title: Axiomatic opportunities and obstacles for inferring a species tree from gene trees.
abstract: The reconstruction of a central tendency "species tree" from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all taxa are present in every gene tree. Here, we list four apparently desirable properties that a method for estimating a species tree from gene trees could have (the strongest property states that building a species tree from input gene trees and then pruning leaves gives a tree that is the same as, or more resolved than, the tree obtained by first removing the taxa from the input trees and then building the species tree). We show that although it is technically possible to simultaneously satisfy these properties when taxon coverage is complete, they cannot all be satisfied in the more general supertree setting. In part two, we discuss a concordance-based consensus method based on Baum's "plurality clusters", and an extension to concordance supertrees.
authors.affiliation: Allan Wilson Centre for Molecular Ecology and Evolution, University of Canterbury, Christchurch, New Zealand; and Department of Philosophy, Texas Tech University, Box 43092, Lubbock, TX 79409, USA; mike.steel@canterbury.ac.nz.
authors.forename: Mike
authors.initials: M
authors.lastname: Steel
authors.affiliation: Allan Wilson Centre for Molecular Ecology and Evolution, University of Canterbury, Christchurch, New Zealand; and Department of Philosophy, Texas Tech University, Box 43092, Lubbock, TX 79409, USA;
authors.forename: Joel D
authors.initials: JD
authors.lastname: Velasco
mesh_terms: D002965:Classification / Q000379:methods*; D008954:Models, Biological; D010802:Phylogeny; D017421:Sequence Analysis; D013045:Species Specificity