Data from: Controlling for p-value inflation in allele frequency change in experimental evolution and artificial selection experiments

dc.contributor.affiliationNorwegian University of Science and Technology - Kemppainen, Petri
dc.contributor.affiliationNorwegian University of Science and Technology - Rønning, Bernt
dc.contributor.affiliationNorwegian University of Science and Technology - Kvalnes, Thomas
dc.contributor.affiliationNorwegian University of Science and Technology - Hagen, Ingerid J.
dc.contributor.affiliationNorwegian University of Science and Technology - Ringsby, Thor Harald
dc.contributor.affiliationNorwegian University of Science and Technology - Billing, Anna M.
dc.contributor.affiliationNorwegian University of Science and Technology - Pärn, Henrik
dc.contributor.affiliationNorwegian University of Life Sciences - Lien, Sigbjorn
dc.contributor.affiliationUniversity of Helsinki - Husby, Arild
dc.contributor.affiliationNorwegian University of Science and Technology - Sæther, Bernt-Erik
dc.contributor.affiliationNorwegian University of Science and Technology - Jensen, Henrik
dc.contributor.affiliationNorwegian University of Science and Technology - Saether, Bernt-Erik
dc.contributor.authorKemppainen, Petri
dc.contributor.authorRønning, Bernt
dc.contributor.authorKvalnes, Thomas
dc.contributor.authorHagen, Ingerid J.
dc.contributor.authorRingsby, Thor Harald
dc.contributor.authorBilling, Anna M.
dc.contributor.authorPärn, Henrik
dc.contributor.authorLien, Sigbjorn
dc.contributor.authorHusby, Arild
dc.contributor.authorSæther, Bernt-Erik
dc.contributor.authorJensen, Henrik
dc.contributor.authorSaether, Bernt-Erik
dc.coverage.spatialNorway
dc.date.accessioned2025-03-24T15:23:19Z
dc.date.issued2016-11-14
dc.date.issued2016-11-14
dc.descriptionExperimental evolution studies can be used to explore genomic response to artificial and natural selection. In such studies, loci that display larger allele frequency change than expected by genetic drift alone are assumed to be directly or indirectly associated with traits under selection. However, such studies report surprisingly many loci under selection, suggesting that current tests for allele frequency change may be subject to p-value inflation and hence be anti-conservative. One factor known from genome wide association (GWA) studies to cause p-value inflation is population stratification, such as relatedness among individuals. Here we suggest that by treating presence of an individual in a population after selection as a binary response variable, existing GWA methods can be used to account for relatedness when estimating allele frequency change. We show that accounting for relatedness like this effectively reduces false positives in tests for allele frequency change in simulated data with varying levels of population structure. However, once relatedness has been accounted for, the power to detect causal loci under selection is low. Finally, we demonstrate the presence of p-value inflation in allele frequency change in empirical data spanning multiple generations from an artificial selection experiment on tarsus length in two wild populations of house sparrow, and correct for this using genomic control. Our results indicate that since allele frequencies in large parts of the genome may change when selection acts on a heritable trait, such selection is likely to have considerable and immediate consequences for the eco-evolutionary dynamics of the affected populations.
dc.identifierhttps://doi.org/10.5061/dryad.vv527
dc.identifier.urihttps://hydatakatalogi-test-24.it.helsinki.fi/handle/123456789/11100
dc.rightsOpen
dc.rights.licensecc-zero
dc.subjectrelatedness
dc.subjectp-value inflation
dc.subjectpopulation stratification
dc.subjectGenome wide association studies
dc.subjectPasser domesticus
dc.subjectArtificial selection
dc.titleData from: Controlling for p-value inflation in allele frequency change in experimental evolution and artificial selection experiments
dc.typedataset
dc.typedataset
Zenodo


: