Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research
Phylogenetic 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 fac...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-07-01
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| Series: | Diversity |
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| Online Access: | https://www.mdpi.com/1424-2818/12/8/288 |
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| author | Nuria Macías-Hernández Marc Domènech Pedro Cardoso Brent C. Emerson Paulo Alexandre Vieira Borges Jesús Lozano-Fernandez Octávio S. Paulo Ana Vieira Alba Enguídanos François Rigal Isabel R. Amorim Miquel A. Arnedo |
| author_facet | Nuria Macías-Hernández Marc Domènech Pedro Cardoso Brent C. Emerson Paulo Alexandre Vieira Borges Jesús Lozano-Fernandez Octávio S. Paulo Ana Vieira Alba Enguídanos François Rigal Isabel R. Amorim Miquel A. Arnedo |
| author_sort | Nuria Macías-Hernández |
| collection | DOAJ |
| description | Phylogenetic 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. |
| first_indexed | 2024-03-10T18:16:07Z |
| format | Article |
| id | doaj.art-9a63b6c0e6184c1481e004c7f2668719 |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-10T18:16:07Z |
| publishDate | 2020-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diversity |
| spelling | doaj.art-9a63b6c0e6184c1481e004c7f26687192023-11-20T07:41:33ZengMDPI AGDiversity1424-28182020-07-0112828810.3390/d12080288Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem ResearchNuria Macías-Hernández0Marc Domènech1Pedro Cardoso2Brent C. Emerson3Paulo Alexandre Vieira Borges4Jesús Lozano-Fernandez5Octávio S. Paulo6Ana Vieira7Alba Enguídanos8François Rigal9Isabel R. Amorim10Miquel A. Arnedo11Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History LUOMUS, University of Helsinki, 00014 Helsinki, FinlandDepartment of Evolutionary Biology, Ecology and Environmental Sciences, & Biodiversity Research institute (IRBio), Universitat de Barcelona, 08028 Barcelona, SpainLaboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History LUOMUS, University of Helsinki, 00014 Helsinki, FinlandIsland Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, 38206 Canary Islands, SpainCentre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group and University of the Azores–Faculty of Agriculture and Environment, PT-9700-042 Angra do Heroísmo, PortugalDepartment of Evolutionary Biology, Ecology and Environmental Sciences, & Biodiversity Research institute (IRBio), Universitat de Barcelona, 08028 Barcelona, SpainCentre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, PortugalCentre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, PortugalDepartment of Evolutionary Biology, Ecology and Environmental Sciences, & Biodiversity Research institute (IRBio), Universitat de Barcelona, 08028 Barcelona, SpainCentre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group and University of the Azores–Faculty of Agriculture and Environment, PT-9700-042 Angra do Heroísmo, PortugalCentre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group and University of the Azores–Faculty of Agriculture and Environment, PT-9700-042 Angra do Heroísmo, PortugalDepartment of Evolutionary Biology, Ecology and Environmental Sciences, & Biodiversity Research institute (IRBio), Universitat de Barcelona, 08028 Barcelona, SpainPhylogenetic 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.https://www.mdpi.com/1424-2818/12/8/288phylogenetic diversitytopological constrainttaxon samplinggenetic markerscalibration |
| spellingShingle | Nuria Macías-Hernández Marc Domènech Pedro Cardoso Brent C. Emerson Paulo Alexandre Vieira Borges Jesús Lozano-Fernandez Octávio S. Paulo Ana Vieira Alba Enguídanos François Rigal Isabel R. Amorim Miquel A. Arnedo Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research Diversity phylogenetic diversity topological constraint taxon sampling genetic markers calibration |
| title | Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research |
| title_full | Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research |
| title_fullStr | Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research |
| title_full_unstemmed | Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research |
| title_short | Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research |
| title_sort | building a robust densely sampled spider tree of life for ecosystem research |
| topic | phylogenetic diversity topological constraint taxon sampling genetic markers calibration |
| url | https://www.mdpi.com/1424-2818/12/8/288 |
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