cladistics

Mark Siddall mes at zoo.toronto.edu
Thu Apr 28 01:29:05 EST 1994


In article <1994Apr26.185539.900 at honte.uleth.ca> std_dickout at hg.uleth.ca writes:
>I am interested in information and/or opinions concerning the use of Maximum
>Parsimony analyses and Distance analyses with respect to the treatment of
>molecular data in the field of cladistics.  Explanations dealing with
>how these two methods differ from one another would also be appreciated.
>Please mail me directly.  
>
>Thank you very much.
>J.L. Burke


Okay, hang on this is gonna take a bit of work.
Maximum Parimony
The reason it's called MAXIMUM parsimony is because reversals are allowed 
with the same rate as unitary changes (apomorphies) as are convergent
changes (> unitary (i.e., occurring more than once)).  That is to say all changes regardles of type are of the same weight.
Parsimony applies a DIRECTION to the the difference between the states observed 
between taxa.  That is, with 3 taxa one with state "a" the other two with 
state "b".  Parsimony requires that one can specify whether "a" or "b"
came first.  If "a" came first then there's a single step uniting the two
taxa with "b" as having descended from a common ancestor that had "b".
If "b" came first, then there's nothing uniting the two with "b" and the one 
with "a" stands alone.  So, only DERIVED changes are considered important to 
relationship.

So... one has a choice of considering only a particular kind of differnece
(i.e., directional; i.e., derived) as informative, or any kind of differnece
(uninformtive of ancestry or informative of ancestry) as informative.  Distance analyses are of the type that calculate absolute difference (irrespective
of KIND of difference).  Thus, by analogy, one might group crocodilians 
with saurians (lizards etc) on the basis of OVERALL SIMILARITY (ABSOLUTE
DIFFERENCE or DISTANCE) in spite of the fact that most of the similarities with
sauriance are ancestral.  Whereas, the DERIVED characteristics suggest that 
they share a most recent common origin with birds.

In short distance measures of any sort are phenetic.
Sneath and Sokal in their original "Numerical Taxonomy: stated quite clearly
in Chapter 9 that phenetic techniques are NOT phylogenetic and should not
be contrued as such.
Thus, if you want to classify organisms, phenetic or phylogenetic methods could be
equally justified.  BUT if you're interested in the pattern of evolutionary
descent of the organisms, the most stalwart adherents have already told you tha

that measures of similarity won't do it!

Thus from an evolutionary point of view, phenetics, distance etc add nothing.
Moreover, from a genetic evolutionary point of view, the most often used method
Fitch-Margoliash Distance, has been criticised by many as being invalid
including one of the authors of the method!!

Good luck
  Mark
-- 
Mark Siddall             The greatest obstacle to discovery is not ignorance,
Department of Zoology       - it is the _illusion_ of knowledge.
University of Toronto                             D. J. Boorstein
mes at zoo.toronto.edu



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