Results 11 to 20 of about 283,425 (262)
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 JP, Kamm JA, Song YS.
europepmc +10 more sources
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.
Lars Nørvang Andersen +2 more
exaly +10 more sources
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
exaly +6 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 ...
Yun S Song, Paul Jenkins
exaly +6 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
openaire +7 more sources
Learning natural selection from the site frequency spectrum. [PDF]
Genetics, 2013 Abstract Genetic adaptation to external stimuli occurs through the combined action of mutation and selection. A central problem in genetics is to identify loci responsive to specific selective constraints. Many tests have been proposed to identify the genomic signatures of natural selection by quantifying the skew in the site frequency ...
Ronen R, Udpa N, Halperin E, Bafna V.
europepmc +6 more sources
Statistical properties of the site-frequency spectrum associated with lambda-coalescents. [PDF]
Genetics, 2013 Abstract Statistical properties of the site-frequency spectrum associated with Λ-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent.
Birkner M, Blath J, Eldon B.
europepmc +5 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
Evaluating the ability of the pairwise joint site frequency spectrum to co-estimate selection and demography [PDF]
Frontiers in Genetics, 2015 The ability to infer the parameters of positive selection from genomic data has many important implications, from identifying drug-resistance mutations in viruses to increasing crop yield by genetically integrating favorable alleles. Although it has been
Lisha eMathew, Jeffrey D. Jensen
doaj +2 more sources