Detecting recombination in evolving nucleotide sequences

Background: Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent residue substitutions, which consequently complicate their detection. While there are many algorithms for the identification of recombination events, little is known about the effects of subsequent substitutions on the accuracy of available recombination-detection approaches. Results: We assessed the effect of subsequent substitutions on the detection of simulated recombination events within sets of four nucleotide sequences under a homogeneous evolutionary model. The amount of subsequent substitutions per site, prior evolutionary history of the sequences, and reciprocality or non-reciprocality of the recombination event all affected the accuracy of the recombination-detecting programs examined. Bayesian phylogenetic-based approaches showed high accuracy in detecting evidence of recombination event and in identify...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Cheong Xin Chan, Robert G. Beiko, Mark A. Ragan
• Keywords: BMCBI 2006, Recombination Breakpoints, Recombination Event, Subsequent Substitutions