10.5061/DRYAD.VV527
Kemppainen, Petri
Norwegian University of Science and Technology
Rønning, Bernt
Norwegian University of Science and Technology
Kvalnes, Thomas
Norwegian University of Science and Technology
Hagen, Ingerid J.
Norwegian University of Science and Technology
Ringsby, Thor Harald
Norwegian University of Science and Technology
Billing, Anna M.
Norwegian University of Science and Technology
Pärn, Henrik
Norwegian University of Science and Technology
Lien, Sigbjorn
Norwegian University of Life Sciences
Husby, Arild
University of Helsinki
Norwegian University of Science and Technology
Sæther, Bernt-Erik
Norwegian University of Science and Technology
Jensen, Henrik
Norwegian University of Science and Technology
Saether, Bernt-Erik
Norwegian University of Science and Technology
Data from: Controlling for p-value inflation in allele frequency change in
experimental evolution and artificial selection experiments
Dryad
dataset
2016
relatedness
p-value inflation
population stratification
Genome wide association studies
Passer domesticus
Artificial selection
2016-11-14T18:33:54Z
2016-11-14T18:33:54Z
en
https://doi.org/10.1111/1755-0998.12631
5840278677 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Experimental 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.
DataThis file contains a folder with all raw data for the simulations.
More instructions can be found in file "Simulated_data.R"
available from the data file "Rproject".RProjectThis file
contains folder with the complete RProject for this manuscript, minus the
original data files for the simulation project (available as file
"Data.tar.gz"). All other temporary (.rda) data files are in in
this folder as well.Rproject.tar.gz
Norway