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We present a new method for inferring species trees from multi-copy genetrees. Our method is based on a generalization of the Robinson-Foulds (RF)distance to multi-labeled trees (mul-trees), i.e., gene trees in which multipleleaves can have the same label. Unlike most previous phylogenetic methods usinggene trees, this method does not assume that gene tree incongruence is causedby a single, specific biological process, such as gene duplication and loss,deep coalescence, or lateral gene transfer. We prove that it is NP-hard tocompute the RF distance between two mul-trees, but it is easy to calculate thegeneralized RF distance between a mul-tree and a singly-labeled tree. Motivatedby this observation, we formulate the RF supertree problem for mul-trees(MulRF), which takes a collection of mul-trees and constructs a species treethat minimizes the total RF distance from the input mul-trees. We present afast heuristic algorithm for the MulRF supertree problem. Simulationexperiments demonstrate that the MulRF method produces more accurate speciestrees than gene tree parsimony methods when incongruence is caused by gene treeerror, duplications and losses, and/or lateral gene transfer. Furthermore, theMulRF heuristic runs quickly on data sets containing hundreds of trees with upto a hundred taxa.

Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance