Tangled Tales from Multiple Markers

Abstract

Supertree methods combine information from multiple phylogenies into a larger, composite phylogeny. When there is no disagreement between the source phylogenies, constructing the supertree is straightforward. But in the (nearly universal) presence of disagreement between source trees, supertree methods seek to either represent or resolve this conflict. Existing supertree methods that resolve conflict between source trees do so in an ad hoc way. Gene tree parsimony is a supertree method that can combine molecular phylogenies for overlapping taxon sets and interprets conflict between these phylogenies in a biologically meaningful way. We review the method and discuss the relationship between gene tree parsimony and other supertree methods. Finally, we suggest that a better understanding of the causes of conflict between source trees should lead to appropriate ways of resolving this conflict when constructing supertrees.Keywordsgene duplicationgene tree parsimonyreconciled trees