ArticlePloS one2008
Phylogenetic detection of recombination with a Bayesian prior on the distance between trees.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Structural and evolutionary insights into the isoprene monooxygenases.FEMS microbiology ecology · 2026Article
- The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics.PLoS genetics · 2024Review
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- Fidelity of hyperbolic space for Bayesian phylogenetic inference.PLoS computational biology · 2023Article
- ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2021Article
- Recombination Located over 2A-2B Junction Ribosome Frameshifting Region of Saffold Cardiovirus.Viruses · 2018Article
- Inferring Local Genealogies on Closely Related Genomes.Comparative genomics : RECOMB ... International Workshop, RCG ... : revised selected papers. RECOMB-CG (Conference) · 2017Article
- A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.Systematic biology · 2016Article
- The inference of gene trees with species trees.Systematic biology · 2015Review
- Codon pairs of the HIV-1 vif gene correlate with CD4+ T cell count.BMC infectious diseases · 2013Article
- Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees.Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America · 2012Article
- Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction.Genome biology and evolution · 2011Article
- Article
- The role of recombination in the emergence of a complex and dynamic HIV epidemic.Retrovirology · 2010Article
- A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies.Evolutionary bioinformatics online · 2009Article
- Phylogenetic inference under recombination using Bayesian stochastic topology selection.Bioinformatics (Oxford, England) · 2009Article
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Authors and funding
3 authors.
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Abstract
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.
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