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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Common variants at ten loci modulate the QT interval duration in the QTSCD Study
Arne Pfeufer,Serena Sanna,Dan E. Arking,Martina Müller,Vesela Gateva,Christian Fuchsberger,Georg B. Ehret,Marco Orr,Cristian Pattaro,Anna Köttgen,Siegfried Perz,Gianluca Usala,Maja Barbalić,Man Li,Benno Pütz,Angelo Scuteri,Ronald J. Prineas,Moritz F. Sinner,Christian Gieger,Samer S. Najjar,W. H. Linda Kao,Thomas W. Mühleisen,Mariano Dei,Christine Happle,Stefan Möhlenkamp,Laura Crisponi,Raimund Erbel,K. H. Jöckel,Silvia Naitza,Gerhard Steinbeck,Fabio Marroni,Andrew A. Hicks,Edward G. Lakatta,Bertram Müller-Myhsok,Peter P. Pramstaller,H.-Erich Wichmann,David Schlessinger,Eric Boerwinkle,Thomas Meitinger,Manuela Uda,Josef Coresh,Stefan Kääb,Gonçalo R. Abecasis,Aravinda Chakravarti +43 more
TL;DR: In this article, the authors analyzed genome-wide data from five population-based cohorts (ARIC, KORA, SardiNIA, GenNOVA and HNR) with a total of 15,842 individuals of European ancestry, to confirm the NOS1AP association and identify nine additional loci at P < 5 x 10(-8).
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Fine-scaled geographical population structuring in a highly mobile marine species: the Atlantic cod.
TL;DR: Findings lend support to the notion that low levels of differentiation are due to passive transport of eggs or larvae by the ocean currents rather than to adult dispersal, the latter being strongly dependent on distance.
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Genome-wide patterns of population structure and admixture among Hispanic/Latino populations
Katarzyna Bryc,Christopher Velez,Tatiana M. Karafet,Andrés Moreno-Estrada,Andrés Moreno-Estrada,Andrew R. Reynolds,Adam Auton,Adam Auton,Michael F. Hammer,Carlos Bustamante,Carlos Bustamante,Harry Ostrer +11 more
TL;DR: The results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.
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Population structure and speciation in tropical seas: global phylogeography of the sea urchin diadema
TL;DR: The phylogeny of the pantropical and subtropical sea urchin genus Diadema is reconstructed, using sequences of mitochondrial DNA from 482 individuals collected around the world, to determine the efficacy of barriers to gene flow and to ascertain the history of possible dispersal and vicariance events that led to speciation.
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Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
Reto Burri,Alexander Nater,Takeshi Kawakami,Carina F. Mugal,Pall I. Olason,Linnéa Smeds,Alexander Suh,Ludovic Dutoit,Stanislav Bureš,László Zsolt Garamszegi,Silje Hogner,Silje Hogner,Juan Moreno,Anna Qvarnström,Milan Ružić,Stein Are Sæther,Glenn-Peter Sætre,János Török,Hans Ellegren +18 more
TL;DR: It is concluded that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination, and the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation is emphasized.
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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