Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees

Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees

Autor Martins, Leonardo de Oliveira Google Scholar
Leal, Elcio Autor UNIFESP Google Scholar
Kishino, Hirohisa Google Scholar
Instituição Univ Tokyo
Universidade Federal de São Paulo (UNIFESP)
Resumo Genomic regions participating in recombination events may support distinct topologies, and phylogenetic analyses should incorporate this heterogeneity. Existing phylogenetic methods for recombination detection are challenged by the enormous number of possible topologies, even for a moderate number of taxa. If, however, the detection analysis is conducted independently between each putative recombinant sequence and a set of reference parentals, potential recombinations between the recombinants are neglected. in this context, a recombination hotspot can be inferred in phylogenetic analyses if we observe several consecutive breakpoints. We developed a distance measure between unrooted topologies that closely resembles the number of recombinations. By introducing a prior distribution on these recombination distances, a Bayesian hierarchical model was devised to detect phylogenetic inconsistencies occurring due to recombinations. This model relaxes the assumption of known parental sequences, still common in HIV analysis, allowing the entire dataset to be analyzed at once. On simulated datasets with up to 16 taxa, our method correctly detected recombination breakpoints and the number of recombination events for each breakpoint. the procedure is robust to rate and transition: transversion heterogeneities for simulations with and without recombination. This recombination distance is related to recombination hotspots. Applying this procedure to a genomic HIV-1 dataset, we found evidence for hotspots and de novo recombination.
Idioma Inglês
Financiador Japan Society for the Promotion of Science (JSPS)
Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Número do financiamento FAPESP: 04/10372-3
FAPESP: 07/52841-8
Data de publicação 2008-07-09
Publicado em Plos One. San Francisco: Public Library Science, v. 3, n. 7, 13 p., 2008.
ISSN 1932-6203 (Sherpa/Romeo, fator de impacto)
Publicador Public Library Science
Extensão 13
Fonte http://dx.doi.org/10.1371/journal.pone.0002651
Direito de acesso Acesso aberto Open Access
Tipo Artigo
Web of Science WOS:000264065800053
Endereço permanente http://repositorio.unifesp.br/handle/11600/30799

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