Some considerations about Cotton and Wilkinson's "majority rule supertrees"

This paper discusses cases where the "majority rule supertree (-)" method of Cotton and Wilkinson (Syst. Biol. 2007, 56, 445) prefers the relationships displayed by a minority of the trees, and is contradicted by the majority. When the trees have different numbers of taxa, the relationships of the bigger tree can be more influential (depending on the specific arrangement of the taxa found in the larger tree but not in the smaller ones). In that case, the smaller tree can occur in an arbitrarily large number of identical copies, and still be disregarded if the big tree has a sufficiently large number of taxa. The "majority rule supertree (+)" method, by contrast, collapses the groups in the bigger tree (instead of resolving them in favour of the bigger tree, as the (-) version).