polyDFE: Inferring the Distribution of Fitness Effects and Properties of Beneficial Mutations from Polymorphism Data
2020; Springer Science+Business Media; Linguagem: Inglês
10.1007/978-1-0716-0199-0_6
ISSN1940-6029
AutoresPaula Tataru, Thomas Bataillon,
Tópico(s)Genetic and phenotypic traits in livestock
ResumoAbstract The possible evolutionary trajectories a population can follow is determined by the fitness effects of new mutations. Their relative frequencies are best specified through a distribution of fitness effects (DFE) that spans deleterious, neutral, and beneficial mutations. As such, the DFE is key to several aspects of the evolution of a population, and particularly the rate of adaptive molecular evolution ( α ). Inference of DFE from patterns of polymorphism and divergence has been a longstanding goal of evolutionary genetics. provides a flexible statistical framework to estimate the DFE and α from site frequency spectrum (SFS) data. Several probability distributions can be fitted to the data to model the DFE. The method also jointly estimates a series of nuisance parameters that model the effect of unknown demography as well data imperfections, in particular possible errors in polarizing SNPs. This chapter is organized as a tutorial for . We start by briefly reviewing the concept of DFE, α , and the principles underlying the method, and then provide an example using central chimpanzees data (Tataru et al., Genetics 207(3):1103–1119, 2017; Bataillon et al., Genome Biol Evol 7(4):1122–1132, 2015) to guide the user through the different steps of an analysis: formatting the data as input to , fitting different models, obtaining estimates of parameters uncertainty and performing statistical tests, as well as model averaging procedures to obtain robust estimates of model parameters.
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