Weighting and congruence: a case study based on three mitochondrial genes in pitvipers.

Weighting strategies in a total evidence approach are often conducted in order to remove homoplasy, with the implicit hope to increase congruence between data partitions. Incongruence was measured using the test of Farris et al. (J. S. Farris, M. Källersjö, A. G. Kluge, and C. Bult, 1995, Cladistics 10, 315-319) within and between three mitochondrial genes from pitvipers (Crotalinae) in partitioning each codon position for the coding genes. Incongruence between codon positions of a gene can be worse than incongruence between genes at analogous positions. Third positions of codons behave very differently in terms of incongruence from one gene to another while showing similar patterns in saturation tests. Instead of removing characters in order to discard homoplasy, which is hopeless and does not increase general congruence, we advocate for the removal of those substitutions that are incongruent with the rest. The genus Calloselasma and its sister group the genus Hypnale are the most basal Crotalinae. Asiatic pitvipers are paraphyletic, while American pitvipers are monophyletic.