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Building a robust, densely-sampled spider tree of life for ecosystem research

2020-07Journal article Open access
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dc.contributor.authorMacías-Hernández, Nuria
dc.contributor.authorDomènech, Marc
dc.contributor.authorCardoso, Pedro
dc.contributor.authorEmerson, Brent C.
dc.contributor.authorBorges, Paulo A. V.
dc.contributor.authorLozano-Fernandez, Jesús
dc.contributor.authorPaulo, Octávio S.
dc.contributor.authorVieira, Ana
dc.contributor.authorEnguídanos, Alba
dc.contributor.authorRigal, François
dc.contributor.authorRosário, Isabel Amorim do
dc.contributor.authorArnedo, Miquel A.
dc.date.accessioned2021-03-22T18:25:30Z
dc.date.available2021-03-22T18:25:30Z
dc.date.issued2020-07
dc.description.abstractPhylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.en
dc.description.sponsorshipMarie Sklodowska-Curie Individual Fellowships (H2020-MSCA-IF-2015); ERA-Net Net-Biome research framework, financed through Portuguese FCT-NETBIOME grant 0003/2011; ERA-Net Net-Biome financed through Canary Islands Government ACIISI grants SE-12/02, SE-12/03, SE-12/04; FEDER; FCT MACDIV-FCT-PTDC/BIABIC/0054/2014; Organismo Autonomo de Parques Nacionales Spain (OAPN #485/2012); Catalan Government; APIF PhD fellowship from the University of Barcelona; Juan de la Cierva Fellowship (FJCI-2015-23723); FCT-Fundação para a Ciência e a Tecnologia (Norma Transitoria-DL57/2016/CP1375/CT0003); University of Helsinki.en
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationMacías-Hernández, N., Domènech, M, Cardoso, P., Emerson, B.C., Borges, P.A.V., Lozano-Fernandez, J., Paulo, O.S., Vieira, A., Enguídanos, A., Rigal, F., Amorim, I.R. & Arnedo, M. (2020). Building a robust, densely-sampled spider tree of life for ecosystem research. “Diversity”, 12(8), 1-23. DOI: 10.3390/d12080288en
dc.identifier.doi10.3390/d12080288pt_PT
dc.identifier.issn1424-2818
dc.identifier.urihttp://hdl.handle.net/10138/317920
dc.identifier.urihttp://hdl.handle.net/10261/217170
dc.identifier.urihttp://hdl.handle.net/10400.3/5809
dc.identifier.wos000577787900001
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherMDPIpt_PT
dc.relationBiodiversity drivers on islands and continents
dc.relation.publisherversionhttps://www.mdpi.com/1424-2818/12/8/288pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectPhylogenetic Diversityen
dc.subjectTopological Constrainten
dc.subjectTaxon Samplingen
dc.subjectGenetic Markersen
dc.subjectCalibrationen
dc.titleBuilding a robust, densely-sampled spider tree of life for ecosystem researchen
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleBiodiversity drivers on islands and continents
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/706482/EU
oaire.citation.conferencePlaceSwitzerlanden
oaire.citation.endPage23pt_PT
oaire.citation.issue(8)pt_PT
oaire.citation.startPage1pt_PT
oaire.citation.titleDiversityen
oaire.citation.volume12pt_PT
oaire.fundingStreamH2020
person.familyNameCardoso
person.familyNameBorges
person.familyNameRigal
person.familyNameAmorim do Rosário
person.givenNamePedro
person.givenNamePaulo
person.givenNameFrançois
person.givenNameIsabel
person.identifier829215
person.identifier.ciencia-id3118-EA4B-B8A3
person.identifier.ciencia-idFA1A-C9CB-9C29
person.identifier.ciencia-idE315-82D2-C35D
person.identifier.ciencia-id9713-F828-9787
person.identifier.orcid0000-0001-8119-9960
person.identifier.orcid0000-0002-8448-7623
person.identifier.orcid0000-0001-6882-1591
person.identifier.orcid0000-0001-6847-3320
person.identifier.ridA-8820-2008
person.identifier.ridB-2780-2008
person.identifier.ridP-5140-2015
person.identifier.scopus-author-id36112709400
person.identifier.scopus-author-id7003533390
person.identifier.scopus-author-id55924714000
person.identifier.scopus-author-id36092499800
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.nameEuropean Commission
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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