The nature of heterotachy
Lockhart P, Novis P, Milligan B, Riden J, Rambaut A & Larkum T(2006) Mol Biol Evol 23, 40-45.
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 (pvar) 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 pvar. For an empirical case with plastid and eubacterial RNA polymerase sequences, we confirm
using capture-recapture estimates and simulations that pvar 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.
