Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes

Two different methods of using paralogous genes for phylogenetic inference have been proposed: reconciled trees (or gene tree parsimony) and uninode coding. Gene tree parsimony suffers from 10 serious problems, including differential weighting of nucleotide and gap characters, undersampling which can be misinterpreted as synapomorphy, all of the characters not being allowed to interact, and conflict between gene trees being given equal weight, regardless of branch support. These problems are largely avoided by using uninode coding. The uninode coding method is elaborated to address multiple gene duplications within a single gene tree family and handle problems caused by lack of gene tree resolution. An example of vertebrate phylogeny inferred from nine genes is reanalyzed using uninode coding. We suggest that uninode coding be used instead of gene tree parsimony for phylogenetic inference from paralogous genes.