title: Controlled recovery of phylogenetic communities from an evolutionary model using a network approach.
abstract: This works reports the use of a complex network approach to produce a phylogenetic classification tree of a simple evolutionary model. This approach has already been used to treat proteomic data of actual extant organisms, but an investigation of its reliability to retrieve a traceable evolutionary history is missing. The used evolutionary model includes key ingredients for the emergence of groups of related organisms by differentiation through random mutations and population growth, but purposefully omits other realistic ingredients that are not strictly necessary to originate an evolutionary history. This choice causes the model to depend only on a small set of parameters, controlling the mutation probability and the population of different species. Our results indicate that for a set of parameter values, the phylogenetic classification produced by the used framework reproduces the actual evolutionary history with a very high average degree of accuracy. This includes parameter values where the species originated by the evolutionary dynamics have modular structures. In the more general context of community identification in complex networks, our model offers a simple setting for evaluating the effects, on the efficiency of community formation and identification, of the underlying dynamics generating the network itself.
authors.affiliation: Instituto de Física, Universidade Federal da Bahia, 40210-210, Salvador, Brazil and Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, G3-52 4259 Nagatsuta-cho, Yokohama 226-8502, Japan.
authors.forename: Arthur M Y R
authors.initials: AM
authors.lastname: Sousa
authors.affiliation: Instituto de Física, Universidade de São Paulo, Caixa Postal 66318, 05314-970, São Paulo, Brazil.
authors.forename: André P
authors.initials: AP
authors.lastname: Vieira
authors.affiliation: Instituto de Física, Universidade de São Paulo, Caixa Postal 66318, 05314-970, São Paulo, Brazil.
authors.forename: Carmen P C
authors.initials: CP
authors.lastname: Prado
authors.affiliation: Instituto de Física, Universidade Federal da Bahia, 40210-210, Salvador, Brazil.
authors.forename: Roberto F S
authors.initials: RF
authors.lastname: Andrade
mesh_terms: D019143:Evolution, Molecular; D008954:Models, Biological; D009154:Mutation; D010802:Phylogeny