Estimating F-statistics for the analysis of population structure.
Bruce S. Weir,C. Clark Cockerham +1 more
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
More filters
Journal ArticleDOI
Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power
TL;DR: Simulated data sets were used to test the power and accuracy of Monte Carlo resampling methods in generating statistical thresholds for identifying F0 immigrants in populations with ongoing gene flow, and hence for providing direct, real‐time estimates of migration rates.
Journal ArticleDOI
What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity.
TL;DR: It is suggested several quantitative criteria that might be used to determine when groups of individuals are different enough to be considered ‘populations’, and a simple algorithm based on a multilocus contingency test of allele frequencies in pairs of samples has high power to detect the true number of populations but requires more rigorous statistical evaluation.
Journal ArticleDOI
Genes mirror geography within Europe.
John Novembre,Toby Johnson,Toby Johnson,Katarzyna Bryc,Zoltán Kutalik,Adam R. Boyko,Adam Auton,Amit Indap,Karen S. King,Sven Bergmann,Matthew R. Nelson,Matthew Stephens,Carlos Bustamante +12 more
TL;DR: Despite low average levels of genetic differentiation among Europeans, there is a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans.
Journal ArticleDOI
Reconstructing Indian Population History
TL;DR: It is predicted that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically and is higher in traditionally upper caste and Indo-European speakers.
Journal ArticleDOI
Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
Paul A. Hohenlohe,Susan Bassham,Paul D. Etter,Nicholas Stiffler,Eric A. Johnson,William A. Cresko +5 more
TL;DR: Overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations and identify several novel regions showing parallel differentiation across independent populations.
References
More filters
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.
Related Papers (5)
Inference of population structure using multilocus genotype data
GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism
Michel Raymond,François Rousset +1 more