Data from: Signatures of local adaptation along environmental gradients in a range-expanding damselfly (Ischnura elegans)

Insect distributions are shifting rapidly in response to climate change and are undergoing rapid evolutionary change. We investigate the molecular signatures underlying local adaptation in the range-expanding damselfly, Ischnura elegans. Using a landscape genomic approach combined with generalized dissimilarity modelling (GDM), we detect selection signatures on loci via allelic frequency change along environmental gradients. We analyse 13,612 Single Nucleotide Polymorphisms (SNPs), derived from Restriction site-Associated DNA sequencing (RADseq), in 426 individuals from 25 sites spanning the I. elegans distribution in Sweden, including its expanding northern range edge. Environmental association analysis (EAA) and the magnitude of allele frequency change along the range expansion gradient revealed significant signatures of selection in relation to high maximum summer temperature, high mean annual precipitation, and low wind speeds at the range edge. SNP annotations with significant signatures of selection revealed gene functions associated with ongoing range expansion, including heat shock proteins (HSP40 and HSP70), ion transport (V-ATPase) and visual processes (long wavelength-sensitive opsin), which have implications for thermal stress response, salinity tolerance and mate discrimination, respectively. We also identified environmental thresholds where climate-mediated selection is likely to be strong, and indicate that I. elegans is rapidly adapting to the climatic environment during its ongoing range expansion. Our findings empirically validate an integrative approach for detecting spatially explicit signatures of local adaptation along environmental gradients.

Usage Notes
Ischnura elegans draft genome assembly Dec 2015This is a draft assembly of the Ischnura elegans genome produced by Pallavi Chauhan, Bengt Hansson, et al. (unpublished). Production date was December, 2015. An updated and annotated reference genome for Ischnura elegans is scheduled to be available on NCBI in 2018.Ischnura_elegans_draftgenome_assemblyDec2015.fastaCompleteness Report for I.elegans draft genome Dec 15Completeness Report for I.elegans draft genome, Dec 2015Ischnura_elegans_draftgenomeDec2015.output.completeness_reportReport for Ischnura_elegans_draftgenomeDec2015Assembly summary data, coverage and statistics for I.elegans draft genome December 2015Ischnura_elegans_draftgenomeDec2015.reportGDM R code for single SNP-based analysisGDM R code for single SNP-based analysis - data formatting, modelling and outputGDM Upload 20180412.REnvironmental dataEnvironmental data for variables used in GDM and EAAUpload1_EnvData.csvSNP_datafileDatafile for 13612 SNPs in genepop format, generated from Stacks 1.40.PlinkMap_datafilePlink .map datafile for 13612 SNPsGDM_TotalmodelOutput_1758snpsTotal model output for GDM of 1758 candidate SNPsSNPannotations and GDMSNP annotations for all candidate loci and GDM output for SNPs meeting criteria for presentation.SNPannotations.xlsxpopmapPopmap of population site IDs and sample IDsOutlier_EAA_SNPs1758List of SNP IDs for all uniquely identified SNPs from Fst Outlier (Bayescan and OutFlank) and Environmental Association Analysis (LFMM) tests.

昆虫分布正迅速响应气候变化而发生变化，并经历着快速的进化变迁。本研究旨在探究范围扩张的蜻蜓物种Ischnura elegans在局部适应中的分子标记。通过结合景观基因组学方法和广义差异模型（GDM），我们通过环境梯度上的等位基因频率变化检测到选择标记在位点上的存在。我们分析了来自瑞典25个地点的426个个体中由限制性位点关联DNA测序（RADseq）得出的13,612个单核苷酸多态性（SNPs）。这些数据覆盖了I. elegans在瑞典的分布范围，包括其向北扩张的边缘。环境关联分析（EAA）和等位基因频率变化在范围扩张梯度上的幅度揭示了与高夏季最高温度、高年均降水量和低风速相关的显著选择标记。具有显著选择标记的SNP注释揭示了与持续范围扩张相关的基因功能，包括热休克蛋白（HSP40和HSP70）、离子运输（V-ATPase）和视觉过程（长波长敏感视蛋白），这些分别与热应激反应、盐度耐受性和配偶选择有关。我们还确定了环境阈值，其中气候介导的选择可能非常强烈，并指出I. elegans正在其持续范围扩张过程中快速适应气候环境。我们的发现从实证角度验证了沿环境梯度检测局部适应空间特异性标记的整合方法。

使用说明
Ischnura elegans基因组草图（2015年12月）
这是由Pallavi Chauhan、Bengt Hansson等人（未发表）生产的Ischnura elegans基因组草图。生产日期为2015年12月。Ischnura elegans的更新和注释参考基因组计划于2018年在NCBI上提供。
Ischnura_elegans_draftgenome_assemblyDec2015.fasta
I.elegans基因组草图完整性报告（2015年12月15日）
I.elegans draft genome, Dec 2015的完整性报告
Ischnura_elegans_draftgenomeDec2015.output.completeness_report
I.elegans draft genome December 2015的组装摘要数据、覆盖率和统计信息
Ischnura_elegans_draftgenomeDec2015.report
基于单个SNP分析的GDM R代码
基于单个SNP分析的GDM R代码 - 数据格式化、建模和输出
GDM Upload 20180412.RE
环境数据
用于GDM和EAA的环境变量数据
Upload1_EnvData.csv
SNP数据文件
由Stacks 1.40生成的13612个SNPs的基因流行病学格式数据文件
PlinkMap数据文件
13612个SNPs的Plink .map数据文件
GDM_TotalmodelOutput_1758snps
1758个候选SNPs的GDM总模型输出
SNP注释和GDM
所有候选位点及满足展示标准的SNPs的GDM输出
SNPannotations.xlsx
popmap
种群站点ID和样本ID的popmap
Outlier_EAA_SNPs1758
来自Fst Outlier（Bayescan和OutFlank）和环境关联分析（LFMM）测试的独特识别SNPs列表。