Data from: Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum)

Widespread species that exhibit both high gene flow and the capacity to occupy heterogeneous environments make excellent models for examining local selection processes along environmental gradients. Here we evaluate the influence of temperature and landscape variables on genetic connectivity and signatures of local adaptation in Phaulacridium vittatum, a widespread agricultural pest grasshopper, endemic to Australia. With sampling across a 900 km latitudinal gradient, we genotyped 185 P. vittatum from 19 sites at 11,408 single nucleotide polymorphisms (SNPs) using ddRAD sequencing. Despite high gene flow across sites (pairwise Fst = 0.0003-0.08), landscape genetic resistance modelling identified a positive non-linear effect of mean annual temperature on genetic connectivity. Urban areas and water bodies had a greater influence on genetic distance among sites than pasture, agricultural areas, and forest. Together, Fst outlier tests and Environmental Association Analysis (EAA) detected 242 unique SNPs under putative selection, with the highest numbers associated with latitude, mean annual temperature, and body size. A combination of landscape genetic connectivity analysis together with EAA identified mean annual temperature as a key driver of both neutral gene flow and environmental selection processes. Gene annotation of putatively adaptive SNPs matched with gene functions for olfaction, metabolic detoxification and ultra-violet light shielding. Our results imply that this widespread agricultural pest has the potential to spread and adapt under shifting temperature regimes and land cover change.

Usage Notes
3257_snps_PvittFiltered dataset PED format consisting of 3,257 SNPs genotyped in 185 individuals of Phaulacridium vittatum.3257_snps_PvittDatafile (map format) consisting names of 3257 loci11408_snps_PvittFiltered dataset consisting of 11,408 SNPs genotyped in 185 individuals used for adaptive genetic analysis11408_snps_PvittMap file containing 11,408 SNP loci name.Model_selection_LandcoverR script to perform model selectionalpha_gamma_valuesDatafile consisting values of of alpha and gamma. Required to generate resistance surfaces.Landcover_150m_resRe-classified landcover raster file used to generate multiple resistance surfaces.BIO1_Mean_annual_tempAnnual mean temperature raster file used to generate multiple resistance surfacesMorphology_185_ind_PvittMorphological data of 185 individuals used to test morph-environment association in LFMM.

兼具高基因流与异质环境适应能力的广布物种，是探究环境梯度下局域选择过程的绝佳研究模型。本研究以澳大利亚特有广布农业害虫——条纹澳蝗（Phaulacridium vittatum）为对象，探究温度与景观变量对其遗传连通性及局域适应信号的影响。本研究沿900公里纬度梯度开展采样，通过双酶切限制性位点相关DNA测序（ddRAD sequencing）技术，对19个采样点的185头条纹澳蝗个体进行了11408个单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点的基因分型。尽管各采样点间基因流水平较高（成对固定指数Fst = 0.0003~0.08），景观遗传抗性模型分析结果显示，年均温对遗传连通性存在显著的正向非线性效应。相较于草地、农业用地与林地，城市区域与水体对采样点间遗传距离的影响更为显著。综合固定指数异常位点检测与环境关联分析（Environmental Association Analysis, EAA），本研究共鉴定出242个处于潜在选择压力下的独特SNPs位点，其中与纬度、年均温和体型关联的位点数量最多。结合景观遗传连通性分析与环境关联分析结果，本研究确认年均温是驱动中性基因流与环境选择过程的关键因子。潜在适应性SNPs的基因注释结果显示，其相关基因功能涵盖嗅觉、代谢解毒与紫外线防护。本研究结果表明，这种广布农业害虫在温度格局变化与土地覆盖改变的背景下，具备进一步扩散与适应新环境的潜力。

使用说明
3257_snps_PvittFiltered数据集：采用PED格式，包含185头条纹澳蝗个体的3257个SNPs位点基因型数据。
3257_snps_PvittDatafile（map格式）：包含3257个基因座名称的文件。
11408_snps_PvittFiltered数据集：包含用于适应性遗传分析的185头条纹澳蝗个体的11408个SNPs位点基因型数据。
11408_snps_PvittMap文件：包含11408个SNP基因座名称。
Model_selection_LandcoverR脚本：用于开展模型选择分析。
alpha_gamma_valuesDatafile：包含alpha与gamma参数值的文件，用于生成抗性表面。
Landcover_150m_res：重分类土地覆盖栅格文件，用于生成多组抗性表面。
BIO1_Mean_annual_temp：年均温栅格文件，用于生成多组抗性表面。
Morphology_185_ind_Pvitt：185头条纹澳蝗的形态学数据，用于LFMM中的形态-环境关联检验。