experiments exploring 'molecular clocks'

Andreas Matern alm13 at cornell.edu
Wed Sep 24 13:31:04 EST 1997

In article <604j3h$9k1 at gap.cco.caltech.edu>, pwkr at ugcs.caltech.edu (paul
wilhelm karl rothemund) wrote:

> Hi all,
> A biology post-doc friend of mine is interested in exploring
> research which is somewhat far out of field for her, molecular evolution,
> and specifically 'molecular clocks.' That is, she'd like to understand
> the way in which we calculate the date of divergence for a pair of 
> organisms based on the divergence of their DNAs and go on to build trees
> using this data. She understands the growing prevalence of this method
> in building phylogenetic trees, and is interested mostly in the 
> details of how we calibrate these clocks, and the subtleties of our
> assumptions about how they work (assumptions like, a particular sequence
> for a clock is not under strong selective pressure, etc.) 
> She is particularly interested in any experimental studies in E. Coli or 
> other experimental organisms that verify our assumptions about 
> molecular clocks--perhaps studies that show the rates of evolution
> of sequence in a lab strain of E. Coli after many serial passages. 
> I'd like to know of any references to the use and calibration of
> molecular clocks that will introduce her to the debate and, in
> particular experimental studies that speak to the issue. 
> Please respond via email to my post in addition to responding to the 
> list since I read news so infrequently.
> Thanks very much,
> Paul Rothemund
> rothemun at pollux.usc.edu
> Graduate Student
> Department of Computer Science
> University of Southern California

This should get you started:  

TI  Vagaries of the molecular clock.
AU  Ayala-F-J.
SO  Proceedings of the National Academy of Sciences of the United States
    of America.
    94 (15). 1997. 7776-7783.

A VERY recent article by a VERY well-known geneticist.  Talks about fruit
fly genes, but the references contained therein (and the discussion in
general) will be helpful.

TI  Molecular evidence from the nuclear genome for the time frame of human
AU  Easteal-S. Herbert-G.
SO  Journal of Molecular Evolution.
    44 (SUPPL. 1). 1997. S121-S132.

People tend to understand how evolutionary principles work best when
confronted with a human example.  This is another timely article which may
be of interest.

TI  Transkingdom transfer of the phosphoglucose isomerase gene.
AU  Katz-L-A.
SO  Journal of Molecular Evolution.
    43 (5). 1996. 453-459.

A fairly recent article which deals with how a gene may have been
transferred from from a bacterium to a eukaryote.  The E. Coli genome is
discussed and an estimated molecular clock based on the E.Coli and
Haemophilus influenzae genomes is described.  Decent references.

TI  Bias-corrected paralinear and LogDet distances and tests of molecular
    clocks and phylogenies under nonstationary nucleotide frequencies.
AU  Gu-X. Li-W-H.

SO  Molecular Biology and Evolution.
    13 (10). 1996. 1375-1383.

A rigorous mathematical approach to understanding clocks -- a bit on the
computationally heavy side, but I thought it may interest you.

Need more?  Just ask!

Andreas Matern
alm13 at cornell.edu
266 Emerson Hall
Dept of Plant Breeding and Biometry
Cornell University
Ithaca, NY  14853

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