On the Comparison of Bacteriophage Populations

The production of cheese and other dairy products relies on the constant monitoring viruses, called bacteriophages, that attack organisms responsible for fermentation process. Bacteriophage species are characterized by a stable core genome, ‘genetic reservoir’ gene variants exchanged through recombination. Phylogenetic analysis phage populations notably difficult due not only to extreme levels horizontal exchange at borders functional modules, but also inside them. In this paper we present first known attempt directly modeling flux between populations. This represents an important departure from gene-based alignment phylogenetic reconstruction, shifting focus genetic reservoir-based evolutionary inference. We combinatorial framework comparison bacteriophage populations, use it compute recombination scenarios generate one population another. apply our heuristic, based framework, four sampled Dutch factories Murphy [14]. find that, far being random, these highly constrained. method test factory-specific diversity, there was likely large amount in ancestral population. Find instructions reproducing results at: https://bitbucket.org/thekswenson/phage_population_comparison code is publicly available https://bitbucket.org/thekswenson/phagerecombination