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

John Grehan jgrehan at sciencebuff.org
Mon Sep 15 08:13:03 CDT 2008

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Mario Blanco
but if you have too many bases of ambiguous alignment, then the
> number of additional analyses necessary can become too large to be
> practical.

All alignment is ambiguous because it is one of any number of
alternatives depending on what algorithm of reality you believe in.

> Different ways of dealing
> with quantitative-continuous data have been proposed, but as far as I
> know there is no agreed-upon best solution. This is admittedly a big
> limitation of current cladistic methods.

It's a limitation on ANY method (I've often enough seen systematics
problems being characterized as purely cladistic problems when they are
really general systematic problems). One of the major problems I have
seen with hominid phylogeny is using measurements as homologies without
demonstrating that the futures are also structurally homologous. I have
used measurement data in my current analysis of hominid origins and
decided to limit the informative statement to the two most derived
measurements (although the supplemental information will contain
measurements for all taxa so if anyone wanted to carry out a different
kind of analysis they could).

John Grehan

> -------- Original Message --------
> Subject: 	Re: [Taxacom] Why character-tracking doesn't happen?
> Date: 	Mon, 15 Sep 2008 09:17:12 +1000
> From: 	Bob Mesibov <mesibov at southcom.com.au>
> To: 	mblanco at flmnh.ufl.edu
> CC: 	TAXACOM <taxacom at mailman.nhm.ku.edu>
> 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
> The characters analysed are the numbered columns, not the nucleotide
> positions. The 5 character states are A,G,C,T and -. No problem.
> 123456789
> Now watch. Imagine sequence 3 was never found. The alignment is now
> 123456789
> 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
> 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
> 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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