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Re: where have all the etc.
I wrote...
Referees have brought this up, suggesting I use 20,000 taxa
and as many characters,
For 20,000 characters you'd obviously need a lot more than 20,000
characters!!!
Er... for 20,000 _taxa_ you'd need lots more characters... :-]
While I am at it:
----- Original Message -----
From: "david peters" <davidrpeters@earthlink.net>
Sent: Tuesday, July 05, 2005 7:16 PM
> No, as David mentioned, adding taxa while holding character
> number constant will only *decrease* resolution.
>
> Nick Pharris
> Department of Linguistics
> University of Michigan
NOW we're getting to the meat of the matter. Where is the reference that
supports this? [...] What are the "ideal" ratios? And how were these
numbers validated?
The numbers were found by simulation. The principle, which was corroborated
by the numbers, is mere common sense, as I tried to explain via the
signal/noise ratio.
One more thing. If you had no convergence at all in your data set, the
numbers of characters and taxa could in principle be identical and still
give you a fully resolved tree (if you happened to make a fortunate choice
of characters -- one autapomorphy for every node). So, getting a fully
resolved tree with a characters/taxon ratio of 1.2 is not a priori
impossible. But you have told us how the homoplasy index in the tree you get
is way higher than usual, instead of way lower. The more noise you have, the
more characters you need to cancel out the noise and increase the signal.