Regulatory cascades (was: Orangutan-human clade)

[John Grehan]

At 04:54 PM 4/9/2003 +0000, Ken Kinman wrote:
>John,
>     "If one chooses to be skeptical... one is free to do so."  ????  Your
>enthusiasm is rather "underwhelming".  ;-)   I think it would be foolish for
>me NOT to be skeptical.

I would not suggest otherwise. One may be skeptical about any characters.

>      I detected a definite pattern in the character suite you presented,
>and if most of those transformations COULD be traced back to a single
>mutation in a regulatory gene, you are going to be just spinning your wheels
>no matter what kind of analysis you use.

As you point out such circumstances may be possible for many characters so
the problem is of a general nature - not just for the orangutan. So one may
raise the question with respect to other human-ape phylogenies as well. It
is possible that even if they were traced back to a single mutation - that
mutation may still represent the real phylogeny.

>    So yes, I am invoking this possibility for other phylogenies where I
>discern a pattern.  It is a very disturbing thought that a single base
>change in a regulatory gene could be equivalent to dozens or even hundreds
>of disparate morphological characters, but we cannot afford to ignore it
>(especially when an interesting pattern jumps out at you).

If someone analyzes the characters and identifies the regulatory genes
involved then the data can be addressed accordingly. At this time what I
have is a list of characters as morphological evidence of a particular
relationship.

>My view is that there isn't nearly enough skepticism in evaluating
>cladistic analyses, thus
>diluting the much greater potential that cladistics has an analytical tool.

The role of regulatory genes being involved with a series of characters
would be something that can affect any kind of systematic analysis.

>Whether the orangutan-human data set suffers from the above-mentioned
>problem remains to be seen, but I hope I am scaring you enough to take it
>very seriously.

I'm not a primate geneticist so I leave the issue in the hands of others
who are in a position to investigate the matter further with respect to any
primate phylogeny. What I will deal with is the presentation of characters
so far proposed. I will take seriously any developments as they arise. Its
certainly an interesting point and perhaps others on the list are in a
better position to comment.

John Grehan

>           ------ Ken
>
>****************************************
>>From: John Grehan <jgrehan at SCIENCEBUFF.ORG>
>>Reply-To: John Grehan <jgrehan at SCIENCEBUFF.ORG>
>>To: TAXACOM at USOBI.ORG
>>Subject: Re: Orangutan-human clade (brainstorming a little)
>>Date: Wed, 9 Apr 2003 08:16:57 -0400
>>
>>At 03:34 AM 4/9/2003 +0000, Ken Kinman wrote:
>>>John,
>>>     Thanks for posting that list of putative synapomorphies of the
>>>putative human-orangutan clade.  It was rather impressive at first, but I
>>>quickly became more skeptical.
>>>     These characters tend to cluster in areas like the shoulder, lower
>>>head (incl. teeth), and urogenital system.
>>
>>If one chooses to be skeptical about characters because they are clustered
>>in a particular body 'area' then one is free to do so.
>>
>>>Unfortunately, a single base mutation in a TBox gene can cause changes in
>>>these same disparate body regions (e.g., Pallister's
>>>Syndrome).  Therefore, the possibility that some mutation or two could
>>>likewise have caused convergence (homoplasy) between humans and orangutans
>>>must be raised.
>>>     I don't have the time to explore this possibility more deeply right
>>>now, but perhaps it is something you might want to consider.  I can only
>>>speculate whether this could be a rather complex "peanut butter sandwich"
>>>phenomenon, but I certainly wouldn't rule it out.
>>
>>So could the other phylogenies.
>>
>>Thanks for the feedback.
>>
>>Dr. John Grehan
>>Director of Science and Collections
>>Buffalo Museum of Science
>>1020 Humboldt Parkway
>>Buffalo, New York 14211-1293
>>Voice 716-896-5200 x372
>>Fax 716-897-6723
>>jgrehan at sciencebuff.org
>
>
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Dr. John Grehan
Director of Science and Collections
Buffalo Museum of Science
1020 Humboldt Parkway
Buffalo, New York 14211-1293
Voice 716-896-5200 x372
Fax 716-897-6723
jgrehan at sciencebuff.org