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