chloroplast and other genes (was Lucy in Newsweek)

Fri Apr 2 09:21:54 CST 2004

A while back (Syst. Biol. 50: 425-437, 2001) I re-evaluated the data from
Satta, Y., J. Klein & N. Takahata. 2000. DNA archives and our nearest
relative: the trichotomy problem revisited. Mol. Phylog. Evol. 14: 259--275.
They reviewed molecular data on Homo, Pan and Gorilla (ignoring Orangutan).

They gave cladograms for 45 loci:  23 supported ((Homo Pan) Gorilla), 8
supported ((Homo Gorilla) Pan), 8 supported ((Gorilla Pan) Homo), and 6
produced trichotomies. I used Doyle's (Syst. Bot. 17: 144-163, 1992)
suggestion that a gene can be used as a character. Ignoring the equivocal
results, my chi-squared analysis showed that 23 out of 23+8+8 trials would
occur by chance alone (assuming a trichotomy and parallelism) only 3 out of
1000 times, giving ((Homo Gorilla) Pan) a confidence level of 0.997. Satta
did not go far but suggested that the contrary results were probably largely
the result of different gene histories.

Well, if some combination of parallelism and retained ancestral polymorphism
occurs in Homo, Pan and Gorilla, and serves to make phylogenetic analysis
difficult, why can't such be the case with the four taxa including
Orangutan? Because many of the 45 loci analyzed were exons, they are able to
be selected for and against, and are doubtless effective in evolution.

If that's the case, why not accept (((Homo Pan))Gorilla)Orangutan)Gibbon) as
is probably indicated by theoretically neutral and nonneutral genes that
agree with species history, and allow Homo to retain doubtless
evolutionarily important polymorphically ancestral morphological traits of
the Orangutan through differential lineage sorting?

If so, this may indicate that morphological traits are poor indicators of
evolutionary patterns (in this group), and may also indicate that
evolutionarily neutral genes are poor indicators of evolutionary process (as
opposed to pattern). Thus, the data indicate that ancestor of Homo was a
population of chimp-like organisms genetically polymorphic with orangutan
morphological traits.

This idea is uncomfortable and even ugly, but answers Smisson's query:
"From even the very
little mitochondrial DNA sequence data I've actually looked at, it is
numbingly difficult to explain the similarities between humans and
chimpanzees (as compared other apes) by simple parallelism or
convergence. What other explanations are available? Lineage sorting?
Human-chimp introgression? Genetic engineering by extraterrestrial
aliens? Divine humour? Do they also explain similarities in nuclear
genomes?  On the other hand, what governs the evolution of the sorts of
morphological characters linking humans to Orang-utans - are some of
them based on quantitative variation under polygenic control and thus
likely to shift quickly back and forth under moderate selection?"

______________________
Richard H. Zander
Bryology Group
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299
richard.zander at mobot.org <mailto:richard.zander at mobot.org>
Voice: 314-577-5180
Fax: 314-577-9595
Websites
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-----Original Message-----
From: Ken Kinman [mailto:kinman2 at YAHOO.COM]
Sent: Friday, April 02, 2004 8:51 AM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: [TAXACOM] chloroplast and other genes (was Lucy in
Newsweek)

Brian,
    I totally agree, and my comments on characterizing "molecular data as
phenetic and unreliable" were certainly not directed at you.  They were
directed mainly at John Grehan who continues to downplay the importance of
molecular data.  And John may think my use of words like "balance" are
somewhat political in nature, but to me it is just common sense.  I look at
it this way------just as it is prudent to diversify a stock portfolio, it is
likewise prudent for biologists to diversify their data portfolios.  The
portfolio for an orangutan-man clade is not balanced if it has no molecular
component.  Likewise the Pan-Homo portfolio needs more morphology added to
it.  John embraces the latter, but seems reluctant to admit to the former as
well.

     To answer Don's question, I also rely heavily on "gut feeling", even
when it runs counter to what appears to be lots of evidence.  A prime
example is my "gut feeling" that bivalves evolved first, and that they
evolved into radulate molluscs (NOT the other way around).  When I offered
evidence in favor of my viewpoint, many malacologists seemed to think I was
just engaging in unscientific storytelling.  I guess only time will tell if
my gut feelings about that one are right or not.  I always liked Darwin's
quote about speculation being good for science (and that includes the
orangutan-man hypothesis if more evidence can be found for it).
             ------ Cheers,
                         Ken Kinman