Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | LOCUS Repositório Institucional da UFV |
Texto Completo: | https://doi.org/10.1016/j.ecoinf.2018.06.008 http://www.locus.ufv.br/handle/123456789/21785 |
Resumo: | Soft polytomies emerge due to the application of handmade supertrees in phylogenetic community analysis, thus increasing uncertainties regarding phylogenetic diversity or community structure indices. Real-time integration of advances in phylogenetic knowledge among species from public data repositories, such as Open Tree of Life, may reduce this uncertainty. Based on an interface with Open Tree of Life, the Community Tree Optimizer (ComTreeOpt) classifies families from user-specific lists into resolvable and non-resolvable families, builds resolved subtrees for resolvable families and inserts them in the megatree previously pruned to species from non-resolvable families. Community trees optimized by ComTreeOpt show 30–50% fewer polytomies than non-optimized community trees, reducing the uncertainties in phylogenetic diversity and dispersion metrics that are due to a lack of phylogenetic resolution. ComTreeOpt enhances user-specific community trees in a rapid and inexpensive way based on available phylogenetic information, thus increasing the confidence in the metrics of phylogenetic diversity and dispersion. |
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Trotter, IanGastauer, MarkusCaldeira, Cecílio FroisRamos, Silvio JunioMeira Neto, João Augusto Alves2018-09-12T19:02:07Z2018-09-12T19:02:07Z2018-0715749541https://doi.org/10.1016/j.ecoinf.2018.06.008http://www.locus.ufv.br/handle/123456789/21785Soft polytomies emerge due to the application of handmade supertrees in phylogenetic community analysis, thus increasing uncertainties regarding phylogenetic diversity or community structure indices. Real-time integration of advances in phylogenetic knowledge among species from public data repositories, such as Open Tree of Life, may reduce this uncertainty. Based on an interface with Open Tree of Life, the Community Tree Optimizer (ComTreeOpt) classifies families from user-specific lists into resolvable and non-resolvable families, builds resolved subtrees for resolvable families and inserts them in the megatree previously pruned to species from non-resolvable families. Community trees optimized by ComTreeOpt show 30–50% fewer polytomies than non-optimized community trees, reducing the uncertainties in phylogenetic diversity and dispersion metrics that are due to a lack of phylogenetic resolution. ComTreeOpt enhances user-specific community trees in a rapid and inexpensive way based on available phylogenetic information, thus increasing the confidence in the metrics of phylogenetic diversity and dispersion.engEcological Informaticsv. 46, p. 192- 198, jul. 2018Elsevier B.V.info:eu-repo/semantics/openAccessPhylogenetic community analysisPhylogenetic resolutionPolytomiesEcological misinterpretationOptimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indicesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALartigo.pdfartigo.pdftexto completoapplication/pdf2060953https://locus.ufv.br//bitstream/123456789/21785/1/artigo.pdf3ed22f7a6a8e2751ce568aa02c575de8MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://locus.ufv.br//bitstream/123456789/21785/2/license.txt8a4605be74aa9ea9d79846c1fba20a33MD52THUMBNAILartigo.pdf.jpgartigo.pdf.jpgIM Thumbnailimage/jpeg6306https://locus.ufv.br//bitstream/123456789/21785/3/artigo.pdf.jpg832d5a8e7b52e7f72196175337d38425MD53123456789/217852018-09-12 23:00:31.964oai:locus.ufv.br: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Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452018-09-13T02:00:31LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false |
dc.title.en.fl_str_mv |
Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices |
title |
Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices |
spellingShingle |
Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices Trotter, Ian Phylogenetic community analysis Phylogenetic resolution Polytomies Ecological misinterpretation |
title_short |
Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices |
title_full |
Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices |
title_fullStr |
Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices |
title_full_unstemmed |
Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices |
title_sort |
Optimizing community trees using the open tree of life increases the reliability of phylogenetic diversity and dispersion indices |
author |
Trotter, Ian |
author_facet |
Trotter, Ian Gastauer, Markus Caldeira, Cecílio Frois Ramos, Silvio Junio Meira Neto, João Augusto Alves |
author_role |
author |
author2 |
Gastauer, Markus Caldeira, Cecílio Frois Ramos, Silvio Junio Meira Neto, João Augusto Alves |
author2_role |
author author author author |
dc.contributor.author.fl_str_mv |
Trotter, Ian Gastauer, Markus Caldeira, Cecílio Frois Ramos, Silvio Junio Meira Neto, João Augusto Alves |
dc.subject.pt-BR.fl_str_mv |
Phylogenetic community analysis Phylogenetic resolution Polytomies Ecological misinterpretation |
topic |
Phylogenetic community analysis Phylogenetic resolution Polytomies Ecological misinterpretation |
description |
Soft polytomies emerge due to the application of handmade supertrees in phylogenetic community analysis, thus increasing uncertainties regarding phylogenetic diversity or community structure indices. Real-time integration of advances in phylogenetic knowledge among species from public data repositories, such as Open Tree of Life, may reduce this uncertainty. Based on an interface with Open Tree of Life, the Community Tree Optimizer (ComTreeOpt) classifies families from user-specific lists into resolvable and non-resolvable families, builds resolved subtrees for resolvable families and inserts them in the megatree previously pruned to species from non-resolvable families. Community trees optimized by ComTreeOpt show 30–50% fewer polytomies than non-optimized community trees, reducing the uncertainties in phylogenetic diversity and dispersion metrics that are due to a lack of phylogenetic resolution. ComTreeOpt enhances user-specific community trees in a rapid and inexpensive way based on available phylogenetic information, thus increasing the confidence in the metrics of phylogenetic diversity and dispersion. |
publishDate |
2018 |
dc.date.accessioned.fl_str_mv |
2018-09-12T19:02:07Z |
dc.date.available.fl_str_mv |
2018-09-12T19:02:07Z |
dc.date.issued.fl_str_mv |
2018-07 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://doi.org/10.1016/j.ecoinf.2018.06.008 http://www.locus.ufv.br/handle/123456789/21785 |
dc.identifier.issn.none.fl_str_mv |
15749541 |
identifier_str_mv |
15749541 |
url |
https://doi.org/10.1016/j.ecoinf.2018.06.008 http://www.locus.ufv.br/handle/123456789/21785 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartofseries.pt-BR.fl_str_mv |
v. 46, p. 192- 198, jul. 2018 |
dc.rights.driver.fl_str_mv |
Elsevier B.V. info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Elsevier B.V. |
eu_rights_str_mv |
openAccess |
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application/pdf |
dc.publisher.none.fl_str_mv |
Ecological Informatics |
publisher.none.fl_str_mv |
Ecological Informatics |
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LOCUS Repositório Institucional da UFV |
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