Rate of substitution of genomic regions is among the most debated intrinsic 
features that impact phylogenetic informativeness. However, this variable is 
also coupled with rates of nonsynonymous substitutions that underscore the 
nature and degree of selection on the selected genes. To empirically address 
these variables, we constructed four completely overlapping data sets of plastid 
matK, atpB, rbcL, and mitochondrial matR genes and used the rosid lineage 
(angiosperms) as a working platform. The genes differ in combinations of overall 
rates of nucleotide and amino acid substitutions. Tree robustness, homoplasy, 
accuracy in contrast to a reference tree, and phylogenetic informativeness are 
evaluated. The rapidly evolving/unconstrained matK faired best, whereas 
remaining genes varied in degrees of contribution to rosid phylogenetics across 
the lineage's 108 million years evolutionary history. Phylogenetic accuracy was 
low with the slowly evolving/unconstrained matR despite least amount of 
homoplasy. Third codon positions contributed the highest amount of parsimony 
informative sites, resolution and informativeness, but magnitude varied with 
gene mode of evolution. These findings are in clear contrast with the views that 
rapidly evolving regions and the 3rd codon position have inevitable negative 
impact on phylogenetic reconstruction at deep historic level due to accumulation 
of multiple hits and subsequent elevation in homoplasy and saturation. Relaxed 
evolutionary constraint in rapidly evolving genes distributes substitutions 
across codon positions, an evolutionary mode expected to reduce the frequency of 
multiple hits. These findings should be tested at deeper evolutionary histories.