Data from: Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants

Gompert Z, Lucas LK, Buerkle CA, Forister ML, Fordyce JA, Nice CC

Date Published: May 5, 2014

DOI: http://dx.doi.org/10.5061/dryad.pq93h

 

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 entropy.tar
Downloaded 51 times
Description This compressed directory contains the source code (C++), example files, and a README file for the admixture proportion and admixture class models described in the publication. Compile the pogram and type the program name for a list of command line options. Source code for a second program (estpost_h5_entropy.c) is incluced to summarize the MCMC output from the analysis.
Download entropy.tar.gz (9.748 Mb)
Details View File Details
Title isolationByDistanceAndTaxon
Downloaded 20 times
Description R code to test for isolation by distance and isolation by taxon. This is a Bayesian implementation of the mixed model described by Clarke et al. 2002 to model the lack of independence among pair-wise distances. This code requires JAGS and rjags.
Download isolationByDistanceAndTaxon.R (4.979 Kb)
Details View File Details
Title maf_0.05_0.5_lycaeides_gbs_admix_d80
Downloaded 11 times
Description Variant call format (VCF) file for the full set of common variants identified in Lycaeides. Rare and low-frequency VCF files are too large to include on Dryad, but are available from the authors upon request.
Download maf_0.05_0.5_lycaeides_gbs_admix_d80.vcf (654.4 Mb)
Details View File Details
Title lycaeides_gbscontigs_reference
Downloaded 7 times
Description Lycaeides reference sequence set generated from the GBS data. This was used for the reference based alignments with bwa.
Download lycaeides_gbscontigs_reference.fasta (28.40 Mb)
Details View File Details

When using this data, please cite the original publication:

Gompert Z, Lucas LK, Buerkle CA, Forister ML, Fordyce JA, Nice CC (2014) Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants. Molecular Ecology, 23(18): 4555-4573. http://dx.doi.org/10.1111/mec.12811

Additionally, please cite the Dryad data package:

Gompert Z, Lucas LK, Buerkle CA, Forister ML, Fordyce JA, Nice CC (2014) Data from: Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.pq93h
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: