Integrated and Open Butterfly Database

The Integrated and Open Butterfly Database provide a massive dataset of curated COI sequences for West Palearctic butterflies and an updated checklist. Functions to manage the dataset are also provided.

Detalhes bibliográficos
Autor: Dapporto, Leonardo
Formato: conjunto de datos
Fecha de publicación:2022
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/311507
Acesso em linha:http://hdl.handle.net/10261/311507
https://doi.org/10.20350/digitalCSIC/15330
Access Level:acceso abierto
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spelling Integrated and Open Butterfly DatabaseIOdatabaseDapporto, LeonardoThe Integrated and Open Butterfly Database provide a massive dataset of curated COI sequences for West Palearctic butterflies and an updated checklist. Functions to manage the dataset are also provided.The IOdatabase is intended as a project integrating several datasets of butterflies from Western Palaearctic harmonised with a shared taxonomy. IOdatabase now includes a revised version of the species checklist from West Palerarctic (Wiemers et al. 2016 and Middleton Welling et al. 2020) and more than 30000 COI sequences for 532 species. COI sequences belong to three main sources: 1) De novo sequencing mostly for Maghreb and Macaronesia 2) Published DNA-barcode libraries and public BOLD projects compiled at regional level 3) Studies providing COI of single species or genera. In the latter case, we checked whether haplotypes, instead of specimens, were included in repositories (Paz‐Vinas et al. 2021). If the number of specimens sharing a given haplotype in a particular location was reported, we replicated the haplotype sequences to obtain data at the specimen level, otherwise the sequences were excluded. We verified species identifications by building neighbor-joining trees for each genus. When morphology could not be verified, we removed sequences not clustering within the species to which they were attributed if the mismatch did not involve one of the 74 species showing DNA-barcode sharing. Metadata are also available: coordinates in WGS84 (degrees) and Lambert projections (meters), BOLD and Genbank codes, Continental areas and country obtained by an autmatic attribution using the rworldextra R package. Using these data we also calculated some basic indexes of genetic diversity (number of haplotypes observed and predicted based on rarefaction curves, GST, DST, haplotype diversity and nucleotide diversity).Peer reviewedGitHubDapporto, Leonardo [0000-0001-7129-4526]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202320232022info:eu-repo/semantics/datasethttp://purl.org/coar/resource_type/63NG-B465info:eu-repo/semantics/othertext/x-r-syntaxhttp://hdl.handle.net/10261/311507https://doi.org/10.20350/digitalCSIC/15330reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésDapporto, Leonardo; Menchetti, Mattia; Vodă, Raluca; Corbella, Cecilia; Cuvelier, Sylvain; Djemadi, Imed; Gascoigne-Pees, Martin; Hinojosa, Joan Carles; Ting Lam, Nok; Serracanta, Maria; Talavera, Gerard; Dincă, Vlad; Vila, Roger. The atlas of mitochondrial genetic diversity for Western Palaearctic butterflies. https://doi.org/10.1111/geb.13579 . http://hdl.handle.net/10261/281535Dapporto, Leonardo; 2022; The Atlas of mitochondrial genetic diversity for Western Palearctic butterflies [Dataset]; Dryad; https://doi.org/10.5061/dryad.9w0vt4bjjDapporto, Leonardo; 2022; The Atlas of mitochondrial genetic diversity for Western Palearctic butterflies [Software]; Zenodo; https://doi.org/10.5281/zenodo.6841163https://github.com/leondap/iodatabase.gitSíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3115072026-05-22T06:33:51Z
dc.title.none.fl_str_mv Integrated and Open Butterfly Database
IOdatabase
title Integrated and Open Butterfly Database
spellingShingle Integrated and Open Butterfly Database
Dapporto, Leonardo
title_short Integrated and Open Butterfly Database
title_full Integrated and Open Butterfly Database
title_fullStr Integrated and Open Butterfly Database
title_full_unstemmed Integrated and Open Butterfly Database
title_sort Integrated and Open Butterfly Database
dc.creator.none.fl_str_mv Dapporto, Leonardo
author Dapporto, Leonardo
author_facet Dapporto, Leonardo
author_role author
dc.contributor.none.fl_str_mv Dapporto, Leonardo [0000-0001-7129-4526]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
description The Integrated and Open Butterfly Database provide a massive dataset of curated COI sequences for West Palearctic butterflies and an updated checklist. Functions to manage the dataset are also provided.
publishDate 2022
dc.date.none.fl_str_mv 2022
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/dataset
http://purl.org/coar/resource_type/63NG-B465
dc.type.openaire.fl_str_mv info:eu-repo/semantics/other
format dataset
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/311507
https://doi.org/10.20350/digitalCSIC/15330
url http://hdl.handle.net/10261/311507
https://doi.org/10.20350/digitalCSIC/15330
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Dapporto, Leonardo; Menchetti, Mattia; Vodă, Raluca; Corbella, Cecilia; Cuvelier, Sylvain; Djemadi, Imed; Gascoigne-Pees, Martin; Hinojosa, Joan Carles; Ting Lam, Nok; Serracanta, Maria; Talavera, Gerard; Dincă, Vlad; Vila, Roger. The atlas of mitochondrial genetic diversity for Western Palaearctic butterflies. https://doi.org/10.1111/geb.13579 . http://hdl.handle.net/10261/281535
Dapporto, Leonardo; 2022; The Atlas of mitochondrial genetic diversity for Western Palearctic butterflies [Dataset]; Dryad; https://doi.org/10.5061/dryad.9w0vt4bjj
Dapporto, Leonardo; 2022; The Atlas of mitochondrial genetic diversity for Western Palearctic butterflies [Software]; Zenodo; https://doi.org/10.5281/zenodo.6841163
https://github.com/leondap/iodatabase.git
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv text/x-r-syntax
dc.publisher.none.fl_str_mv GitHub
publisher.none.fl_str_mv GitHub
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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