Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness

Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders from ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co-occurring moth pests across their common native range of China, one of which (the peach fruit moth, Carposina sasakii) has maintained its native distribution, while the other (the oriental fruit moth, Grapholita molesta) has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive spe..., Sample collection and library construction

Larvae of the OFM were sampled from 19 geographical locations from peach shoots, while larvae of the PFM were sampled from 12 locations from multiple hosts, both across their native range of China (Table S1). In total, 358 OFM and 220 PFM were used for genotyping. The genotyped individuals from the same orchard were collected from different trees separated by a distance of at least five meters.

Genomic DNA was extracted from a segment of an individual larva using DNeasy Blood and Tissue Kit (Qiagen, Germany). ddRAD libraries were prepared following a protocol from Peterson et al. (2012). Briefly, 120 ng of extracted genomic DNA from each sample was digested by the restriction enzymes NlaIII and AciI (New England Biolabs, USA), and then ligated to adapters barcoded with a combinatorial index. Each population was discriminated by a 6-bp index and each sample was discriminated by a unique 5 bp barcodes. Uniquely barcoded samples were pooled ...,

File name
Content

Admixture.txt
Commands for Admixture analysis

baypass.workflow.R
R script for Baypass analysis

cs.ind188.mac2.430740.vcf.zip
VCF file of PFM

gm.ind306.4-200gm.ind306.4-200x.mac2.177951snp.vcf.zipx.mac2.17795...
VCF file of OFM

gradient_forest_Scripts.R
R script for Gradient forest analysis

lfmm.R
R script for lfmm analysis

PCA_principle_componePCA_principle_component_analysis.Rnt_ana...
Script for PCA analysis

plot_LDdecay_from_VCF.txt
Script for Lddecay analysis

RAD_qualitRAD_quality_control.update-20200427.Ry_control.update-...
R script for quality control of SNPs

redundancy_analyses.R
R script of Redundacy analysis (RDA)