Sequence data and cladistics

Joe Felsenstein joe at evolution.genetics.washington.edu
Sat May 13 11:48:45 EST 1995

In article <3oovim$b7i at studium.student.umu.se>,
Ludvig Mortberg <Agneta.Guillemot at historia.umu.se> wrote:
>Has anyone ever been able to prove anything in  
>a true cladistic analysis with sequence data  
>from proteins or DNA?
>I want to see with my own eyes are unique sequences  
>in DNA or proteins (not single substitutions of  
>an amino acid or a base pair) shared by the taxa  
>you want group together, while the other candidates  
>for inclusion into this group have the primitive  
>sequence as determined by outgroup comparison.
>If you belive that the genom of an organism ultimatly 
>controls the sequences of all proteins, and therefore 
>the signals that determines what an organism is, and  
>you also have a basic grasp of cladistics (and of course 
>belives in evolution) you must also belive that sequence 
>data from proteins and DNA can be used in a cladistic 
>analysis. "shared derived sequences" must exist. The 
>tricky business is to find them among the billions of  
>base pairs in a genom. 

No, no one has ever "proved anything" with sequence data in
this sense.  While one can find sites where a group
shares the same state and all others have the outgroup state,
these are scattered among many other sites showing homoplasy,
and also showing other states that have arisen elsewhere.
Selecting the sites that have a clear and self-consistent
pattern is the aim of compatibility analysis (called "cliques
analysis" by those who dislike it).  Even this is done numerically
after looking at all states, and like all other methods is
subject to error.

Phylogenetic systematists in the 1980's liked to take the
hypothetico-deductive method as their basic framework (this is
now mostly superseded by the "logical parsimony" framework).
Even they did not search for compatible sites but took individual
substitutions as refutations of each other, not whole sites.

You should therefore look in the compatibility literature.  But
"proof" is too strong a word, whether we are talking about
molecular or morphological characters.

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360

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