DOI: 10.5061/dryad.0tr36fp
title: Data from: Dynamics of genomic change during evolutionary rescue in the seed beetle Callosobruchus maculatus

description: Rapid adaptation can be necessary to prevent extinction when populations
 are exposed to extremely marginal or stressful environments. Factors that
 affect the likelihood of evolutionary rescue from extinction have been
 identified, but much less is known about the evolutionary dynamics and
 genomic basis of successful evolutionary rescue, particularly in
 multicellular organisms. We conducted an evolve-and-resequence experiment
 to investigate the dynamics of evolutionary rescue at the genetic level in
 the cowpea seed beetle, Callosobruchus maculatus, when it is
 experimentally shifted to a stressful host plant, lentil (Lens culinaris).
 Low survival (~1%) at the onset of the experiment caused population
 decline. But adaptive evolution quickly rescued the population with
 survival rates climbing to 69\% by the F5 generation and 90\% by the F10
 generation. Population genomic data showed that rescue likely was caused
 by rapid evolutionary change at multiple loci, with many alleles fixing or
 nearly fixing within five generations of selection on lentil. By comparing
 estimates of selection across five lentil-adapted C. maculatus populations
 (two new sublines and three long-established lines), we found that
 adaptation to lentil can involve a mixture of repeated and idiosyncratic
 evolutionary changes. Parallel evolutionary changes were particularly
 pronounced in sublines formed after the parent line had passed through an
 initial bottleneck. Overall, our results suggest that evolutionary rescue
 in this system can be driven by very strong selection on a modest number
 of loci, and these results provide empirical evidence that ecological
 dynamics during evolutionary rescue can cause distinct evolutionary
 trajectories and genomic signatures.
description: C. maculatus reference
 genomeThis compressed fastq
 file contains our de novo C. maculatus genome assembly. This was produced
 with ALLPATHS-LG.cmacgenome.fasta.gzWFABC-dyn source codeThis compressed directory contains the C++ source code for the ABC simulations for the L14 line. This program simulates evolution by drift and selection based on a known ancestral allele frequency. This code requires the Gnu Scientific Library.wfabc-dyn.tar.gzWFABC-const source codeThis compressed directory contains the C++ source code for the ABC simulations for the L1, L2 and L3 lines. This programs first simulates evolution in genetic drift backwards in time to obtain ancestral allele frequencies for the forward in time simulations of evolution by drift and selection in the lentil lines. This code requires the Gnu Scientific Library.wfabc-const.tar.gzWFABC-simpleThis compressed directory contains the C++ source code for the ABC simulations for the L11 line. This program assumes a known ancestral allele frequency and only outputs the final allele frequency after four generations of evolution by drift and selection. This code requires the Gnu Scientific Library.wfabc-simple.tar.gzL14 ABC summary scriptThis R script provides summaries of the credibility and magnitude of estimates of selection, as well as scatterplots of selection coefficient estimates a plot of posterior probabilities for different models.L14_Selection.RPop. genetic comparisons R scriptThis R script provides analyses comparing patterns of allele frequency change and selection among lines.SelComps.RLinkage disequilibrium scriptThis R script plots LD dendrograms, heatmaps, and networks, and plots patterns of allele frequency change by LD cluster.LD.RAllele frequency dataThis compressed directory contains the allele frequency estimates for the L11 and L14 lines, sublines and generations. There is one file per line/subline/generation. Each file has one row per locus (21,342 rows), with posterior means, medians and 95% ETPIs for the non-reference allele frequency at each locus.popgen.tar.gzGenotype dataThis compressed directory contains genotype estimates for L11 and L14. There is one file per line, subline and generation. Each file has one row per individual beetle and one column per SNP locus (columns are comma-separated). Genotype estimates given the number of non-reference alleles but are the mean of the posterior and thus not constrained to be integer valued.genotypes.tar.gzL14 ABC infileThis is the infile for the ABC analyses of L14. This file contains only the focal SNPs with one row per SNP (plus a header row with variance effective population sizes). Allele frequencies are then given per generation with sublines A and then B. Each row begins with a locus ID, coded as scaffold and position (in bp).pLentilSnps.txtABC infiles/genetic data for L1, L2 and L3This compressed directory contains three files, one for each of the long-established lentil lines (L1, L2 and L3). These contain allele frequency data for the focal SNPs (one locus per row, these are the data for the reference mung bean sample) along with locus IDs. The header rows (first two rows) give the variance effective populations sizes and generation times for the ABC simulations.L1_L2_L3popgen.tar.gz