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

John Grehan jgrehan at sciencebuff.org
Mon Sep 15 08:06:00 CDT 2008


One might criticise cladists for being out of reality, but to base
phylogenies on invented homologies (i.e. creating them out of alignment)
is about as bizaree as it gets.

John Grehan

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Bob Mesibov
> Sent: Sunday, September 14, 2008 7:17 PM
> To: mblanco at flmnh.ufl.edu
> Cc: TAXACOM
> Subject: Re: [Taxacom] Why character-tracking doesn't happen?
> 
> 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
> 
> 
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