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Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization
Vittori, Karla; Delbem, Alexandre C. B; Pereira, Sérgio L.
Afiliação
  • Vittori, Karla; Universidade de São Paulo. Departamento de Ciência da Computação. São Carlos. BR
  • Delbem, Alexandre C. B; Universidade de São Paulo. Departamento de Ciência da Computação. São Carlos. BR
  • Pereira, Sérgio L; Royal Ontario Museum. Department of Natural History. Toronto. CA
Genet. mol. biol ; Genet. mol. biol;31(4): 974-981, Sept.-Dec. 2008. ilus, graf, tab
Article em En | LILACS | ID: lil-501455
Biblioteca responsável: BR26.1
ABSTRACT
We propose a new distance algorithm for phylogenetic estimation based on Ant Colony Optimization (ACO), named Ant-Based Phylogenetic Reconstruction (ABPR). ABPR joins two taxa iteratively based on evolutionary distance among sequences, while also accounting for the quality of the phylogenetic tree built according to the total length of the tree. Similar to optimization algorithms for phylogenetic estimation, the algorithm allows exploration of a larger set of nearly optimal solutions. We applied the algorithm to four empirical data sets of mitochondrial DNA ranging from 12 to 186 sequences, and from 898 to 16,608 base pairs, and covering taxonomic levels from populations to orders. We show that ABPR performs better than the commonly used Neighbor-Joining algorithm, except when sequences are too closely related (e.g., population-level sequences). The phylogenetic relationships recovered at and above species level by ABPR agree with conventional views. However, like other algorithms of phylogenetic estimation, the proposed algorithm failed to recover expected relationships when distances are too similar or when rates of evolution are very variable, leading to the problem of long-branch attraction. ABPR, as well as other ACO-based algorithms, is emerging as a fast and accurate alternative method of phylogenetic estimation for large data sets.
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Texto completo: 1 Coleções: 01-internacional Base de dados: LILACS Assunto principal: Formigas / Algoritmos / DNA Mitocondrial Tipo de estudo: Prognostic_studies Limite: Animals Idioma: En Revista: Genet. mol. biol Assunto da revista: GENETICA Ano de publicação: 2008 Tipo de documento: Article País de afiliação: Brasil / Canadá País de publicação: Brasil
Texto completo: 1 Coleções: 01-internacional Base de dados: LILACS Assunto principal: Formigas / Algoritmos / DNA Mitocondrial Tipo de estudo: Prognostic_studies Limite: Animals Idioma: En Revista: Genet. mol. biol Assunto da revista: GENETICA Ano de publicação: 2008 Tipo de documento: Article País de afiliação: Brasil / Canadá País de publicação: Brasil