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
doaj +8 more sources
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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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
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A General Framework for Neutrality Tests Based on the Site Frequency Spectrum. [PDF]
Genes (Basel), 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 ...
Ramos-Onsins SE +3 more
europepmc +6 more sources
Spatial structure alters the site frequency spectrum produced by hitchhiking. [PDF]
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
Min J, Gupta M, Desai MM, Weissman DB.
europepmc +4 more sources
Controlling for Variable Transposition Rate with an Age-Adjusted Site Frequency Spectrum. [PDF]
Genome Biol Evol, 2022 Abstract Recognition of the important role of transposable elements (TEs) in eukaryotic genomes quickly led to a burgeoning literature modeling and estimating the effects of selection on TEs. Much of the empirical work on selection has focused on analyzing the site frequency spectrum (SFS) of TEs.
Horvath R +3 more
europepmc +8 more sources
Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests. [PDF]
Genetics, 2017 Abstract We investigate the dependence of the site frequency spectrum (SFS) on the topological structure of genealogical trees. We show that basic population genetic statistics – for instance estimators of θ or neutrality tests such as Tajima’s D –
Ferretti L +4 more
europepmc +7 more sources
The aggregate site frequency spectrum for comparative population genomic inference. [PDF]
Mol Ecol, 2015 AbstractUnderstanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, an endeavour that has increasing potential to integrate with community ecology.
Xue AT, Hickerson MJ.
europepmc +5 more sources
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 +6 more sources
Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. [PDF]
PLoS ONE, 2011 Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology.
Aurélien Tellier +7 more
doaj +11 more sources