Alleles and phylogenetic results

[John Grehan]

Ken,

I'll continue to be critical when it comes to assumptions that DNA
similarities necessarily over-ride morphology. Although it's interesting
to see that you now at least recognize that some genetic similarities
might be better than others. If sequences do not match morphology there
is a problem and simply appealing to homoplasy does not work (and my
understanding of homoplasy is that it only exists once one has decided
on a particular phylogeny, not before). And as far as the facts are
apparent to me, hominoids (at least the large bodied) don't show much of
that problem unless one ignores all the orangutan-clade related
characters in humans.

It's fine if one can go and find morphological support for a molecular
tree, but in the case of the chimpanzee the contrary has happened, not
only for the living but also the fossil (as australopiths not only look
more like orangutans, but also share various unique features with the
orangutan clade).

Whether the morphological features might be developmentally connected or
not does not matter. The empirical fact remains that there are more
uniquely shared features found between humans and orangutans than humans
and chimpanzees (actually for the latter the number may even be
non-existent).

I would add that in my view systematic analysis of DNA sequence
similarities is not 'genetics', but another form of morphology (what I
would call DNA morphology). 

Thanks for spelling out 'for the record'. I grew up with English
language in its whole, not in its alphabet. 

John Grehan

> -----Original Message-----
> From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
> Behalf Of Ken Kinman
> Sent: Wednesday, January 25, 2006 10:29 PM
> To: TAXACOM at LISTSERV.NHM.KU.EDU
> Subject: Re: [TAXACOM] Alleles and phylogenetic results
> 
> Hi Richard,
>       Thanks for the citation to Stace, 2005.  Just hope our library's
> copy isn't at the bindery (would be just my luck).  I did read the
> abstract online, and it sounds very interesting, including an apparent
> discussion on the "desirability of insisting on a monophyletic
> classification".  That sounds particularly interesting.  As I have
> remarked before, maybe I should have been a botanist.   :-)
> 
>       And to John Grehan:  FTR (= for the record), I think you are
overly
> critical of molecular phylogenetics.  Just yesterday, I was reading
> information about ASPM gene msequences.  That gene has a large,
53-base
> pair, insertion which unites the African hominoids (to the exlusion of
> Pongo).  This kind of major "indel" is far more convincing than just
> sequence similarity overall, so I encourage you to look for large
indels
> which Pongo and Homo have in common (but not found in Pan and
Gorilla).
> Try following the lead of Fain and Houde, 2004, who discovered a major
> dichotomy (Metaves and Coronaves) within the large radiation of
neoavian
> bird Orders.  Not only does overall genetic similarity support it, but
> indels give even stronger (far more convincing) support.  Then they
went
> on to find new morphological evidence to back it up, just as
morphological
> evidence is being found to back up the relationship of flamingos and
> grebes (whose morphological divergence has masked their re
>  lationship).  The morphology of birds is so full of homoplasy, that
it
> has led us astray until now.  The hominoids appear to have very
similar
> problems, so until you find some genetic support (and even one
exclusive
> indel would be great) for your Pongo-Homo clade, I still think your
list
> of "synapomorphies" are probably developmentally connected (non-
> independent) and therefore leading you and Schwartz astray.
>     -----Ken Kinman