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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Environmentally related patterns of reproductive modes in the aphid Myzus persicae and the predominance of two ‘superclones’ in Victoria, Australia
TL;DR: Interestingly, obligate parthenogens were, on average, more heterozygous and exhibited larger allele size differences between the two alleles at individual loci than cyclical parthenogenesis, which may reflect the previously proposed model of biased mutational divergence of microsatellite alleles within asexual aphid lineages.
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Reconciling patterns of inter‐ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans)
TL;DR: The results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci, and show that divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration.
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Genetic spatial autocorrelation can readily detect sex‐biased dispersal
Sam C. Banks,Rodney Peakall +1 more
TL;DR: Congruence was found between simulation predictions and empirical data from the agile antechinus, a species that exhibits male‐biased dispersal, confirming the power of individual‐based genetic analysis to provide insights into asymmetries in male and female dispersal.
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Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm.
Ibrokhim Y. Abdurakhmonov,Russell J. Kohel,John Z. Yu,Alan E. Pepper,Alisher A. Abdullaev,Fakhriddin N. Kushanov,Ilkhom B. Salakhutdinov,Zabardast T. Buriev,Sukumar Saha,Brian E. Scheffler,Johnie N. Jenkins,Abdusattor Abdukarimov +11 more
TL;DR: The results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and stratification existing in cotton germplasm resources, and demonstrate the existence of useful genetic diversity within exotic cotton germ plasm.
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Fast-evolving noncoding sequences in the human genome
Christine P. Bird,Barbara E. Stranger,Maureen Liu,Daryl J. Thomas,Catherine E. Ingle,Claude Beazley,Webb Miller,Matthew E. Hurles,Emmanouil T. Dermitzakis +8 more
TL;DR: This analysis suggests that ANC sequences have until very recently played a role in human evolution, potentially through lineage-specific changes in gene regulation.
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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