Changing the landscape: A new strategy for estimating large phylogenies

In this paper we describe a new heuristic strategy designed to find optimal (parsimonious) trees for data sets with large numbers of taxa and characte rs. This new strategy uses an iterative searching process of branch swappin g with equally weighted characters, followed by swapping with reweighted ch aracters. This process increases the efficiency of the search because, afte r each round of swapping with reweighted characters, the subsequent swappin g with equal weights will start from a different group (island) of trees th at are only slightly, if at all, less optimal. In contrast, conventional he uristic searching with constant equal weighting can become trapped on islan ds of suboptimal trees. We test the new strategy against a conventional str ategy and a modified conventional strategy and show that, within a given ti me, the new strategy finds trees that are markedly more parsimonious. We al so compare our new strategy with a recent, independently developed strategy known as the Parsimony Ratchet.