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.
Single nucleotide variants for C. maculatus
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
cmacvariants.vcf.gz
Reference genome sequence
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.
cmacbbg9jan14gbs.fasta
C. maculatus allele frequencies
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.
cmacAlleleFreqs.tar.gz
Source code for ABC model
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.
beetleAbc.tar.gz
Source code for Ne estimation program
This compressed directory contains the source code for the program used to infer contemporary effective population sizes and implement the Bayesian bootstrap analyses.
varne.tar.gz
C. maculatus survival data
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).
formatedSurviva.csv
C. maculatus DNA sequence alignment L1LR
Compressed directory with bam format alignments
cmacAlnsL1LR.tar
C. maculatus DNA sequence alignment 2L2R
Compressed directory with bam format alignments
cmacAlnsL2L2R.tar
C. maculatus DNA sequence alignment 3L3R
Compressed directory with bam format alignments
cmacAlnsL3L3R.tar
C. maculatus DNA sequence alignment M
Compressed directory with bam format alignments
cmacAlnsM.tar
C. maculatus DNA sequence data parsed_gomp003_combined
DNA sequence (GBS) data used in this study. Header lines include individual beetle IDs.
parsed_gomp003_combined.fastq.gz
C. maculatus DNA sequence data parsed_gomp004_NoIndex_L006_R1_001
DNA sequence (GBS) data used in this study. Header lines include individual beetle IDs.
parsed_gomp004_NoIndex_L006_R1_001.fastq.gz
C. maculatus DNA sequence data parsed_gomp005_NoIndex_L007_R1_001
DNA sequence (GBS) data used in this study. Header lines include individual beetle IDs.
parsed_gomp005_NoIndex_L007_R1_001.fastq.gz