[Taxacom] shared derived molecular similarities

[John Grehan]

My understanding is that one is not dealing with character states, but
four different characters that replace each other so one really does not
know what came before. Even with coding genes the genes are not
necessarily the same length so one has to invent the homologies even
before theorizing the replacement. And in practice the outgroup is often
so limited in taxonomic representation as to almost be meaningless. That
is another reason I have more confidence in the morphogenetic result for
the orangutan where the outgroup test at least encompasses gibbons and
OW monkeys. 

Perhaps there is a solution to the above for molecular sequences, but I
have not yet seen it (and what of non-coding sequences?). Some molecular
theorists admit that sequencing is, after all, unreliable and now
salvation lies with LINE's and SINE's - once again repeating the history
of molecular systematics which is to jump from one to another and
another technique as problems emerge with each, but the faith holds
true.

John Grehan
 

-----Original Message-----
From: Sergio Vargas [mailto:sevragorgia at gmail.com] 
Sent: Sunday, April 03, 2011 2:30 PM
To: John Grehan; taxacom at mailman.nhm.ku.edu
Subject: shared derived molecular similarities



Hi,

>I have a personal preference for the morphology being more likely 
>correct simply because the latter can be evaluated in terms of shared 
>derived similarities
>  for each character individually...

I have a question regarding the statement above. I'm kind of lost
here... Why exactly is that you cannot evaluate individual molecular
characters and establish shared derived (molecular) similarities? say
you have protein coding genes and no gaps and you can compare the
sequence/structure of the proteins, etc. and use an outgroup criterion
to find these shared derived similarities, I cannot see why this is not
possible...

tnx in advance

sergio