Farewell to: Farewell to Species - reticulation

Hubert Turner turner at RULSFB.LEIDENUNIV.NL
Fri Feb 4 15:31:17 CST 2000


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<blockquote type="cite" cite>On Thu, 3 Feb 2000, A Mitchell wrote:<br>
<br>
> Well how many of us deal with "the ideal case" in our
(real life) every<br>
> day work?  If any of us did, we would soon be out of a job
because nobody<br>
> needs a Ph.D. and years of experience to do something as easy
"the ideal<br>
> case" (every character has a consistency index of 1 and
phylogeny<br>
> reconstruction is child's play).  So in the
"practical, ordinary,<br>
> conventional, usual, everyday case" cladistics will fail to
accurately<br>
> represent hybridization events.<br>
><br>
> SIGH!!<br>
><br>
<br>
Years ago (late '70s-early '80s), when the phenetocladistic wars
were<br>
being hotly contested, I  observed two things.  First,
the<br>
original examples of parsimony analysis (e.g., the first
Farris/Kluge<br>
paper), were done with very clean data sets (i.e., CI of
approximately 1);<br>
at a meeting I presented my attempts with oaks and Walter Fitch and
others<br>
were quite interested to see the numerous "most parsimonious
trees" and<br>
the high levels of homoplasy in my data set.  And, I was able to
find<br>
shorter trees by intuitive branch-swapping and simply shuffling the
deck<br>
(in the days when the data were on key-punched cards).<br>
<br>
Second, I have always suspected that one reason cladistics caught on
so<br>
quickly, compared to classical NT, was the relative simplicity of
doing a<br>
cladistic analysis.  After all, it is quite easy to conduct a
cladistic<br>
analysis by hand and the mathematical approach (as presented in
Farris'<br>
early papers) was also quite simple. NT, on the other hand, based
on<br>
multivariate statistics, was much more esoteric.  While a
cluster analysis<br>
can also be done simply by hand (maybe with a calculator),
ordinations are<br>
far more demanding.<br>
<br>
Admittedly, from the view of getting a solution, parsimony analysis
is a<br>
far more difficult problem than conducting a principal components<br>
analysis.  But in those days, many were not aware of the fact
that a<br>
single data set could produce so many equally parsimonious trees.<br>
<br>
Besides, cladistics was designed specifically to construct
phylogenetic<br>
hypotheses while phenetics is based on the criterion of overall<br>
similarity, which may yield a very good approximation of
phylogenetic<br>
relationships, but is not intended to do so.  I believe many of
the<br>
questons related to the informaton-content and utility of the
resultant<br>
classifications are as yet unresolved.<br>
<br>
So, I use phenetics quite a bit because of the ubiquity of hybrids in
my<br>
favorite organisms (oaks).  But, I do not claim that my results
reflect<br>
phylogenetic relationships.  At this point, my view is that a
phenetic<br>
classification of oaks is much more desirable than a cladistic<br>
classification, especially with respect to utility.  That
doesn't mean<br>
that cladistics should not be applied, just that the cladistic
results are<br>
a hypothesis that is likely to change, perhaps significantly, as
more<br>
data are gathered and we develop a better understanding of exactly
what<br>
constitutes a species (however defined) in oaks.<br>
<br>
<br>
Richard J. Jensen      |   E-MAIL:
rjensen at saintmarys.edu<br>
Dept. of Biology       |  
TELEPHONE: 219-284-4674<br>
Saint Mary's College   |   FAX: 219-284-4716<br>
Notre Dame, IN  46556  |</blockquote>
<div><br></div>
<div>A very nice rebuttal of Mitchell's coarse reaction to my
posting. I had already given up and wasn't going to respond to it. I
suppose I am different from many other participants in these
discussions in that my first interest is in the methodology of
phylogenetic analysis rather than in practical systematic issues.
Thus I firmly believe that a sound theoretical and methodological
basis is essential for practical improvements, and as such I do want
to consider ideal cases. But I am acutely aware that ideal cases are
very rare out there. Nevertheless, I consider them essential in
understanding what the methods really do, and which assumptions they
do and do not make.</div>
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*******************************************************
Dr. Hubert Turner
EEW, Sect. Theoretical Biology & Phylogenetics
PO Box 9516, 2300 RA  Leiden, The Netherlands
Visiting address: Van der Klaauw Laboratory, Kaiserstraat 63, Leiden
Phone: +31-71-5274904    Fax: +31-71-5274900
E-mail: turner at rulsfb.leidenuniv.nl
WWW: http://wwwbio.leidenuniv.nl/~turner/index.html

FROM 18 JANUARY TILL MID-APRIL I WILL BE VISITING THE NEW YORK
BOTANICAL GARDEN AS VISITING SCHOLAR, DOING MOLECULAR
PHYLOGENETIC RESEARCH ON ANACARDIACEAE. THIS E-MAIL ADDRESS
WILL REMAIN FUNCTIONAL DURING THAT PERIOD.
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