DOI: 10.5061/dryad.3j9kd51dw
title: Data from: Combining experimental evolution and genomics to understand how seed beetles adapt to a marginal host plant

description: Genes that affect adaptive traits have been identified, but our knowledge
 of the genetic basis of adaptation in a more general sense (across
 multiple traits) remains limited. We combined population-genomic analyses
 of evolve and resequence experiments, genome-wide association mapping of
 performance traits, and analyses of gene expression to fill this knowledge
 gap, and shed light on the genomics of adaptation to a marginal host
 (lentil) by the seed beetle Callosobruchus maculatus. Using
 population-genomic approaches, we detected modest parallelism in allele
 frequency change across replicate lines during adaptation to lentil.
 Mapping populations derived from each lentil-adapted line revealed a
 polygenic basis for two host-specific performance traits (weight and
 development time), which had low to modest heritabilities. We found less
 evidence of parallelism in genotype-phenotype associations across these
 lines than in allele frequency changes during the experiments.
 Differential gene expression caused by differences in recent evolutionary
 history exceeded that caused by immediate rearing host. Together, the
 three genomic data sets suggest that genes affecting traits other than
 weight and development time are likely to be the main causes of parallel
 evolution, and that detoxification genes (especially cytochrome P450s and
 beta-glucosidase) could be especially important for colonization of lentil
 by C. maculatus.
description: We analyzed six experimental lines in the current study: the M
 line, which was originally collected from South India and has since been
 maintained in the lab on its ancestral mung-bean host
 \cite{messina1991life, mitchell1991traits}, three lentil-adapted lines
 (L1, L2, and L14, each independently derived from M), and two reversion
 lines (L1R and L2R) that were switched back to mung bean after many
 generations on lentil (Fig.\ \ref{lines}, Table \ref{linesummtab}). The
 South India M line has been maintained at a census population size of
 2000-2500 individuals for $&gt;$300 generations; past genetic analyses
 suggest a variance effective population size of 1149 beetles
 \cite{gompert16}. Details on the establishment of L1, L2 and L14 can be
 found in \cite{messina2009experimentally,gompert16} (L1 and L2) and
 \cite{rego19} (L14). The reversion lines, L1R and L2R, were initiated to
 test for genetic trade-offs between performance on mung bean versus
 lentil. These lines were shifted back onto the ancestral host in order to
 examine whether there would be a decrease in the ability to use lentil (as
 predicted by a trade-off hypothesis) \cite{messina2015loss}. Thus, allele
 frequency change in the lentil lines should reflect adaptation to lentil
 (and genetic drift), whereas changes in the reversion lines relative to
 their source lentil lines should reflect adaptation back to mung bean (and
 perhaps drift to a lesser extent) (past work has attempted to parse the
 roles of selection and drift \cite{gompert16, rego19}, but here we simply
 focus on change). Herein, we analyze patterns of genome-wide allele
 frequency change for combinations of all six of these lines (we ignore two
 additional lines, L3 and L3R, as we lack trait-mapping data for these
 lines). Trait-mapping data come from backcross mapping populations created
 by crossing M with L1, L2 and L14 (denoted BC-L1, BC-L2, and BC-L14). Gene
 expression data comes from M, L1 and L1R, that is from the source mung
 bean line, a lentil line, and its corresponding reversion line. We
 measured gene expression in all three lines when reared in mung bean
 (L1$^\mathrm{M}$, L1R$^\mathrm{M}$, M$^\mathrm{M}$), and for L1 and L1R
 when reared in lentil (L1$^\mathrm{L}$, L1R$^\mathrm{L}$) (rearing the M
 line on lentil for expression data was not possible given the extremely
 low survival rates).
description: This data publication contains the following data and script
 files: C_Maculates_Lentil_QTL_Raw_Data_isolations.xlsx
 - Raw data collected from the trait mapping experiment for all eggs
 generated from the backcross. Each line cross is located on a separate
 sheet. L1_phenotypes.txt - Text file of only the L1
 backcross individuals used in the trait mapping analysis. The first column
 is individual IDs, the second is weight (mg), and the third is development
 time (days). L2_phenotypes.txt - Text file of only the
 L2 backcross individuals used in the trait mapping analysis. The first
 column is individual IDs, the second is weight (mg), and the third is
 development time (days). L14_phenotypes.txt - Text file
 of only the L14 backcross individuals used in the trait mapping analysis.
 The first column is individual IDs, the second is weight (mg), and the
 third is development time (days). phenos.R - R script
 used for analysis of phenotypic data of backcrossed individuals.
 wrap_qsub_slurm_bwa_mem.pl - Wrapper perl script used to align
 reads to reference genome. Callvar.sh - Bash script
 used to call variants. vcfFilter.pl - Perl script used
 to filter variants for the VCF which contained all individuals.
 vcfFilterwoCross.pl - Perl script used to filter variants for the
 VCF which excluded the backcross individuals.
 filterSomeMore.pl - Follow-up filtering for all individuals to
 remove high-coverage loci. filterSomeMore_woCross.pl -
 Follow-up filtering for subset of individuals which excluded the
 backcross. vcf2gl.pl - Converts VCF to genotype
 likelihood format. DPupdate.pl - Script used to update
 depth field in VCF files after subsetting out backcross
 individuals. parse_barcodes768.pl - Perl script used to
 remove sequence barcodes and replace fastq header with associated
 individual IDs. ratesCode.R - R script for calculating 
 evolutionary rates/change and fitting the associated hidden Markov
 model. grabBvs.R - R script for breeding value
 analyses. mod_tr_g_L1X_full.txt - Input genotype file
 for backcross line L1 for genome-wide association mapping with
 Gemma. mod_tr_g_L2X_full.txt - Input genotype file for
 backcross line L2 for genome-wide association mapping with
 Gemma. mod_tr_g_L14X_full.txt - Input genotype file for
 backcross line L14 for genome-wide association mapping with
 Gemma.