Data from: Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect

Lindtke D, Lucek K, Soria-Carrasco V, Villoutreix R, Farkas TE, Riesch R, Dennis SR, Gompert Z, Nosil P

Date Published: August 24, 2017

DOI: https://doi.org/10.5061/dryad.jt644

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 N1_sampleCoordinates.csv
Downloaded 12 times
Description Coordinates for Timema cristinae sampled in population N1
Download N1_sampleCoordinates.csv (21.34 Kb)
Download README (297 bytes)
Details View File Details
Title N1_variants.tar.gz
Downloaded 10 times
Description Genetic variants called for population N1 of Timema cristinae using Samtools and Bcftools. Uncompressed file sizes: 2.5G and 0.5G
Download N1_variants.tar.gz (520.5 Mb)
Download README (404 bytes)
Details View File Details
Title FHA_variants.tar.gz
Downloaded 13 times
Description Genetic variants called for population FHA of Timema cristinae using Samtools and Bcftools. Uncompressed file sizes: 4.4G and 2.0G
Download FHA_variants.tar.gz (1.174 Gb)
Download README (407 bytes)
Details View File Details
Title Combined21pop_variants.tar.gz
Downloaded 11 times
Description Genetic variants called for the combined set of 21 Timema cristinae populations using Samtools and Bcftools. Uncompressed file sizes: 4.3G and 0.7G
Download Combined21pop_variants.tar.gz (829.6 Mb)
Download README (444 bytes)
Details View File Details
Title Timema5species_variants.gz
Downloaded 10 times
Description Genetic variants called for five related Timema species using Samtools and Bcftools. Uncompressed file size: 258M
Download Timema5species_variants.flt_s085p001.vcf.gz (43.94 Mb)
Download README (324 bytes)
Details View File Details
Title Input_N1.tar.gz
Downloaded 9 times
Description Input files for various analyses for population N1 of Timema cristinae
Download Input_N1.tar.gz (19.41 Mb)
Download README (1.633 Kb)
Details View File Details
Title Input_FHA.tar.gz
Downloaded 9 times
Description Input files for various analyses for population FHA of Timema cristinae
Download Input_FHA.tar.gz (37.96 Mb)
Download README (1.641 Kb)
Details View File Details
Title Input_Combined21pop.tar.gz
Downloaded 10 times
Description Input files for various analyses for the combined set of 21 Timema cristinae populations
Download Input_Combined21pop.tar.gz (6.110 Mb)
Download README (1.252 Kb)
Details View File Details
Title Gemma.tar.gz
Downloaded 10 times
Description Input files for running GEMMA software for population FHA of Timema cristinae
Download Gemma.tar.gz (289.7 Mb)
Download README (753 bytes)
Details View File Details
Title beast_div_times.tar.gz
Downloaded 12 times
Description Files and scripts for conducting BEAST 2 phylogenetic analyses for estimating divergence times between chromosomal variants
Download beast_div_times.tar.gz (1.017 Gb)
Download README (4.072 Kb)
Details View File Details
Title ABC.tar.gz
Downloaded 10 times
Description Files and scripts for conducting ABC for estimating divergence time between color morphs of Timema cristinae
Download ABC.tar.gz (33.20 Kb)
Download README (1.329 Kb)
Details View File Details
Title selectionmodels.tar.gz
Downloaded 10 times
Description Files and scripts for testing different models of selection and mating preferences for generating observed karyotype frequencies in Timema cristinae populations
Download selectionmodels.tar.gz (5.032 Kb)
Download README (825 bytes)
Details View File Details
Title N1_samplePhenotypes.csv
Downloaded 9 times
Description Information on phenotype for samples from population N1
Download N1_samplePhenotypes.csv (7.876 Kb)
Download README (352 bytes)
Details View File Details
Title FHA_samplePhenotypes.csv
Downloaded 10 times
Description Information on phenotype for samples from population FHA
Download FHA_samplePhenotypes.csv (60.02 Kb)
Download README (524 bytes)
Details View File Details
Title Combined21pop_samplePhenotypes.csv
Downloaded 9 times
Description Information on phenotype for samples from the combined set of 21 Timema cristinae populations
Download Combined21pop_samplePhenotypes.csv (14.91 Kb)
Download README (440 bytes)
Details View File Details
Title N1_assignments.csv
Downloaded 10 times
Description PCA cluster and STRUCTURE karyotype assignments and PCA outlier individuals for population N1
Download N1_assignments.csv (8.308 Kb)
Download README (452 bytes)
Details View File Details
Title FHA_assignments.csv
Downloaded 9 times
Description PCA cluster and STRUCTURE karyotype assignments and PCA outlier individuals for population FHA
Download FHA_assignments.csv (11.44 Kb)
Download README (449 bytes)
Details View File Details
Title Combined21pop_assignments.csv
Downloaded 9 times
Description STRUCTURE karyotype assignments for combined set of 21 Timema cristinae populations
Download Combined21pop_assignments.csv (9.595 Kb)
Download README (333 bytes)
Details View File Details
Title N1_gprob_s090p001.txt.bz2
Downloaded 11 times
Description Posterior genotype probabilities that were determined by MCMC from N1_variants.flt_s090p001.bcf. Uncompressed file size: 4.3G
Download N1_gprob_s090p001.txt.bz2 (458.8 Mb)
Download README (596 bytes)
Details View File Details
Title N1_inVar_snpIDs_bins_s090p001.txt.bz2
Downloaded 13 times
Description Positions of all sites (variants and invariant nucleotides) and their 20-kb bins for population N1, discarding variants where less than 90% of individuals were covered
Download N1_inVar_snpIDs_bins_s090p001.txt.bz2 (23.12 Mb)
Download README (317 bytes)
Details View File Details
Title FHA_gprob_s090p001.txt.bz2
Downloaded 13 times
Description Posterior genotype probabilities that were determined by MCMC from FHA_variants.flt_s090p001.bcf. Uncompressed file size: 7.5G
Download FHA_gprob_s090p001.txt.bz2 (725.8 Mb)
Download README (597 bytes)
Details View File Details
Title FHA_inVar_snpIDs_bins_s090p001.txt.bz2
Downloaded 14 times
Description Positions of all sites (variants and invariant nucleotides) and their 20-kb bins for population FHA, discarding variants where less than 90% of individuals were covered
Download FHA_inVar_snpIDs_bins_s090p001.txt.bz2 (28.24 Mb)
Download README (317 bytes)
Details View File Details

When using this data, please cite the original publication:

Lindtke D, Lucek K, Soria-Carrasco V, Villoutreix R, Farkas TE, Riesch R, Dennis SR, Gompert Z, Nosil P (2017) Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect. Molecular Ecology, online in advance of print. https://doi.org/10.1111/mec.14280

Additionally, please cite the Dryad data package:

Lindtke D, Lucek K, Soria-Carrasco V, Villoutreix R, Farkas TE, Riesch R, Dennis SR, Gompert Z, Nosil P (2017) Data from: Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect. Dryad Digital Repository. https://doi.org/10.5061/dryad.jt644
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: