Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 23, Issue 10, Pages 1891-1901Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msl051
Keywords
recombination; phylogenetic incongruence; model selection; genetic algorithms; multimodel inference
Funding
- NIAID NIH HHS [AI57167, AI36214, AI47745, AI43638] Funding Source: Medline
- NIGMS NIH HHS [R01-GM66276] Funding Source: Medline
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The evolution of homologous sequences affected by recombination or gene conversion cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for sequence analysis, for example, those used for detecting sites evolving nonneutrally, have been shown to fail if such phylogenetic incongruity is ignored. However, it may be possible to propose several phylogenies that can correctly model the evolution of nonrecombinant fragments. We propose a model-based framework that uses a genetic algorithm to search a multiple-sequence alignment for putative recombination break points, quantifies the level of support for their locations, and identifies sequences or clades involved in putative recombination events. The software implementation can be run quickly and efficiently in a distributed computing environment, and various components of the methods can be chosen for computational expediency or statistical rigor. We evaluate the performance of the new method on simulated alignments and on an array of published benchmark data sets. Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection.
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