New Lucy

B.J.Tindall bti at DSMZ.DE
Sat Mar 27 10:32:39 CST 2004


There are a lot of "hidden" aspects in Ken's reply. "Sequence similarity" -
sounds a bit like a "phenetic" approach. If I understand correctly, all
forms of gene or protein sequence comparisons correctly all have an in
built assumption about "parsimony" and they probably also assume you are
comparing orthologs, and that homoplassy is not present. Perhaps even the
more ultrametric the data set the better the true reflection of evolution?

If "some genes are a lot more informative than others" then we are also
making some initial choice about which genes are "more informative" - i.e.
you already have a hypothesis which you probably want to confirm, rather
than test in a neutral fashion.

Perhaps one should also remember that gene sequences also code for things
like either enzymes or structural proteins, both of which have "structure
and function" - that is structure and function (i.e. phenotype) probably
plays a role in determining how genes change, an aspect which is also
generally forgotten - in other words both proteins and RNAs have strongly
expressed "mophologies" - perhaps a rather strange word to use, but these
morphologies are expressed at the molecular level, a level which we are
just beginning to appreciate again.

The more data we have, whether classical moprhological or gene sequence the
more interesting the story becomes. Perhaps in 10 years we will have solved
all the problems, perhaps we will have simply discovered that that are even
more questions to be answered.
Brian


At 22:31 26.3.2004 -0600, Ken Kinman wrote:
>John Grehan wrote:
>The preponderance of the morphological evidence is that the
orangutan-human similarities are synapomorphies as they are uniquely shared
features and there are far more of these for humans and orangutans than any
other human-ape combination.
>If one views gene sequence similarity as the basis of phylogeny then of
course the morphology does not count.  The morphological evidence conflicts
with most (but not all) molecular sequence studies....
>********************************************************
>John,
>     Molecular evidence is not confined to sequence similarity---there is
also the "morphology of genes" (gene order) which can be extremely
important, especially when that order is very improbable and thus
relatively resistance to arguments about homoplasy.  Also, my experience is
that some genes are a lot more informative than others----an angiosperm
phylogeny based on maturase genes seems a whole lot more reliable than
certain other genes (which may have resulted in some of the overlumping of
angiosperm ordinal taxa by APG).  Of course, whole genomes will be even
better.
>      If humans and orangutans form a true clade, there should be at least
some evidence on the molecular side.  If there isn't any, then I have no
choice but to remain skeptical.  I also do not like to play number games
with synapomorphies.  Many of your characters could be combined with others
(being clearly non-independent of one another).  I had many arguments (a
few years back) with a dinosaur cladist on the Dinosaur Mailing List where
he would claim to have more synapomorphies than I did, so his hypothesis
was therefore "better".  What a bunch of poppycock.  I see that recently he
was having trouble keeping one of his favorite "clades" from splitting up.
My arguments that it was paraphyletic had been rejected just because I had
fewer synapomorphies than he did.  I was delighted to recently read that
(partially in jest) he even expressed his frustration by exclaiming "damn
the ghost of Ken Kinman".   I also expect to be "haunting" the
overconfidence of other strict cla!
> dists in years to come, and some eclecticists as well (both sides have
their problems).
>     I would admittedly be delighted if an orangutan-human clade existed,
but inflating the number of synapomorphies and casually dismissing
molecular evidence is not going to convince me that your hypothesis is
correct.  Which genus of the traditional (paraphyletic) Pongidae (sensu
lato) is sister group to Family Hominidae is still an open question in my
mind.  Those who prefer a Pan-hominid clade need morphological evidence to
substantiate their claim, and those who prefer a Pongo-hominid clade need
molecular evidence to substantiate theirs.  Until then, I am sitting on the
fence and even considering the alternative phylogeny I mentionned earlier
(hominids as sister group to a Pan-Gorilla clade).  I certainly never said
"morphology does not count", but one can be mislead by morphological
evidence just as easily as one can be mislead by molecular evidence.
>             -------- Ken Kinman
>


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