Nature 425, 798-804 (23 October 2003) | doi:10.1038/nature02053; Received 4 June 2003; Accepted 15 September 2003

Genome-scale approaches to resolving incongruence in molecular phylogenies

Antonis Rokas1,2, Barry L. Williams1,2, Nicole King1 & Sean B. Carroll1

  1. Howard Hughes Medical Institute, Laboratory of Molecular Biology, R. M. Bock Laboratories, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin 53706, USA
  2. These authors contributed equally to this work

Correspondence to: Sean B. Carroll1 Email:


One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.