Adaptation repeatedly uses complex structural genomic variation: Data and scripts

This archive contains data and scripts used in the paper "Adaptation repeatedly uses complex structural genomic variation" (by Gompert et al.).

The abstract of the manuscript follows:

Structural elements are widespread across genomes but their complexity and role in repeatedly driving local adaptation remains unclear. Here we use phased genome assemblies to show that adaptive divergence in cryptic color pattern in a stick insect is repeatedly underlain by structural variation, but not a simple chromosomal inversion. We find that color pattern in populations of stick insects on two mountains is associated with translocations that have also been inverted. These translocations differ in size and origin on each mountain, but they overlap partially and involve some of the same gene regions. Moreover, this structural variation is subject to divergent selection and arose without introgression between species. Our results show how the origin of structural variation provides a mechanism for repeated bouts of adaptation.

Summary of files included:

Data files:

sample_sp_loc_host_morph.dsvpattern_gen_h154_gs.geno.gzpattern_gen_h154_gus.geno.gzpattern_gen_h154_no8_gs.geno.gzpattern_g_tcr_refugio_gs.geno.gzpattern_g_tcr_refugio_gus.geno.gzpattern_no8_g_tcr_refugio_gs.geno.gzpattern_no8_g_tcr_refugio_gus.geno.gzfiltered_vars_noch8.vcf.gzfiltered_tcr_h154_variants_gus.gl.gzg_tcr_refugio_gs.txt.gzg_tcr_refugio_gus.txt.gzfiltered_tcr_refugio_variants_gs.gl.gzfiltered_tcr_refugio_variants_gus.gl.gzfiltered_tcr_h154_variants_gs.gl.gzpntest_filtered_tcr_refugio_variants_gs.txt.gzpntest_filtered_tcr_refugio_variants_gus.txt.gz

General workflow scripts, including scripts for processing raw sequence data, alignments and variant files:

BwaAlign.shRunBcfCall.shcallvar_gs1.shcallvar_gus.shrun_entropy.shSam2Bam.shSubDedup.shsummarizeEntropy.sh

splitPops.plBcfForkLg.plBwaAlignWgsFork2.plBwaAlignWgsFork.plfixHeader.plforBam2Fq.plforkEntropy.plindexFork.plmakeClean.plMergeFork.plRemoveDupsFork.plSam2BamFork.plvcf2gl.plVarFiltFork.plgl2genest.plrunEstP.pl

initq.R

Scripts for demographic analyses:

am_sub_moments.pyim_sub_moments.pysc_sub_moments.pysi_sub_moments.pydemcalc.R

Scripts for GWA mapping:

FormatPheno.Rrun_gemma.shsummarize_gemma_gs.Rsummarize_gemma_gus.R

Scripts for comparative alignments:

forkCactus.sh

halSynteny.pl

figSXsvpca.RSynPlotsHwy154.RSynPlotsRefugio.RSVexplor.R

Files for cline analyses:

cline.stancline_con.stanllcline.stanClineAnalyses.R

Scripts and files for treemix:

run_treemix.shtreemix_in_ch8.txt.gztreemix_in_other.txt.gzsummarizeTreemix.R

Scripts and files for annotations and gene-based analyses:

extractFq.shrun_braker3.shRunRMGenomesAnnotHaps.sh

CreateGoTable.plSVgenes_h154_gs_h1.plSVgenes_h154_gus_h2.plSVgenes_refugio_gus_h1.plSVgenes_refugio_gs_h1.plSVGO_h154_gs_h1.plSVGO_h154_gus_h2.plSVGO_refugio_gus_h1.plSVGO_refugio_gs_h1.pl

genespace_ch8_4.Rgenespace_ch8_8.Rgenespace_ch8_5.RGeneSVCounts.Roverlap.RSummarizeTEData_phased_genomes.RSummarizeTEData_phased.R

ojincantatabio-cen4280-hap1-mb-hirise-ig5ps__01-30-2024__hic_output.fasta.out.gff.gzojincantatabio-cen4280-hap2-mb-hirise-i2xb7__01-30-2024__hic_output.fasta.out.gff.gzojincantatabio-cen4120-hap1-mb-hirise-wlbll__08-15-2023__final_assembly.fasta.out.gff.gzojincantatabio-cen4120-hap2-mb-hirise-bn0ko__08-15-2023__final_assembly.fasta.out.gff.gzojincantatabio-cen4122-hap2-mb-hirise-14fv0__08-10-2023__final_assembly.fasta.out.gff.gzojincantatabio-cen4122-hap1-mb-hirise-g4hzf__08-10-2023__final_assembly.fasta.out.gff.gz

t_crist_h154_green_h2.bedt_crist_h154_stripe_h1.bedt_crist_refug_green_h1.bedt_crist_refug_stripe_h1.bed

t_crist_refug_stripe_h1.fa.gzt_crist_refug_green_h1.fa.gzt_crist_h154_green_h2.fa.gzt_crist_h154_stripe_h1.fa.gz

gspace.rdat