Humans and apes

[A.P. Jason de Koning]

B.J. Tindall wrote:
> I am not in a position to judge the accuracy of the data, but it indicates
> that one may not be able to apply a "constant" substitution rate.

Indeed assumption of a constant molecular clock is highly unrealistic, and
development of statistical methods, which 'relax' that constraint are being
actively developed.  There are both parametric and non-parametric approaches
for doing this, and they both give consistent dates for hominoid branchings
(when using reasonable calibration points).  For those interested, see:

Huelsenbeck, Larget, and Swofford, 2000. A compound poisson process for
relaxing the molecular clock. Genetics. 2000 Apr;154(4):1879-92. (This one
is a highly promising parametric approach using reversible-jump Markov Chain
Monte Carlo.)

> has also pointed out that molecular substitution rates appear to be
> calibrated against the fossil record.

This is also correct.  Since rates of molecular evolution are measured as
the product of rate and time [i.e., observed substitutions = f(rate of
evolution, time)], once rate differences are modelled, an external source of
time information is needed to convert between units.  This is not a problem
per se, since you can use any (or multiple) calibration points.

> John Grehan wrote:
> > This is incorrect. The human-orangutan hypothesis is still being
promoted
> >within primate systematics.

This may be true in small circles, but to suggest that this is an active
question of debate would make most primate systematicists incredulous.  The
weight of evidence from all types of information is quite consistent on this
(see below).

> > Jason de Koning wrote:
> > There is little doubt left by a wide array of consistent molecular data
> >that bonobo and chimpanzee are sister species, separated by only a few
> >million years, and that the chimpanzee lineage (including both Pan spp.)
is
> >the sister group to humans.

> > Grehan wrote:
> > While may be little doubt left if one accepts the molecular data as
having
> >the last word, the orangutan hypothesis presents an alternative that
might
> >suggest the molecular data is, in this case, incorrect about the nearest
> >living relative to humans.

You don't have to accept that the molecular data (i.e., nuclear and
mitochondrial DNA, protein sequences; DNA-DNA hybridization, etc.) has the
"last word" on this issue.  Have a look at the cytological literature for
example [just look at HCGO karyotypes!  For an old data-set, go to
http://www.indiana.edu/~ensiweb/lessons/chr.clad.html (Yunis, 1982).  More
recent work bears out the general conclusion (e.g., Roscoe Stanyon's work).]

In addition, there is plenty of morphological data that gives strong support
to a basal position for Orangutan.  For instance, cladistic analysis of 264
cranial/post-cranial morphological characters in Shoshani et al., showed
strong support for (O(G(HC)).  (Mol Phyl Evol 1996, 5:102-154)  This is not
a molecules versus morphology question.

> > It remains a problem in the sense that it is incongruent with the set of
> >morphological synapomorphies that have been proposed to support a
> >human-orangutan clade.

In good fun, I can find you a few morphological characters that group humans
and peanut butter sandwiches, but that doesn't mean much when there is so
much other evidence suggesting that sandwiches are lunch, not our closest
living relative...

Seriously though, there are lots of reasons why molecular markers and
morphological characters can give misleading and/or inconsistent phylogenies
(selection and convergence being chief among them).  Should not the best
approach to be to look at as many *independently evolving* characters as
possible?  And while we're at it, should we not prefer the neutrally
evolving ones, which are less susceptible to 'corruption' by selection?

Cheers,
- Jason

__________________________________________________________________________
 A.P. Jason de Koning, Doctoral student       Email: apjdk at albany.edu
   Department of Biological Sciences            Lab: (518) 442-4347
   University at Albany, SUNY                   FAX: (518) 442-4767
   1400 Washington Ave., Albany NY 12222, USA Mobil: (518) 210-4504
__________________________________________________________________________