The nature of heterotachy at the center of recent controversy over the relative 
performance of tree-building methods is different from the form of heterotachy 
that has been inferred in empirical studies. The latter have suggested that 
proportions of variable sites (p(var)) vary among orthologues and among 
paralogues. However, the strength of this inference, describing what may be one 
of the most important evolutionary properties of sequence data, has remained 
weak. Consequently, other models of sequence evolution have been proposed to 
explain some long-branch attraction (LBA) problems that could be attributed to 
differences in p(var). For an empirical case with plastid and eubacterial RNA 
polymerase sequences, we confirm using capture-recapture estimates and 
simulations that p(var) can differ among orthologues in anciently diverged 
evolutionary lineages. We find that parsimony and a least squares distance 
method that implements an overly simple model of sequence evolution are 
susceptible to LBA induced by this form of heterotachy. Although homogeneous 
maximum likelihood inference was found to be robust to model misspecification in 
our specific example, we caution against assuming that it will always be so.