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Data from: Signatures of local adaptation along environmental gradients in a range-expanding damselfly (Ischnura elegans)
datasetposted on 2022-06-10, 02:57 authored by Rachael Y. Dudaniec, Chuan Ji Yong, Lesley T. Lancaster, Erik I. Svensson, Bengt Hansson
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 NotesIschnura 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 (unpublished).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.
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