scholarly journals Genomic scans for selective sweeps using SNP data

2005 ◽  
Vol 15 (11) ◽  
pp. 1566-1575 ◽  
Author(s):  
R. Nielsen
Keyword(s):  
Selective Sweeps ◽  
Snp Data ◽  
Genomic Scans

scholarly journals How reliable are empirical genomic scans for selective sweeps?

2006 ◽  
Vol 16 (6) ◽  
pp. 702-712 ◽  
Author(s):  
K. M. Teshima
Keyword(s):  
Selective Sweeps ◽  
Genomic Scans

scholarly journals A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

PLoS ONE ◽  
2019 ◽  
Vol 14 (3) ◽  
pp. e0214201 ◽  
Author(s):  
Mark Charles Derbyshire ◽  
Matthew Denton-Giles ◽  
James K. Hane ◽  
Steven Chang ◽  
Mahsa Mousavi-Derazmahalleh ◽  
...  
Keyword(s):  
Host Range ◽  
Sclerotinia Sclerotiorum ◽  
Pathogenic Fungus ◽  
Genome Scan ◽  
Broad Host Range ◽  
Whole Genome ◽  
Selective Sweeps ◽  
Plant Pathogenic Fungus ◽  
Snp Data ◽  
Whole Genome Scan

scholarly journals Considering Genomic Scans for Selection as Coalescent Model Choice

2020 ◽  
Vol 12 (6) ◽  
pp. 871-877
Author(s):  
Rebecca B Harris ◽  
Jeffrey D Jensen
Keyword(s):  
Genomic Analysis ◽  
Selective Sweeps ◽  
Demographic Parameter ◽  
Demographic Models ◽  
Sufficient Power ◽  
Selective Neutrality ◽  
Neutral Models ◽  
Modern Population ◽  
Theoretical Results ◽  
Genomic Scans

Abstract First inspired by the seminal work of Lewontin and Krakauer (1973. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74(1):175–195.) and Maynard Smith and Haigh (1974. The hitch-hiking effect of a favourable gene. Genet Res. 23(1):23–35.), genomic scans for positive selection remain a widely utilized tool in modern population genomic analysis. Yet, the relative frequency and genomic impact of selective sweeps have remained a contentious point in the field for decades, largely owing to an inability to accurately identify their presence and quantify their effects—with current methodologies generally being characterized by low true-positive rates and/or high false-positive rates under many realistic demographic models. Most of these approaches are based on Wright–Fisher assumptions and the Kingman coalescent and generally rely on detecting outlier regions which do not conform to these neutral expectations. However, previous theoretical results have demonstrated that selective sweeps are well characterized by an alternative class of model known as the multiple-merger coalescent. Taken together, this suggests the possibility of not simply identifying regions which reject the Kingman, but rather explicitly testing the relative fit of a genomic window to the multiple-merger coalescent. We describe the advantages of such an approach, which owe to the branching structure differentiating selective and neutral models, and demonstrate improved power under certain demographic scenarios relative to a commonly used approach. However, regions of the demographic parameter space continue to exist in which neither this approach nor existing methodologies have sufficient power to detect selective sweeps.

scholarly journals Detection of selective sweeps in cattle using genome-wide SNP data

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 382 ◽  
Author(s):  
Holly R Ramey ◽  
Jared E Decker ◽  
Stephanie D McKay ◽  
Megan M Rolf ◽  
Robert D Schnabel ◽  
...  
Keyword(s):  
Selective Sweeps ◽  
Snp Data ◽  
Genome Wide

Haplotype-based analysis of selective sweeps in sheep

Genome ◽  
2014 ◽  
Vol 57 (8) ◽  
pp. 433-437 ◽  
Author(s):  
James W. Kijas
Keyword(s):  
Type I Error ◽  
Domestic Animal ◽  
Population History ◽  
Phenotypic Traits ◽  
Type I ◽  
Selective Sweeps ◽  
Elevated Type ◽  
Snp Data ◽  
Simulation Based ◽  
Genomic Regions

Domestic animals represent an extremely useful model for linking genotypic and phenotypic variation. One approach involves identifying allele frequency differences between populations, using FST, to detect selective sweeps. While simple to calculate, FST may generate false positives due to aspects of population history. This prompted the development of hapFLK, a metric that measures haplotype differentiation while accounting for the genetic relationship between populations. The focus of this paper was to apply hapFLK in sheep with available SNP50 genotypes. The hapFLK approach identified a known selective sweep on chromosome 10 with high precision. Further, five regions were identified centered on genes with strong evidence for positive selection (COL1A2, NCAPG, LCORL, and RXFP2). Estimation of global FST revealed many more genomic regions, providing empirical data in support of published simulation-based results concerning elevated type I error associated with FST when it is being used to characterize sweep regions. The findings, while conducted using sheep SNP data, are likely to be applicable across those domestic animal species that have undergone artificial selection for desirable phenotypic traits.

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