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arXiv · 1709.04459

Gene tree reconciliation including transfers with replacement is hard and FPT

Damir Hasic·Eric Tannier
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Abstract

Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the gene level like duplication or transfer. These differences are handled by phylogenetic reconciliation, which formally is a mapping between gene tree nodes and species tree nodes and branches. We investigate models of reconciliation with a gene transfer that replaces existing gene, which is a biological important event but never included in reconciliation models. Also the problem is close to a dated version of the classical subtree prune and regraft (SPR) distance problem, where a pruned subtree has to be regrafted only on a branch closer to the root. We prove that the reconciliation problem including transfer and replacement is NP-hard, and that if speciations and transfers with replacement are the only allowed evolutionary events, then it is fixed-parameter tractable (FPT) with respect to the reconciliation's weight. We prove that the results extend to the dated SPR problem.

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Damir Hasic, Eric Tannier. 2017-09-13. Gene tree reconciliation including transfers with replacement is hard and FPT. https://doi.org/10.1007/s10878-019-00396-z

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