Removing Noise from Gene Trees

Reconciliation is the commonly used method for inferring the evolutionary scenario for a gene family. It consists in “embedding” an inferred gene tree into a known species tree, revealing the evolution of the gene family by duplications and losses. The main complaint about reconciliation is that the inferred evolutionary scenario is strongly dependant on the considered gene tree, as few misplaced leaves may lead to a completely different history, with significantly more duplications and losses. As using different phylogenetic methods with different parameters may lead to different gene trees, it is essential to have criteria to choose, among those, the appropriate one for reconciliation. In this paper, following the conclusion of a previous paper, we flag certain duplication vertices of a gene tree, the “non-apparent duplication” (NAD) vertices, as resulting from the misplacement of leaves, and consider the optimization problem of removing the minimum number of leaves leading to a tree without any NAD vertex. We develop a polynomial-time algorithm that is exact for two special classes of gene trees, and show a good performance on simulated data sets in the general case.