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A Composite-Likelihood Method for Detecting Incomplete Selective Sweep from Population Genomic Data

Title
A Composite-Likelihood Method for Detecting Incomplete Selective Sweep from Population Genomic Data
Authors
Vy, Ha My T.Kim, Yuseob
Ewha Authors
김유섭
SCOPUS Author ID
김유섭scopus
Issue Date
2015
Journal Title
GENETICS
ISSN
0016-6731JCR Link1943-2631JCR Link
Citation
vol. 200, no. 2, pp. 633 - +
Keywords
positive selectionselective sweepcomposite likelihoodpolymorphism
Publisher
GENETICS SOCIETY AMERICA
Indexed
SCI; SCIE; SCOPUS WOS scopus
Abstract
Adaptive evolution occurs as beneficial mutations arise and then increase in frequency by positive natural selection. How, when, and where in the genome such evolutionary events occur is a fundamental question in evolutionary biology. It is possible to detect ongoing positive selection or an incomplete selective sweep in species with sexual reproduction because, when a beneficial mutation is on the way to fixation, homologous chromosomes in the population are divided into two groups: one carrying the beneficial allele with very low polymorphism at nearby linked loci and the other carrying the ancestral allele with a normal pattern of sequence variation. Previous studies developed long-range haplotype tests to capture this difference between two groups as the signal of an incomplete selective sweep. In this study, we propose a composite-likelihood-ratio (CLR) test for detecting incomplete selective sweeps based on the joint sampling probabilities for allele frequencies of two groups as a function of strength of selection and recombination rate. Tested against simulated data, this method yielded statistical power and accuracy in parameter estimation that are higher than the iHS test and comparable to the more recently developed nS(L) test. This procedure was also applied to African Drosophila melanogaster population genomic data to detect candidate genes under ongoing positive selection. Upon visual inspection of sequence polymorphism, candidates detected by our CLR method exhibited clear haplotype structures predicted under incomplete selective sweeps. Our results suggest that different methods capture different aspects of genetic information regarding incomplete sweeps and thus are partially complementary to each other.
DOI
10.1534/genetics.115.175380
Appears in Collections:
자연과학대학 > 생명과학전공 > Journal papers
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