Efficient algorithms for lateral gene transfer problems

This paper develops a model for lateral gene transfer events (a.k.a. horizontal gene transfer events) between a set of gene trees T1, T2, …, Tk and a species tree S. To the best of our knowledge, this model possesses a higher degree of biological and mathematical soundness than any other model proposed in the literature. Among other biological considerations, the model respects the partial order of evolution implied by S. Within our model, we identify an activity parameter that measures the number of genes that are allowed to be simultaneously active in the genome of a taxa and show that finding the most parsimonious scenario that reconciles the disagreeing gene trees with the species tree is doable in polynomial time when the activity level and number of transfers are small, but intractable in general. To the best of our knowledge, all other models proposed in the literature assume implicitly that the activity is one. Finally, using a dataset of bacterial gene sequences from [4], our implementations found 5 optimal scenarios; one of which is the scenario proposed by the authors in [4].