Abstract
BackgroundGenetic 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.ResultsWe 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 identifying recombination breakpoints. These approaches were less sensitive to parameter settings than other methods we tested, making them easier to apply to various data sets in a consistent manner.ConclusionPost-recombination substitutions tend to diminish the predictive accuracy of recombination-detecting programs. The best method for detecting recombined regions is not necessarily the most accurate in identifying recombination breakpoints. For difficult detection problems involving highly divergent sequences or large data sets, different types of approach can be run in succession to increase efficiency, and can potentially yield better predictive accuracy than any single method used in isolation.
Highlights
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes
Using simulated sequence data and multiple regression analysis, we have shown that the prediction accuracy of recombination-detecting programs is affected by the reciprocal and non-reciprocal nature of the recombination event, prior evolutionary history, subsequent substitutions after the recombination event, and the choice of parameter settings in certain programs
We demonstrated differences in phylogenetic signals within recombined and non-recombined regions, between a reciprocal and a non-reciprocal event, and how these signals affect prediction accuracy of different approaches in detecting occurrence and identifying breakpoints of a recombination event
Summary
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent residue substitutions, which complicate their detection. Genetic information is transferred or exchanged between two similar DNA sequences. In non-reciprocal recombination, a contiguous region of DNA is replaced by, rather than exchanged with, the transferred region. Both types of recombination are a consequence of the DNA mismatch repair mechanism which protects genetic information from damage. For example, is a cross-over process between homologous sequences in which a DNA strand replaces a damaged partner DNA strand with a copy of its own sequence [1]. Gene conversion events can lead to reshuffling of parental open reading frames, or of structural and functional motifs within protein domains, and these can generate a gene with novel (page number not for citation purposes)
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