Results 1 to 10 of about 596 (200)
The Site Frequency/Dosage Spectrum of Autopolyploid Populations [PDF]
Frontiers in Genetics, 2018 The Site Frequency Spectrum (SFS) and the heterozygosity of allelic variants are among the most important summary statistics for population genetic analysis of diploid organisms.
Luca Ferretti +2 more
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Correcting the site frequency spectrum for divergence-based ascertainment. [PDF]
PLoS ONE, 2009 Comparative genomics based on sequenced referenced genomes is essential to hypothesis generation and testing within population genetics. However, selection of candidate regions for further study on the basis of elevated or depressed divergence between ...
Andrew D Kern
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Multivariate phase-type theory for the site frequency spectrum [PDF]
Journal of Mathematical Biology, 2021 Linear functions of the site frequency spectrum (SFS) play a major role for understanding and investigating genetic diversity. Estimators of the mutation rate (e.g. based on the total number of segregating sites or average of the pairwise differences) and tests for neutrality (e.g. Tajima's D) are perhaps the most well-known examples.
Asger Hobolth +2 more
exaly +8 more sources
Joint effect of changing selection and demography on the site frequency spectrum [PDF]
Theoretical Population Biology, 2022 Abstract The site frequency spectrum (SFS) is an important statistic that summarizes the molecular variation in a population, and used to estimate population-genetic parameters and detect natural selection. While the equilibrium SFS in a constant environment is quite well studied, recent research has focused on nonequilibrium SFS to ...
Kavita Jain, Sachin Kaushik
exaly +3 more sources
The Site-Frequency Spectrum of Linked Sites [PDF]
Bulletin of Mathematical Biology, 2010 The site-frequency spectrum, representing the distribution of allele frequencies at a set of polymorphic sites, is a commonly used summary statistic in population genetics. Explicit forms of the spectrum are known for both models with and without selection if independence among sites is assumed.
Xiaohui Xie, Xie Xiaohui
exaly +3 more sources
The yule approximation for the site frequency spectrum after a selective sweep. [PDF]
PLoS ONE, 2013 In the area of evolutionary theory, a key question is which portions of the genome of a species are targets of natural selection. Genetic hitchhiking is a theoretical concept that has helped to identify various such targets in natural populations. In the
Sebastian Bossert, Peter Pfaffelhuber
doaj +5 more sources
The site frequency spectrum of dispensable genes [PDF]
Theoretical Population Biology, 2015 The differences between DNA-sequences within a population are the basis to infer the ancestral relationship of the individuals. Within the classical infinitely many sites model, it is possible to estimate the mutation rate based on the site frequency spectrum, which is comprised by the numbers $C_1,...,C_{n-1}$, where n is the sample size and $C_s$ is ...
Franz Baumdicker
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Correction: The Yule Approximation for the Site Frequency Spectrum after a Selective Sweep
PLoS ONE, 2014 This article was republished on January 17th, 2014 to include a document containing the Supporting Information for the article that was incorrectly omitted from the original edition of the article. The original edition of the article is available here: http://plosone.org/corrections/pone.0081738.original.cn ...
Sebastian Bossert, Peter Pfaffelhuber
doaj +5 more sources
Spatial structure alters the site frequency spectrum produced by hitchhiking
Genetics, 2022 Abstract The reduction of genetic diversity due to genetic hitchhiking is widely used to find past selective sweeps from sequencing data, but very little is known about how spatial structure affects hitchhiking. We use mathematical modeling and simulations to find the unfolded site frequency spectrum left by hitchhiking in the genomic
Jiseon Min +2 more
exaly +3 more sources
A General Framework for Neutrality Tests Based on the Site Frequency Spectrum
Genes, 2023 One of the main necessities for population geneticists is the availability of sensitive statistical tools that enable to accept or reject the standard Wright–Fisher model of neutral evolution. A number of statistical tests have been developed to detect specific deviations from the null frequency spectrum in different directions (e.g., Tajima’s D, Fu ...
Sebastian E Ramos-Onsins +2 more
exaly +5 more sources