Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection.
TLDR
It is found that the polymorphic patterns in a DNA sample under logistic population growth and genetic hitchhiking are very similar and that one of the newly developed tests, Fs, is considerably more powerful than existing tests for rejecting the hypothesis of neutrality of mutations.Abstract:
The main purpose of this article is to present several new statistical tests of neutrality of mutations against a class of alternative models, under which DNA polymorphisms tend to exhibit excesses of rare alleles or young mutations. Another purpose is to study the powers of existing and newly developed tests and to examine the detailed pattern of polymorphisms under population growth, genetic hitchhiking and background selection. It is found that the polymorphic patterns in a DNA sample under logistic population growth and genetic hitchhiking are very similar and that one of the newly developed tests, Fs, is considerably more powerful than existing tests for rejecting the hypothesis of neutrality of mutations. Background selection gives rise to quite different polymorphic patterns than does logistic population growth or genetic hitchhiking, although all of them show excesses of rare alleles or young mutations. We show that Fu and Li's tests are among the most powerful tests against background selection. Implications of these results are discussed.read more
Citations
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Worldwide Phylogenetic Distributions and Population Dynamics of the Genus Histoplasma.
Marcus de Melo Teixeira,Marcus de Melo Teixeira,José S. L. Patané,Maria Lucia Taylor,Beatriz L. Gómez,Raquel Cordeiro Theodoro,Sybren de Hoog,David M. Engelthaler,Rosely Maria Zancopé-Oliveira,Maria Sueli Soares Felipe,Bridget M. Barker +10 more
TL;DR: The genetic isolation of Histoplasma could be a result of differential dispersion potential of naturally infected bats and other mammals, and isolate selection for future population genomics and genome wide association studies in this important pathogen complex.
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DNA Variation in a Conifer, Cryptomeria japonica (Cupressaceae sensu lato)
TL;DR: The frequency spectrum of the nucleotide polymorphism revealed excesses of intermediate-frequency variants, which suggests that the population was not panmictic and a constant size in the past, and suggested possibilities of natural selection acting at some of the loci.
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Did glacial advances during the Pleistocene influence differently the demographic histories of benthic and pelagic Antarctic shelf fishes?--Inferences from intraspecific mitochondrial and nuclear DNA sequence diversity.
Karel Janko,Guillaume Lecointre,Arthur L. DeVries,Arnaud Couloux,Corinne Cruaud,Craig J. Marshall +5 more
TL;DR: Benthic and pelagic species reacted differently to the Pleistocene ice-sheet expansions that probably significantly reduced the suitable habitat for benthic species, and the asynchronous timing of major demographic events observed in different species within both "ecological guilds".
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Allele Frequency Distribution Under Recurrent Selective Sweeps
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The whereabouts of an ancient wanderer: global phylogeography of the solitary ascidian Styela plicata.
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References
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Journal Article
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
Journal ArticleDOI
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
TL;DR: The relationship between the two estimates of genetic variation at the DNA level, namely the number of segregating sites and the average number of nucleotide differences estimated from pairwise comparison, is investigated in this article.
Journal ArticleDOI
Statistical tests of neutrality of mutations
Yunxin Fu,Wen-Hsiung Li +1 more
TL;DR: From these properties, several new statistical tests based on a random sample of DNA sequences from the population are developed for testing the hypothesis that all mutations at a locus are neutral.
Journal ArticleDOI
On the number of segregating sites in genetical models without recombination.
TL;DR: The distribution is obtained for the number of segregating sites observed in a sample from a population which is subject to recurring, new, mutations but not subject to recombination, and applies approximately to three population models.
Journal ArticleDOI
Evolutionary relationship of dna sequences in finite populations
TL;DR: These studies indicate that the estimates of the average number of nucleotide differences and nucleon diversity have a large variance, and a large part of this variance is due to stochastic factors.