tinyurl.com/uh3t wrote:
> > From: syvanen{at}ucdavis.edu
> > #11 at: http://www.vme.net/hgt/
>    Ribosomal RNA sequences are used to obtain molecular
>    distances that are used to estimate divergence times. This work
shows
>    that many major clades (angiosperm families and three metazoan
groups)
>    arose at times significantly earlier than is indicated by the
fossil
>    record. This is further evidence that major evolutionary
radiations
>    were possibly accompanied by extensive horizontal gene transfers.
>
> Two alternate explanations for the evidence:
> - The calibration of molecular distances is wrong, that the
divergences
> happened much more recently than the wrong calibration would
indicate.
> I.e. mutations happened more rapidly than assumed.

Think this through. Accept that mutations happened more rapidly than
assumed.  How would this affect the relative rate test?  I have thought
about this.  It leads to a number of conclusions that are quite ad hoc
and begin to fail on the parsimony principle.


> - The fossil record is incomplete. We simply don't happen to have
> fossils from the earliest time after the divergences happened. So the
> fossil record underestimates the time since divergence.

This requires that we reject much of the fossil record.  There is no
evidence of calcareous or silicate based life before the cambrian.
This type of life definetly appears in the Cambrian.  I think it is
safe to assume that this life form did not exist before then.  Please
keep in mind that we are talking about at least 2.5 billion years
before the Cambrian. Is it reasonable to postulate the presence of
these complex organisms in a 600 million year period without any fossil
evidence?

Mike Syvanen

>
> How do you dismiss those alternate explanations?
>
> The real test of horizontal gene transfer is to compute trees for
lots
> of different DNA loci, not trying to calibrate it by absolute years
but
> only structurally i.e. which way it branched first then which
> sub-branches happened later, and then check whether the structure
> obtained for different loci agree or disagree. If they all agree,
then
> they all co-evolved together, refuting horizontal gene transfer among
> those particular sections of DNA. If different sections of the DNA
show
> differently-structured evolutionary trees, then that would show that
> the portions of the trees where they disagreed happened before a
> horizontal gene transfer event and the later portions where they all
> run in parallel happened after the event. Some outgroup needs to be
> included to root all the trees, but otherwise no calibration of
> rate-of-mutation needs to be done. (Actually even unrooted trees are
> sufficient to check what recent i.e. near-leaf parts run in parallel
> and what parts near the "center" don't.)
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