Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

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dc.creatorAristóteles Góes-Neto
dc.creatorMarcelo V.C. Diniz
dc.creatorDaniel Santana de Carvalho
dc.creatorGilberto Cafezeiro Bomfim
dc.creatorAngelo Amâncio Duarte
dc.creatorJerzy A. Brzozowski
dc.creatorThierry C. Petit Lobão
dc.creatorSuani T.R. Pinho
dc.creatorCharbel N. El-Hani
dc.creatorRoberto Fernandes Silva Andrade
dc.date.accessioned2023-06-20T19:30:02Z
dc.date.accessioned2025-09-08T23:01:28Z
dc.date.available2023-06-20T19:30:02Z
dc.date.issued2018
dc.description.sponsorshipCNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico
dc.format.mimetypepdf
dc.identifier.doihttp://dx.doi.org/10.7717/peerj.4349
dc.identifier.issn2167-8359
dc.identifier.urihttps://hdl.handle.net/1843/55174
dc.languageeng
dc.publisherUniversidade Federal de Minas Gerais
dc.relation.ispartofPeerJ
dc.rightsAcesso Aberto
dc.subjectRedes complexas
dc.subjectFilogenia
dc.subjectBasidiomycota
dc.subjectQuitina sintase
dc.subject.otherComplex networks
dc.subject.otherCommunity detection
dc.subject.otherPhylogenetic methods
dc.subject.otherStatistical support
dc.subject.otherBasidiomycota
dc.subject.otherChitin synthases
dc.titleComparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method
dc.title.alternativeComparação de redes complexas e métodos baseados em árvores de análise filogenética e proposta de um método bootstrap
dc.typeArtigo de periódico
local.citation.issuee4349
local.citation.volume6
local.description.resumoComplex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.
local.identifier.orcidhttps://orcid.org/0000-0002-7692-6243
local.identifier.orcidhttps://orcid.org/0000-0003-1772-7727
local.identifier.orcidhttps://orcid.org/0000-0001-6590-4287
local.identifier.orcidhttps://orcid.org/0000-0002-0053-3574
local.identifier.orcidhttps://orcid.org/0000-0001-7446-1342
local.identifier.orcidhttps://orcid.org/0000-0002-8667-9530
local.identifier.orcidhttps://orcid.org/0000-0003-1404-3485
local.identifier.orcidhttps://orcid.org/0000-0002-2308-3983
local.identifier.orcidhttps://orcid.org/0000-0002-9323-1400
local.publisher.countryBrasil
local.publisher.departmentICB - DEPARTAMENTO DE MICROBIOLOGIA
local.publisher.initialsUFMG
local.url.externahttps://peerj.com/articles/4349/#p-1

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