[Taxacom] Why character-tracking doesn't happen?

[Bob Mesibov]

Gotta run, but:

Mario Blanco wrote:

"This is analogous to the situation in which you score morphological
data 
(e.g., color of petals), and then you hava a species with no petals.  
For this species, the character state here becomes "missing", and you 
effectively create a gap in the matrix (and indels are simply gaps in
an 
aligned matrix)."

Sorry I wasn't clear enough. Look at the three aligned sequences below.
The characters analysed are the numbered columns, not the nucleotide
positions. The 5 character states are A,G,C,T and -. No problem.

123456789
AATGATATA
AGT--GCTA
AGTGACGTA

Now watch. Imagine sequence 3 was never found. The alignment is now

123456789
AATGATATA
AGTGCTAxx

See what happened? The 4 nucleotides at 'positions' 6-9 in the second
sequence are now at 'positions' 4-7. They've shifted from character to
character, and their positions in the native sequence are definitely not
themselves characters.

I admit this is a contrived example, but I'm pretty sure this often
happens with indels in multiple sequence alignments. Column characters
and their states change depending on which sequences are analysed.

Some molecular phylogeny gurus suggest that uncertain sections of
alignments shouldn't be used in an analysis, just as some morphological
phylogeny gurus suggest that uncertain homologies should be omitted.
Don't know where that fits with the 'total evidence' philosophy...
-- 
Dr Robert Mesibov
Honorary Research Associate
Queen Victoria Museum and Art Gallery and
School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
(03) 64371195; 61 3 64371195
http://www.qvmag.tas.gov.au/mesibov.html