Data from: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations

Franssen SU, Nolte V, Tobler R, Schlötterer C

Date Published: December 7, 2016

DOI: http://dx.doi.org/10.5061/dryad.403b2.2

 

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 Scripts
Description This zip archive includes two python scripts referenced in the associated publication. Functionality includes: 1) Estimation of short and long range LD from haplotype data, 2) Identification of haplotype-blocks through singleton markers. Each script comes with an associated README file, parameter specifications and example data. See Material and Methods and a description in the Supplemental Material for more details.
Download scripts.zip (17.27 Kb)
Details View File Details
Title Dmel_haplotype_fasta_base
Description This zip archive contains fasta files of 29 haploid D. melanogaster genomes associated with the experimental evolution experiment in the referenced publication. They correspond to 29 haploid genomes for the experimental starting population. Provided are the major chromosomal arms X, 2L, 2R, 3L and 3R. See Material and Methods for more details.
Download Dmel_haplotype_fasta_base.zip (944.9 Mb)
Details View File Details
Title Dmel_haplotype_fasta_F67
Description This zip archive contains fasta files of 29 haploid D. melanogaster genomes associated with the experimental evolution experiment in the referenced publication. They correspond to 29 haploid genomes for a (hot) evolved population at generation 67 (2nd replicate). Provided are the major chromosomal arms X, 2L, 2R, 3L and 3R. See Material and Methods for more details.
Download Dmel_haplotype_fasta_F67.zip (926.0 Mb)
Details View File Details
Title Sync file for 3 time points for 3 replicates
Description Sync file of allele coverage counts for 1,453,774 called SNPs in the euchromatin of the *D. melanogaster* genome (for format specification see Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011;27:3435-3436.). To the sync file a header line is added, which specifies the time points, replicates and treatment abbreviations (FX: time point at generation X, RY: replicate number Y, H: hot treatment). The sync file contains time points for generations: 0, 15, 37 and 59. For generations 0, 15 and 38 please additionally cite: Orozco-terWengel P, Kapun M, Nolte V, Kofler R, Flatt T, Schlötterer C. Adaptation of *Drosophila* to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol Ecol. 2012;21:4931-4941.
Download AllDmelCagePops_F0toF59_RepIndMasked_pub_E...nc.gz (62.05 Mb)
Details View File Details

When using this data, please cite the original publication:

Franssen SU, Nolte V, Tobler R, Schlötterer C (2015) Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations. Molecular Biology and Evolution 32(2): 495-509. http://dx.doi.org/10.1093/molbev/msu320

Additionally, please cite the Dryad data package:

Franssen SU, Nolte V, Tobler R, Schlötterer C (2014) Data from: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.403b2.2
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Version History

Item Version Date Summary

* Selected Version

Submissions have been temporarily disabled.

Search for data

Be part of Dryad

We encourage organizations to: