M. Sefc,M. S. Lopes,François Lefort,R. Botta,Kalliopi A. Roubelakis-Angelakis,Javier Ibáñez,Ivan Pejić,H. W. Wagner,Josef Glössl,Herta Steinkellner +9 more
TL;DR: The observed genetic differentiation among vine-growing regions suggested that cultivars could possibly be assigned to their regions of origin according to their genotypes, and the assignment procedure proved to work for cultivars from the higher differentiated regions, as for example from Austria and Portugal.
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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