A Reconciliation with Non-binary Gene Trees Revisited

By reconciling the phylogenetic tree of a gene family with the corresponding species tree, it is possible to infer lineage-specific duplications and losses with high confidence and hence to annotate orthologs and paralogs. The currently available reconciliation methods for non-binary gene trees are computationally expensive for genome-scale applications. We present four O(|G| + |S|) algorithms to reconcile an arbitrary gene tree G with its corresponding species tree S in the mutation, duplication, loss and deep coalescence cost models, where | · | denotes the number of nodes in the corresponding tree. The improvement is achieved through two innovations: a linear-time computation of compressed child-image subtrees and efficient reconstruction of irreducible duplication histories. Our technique for child-image subtree compression also results in an order of magnitude speedup in run time for the dynamic programming and Wagner-parsimony-based methods for tree reconciliation in the affine cost model.