[Taxacom] Protist systematics

David Campbell pleuronaia at gmail.com
Fri Jan 24 10:35:28 CST 2014

Unfortunately, the estimated dates of divergence are often based on
statistically invalid and/or badly calibrated molecular clock calculations,
so there's little basis for trusting cited estimates.  Not all molecular
clock calculations are quite as bad as those critiqued, e.g., by Graur and
Martin (http://www.cell.com/trends/genetics/abstract/S0168-9525(03)00342-1),
but they remain highly vulnerable to miscalibration, incorrect algorithms
(I recently saw a paper where the fossil divergence times were misassigned
to be the date of the divergence of the taxa within a clade that happened
to be sampled, rather than to the origin of the clade containing the fossil
in question, not sure if user or BEAST was at fault), and poor knowledge of
geology and paleontology.

On the other hand, it is fairly easy to recognize clades that seem to
diverge at a common level in a tree and assign them a particular rank,
without falling into the temptation of trying to assign a numeric date
without serious study of the paleontological record or to engage in
fanciful speculation about how the fact about that time period that you
happen to have must have caused the origin of the clades.

Some categories are necessary for communication.  The challenge is deciding
which categories are most useful.  Monophyly is a nice feature for a
category, but some paraphyletic groups are also useful for certain
purposes.  Most importantly, a category must be recognizable.  Unless the
user can remember what a particular category includes, it does no good.  As
a result, venerable, though paraphyletic, groups are likely to be good
options for purposes of communication.

On Fri, Jan 24, 2014 at 10:25 AM, Fred Schueler <bckcdb at istar.ca> wrote:

> Quoting Ken Kinman <kinman at hotmail.com>:
> > > Too bad limited paraphyly is still seen as a bad thing, and those
> > who bash paraphyly can still get rewarded for doing so.
> * or, we might say, "too bad categories are still seen as a good
> thing." Surely we're at the state now where we can characterize at
> least these higher taxa by their estimated age of divergence, and the
> genomic difference between their surviving descendents.
> fred.
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Dr. David Campbell
Assistant Professor, Geology
Department of Natural Sciences
Box 7270
Gardner-Webb University
Boiling Springs NC 28017

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