I am responding to comments made in a posting from site rhoneycu at NSF.GOV.
There was no signature so I don't know the name of the individual who
made the comments.
"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."
I'm curious to know what you mean by "generation time effects". There are
those who argue that evoluton is faster in rodents than in some other mammals
because rodents have shorter generation times. I don't think that the data
for a rate differential is very good but even if it was it does not
necessarily follow that generation times are the cause.
If one uses an appropriate outgroup then the rates of change in most mammalian
lineages are similar for a number of genes. In other words all of the tips
of the branches of the dendrogram are equidistant from the root. This suggests
to me that there has been a (relatively) constant rate of change since the
time of the main mammalian radiation (about 100 myr). Why is this "wrong-
minded"?
I agree with the rest of the article posted from rhoneycu at NSF.GOV where
he/she said that calibration points are necessary in order to calculate
absolute rates or divergent times. Where we differ, I suspect, is that
I believe that only a single calibration point (ie. mammalian radiation
at 100 myr) is necessary to provide an estimate of the rat/mouse divergence
because rates of change in all lineages are about equal. Thus if the
rat/mouse node is two thirds of the distance from the root then these
organisms likely shared a common ancestor 33 million years ago.
In that case the fossil record could be misleading or incomplete because
palaeontologists estimate about 15 million years. There are at least as
many reasons why the fossil evidence could be incomplete as there are
criticisms concerning molecular data.
Let's look at a hypothetical example.
|------------------------------------- whales
|
----|
| |------------ mouse
|------------------------|
|------------ rat
100 15 ages from
myr myr fossil record
One interpretation of this data is that the 15 myr age must be incorrect
and the last common ancestor of mice and rats actually lived much earlier.
Another interpretation is that the 15 myr estimate is accurate and the
rates of change in both mice and rats since the time of divergence have
been much more rapid than in other lineages.
Laurence A. Moran (Larry)
