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

Autor(es)

Martins, Leonardo de Oliveira ^[1] ; Leal, Elcio ^[2] ; Kishino, Hirohisa ^[1]

Afiliação do(s) autor(es)

^[1] Univ Tokyo, Grad Sch Agr & Life Sci, Tokyo - Japan

^[2] Univ Fed Sao Paulo, Sao Paulo - Brazil

• Tipo de documento: Artigo Científico
• Fonte: PLoS One; v. 3, n. 7, p. e2651, 2008.
• Citações Web of Science: 13

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. (AU)

• Processo FAPESP: 07/52841-8 - Análise bayesiana de aspectos filogenética e seletivos do HIV-1 na epidemia brasileira
• Beneficiário: Elcio de Souza Leal
• Modalidade de apoio: Bolsas no Exterior - Pesquisa
• Processo FAPESP: 04/10372-3 - Dinâmica evolutiva do vírus da imunodeficiência humana, tipo 1 (HIV-1) em populações sob tratamento antiretroviral
• Beneficiário: Elcio de Souza Leal
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado