Phylogenetic trees

Alan Harvey aharvey at AMNH.ORG
Wed Feb 26 09:59:11 CST 1997

Don Colless wrote:

>     Curiously, this [i.e., "the notion that one must rigorously
>discriminate between apomorphy and plesiomorphy when reconstructing a
>is not directly true in most modern applications of
>phylogenetic reconstruction. Using, e.g., PAUP, one inserts an outgroup to
>provide a root and the apomorphies and plesiomorphies are read off afterwards!
>This is, of course, because the outgroup(s) is/are credited with providing
>that information directly to the programme. Any rigorous discrimination will
>only come about during the not-very-common practice, of evaluating one's
>>tree(s) per the implied plesiomorphies, etc.

What I find curious is the notion that character polarity (and ordering,
for that matter) should be done _prior_ to the phylogenetic analysis. This
is tantamount to saying that we don't know the evolutionary history of the
taxa (else why would we be doing the phylogenetic analysis?), but we _do_
know the evolutionary history of the characters that constitute the taxa
(else how could we provide a priori polarities and ordering?). Phylogenies
generated by PAUP and other such programs are hypotheses of relationship
among character states as much as they are hypotheses of relationship among




Alan W. Harvey (aharvey at
Assistant Curator of Invertebrates
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024
(212) 769-5638; fax (212) 769-5783

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