A simple method to improve the reliability of tree reconstructions

Abstract

The efficiencies of distance-matrix methods for correct tree reconstruction under a variety of substitution rates, transition-transversion biases, and different model trees were studied. If substitution rates are high and the ratio of transitions and transversions is large, even a Kimura two-parameter correction fails very often to reconstruct the model tree. We show that a combination of combinatorial weighting by Williams and Fitch and the Jukes-Cantor correction significantly increases the efficiency of tree-reconstruction methods, for a large fraction of evolutionary parameters. We explain why this approach is superior to any other weighting/correction scheme tested, as long as sequences are sufficiently long or substitution rates are sufficiently large. An approximate threshold for switching to a different weighting scheme is given.