Data from: Highly variable reproductive isolation among pairs of Catostomus species

Mandeville EG, Parchman TL, McDonald DB, Buerkle CA

Date Published: May 26, 2015

DOI: http://dx.doi.org/10.5061/dryad.r31sg.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 VCF file
Downloaded 6 times
Description This is the raw VCF file containing all 32,978 variant genetic sites initially identified from assembled reads.
Download variants_0.5.vcf (412.9 Mb)
Details View File Details
Title names_common_variants_0.5
Downloaded 6 times
Description This file is the formatted input file for entropy, the hierarchical Bayesian model used in this study. The file contains data for a subset of SNPs, in a simplified genotype likelihood format. SNPs in this file have a minor allele frequency >0.05, and a maximum of 1 alternate allele. This file also contains only one locus per contig.
Download names_common_variants_0.5.mpgl (21.59 Mb)
Details View File Details
Title artificial reference genome
Downloaded 5 times
Description This artificial reference genome was constructed via a de novo assembly (using DNAstar's smng) of a subset of 25 million short sequence reads, distributed across all taxa. We then assembled short reads to this
Download split_sucker_ref_long.fasta (50.96 Mb)
Details View File Details
Title Allele frequencies
Downloaded 4 times
Description This file gives allele frequencies at 4095 genetic loci for 21 different populations of fish, spanning 5 species. This is the input file for calculation of Nei's D and construction of a neighbor joining tree, visualizing genetic distance among populations.
Download ID_afreq_matrix.txt (674.6 Kb)
Details View File Details
Title R script for Nei's D
Downloaded 20 times
Description This is an R script that calculates Nei's genetic distance between pairs of populations, using allele frequencies. The input file for this script is "ID_afreq_matrix.txt"
Download distAnalysis.R (1.349 Kb)
Details View File Details
Title Locations
Downloaded 5 times
Description Approximate latitude and longitude of samped populations. NOTE: these are estimated from maps, and do not represent exact sampling locations, as GPS coordinates were not taken in the field.
Download locations.csv (395 bytes)
Details View File Details
Title lib1_sucker_barcode_key
Downloaded 9 times
Description Barcode-ID pairs for individual fish for lane 1 of sequencing. (Please note that there are individuals included in this barcode file that belong to a different project, and are not discussed in the related paper. )
Download lib1_sucker_barcode_key.csv (22.13 Kb)
Details View File Details
Title lib2_sucker_barcode_key
Downloaded 4 times
Description Barcode-ID pairs for individual fish for lane 2 of sequencing. (Please note that there are individuals included in this barcode file that belong to a different project, and are not discussed in the related paper. )
Download lib2_sucker_barcode_key.csv (23.93 Kb)
Details View File Details
Title Assemblies
Downloaded 8 times
Description This is a tarred (compressed) file that contains assemblies to an artificial reference genome. When untarred, this file will contain >800 files in .bam format, one for each individual fish. These files were produced using bwa (Burrows-Wheeler Aligner, Li and Durbin 2009).
Download assembled.tgz (8.998 Gb)
Details View File Details

When using this data, please cite the original publication:

Mandeville EG, Parchman TL, McDonald DB, Buerkle CA (2015) Highly variable reproductive isolation among pairs of Catostomus species. Molecular Ecology 24(8): 1856-1872. http://dx.doi.org/10.1111/mec.13118

Additionally, please cite the Dryad data package:

Mandeville EG, Parchman TL, McDonald DB, Buerkle CA (2015) Data from: Highly variable reproductive isolation among pairs of Catostomus species. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r31sg.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

Search for data

Be part of Dryad

We encourage organizations to: