CHASE, MARK W., VINCENT SAVOLAINEN*, KEI TAKAHASHI, DOUGLAS E. SOLTIS, AND PAMELA S. SOLTIS. Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS UK; Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, PA 16802 USA; Department of Botany, Washington State University, Pullman, Washington 99164-4238 USA. - Large-scale phylogeny of flowering plants 1: simple tree-building methods work better.
Large-scale molecular phylogenies have been thought to be
non-tractable due to computer limitation (extensive searches),
resulting in the need for years of CPU time or a parallel computing
environment. Using simulated and real 3-gene data sets for ca. 150
angiosperms, we evaluated various tree-building algorithms. We used
minimum evolution (neighbor-joining with corrected distances), no
swapping or NNI and TBR swapping with maximum parsimony, and maximum
likelihood. We compared tree lengths versus topological distances of
individual searches to the best trees (viz. combined tree with real
data and model tree in simulations). We found that the simplest
tree-building algorithms (e.g. fast swapping) performed equally well
or better compared to other methods. These results imply that
large-scale phylogenies can be built easily and accurately without
extensive computer power. It also explains why incorrect trees are
built when not enough data are used, no matter how complex and
time-consuming the tree-building methods employed.
Key words: large-scale phylogeny, tree-building methods