Data from: Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

Egan SP, Ragland GJ, Assour L, Powell THQ, Hood GR, Emrich S, Nosil P, Feder JL

Date Published: January 27, 2016

DOI: http://dx.doi.org/10.5061/dryad.mb2tj

 

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Title VCF file for experimental and natural populations
Downloaded 15 times
Description This is the VCF file for the experimental and natural population comparisons. To test for differentiation genome wide among sympatric populations, we contrasted our apple7 and haw7 groups; for a response to selection in our experiment, we compared haw7 and haw30. Haw or apple represents the host plant from which the flies were collected; the number - 7 or 30 - represents the pre-winter warm period experienced by larvae/pupae prior to overwintering to match that found in nature on haw or apple plants. See txt file to match individual MID labels in the VCF file with the experimental group they were part of.
Download snps.ScottSelection.05-400-20.filteredHwe...ed.vcf (123.3 Mb)
Download README.txt (4.018 Kb)
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Title R_pomonella_denovo_assembly
Downloaded 28 times
Description This file is the de novo assembly of Illumina sequence reads (20 million reads; 3% of total data) generated by Seqman NGen 4.0.0 (DNASTAR) using parameter values described in Gompert et al. 2012. See methods for more details.
Download LatestRadFakeGenome.cut.fa.txt (29.09 Mb)
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Title R. pomonella Linkage Map
Downloaded 9 times
Description Linkage map giving the linear order of SNPs on each of the five chromosomes/linkage groups. Column labels: chromosome (1 to 5), Sn = SNP number ID (1-N by chromosome), locus = location of SNP in our de novo assembly by contig, then by location along contig, separated by an underscore, Position = distance along each linkage group/chromosome in centiMorgans.
Download MapLinearOrderAllChrom.txt (103.1 Kb)
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When using this data, please cite the original publication:

Egan SP, Ragland GJ, Assour L, Powell THQ, Hood GR, Emrich S, Nosil P, Feder JL (2015) Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow. Ecology Letters 18(8): 817-825. http://dx.doi.org/10.1111/ele.12460

Additionally, please cite the Dryad data package:

Egan SP, Ragland GJ, Assour L, Powell THQ, Hood GR, Emrich S, Nosil P, Feder JL (2015) Data from: Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.mb2tj
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