A Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes

Recombination is an evolutionary force that results in mosaic genomes for microorganisms. The evolutionary history of microorganisms cannot be properly inferred if recombination has occurred among a set of taxa. That is, polymorphic sites of a multiple sequence alignment cannot be described by a single phylogenetic tree. Thus, detecting the presence of recombination is crucial before phylogeny inference. The phylogenetic-based methods are commonly utilized to explore recombination, however, the compatibility-based methods are more computationally efficient since the phylogeny construction is not required. We propose a novel approach focusing on the pairwise compatibility of polymorphic sites of given regions to characterize potential breakpoints in recombinant bacterial and viral genomes. The performance of average compatibility ratio (ACR) approach is evaluated on simulated alignments of different scenarios comparing with two programs, GARD and RDP4. Three empirical datasets of varying genome sizes with varying levels of homoplasy are also utilized for testing. The results demonstrate that our approach is able to detect the presence of recombination and identify the recombinant breakpoints efficiently, which provides a better understanding of distinct phylogenies among mosaic sequences.