DOI: 10.5061/dryad.1p0rm
title: Data from: Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle

description: Trade-offs have often been invoked to explain the evolution of ecological
 specialization. Phytophagous insects have been especially well studied,
 but there has been little evidence that resource-based trade-offs
 contribute to the evolution of host specialization in this group. Here, we
 combine experimental evolution and partial genome resequencing of
 replicate seed beetle selection lines to test the trade-off hypothesis and
 measure the repeatability of evolution. Bayesian estimates of selection
 coefficients suggest that rapid adaptation to a poor host (lentil) was
 mediated by standing genetic variation at multiple genetic loci and
 involved many of the same variants in replicate lines. Sublines that were
 then switched back to the ancestral host (mung bean) showed a more gradual
 and variable (less repeatable) loss of adaptation to lentil. We were able
 to obtain estimates of variance effective population sizes from
 genome-wide differences in allele frequencies within and between lines.
 These estimates were relatively large, which suggests that the
 contribution of genetic drift to the loss of adaptation following
 reversion was small. Instead, we find that some alleles that were favored
 on lentil were selected against during reversion on mung bean, consistent
 with the genetic trade-off hypothesis.
description: Single nucleotide
 variants for C. maculatusThis 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 &gt; cmacvariants.bcf
 bcftools view -c -d 0.8 -g -p 0.01 -P full -t 0.001 -v cmacvariants.bcf
 &gt; cmacvariants.vcfcmacvariants.vcf.gzReference genome sequenceAn 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.cmacbbg9jan14gbs.fastaC. maculatus allele frequenciesThis 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.cmacAlleleFreqs.tar.gzSource code for ABC modelThis 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.beetleAbc.tar.gzSource code for Ne estimation programThis compressed directory contains the source code for the program used to infer contemporary effective population sizes and implement the Bayesian bootstrap analyses.varne.tar.gzC. maculatus survival dataThis 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).formatedSurviva.csvC. maculatus DNA sequence alignment L1LRCompressed directory with bam format alignmentscmacAlnsL1LR.tarC. maculatus DNA sequence alignment 2L2RCompressed directory with bam format alignmentscmacAlnsL2L2R.tarC. maculatus DNA sequence alignment 3L3RCompressed directory with bam format alignmentscmacAlnsL3L3R.tarC. maculatus DNA sequence alignment MCompressed directory with bam format alignmentscmacAlnsM.tarC. maculatus DNA sequence data parsed_gomp003_combinedDNA sequence (GBS) data used in this study. Header lines include individual beetle IDs.parsed_gomp003_combined.fastq.gzC. maculatus DNA sequence data parsed_gomp004_NoIndex_L006_R1_001DNA sequence (GBS) data used in this study. Header lines include individual beetle IDs.parsed_gomp004_NoIndex_L006_R1_001.fastq.gzC. maculatus DNA sequence data parsed_gomp005_NoIndex_L007_R1_001DNA sequence (GBS) data used in this study. Header lines include individual beetle IDs.parsed_gomp005_NoIndex_L007_R1_001.fastq.gz