A Bayesian model for detecting past recombination events in DNA multiple alignments

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
G McGuireM J Prentice

Abstract

Most phylogenetic tree estimation methods assume that there is a single set of hierarchical relationships among sequences in a data set for all sites along an alignment. Mosaic sequences produced by past recombination events will violate this assumption and may lead to misleading results from a phylogenetic analysis due to the imposition of a single tree along the entire alignment. Therefore, the detection of past recombination is an important first step in an analysis. A Bayesian model for the changes in topology caused by recombination events is described here. This model relaxes the assumption of one topology for all sites in an alignment and uses the theory of Hidden Markov models to facilitate calculations, the hidden states being the underlying topologies at each site in the data set. Changes in topology along the multiple sequence alignment are estimated by means of the maximum a posteriori (MAP) estimate. The performance of the MAP estimate is assessed by application of the model to data sets of four sequences, both simulated and real.

References

Sep 1, 1992·Molecular Phylogenetics and Evolution·H J Bandelt, A W Dress
Jan 1, 1988·Annual Review of Genetics·J Felsenstein
Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Nov 1, 1995·AIDS Research and Human Retroviruses·M O SalminenF E McCutchan
Jan 1, 1996·Molecular Biology and Evolution·J Felsenstein, G A Churchill
May 1, 1996·Molecular Biology and Evolution·J L ThorneD T Jones
Mar 1, 1997·Molecular Biology and Evolution·N C Grassly, E C Holmes
Nov 19, 1997·Molecular Biology and Evolution·G McGuireM J Prentice
May 15, 1998·Molecular Biology and Evolution·J Maynard Smith, N H Smith

Citations

Jun 9, 2005·Molecular Phylogenetics and Evolution·Nicolas DevosPaul S Manos
Sep 26, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·D Husmeier, F Wright
Apr 5, 2003·Molecular Ecology·De-Xing Zhang, Godfrey M Hewitt
Nov 13, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yufeng Wu
Nov 14, 2002·Annual Review of Genetics·David PosadaEdward C Holmes
Oct 1, 2004·American Journal of Botany·C Randal Linder, Loren H Rieseberg
Sep 15, 2001·Molecular Biology and Evolution·C WiufJ Hein
Jul 30, 2014·Systematic Biology·Gergely J SzöllősiBastien Boussau

Related Concepts

Bayesian Prediction
DNA, Double-Stranded
DNA, Bacterial
Markov Chains
Neisseria
Phylogeny
Recombination, Genetic
Two-Parameter Models
Determination, Sequence Homology

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