[Taxacom] was contamination

[Doug Yanega]

Jason Mate wrote:

>The location of a nucleotide is the character and the state is the 
>particular nucleotide you find there. Similarly with proteins and 
>practically any character you can think of (segment 3 is defined in 
>relation to segments 2 and 4, unless you have developemental 
>information which is quite rare and even then the homology is 
>relational).

Ummm...not quite. The character state of a nucleotide is free to 
change back and forth between states repeatedly (even in a conserved 
coding region this is true for roughly 1/3rd of all the nucleotides), 
in precisely such a way as to utterly confound attempts to establish 
homology. This can be true even within a species - and we all know 
how useless polymorphic or homoplastic characters tend to be in a 
morphological matrix. Most morphologists intentionally exclude 
characters that are too variable, and/or suspected to have high 
likelihood of homoplasy, whereas nucleotide states are accepted 
despite such shortcomings. In fact, one cannot use nucleotide states 
in one's analyses unless one includes an additional level of modeling 
designed to account for the differential probabilities of state 
changes between different pairs of bases (on top of which there are 
other confounding meta-properties such as "A-T rich" genomes). I can 
think of lots of characters that do NOT require secondary models of 
transformation probabilities in order to be informative, and - as 
such - nucleotides are demonstrably a very different type of 
character.
Insertions, deletions, and segment polarity reversals can be quite 
different, and far more akin to "traditional" characters, especially 
as the chunks involved get larger. After all, what are the odds that 
two taxa will uniquely share a 75-base-pair long deletion/insertion 
at the exact same spot in their genomes and it NOT be homologous? 
Myself, I tend to have greater faith in trees built by human beings 
who subjectively choose to ignore certain characters, than I do in 
algorithms that are objective and try to work with every single 
possible character and hope to find the signal amidst the noise - 
though, naturally, there are some human beings that are good at 
taxonomy, and some that are terrible. Traditional character anaylses 
have their pros and cons...

Peace,
-- 

Doug Yanega        Dept. of Entomology         Entomology Research Museum
Univ. of California, Riverside, CA 92521-0314        skype: dyanega
phone: (951) 827-4315 (standard disclaimer: opinions are mine, not UCR's)
              http://cache.ucr.edu/~heraty/yanega.html
   "There are some enterprises in which a careful disorderliness
         is the true method" - Herman Melville, Moby Dick, Chap. 82