Phylogenetic signal common to three data sets: combining data which initially appear heterogeneous

This study makes use of three sources of data, morphology and two chloroplast DNA sequences, ndhF and rbcL, to resolve relationships in Gesneriaceae. Cladograms from each of the three data sets separately are not topologically congruent. Statistical indices suggest that each data set is congruent with the ndhF data although, rbcL and morphology are themselves incongruent. Consensus methods provide no resolution of taxonomic relationships when trees from the different data sets are combined. Combining data sets generally results in cladograms that are more fully resolved than each of the data sets analyzed separately and support for the clades increases based on higher decay index and bootstrap values. These results indicate that there is a phylogenetic signal common to each of the data sets, however, the noise (errors due to homoplasy, mis-scoring, etc.) unique to each data source masks this signal. In combining the data, the evidence for the common evolutionary history in each data set overcomes the noise and is apparent in the resulting trees.