Data from: Multilocus approaches for the measurement of selection on correlated genetic loci

Gompert Z, Egan SP, Barrett RDH, Feder JL, Nosil P

Date Published: September 29, 2016

DOI: http://dx.doi.org/10.5061/dryad.ns47q

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Null model simulations
Downloaded 9 times
Description This R script was used to simulate random mortality and then infer total selection on genotypes based on allele frequency changes while ignoring the effect of genetic drift.
Download nullSim.R (1.209 Kb)
Details View File Details
Title Simulated phenotypes based on Timema GBS data
Downloaded 4 times
Description This compressed folder contains the simulated data sets where Timema cristinae GBS data were used as the starting point. It contains three gemma formatted genotype files (geno_sims.txt, geno2500_sims.txt, and geno592r_sims.txt) that contain the underlying genotypic data for the base simulations, those with 2500 individuals and those with replicated genotypes, respectively. The remaining files are named based on the simulations condition (simsN): 1, h2=0.3, L = 100; 2, h2=0.3, L=10; 3, h2=0.05, L=100; 4, h2=0.05, L=10; 5, h2=0.3, L=1000; and 6, h2=0.05, L=1000. Files with 'bin' in their name correspond to results with a binary measure of fitness (e.g., alive or dead). The general file types are as follows: pheno* = gemma formatted phenotype file with one column per simulated phenotypic data set, bv* = breeding values (expected phenotypic values) for each individual based on the genotypic data, effect* = phenotypic effect sizes for causal variants, functvar* = a list of the causal variants (by SNP number, and in the same order as in effect*).
Download simdata_timema.tar.gz (884.8 Mb)
Details View File Details
Title Simulated phenotypes based on the Rhagoletis GBS data
Downloaded 3 times
Description This compressed folder contains the simulated data sets where Rhagoletis pomonella GBS data were used as the starting point. It contains two gemma formatted genotype files (geno_sims.txt and geno592r_sims.txt) that contain the underlying genotypic data for the base simulations and those with replicated genotypes, respectively. The remaining files are named based on the simulations condition (simsN): 1, h2=0.3, L = 100; 2, h2=0.3, L=10; 3, h2=0.05, L=100; 4, h2=0.05, L=10; 5, h2=0.3, L=1000; and 6, h2=0.05, L=1000. The general file types are as follows: pheno* = gemma formatted phenotype file with one column per simulated phenotypic data set, bv* = breeding values (expected phenotypic values) for each individual based on the genotypic data, effect* = phenotypic effect sizes for causal variants, functvar* = a list of the causal variants (by SNP number, and in the same order as in effect*).
Download simdata_rhag.tar.gz (29.59 Mb)
Details View File Details
Title Timema simulation scripts
Downloaded 5 times
Description This compressed directory contains four R scripts. The first three sims.R, sims2500.R and sims592r.R were used to simulate the quantitative phenotypes (fitness values) from the Timema GBS data for the original genotypic data, data with 2500 individuals, and with replicated genotypes, respectively. The last script, liability2binary.R, was used to convert quantitative fitness values to binary data.
Download simscripts_timema.tar.gz (2.004 Kb)
Details View File Details
Title Rhagoletis simulation scripts
Downloaded 4 times
Description This compressed directory contains two R scripts. These scripts (sims.R and sims592r.R) were used to simulate the quantitative phenotypes (fitness values) from the Rhagoletis GBS data for the original genotypic data and data with replicated genotypes, respectively.
Download simscripts_rhag.tar.gz (1.445 Kb)
Details View File Details
Title Summary scripts
Downloaded 6 times
Description This compressed directory contains the perl scripts used to summarize (1) the posterior distribution of genome-level genetic architecture parameters (calcpost*), and (2) SNP specific selection coefficients (summarizeSNP*pl).
Download analysis_scripts.tar.gz (2.35 Kb)
Details View File Details

When using this data, please cite the original publication:

Gompert Z, Egan SP, Barrett RDH, Feder JL, Nosil P (2017) Multilocus approaches for the measurement of selection on correlated genetic loci. Molecular Ecology 26(1): 365-382. http://dx.doi.org/10.1111/mec.13867

Additionally, please cite the Dryad data package:

Gompert Z, Egan SP, Barrett RDH, Feder JL, Nosil P (2016) Data from: Multilocus approaches for the measurement of selection on correlated genetic loci. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ns47q
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: