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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 Alexandre Vieira
dc.contributor.authorLozano-Fernandez, Jesús
dc.contributor.authorPaulo, Octávio S.
dc.contributor.authorVieira, Ana
dc.contributor.authorEnguídanos, Alba
dc.contributor.authorRigal, François
dc.contributor.authorAmorim, Isabel R.
dc.contributor.authorArnedo, Miquel A.
dc.date.accessioned2021-02-09T20:12:35Z
dc.date.available2021-02-09T20:12:35Z
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.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.doi10.3390/d12080288pt_PT
dc.identifier.urihttp://hdl.handle.net/10451/46257
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherMDPIpt_PT
dc.relationproject BIODIV ISLAND-CONT (Biodiversity drivers on islands and continents–706482)pt_PT
dc.relationFCT-NETBIOME grant 0003/2011pt_PT
dc.relationERA-Net Net-Biome financed through Canary Islands Government ACIISI grants SE-12/02, SE-12/03, SE-12/04 (B.C.E.), co-financed by FEDERpt_PT
dc.relationFCT MACDIV–FCT-PTDC/BIABIC/0054/2014pt_PT
dc.relationOrganismo Autónomo de Parques Nacionales Spain (OAPN #485/2012)pt_PT
dc.relationgrant 2017SGR83 from the Catalan Governmentpt_PT
dc.relationAPIF PhD fellowship from the University of Barcelonapt_PT
dc.relationFCT–Norma Transitória–DL57/2016/CP1375/CT0003pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.titleBuilding a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Researchpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.issue8pt_PT
oaire.citation.startPage288pt_PT
oaire.citation.titleDiversitypt_PT
oaire.citation.volume12pt_PT
person.familyNamePaulo
person.givenNameOctávio
person.identifier119335
person.identifier.ciencia-id471A-1219-9C5F
person.identifier.orcid0000-0001-5408-5212
person.identifier.ridD-9921-2011
person.identifier.scopus-author-id6602677193
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication2be59178-7c2d-4df6-9d6f-3aaef29c0a53
relation.isAuthorOfPublication.latestForDiscovery2be59178-7c2d-4df6-9d6f-3aaef29c0a53

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