Inferring Gene-Species Assignments in the Presence of Horizontal Gene Transfer

Background: Microbial communities from environmental samples show great diversity as bacteria quickly responds to changes in their ecosystems. To assess the scenario of the actual changes, metagenomics experiments aimed at sequencing genomic DNA from such samples are performed. These new obtained sequences together with already known are used to infer phylogenetic trees assessing the taxonomic groups the species with these genes belong to. Here, we propose the first approach to the gene-species assignment problem by using reconciliation with horizontal gene transfer. Results: We propose efficient algorithms that search for optimal gene-species mappings taking into account gene duplication, loss and transfer events under two tractable models of HGT reconciliation. Conclusions: We calculate both the optimal cost and all possible optimal scenarios. Furthermore as the number of optimal reconstructions can be large, we use a Monte-Carlo method for the inference of approximate distributions of gene-species assignments. We demonstrate the applicability on empirical and simulated datasets.