mwooten at ducvax.auburn.edu had several questions concerning
using fossils to calibrate the molecular clock. This is a
response to those questions and comments.
I am not for sure what Mike Wooten is arguing. The
divergence time estimate for Mus and Rattus is based on the
fossil record, and the age of fossils has nothing to do with
the phenotype and the environment. In fact, I don't even
know what this has to do with calibration of the molecular
clock. The best estimate for divergence between Mus and
Rattus is based on the earliest fossils and is between
approximately 11 and 12 million years. The controversy as
to this divergence comes from arguments presented by Vincent
Sarich based on an albumin clock. Here, Sarich estimated a
35 million year divergence. This estimate has nothing to do
with the fossil record. To the contrary, it is based on an
assumption that the albumin clock for rodents should be
similar to other mammals. Given this assumption, the amount
of divergence seen in terms of AID units argues for a much
older divergence time. The problem with many molecular
clocks for rodents is that generation time effects are known
to exist, especially for synonymous substitutions. Thus, it
is difficult to calibrate a clock based on divergence rates
of genes sequenced from other mammalian lineages. In fact,
the whole idea of calibrating clocks using some time of
assumption that the same gene has a constant rate of change
among all mammalian lineages is wrong minded, and in fact,
there is empirical data to suggest otherwise.
Two observations are essential to deriving a molecular
clock. First, one must demonstrate linearity with time and
evidence that rate heterogeneity is not apparent in the
group under study. Second, if an absolute rate is desired,
one must have a calibration point, based either on the
fossil record or biogeography. It would be nice to have
multiple calibration points, so one could get an idea about
error (a point suggested by David Hillis).
Molecules provide no insight into divergence time
without a calibration point, and I feel that in too many
cases the use of a molecular clock is abused. If used
correctly, calibration points based on fossils can be very
informative, especially if one is interested in divergence
times in other parts of the rodent phylogeny. Circularity
arises when one does not use the method correctly and
assumes to much.
I disagree with Wooten's statement that morphology and
fossils have nothing to offer. To the contrary, without
this information it would be difficult to examine processes
of molecular evolution, at least so far as rates are
concerned. Also, Wooten might also remember that
convergence cannot be ruled out at the molecular level.
There is beginning to more and more evidence of convergence
and even positive selection, at least in some cases.
