bad science or good systematics?

Barry Roth barry_roth at YAHOO.COM
Tue Jul 20 10:11:49 CDT 2004

Just off the top of my head:  cladistic analysis of a paraphyletic group (which seems to be what the study-group is here) will tend to underestimate homoplasy.  I don't know what method this study used for estimating sister-group relationship.  Were macaques designated an outgroup for purposes of tree rooting?

Barry Roth

John Grehan <jgrehan at SCIENCEBUFF.ORG> wrote:
For those on this list who think I am as thick as brick when it comes to
systematics I would be grateful for them to show me where I am missing
the obvious with respect to a paper titled "Sister grouping of
chimpanzees and humans as revealed by genome-wide phylogenetic analysis
of brain gene expression profiles". (PNAS 101 (9), 2004, page

Given the title of the paper I expected to see another genetic argument
supporting the sister group relationship of chimpanzees to humans. That
is what is claimed in the abstract where it is stated that "these
profiles demonstrate that chimpanzees are the sister group of humans".

What I did find was that the authors started with the accepted fact that
chimpanzees are the sister group to humans. They then went on to compare
brain expression profiles of humans, chimpanzees, gorillas, and
macaques. In the next to final sentence they conclude that their results
"depict, during descent of several catarrhine primates, gene expression
profile changes that group the chimpanzee clade closest to the human
rather than to the gorilla clade".

It seems to me that what is wrong with this paper is at least the title
and abstract. If there is any sister group relationship demonstrated
between humans and chimpanzees, it is only in the context of comparing
four selected taxa, with the notable absence of the orangutan. To me the
title and abstract are misleading at the least, and moreover possibly

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