Phylogenetic detection of recombination with a Bayesian prior on the distance between trees

• Published in: PloS one 2008-07, Vol.3 (7), p.e2651-e2651
• Main Authors: Martins, Leonardo de Oliveira, Leal, Elcio, Kishino, Hirohisa
• Format: Article
• Language: English
• Subjects: Algorithms; Analysis; Bayes Theorem; Bayesian analysis; Bioinformatics; Breakpoints; Computational Biology/Comparative Sequence Analysis; Computational Biology/Evolutionary Modeling; Computational Biology/Genomics; Computational Biology/Population Genetics; Computer Science/Applications; Computer simulation; Deoxyribonucleic acid; DNA; Evolutionary Biology/Bioinformatics; Evolutionary Biology/Evolutionary and Comparative Genetics; Evolutionary Biology/Microbial Evolution and Genomics; Genetic Heterogeneity; Genetic recombination; Genetics and Genomics/Bioinformatics; Genetics and Genomics/Microbial Evolution and Genomics; Haplotypes; HIV-1 - genetics; Hot spots; Human immunodeficiency virus 1; Infectious Diseases/HIV Infection and AIDS; Information processing; Life sciences; Mathematics/Statistics; Methods; Mitochondrial DNA; Performance evaluation; Phylogenetics; Phylogeny; Population; Recombinants; Recombination; Recombination hot spots; Recombination, Genetic; Taxa; Topology; Transversion; Virology/Immunodeficiency Viruses; Virology/Virus Evolution and Symbiosis
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0002651

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 transitionratiotransversion 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.