Oct 29, 2018

An Efficient Computational Approach for Constructing the Allele Frequency Spectrum of Populations with Arbitrary Complex History

BioRxiv : the Preprint Server for Biology
Hua Chen

Abstract

The allele frequency spectrum (AFS), or site frequency spectrum, is commonly used to summarize the genomic polymorphism pattern of a sample, which is informative for inferring population history and detecting natural selection. Recently, Chen an Chen (2013) developed a method for analytically deriving the AFS for populations with temporally varying size through the coalescence time-scaling function. However, their approach is only applicable for population history scenarios in which the analytical form of the time-scaling function is tractable. In this paper, we propose a computational approach to extend the method to populations with arbitrary complex history by numerically approximating the time-scaling function. We demonstrate the performance of the approach by constructing the AFS for two population history scenarios: the logistic growth model and the Gompertz growth model, for which the AFS are unavailable with existing approaches.

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Mentioned in this Paper

Gene Polymorphism
Size
Patterns
Genome
Site
Genomics
Logistic Models
Alleles
Genetic Polymorphism
Population Group

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