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
More filters
Journal ArticleDOI
Molecular Differentiation at Nuclear Loci in French Host Races of the European Corn Borer (Ostrinia nubilalis)
Thibaut Malausa,Laurianne Leniaud,Laurianne Leniaud,Laurianne Leniaud,Jean Francxois Martin,Philippe Audiot,Denis Bourguet,Sergine Ponsard,Siu F. Lee,Richard J. Harrison,Erik B. Dopman +10 more
TL;DR: Gene genealogies revealed extensive shared polymorphism, but confirmed the previously observed genetic differentiation between the two host races, suggesting that the two taxa diverged recently but probably long before the introduction of maize into Europe.
Journal ArticleDOI
Geodemographic analysis of Borrelia burgdorferi sensu lato using the 5S-23S rDNA spacer region.
Elena Claudia Coipan,Manoj Fonville,Ellen Tijsse-Klasen,Joke van der Giessen,Willem Takken,Hein Sprong,Katsuhisa Takumi +6 more
TL;DR: A genetic trace of population expansion for B. afzelii and B. garinii is consistent with the reported increase in Lyme borreliosis incidence in European countries, and the population genetic analyses of IGS region can resolve subpopulations within a genospecies and detect a large excess of rare genetic variants at the genosPecies level.
Journal ArticleDOI
Tempo and mode of recurrent polyploidization in the Carassius auratus species complex (Cypriniformes, Cyprinidae)
Jing Luo,Yun Gao,Ma W,Bi Xy,Wang Sy,Jing Wang,Yan-Qin Wang,Jing Chai,Rui Du,Wu Sf,Axel Meyer,Zan Rg,Xiao H,Murphy Rw,Ya-Ping Zhang +14 more
TL;DR: This work explores the origin, tempo and frequency of polyploidization in Chinese and Japanese goldfish using both mitochondrial (mtDNA) and nuclear DNA sequences from up to 1202 individuals including the outgroup taxon, Cyprinus carpio.
Journal ArticleDOI
Barriers in the pelagic: population structuring of Calanus helgolandicus and C. euxinus in European waters
TL;DR: Spatial population structuring in European waters of the Atlantic Ocean and Mediterranean Sea of Calanus helgolandicus and its sister species, C. euxinus, is examined to identify barriers to dispersal, relate these to hydrographic characteristics and infer historical patterns of distribution and demography, finding populations are not protected by high levels of dispersal and have been vulnerable to past climatic changes.
Journal ArticleDOI
Phylogeography of the European stalked barnacle (Pollicipes pollicipes): identification of glacial refugia
Daniel Campo,Daniel Campo,Jose Molares,Lucia Garcia,Pino Fernandez-Rueda,Claudia Garcia-Gonzalez,Eva Garcia-Vazquez +6 more
TL;DR: This work analyzed a fragment of the mitochondrial gene cytochrome c oxidase subunit I for 569 individuals of P. pollicipes in order to investigate whether the shifts in climatic conditions that occurred during the Pleistocene influenced the current pattern of distribution of genetic variation of the European stalked barnacle.
References
More filters
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.