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Cladistics and Phylogenetic trees from sequences

fatherdes at hotmail.com fatherdes at hotmail.com
Thu Feb 11 11:25:06 EST 1999

I am missing some posts on the recent cladist threads (my newsreader seems to
be selective) but I believe Joe Felsenstein corrected some of my mistakes in a
post I made about pattern or transformed cladists.  Joe knows this stuff very
well and saw much of this happening so I will accept all of his points and
apologise to the newsgroup if I was a bit arrogant and pushy.

Doug Eernisse posted a nice description of why cladistics is important (to
him and to us) and, again, I will go along with everything he says.  Now,
before I get completely out of control and ask to hug everyone in sight, I
would still like to point out a remaining controversy in the area that stems
from the original cladist/pheneticist debate but which still affects people
today who do not know what any of these terms are but which is of great
practical importance. That is which methods should we use when we want to
estimate/derive/guess at/work out phylogenies from molecular sequence data.

Doug can easily convince me that sound use of a cladistic approach is
important in systematics but the overall debate as to which methods of
phylogenetic inference might be best or most accurate or have most desirable
properties has been enormously influenced by these debates.  Some of these
influences have ben beneficial but some have created bizarre and disasterous
schisms, rows and fights.

I detect a cooling off these days and a coming together as ML methods become
more practical and influential.  Maybe everyone sees these as a way of going
forward without giving in to the other side.  Personally, I imagine Ml methods
will become more and more widely used and with good reason but parsimony and
distance methods still have their uses.

Des Higgins
Department of Biochemistry
University College
Cork Ireland


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