> 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.
- 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.

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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