In article <Pine.SOL.3.91.950414173342.20428A-100000 at corona> Patrick
O'Neil, patrick at corona writes:
>> I know there are several people who have published papers
>> argueing that the "molecular clock rate" of different organisms varies
as
>> a function of reproductive time. That animals such as rodents with a
1
>> or 2 month period between generations have a faster molecular clock
than
>> do primates with generation times of 3 to 30 years.
>> I could not find any references at my fingertips (no MedLine
>>I would think that generation _time_ would be rather irrelevant (Unless
>your generation time is a million years :) ). I would think that the
>fact that mice have a less efficient DNA damage repair system than
humans
>do, for instance, and so THIS would lead to a higher "clock rate" for
>them vs us, that is, sequence variations will occur at a higher rate per
>replication. Correcting for more rapid generation time, the mutation
>rate should itself be more important.
This last paragraph is self contradictory. First you say that generation
time is irrelevant then that it must be corrected for. I think you are
confusing the idea of a mutation rate - the rate at which errors occur
during DNA replication - and substitution rate - the rate at which these
errors
are fixed into the genes of a population. The latter is what we observe
when we compare homologous sequences. It is dependant on a number of
factors
including mutation rate, selection, generation time and possibly
metabolic rate.
>The clock rate for HIV, taking mutation rate into account, should then
be
>extremely fast.
About a million times faster than its host's. However, most of the error
is in the
reverse transcriptase function. This integrates the viral genome into the
host
DNA. Any mutations that occurred during this process are then garenteed
to be
in the resultant progeny viruses because the new viral RNA is then
transcribed
from the integrated DNA.
For references try:
Chao, L., & Carr, D. E. (1993) Evolution 47:668-690.
Martin, A. P., & Palumbi, S. R. (1993) Proc. Natl. Acad. Sci. USA
90:4087-4091
Mooers, A. O., & Harvey, P. H. (1994) Molecular Phylogenies and Evolution
3:344-350
=====================================================================
Andrew Rambaut,
Zoology Department, EMAIL - Andrew.Rambaut at zoology.ox.ac.uk
University of Oxford,
South Parks Road, Oxford, England.
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