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

PeerJ

article

Aristóteles Góes-Neto¹  Marcelo V.C. Diniz¹  Daniel S. Carvalho²  Gilberto C. Bomfim²  Angelo A. Duarte³  Jerzy A. Brzozowski⁴  Thierry C. Petit Lobão⁵  Suani T.R. Pinho⁶  Charbel N. El-Hani²  Roberto F.S. Andrade⁶ 

[1] Department of Microbiology, Universidade Federal de Minas Gerais;Institute of Biology, Universidade Federal da Bahia;Department of Technology, Universidade Estadual de Feira de Santana;Interdisciplinary Graduate Program in Human Sciences, Federal University of Fronteira Sul;Institute of Mathematics, Universidade Federal da Bahia;Institute of Physics, Universidade Federal da Bahia;National Institute of Science & Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution ,(IN-TREE), Instituto de Biologia, Universidade Federal da Bahia

关键词: Complex networks;    Community detection;    Phylogenetic methods;    Statistical support;    Basidiomycota;    Chitin synthases;   

DOI  :  10.7717/peerj.4349

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY