DOI: 10.5061/dryad.w9ghx3fsk
title: Data for: Population genomic insights into invasion success in the polyphagous agricultural pest, Halyomorpha halys

description: Invasive species are increasingly threatening ecosystems and agriculture
 by rapidly expanding their range and adapting to environmental and
 human-imposed selective pressures. The genomic mechanisms that underlie
 such rapid changes remain unclear, especially for agriculturally important
 pests. Here, we use genome-wide polymorphisms derived from native,
 invasive, and intercepted samples and populations of the brown marmorated
 stink bug (BMSB), Halyomorpha halys, to gain insights into population
 genomics processes that have promoted the successful global invasion of
 this polyphagous pest. Our analysis demonstrated that BMSB exhibits
 spatial structure but admixture rates are high among introduced
 populations, resulting in similar levels of genomic diversity across
 native and introduced populations. These spatial genomic patterns suggest
 a complex invasion scenario, potentially with multiple bridgehead events,
 posing a challenge for accurately assigning BMSB incursions to their
 source using reduced-representation genomic data. By associating allele
 frequencies with the invasion status of BMSB populations, we found
 significantly differentiated SNPs located in close proximity to genes for
 insecticide resistance and olfaction. Comparing variations in allele
 frequencies among populations for outlier SNPs suggests that BMSB invasion
 success has likely evolved from standing genetic variation. In addition to
 being a major nuisance of households, BMSB has caused significant economic
 losses to agriculture in recent years and continues to expand its range.
 Despite no record of BMSB insecticide resistance to date, our results show
 high capacity for potential evolution of such characters, highlighting the
 need for future sustainable and targeted management strategies.
description: <strong>allwithNZ_neutral_IQtree.phy:</strong> input
 file for IQtree, containing neutral SNPs of all samples and
 populations
 <strong>allwithNZ_neutral_noNZ_BayesAss.immanc:</strong> input file for BayesAss, containing neutral SNPs of all populations except New Zealand intercepted samples <strong>AllwithNZ_neutral_noNZ_DivMigrate.gen:</strong> input file for DivMigrate, containing neutral SNPs of all populations except New Zealand intercepted samples <strong>AllwithNZ_noNZ_neutral_assignPOP.gen:</strong> input file for assignPOP, containing neutral SNPs of all populations except New Zealand intercepted samples <strong>assignMC_assignPOP.R:</strong> R script for assignPOP cross-validation analysis <strong>assignment probability plot_assignPOP.R:</strong> R script for plotting assignPOP assignment probabilities of New Zealand intercepted samples <strong>BayesAss.sh:</strong> script to run BayesAss <strong>BMSB_allSNPs.vcf:</strong> VCF containing all SNPs (neutral and adaptive) of all samples and populations <strong>BMSB_BayPass.geno:</strong> genotype input file for BayPass, containing all SNPs (neutral and adaptive) of all samples and populations <strong>BMSB_CHvsALL_BayPass.sh:</strong> script to run BayPass <strong>BMSB_neutralSNPs.vcf:</strong> VCF containing only neutral SNPs of all samples and populations <strong>BMSB_popmap.txt:</strong> population map of all samples and populations <strong>ChinavsAllwithNZ_BayPass.ecotype:</strong> ecotype input file for BayPass <strong>DivMigrate_BayesAss_heatmap.R:</strong> R script for plotting heatmaps for BayesAss and DivMigrate results <strong>IQtree_allwithNZneutral.sh:</strong> script for running IQtree