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Ischnura elegans draft genome assembly Dec 2015
This 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 (unpublished).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.fasta
Completeness Report for I.elegans draft genome Dec 15
Completeness Report for I.elegans draft genome, Dec 2015
Ischnura_elegans_draftgenomeDec2015.output.completeness_report
Report for Ischnura_elegans_draftgenomeDec2015
Assembly summary data, coverage and statistics for I.elegans draft genome December 2015
Ischnura_elegans_draftgenomeDec2015.report
GDM R code for single SNP-based analysis
GDM R code for single SNP-based analysis - data formatting, modelling and output
GDM Upload 20180412.R
Environmental data
Environmental data for variables used in GDM and EAA
Upload1_EnvData.csv
SNP_datafile
Datafile for 13612 SNPs in genepop format, generated from Stacks 1.40.
PlinkMap_datafile
Plink .map datafile for 13612 SNPs
GDM_TotalmodelOutput_1758snps
Total model output for GDM of 1758 candidate SNPs
SNPannotations and GDM
SNP annotations for all candidate loci and GDM output for SNPs meeting criteria for presentation.
SNPannotations.xlsx
popmap
Popmap of population site IDs and sample IDs
Outlier_EAA_SNPs1758
List of SNP IDs for all uniquely identified SNPs from Fst Outlier (Bayescan and OutFlank) and Environmental Association Analysis (LFMM) tests.
", "type": { "id": "notes", "title": { "de": "Anmerkungen", "en": "Notes" } } } ], "creators": [ { "affiliations": [ { "name": "Macquarie University" } ], "person_or_org": { "family_name": "Dudaniec", "given_name": "Rachael Y.", "name": "Dudaniec, Rachael Y.", "type": "personal" } }, { "affiliations": [ { "name": "Macquarie University" } ], "person_or_org": { "family_name": "Yong", "given_name": "Chuan Ji", "name": "Yong, Chuan Ji", "type": "personal" } }, { "affiliations": [ { "name": "University of Aberdeen" } ], "person_or_org": { "family_name": "Lancaster", "given_name": "Lesley T.", "name": "Lancaster, Lesley T.", "type": "personal" } }, { "affiliations": [ { "name": "Lund University" } ], "person_or_org": { "family_name": "Svensson", "given_name": "Erik I.", "name": "Svensson, Erik I.", "type": "personal" } }, { "affiliations": [ { "name": "Lund University" } ], "person_or_org": { "family_name": "Hansson", "given_name": "Bengt", "name": "Hansson, Bengt", "type": "personal" } } ], "description": "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.", "locations": { "features": [ { "place": "Sweden" } ] }, "publication_date": "2018-04-13", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "10.1111/mec.14709", "relation_type": { "id": "iscitedby", "title": { "de": "Wird zitiert von", "en": "Is cited by" } }, "scheme": "doi" } ], "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "CC0 waives copyright interest in a work you've created and dedicates it to the world-wide public domain. Use CC0 to opt out of copyright entirely and ensure your work has the widest reach." }, "icon": "cc-cc0-icon", "id": "cc0-1.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" }, "title": { "en": "Creative Commons Zero v1.0 Universal" } } ], "subjects": [ { "subject": "landscape genomics" }, { "subject": "Ischnura elegans" }, { "subject": "environmental association analysis" }, { "subject": "damselfly" }, { "subject": "Ischnura" }, { "subject": "Holocene" } ], "title": "Data from: Signatures of local adaptation along environmental gradients in a range-expanding damselfly (Ischnura elegans)" }, "parent": { "access": { "owned_by": { "user": "90070" } }, "communities": { "default": "734b6452-1f40-4db0-b218-08ab1d568b7f", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_submission_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2020-02-04T14:03:17.992421+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "734b6452-1f40-4db0-b218-08ab1d568b7f", "links": {}, "metadata": { "curation_policy": "

The Dryad collection in Zenodo contains datasets mirrored from the Dryad Digital Repository. If you want your dataset to appear here, submit it through https://datadryad.org. No other datasets will be accepted.

", "description": "Dryad is an international open-access repository of research data, especially data underlying scientific and medical publications. Dryad is a curated general-purpose repository that makes data discoverable, freely reusable, and citable.", "organizations": [ { "id": "00x6h5n95" } ], "page": "

Dryad is a community-governed open data publishing and curation repository. Through Dryad and Zenodo's partnership, Zenodo hosts a preservation copy of Dryad datasets, available through this Zenodo Community. For more information or to access the original published datasets, visit https://datadryad.org.

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