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http://hdl.handle.net/1843/55174| Type: | Artigo de Periódico |
| Title: | Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method |
| Other Titles: | Comparação de redes complexas e métodos baseados em árvores de análise filogenética e proposta de um método bootstrap |
| Authors: | Aristóteles Góes-Neto Marcelo V.C. Diniz Daniel Santana de Carvalho Gilberto Cafezeiro Bomfim Angelo Amâncio Duarte Jerzy A. Brzozowski Thierry C. Petit Lobão Suani T.R. Pinho Charbel N. El-Hani Roberto Fernandes Silva Andrade |
| Abstract: | Complex 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. |
| Subject: | Redes complexas Filogenia Basidiomycota Quitina sintase |
| language: | eng |
| metadata.dc.publisher.country: | Brasil |
| Publisher: | Universidade Federal de Minas Gerais |
| Publisher Initials: | UFMG |
| metadata.dc.publisher.department: | ICB - DEPARTAMENTO DE MICROBIOLOGIA |
| Rights: | Acesso Aberto |
| metadata.dc.identifier.doi: | http://dx.doi.org/10.7717/peerj.4349 |
| URI: | http://hdl.handle.net/1843/55174 |
| Issue Date: | 2018 |
| metadata.dc.url.externa: | https://peerj.com/articles/4349/#p-1 |
| metadata.dc.relation.ispartof: | PeerJ |
| Appears in Collections: | Artigo de Periódico |
Files in This Item:
| File | Description | Size | Format | |
|---|---|---|---|---|
| Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method.pdf | 1.39 MB | Adobe PDF | View/Open |
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