Do others take an HIV molecular clock seriously?
As I understand it, there are estimates of the frequency of occurrence
of changes in the HIV-1 genome for samples whose divergence time can be
estimated accurately. These estimates when applied to the different
subtypes of HIV-1 yield divergence dates consistent with other information.
This estimate is then applied assuming a constant frequency (a uniformly
ticking clock) to earlier divergences (from HIV-2 and from other primate
Since HIV-1 seems to be a recently evolved virus and is probably still
rapidly evolving, I question whether a constant clock can be applied to
these earlier divergences. I expect that the frequencies of substitutions
can change dramatically in situations where viruses are adapting to new
niches. Thus, I take estimates of distant divergence times with several
grains of salt.
Ulrich Melcher umelcher at bmb-fs1.biochem.okstate.edu
Department of Biochemistry Tel: 405-744-6210
and Molecular Biology FAX: 405-744-7799
Oklahoma State University
Stillwater OK 74078-0454 USA