Results 11 to 20 of about 3,871 (235)
The Wright–Fisher site frequency spectrum as a perturbation of the coalescent’s [PDF]
Theoretical Population Biology, 2018 Abstract The first terms of the Wright-Fisher (WF) site frequency spectrum that follow the coalescent approximation are determined precisely, with a view to understanding the accuracy of the coalescent approximation for large samples.
Andrew Melfi, Divakar Viswanath
exaly +5 more sources
The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele [PDF]
Theoretical Population Biology, 2011 The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to be polymorphic. This distribution is widely used in population genetic inferences, including statistical tests of neutrality in which a skew in the observed frequency spectrum across ...
Paul A Jenkins, Yun S Song
exaly +5 more sources
Experiments with the Site Frequency Spectrum [PDF]
Bulletin of Mathematical Biology, 2010 Evaluating the likelihood function of parameters in highly-structured population genetic models from extant deoxyribonucleic acid (DNA) sequences is computationally prohibitive. In such cases, one may approximately infer the parameters from summary statistics of the data such as the site-frequency-spectrum (SFS) or its linear combinations. Such methods
Sainudiin, R +8 more
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The third moments of the site frequency spectrum
Theoretical Population Biology, 2017 Abstract The analysis of patterns of segregating (i.e. polymorphic) sites in aligned sequences is routine in population genetics. Quantities of interest include the total number of segregating sites and the number of sites with mutations of different frequencies, the so-called site frequency spectrum
Klassmann, A., Ferretti, L.
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The Site Frequency Spectrum for General Coalescents [PDF]
Genetics, 2016 Abstract General genealogical processes such as Λ- and Ξ-coalescents, which respectively model multiple and simultaneous mergers, have important applications in studying marine species, strong positive selection, recurrent selective sweeps, strong bottlenecks, large sample sizes, and so on.
Spence, Jeffrey P +2 more
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The aggregate site frequency spectrum for comparative population genomic inference [PDF]
Molecular Ecology, 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.
Alexander T Xue, Michael J Hickerson
exaly +3 more sources
Non-parametric estimation of population size changes from the site frequency spectrum [PDF]
Statistical Applications in Genetics and Molecular Biology, 2017 Abstract The variability in population size is a key quantity for understanding the evolutionary history of a species. We present a new method, CubSFS, for estimating the changes in population size of a panmictic population from the site frequency spectrum.
Waltoft, Berit Lindum, Hobolth, Asger
core +5 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 +10 more sources
Site Frequency Spectrum in stationary branching populations
This paper explores the Site Frequency Spectrum (SFS) in stationary branching populations. We derive estimates for the SFS associated with a sample from a continuous-state branching process conditioned to never go extinct, utilizing a quadratic branching mechanism.
Abraham, Romain +2 more
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The site frequency spectrum for coalescing Brownian motion
Stochastic Processes and their Applications, 2023 We consider an expanding population on the plane. The genealogy of a sample from the population is modelled by coalescing Brownian motion on the circle. We establish a weak law of large numbers for the site frequency spectrum in this model. A parallel result holds for a localized version where the genealogy is modelled by coalescing Brownian motion on ...
Shuai, Yubo
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