On Weighting and Congruence

- A priori differential weighting of molecular characters is a common methodological practice in molecular phylogenetics and evolution. This has been a largely subjective exercise with few criteria for deciding which characters to down-weight and how much to do so. A priori differential weighting is conducted to remove heterogeneity from the data sets and to improve the congruence among the informative, and usually more conservative characters. Herein, we test whether congruence is improved with a priori differential weighting by using the incongruence length difference test on a linked genetic data set consisting of 14 mammalian taxa and the 13 protein coding genes of the mitochondrial genome. Weighting by omitting the third codon position did not improve congruence with respect to the equally weighted data, while weighting transversions did improve the congruence between the 13 protein coding genes. Nonetheless, the most parsimonious tree found from transversion weighting did not differ from one using all of the data equally weighted.