Data from: Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle

Gompert Z, Messina FJ

Date Published: June 10, 2016

DOI: http://dx.doi.org/10.5061/dryad.1p0rm

 

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Title Single nucleotide variants for C. maculatus
Downloaded 8 times
Description This VCF file (VCF v 4.1) contains the full set of unfiltered SNVs identified from the C. maculatus experimental flies. The following commands were used to generate this set of variants: samtools mpileup -C 50 -d 50 -f cmacbbg9jan14gbs.fasta -q 10 -Q 15 -D -g -I *bam > cmacvariants.bcf bcftools view -c -d 0.8 -g -p 0.01 -P full -t 0.001 -v cmacvariants.bcf > cmacvariants.vcf
Download cmacvariants.vcf.gz (182.5 Mb)
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Title Reference genome sequence
Downloaded 2 times
Description An original reference genome sequence was downloaded from http://www.beanbeetles.org/genome/denovo/new/longContigs.fasta. We then added GBS consensus sequences that did not match this reference as additional contigs. This file includes the original reference plus these additional contig sequences.
Download cmacbbg9jan14gbs.fasta (328.3 Mb)
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Title C. maculatus allele frequencies
Downloaded 2 times
Description This compressed directory contains csv text files with allele frequency estimates for each line and generation (one file each). Within each file, rows correspond with different SNVs and the values on each row give the posterior mean, median, and lower and upper bounds of the 95% CIs for the frequency of one of the two alleles at the locus.
Download cmacAlleleFreqs.tar.gz (10.47 Mb)
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Title Source code for ABC model
Downloaded 1 time
Description This compressed directory contains the source code for the ABC program used to infer selection coefficients. The directory includes example data files and a README file with compilation instructions.
Download beetleAbc.tar.gz (161.8 Kb)
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Title Source code for Ne estimation program
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Description This compressed directory contains the source code for the program used to infer contemporary effective population sizes and implement the Bayesian bootstrap analyses.
Download varne.tar.gz (33.44 Mb)
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Title C. maculatus survival data
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Description This csv file contains the data from the survival assays. The files has five columns: line, reverted or non-reverted line (trt), generation (gen), the number of surviving beetles (surv), and the number of dead beetles (dead).
Download formatedSurviva.csv (424 bytes)
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Title C. maculatus DNA sequence alignment L1LR
Downloaded 4 times
Description Compressed directory with bam format alignments
Download cmacAlnsL1LR.tar (8.835 Gb)
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Title C. maculatus DNA sequence alignment 2L2R
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Description Compressed directory with bam format alignments
Download cmacAlnsL2L2R.tar (8.637 Gb)
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Title C. maculatus DNA sequence alignment 3L3R
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Description Compressed directory with bam format alignments
Download cmacAlnsL3L3R.tar (8.481 Gb)
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Title C. maculatus DNA sequence alignment M
Downloaded 4 times
Description Compressed directory with bam format alignments
Download cmacAlnsM.tar (6.099 Gb)
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Title C. maculatus DNA sequence data parsed_gomp003_combined
Downloaded 3 times
Description DNA sequence (GBS) data used in this study. Header lines include individual beetle IDs.
Download parsed_gomp003_combined.fastq.gz (6.772 Gb)
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Title C. maculatus DNA sequence data parsed_gomp004_NoIndex_L006_R1_001
Downloaded 4 times
Description DNA sequence (GBS) data used in this study. Header lines include individual beetle IDs.
Download parsed_gomp004_NoIndex_L006_R1_001.fastq.gz (12.94 Gb)
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Title C. maculatus DNA sequence data parsed_gomp005_NoIndex_L007_R1_001
Downloaded 3 times
Description DNA sequence (GBS) data used in this study. Header lines include individual beetle IDs.
Download parsed_gomp005_NoIndex_L007_R1_001.fastq.gz (12.77 Gb)
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When using this data, please cite the original publication:

Gompert Z, Messina FJ (2016) Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle. Evolution 70(6): 1249-1264. http://dx.doi.org/10.1111/evo.12933

Additionally, please cite the Dryad data package:

Gompert Z, Messina FJ (2016) Data from: Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.1p0rm
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