Reality

[Richard Zander]

Well, let's see. We have equal evidence supporting two different hypotheses: 3 gene trees supporting, say, ((AB)C) and 3 gene trees supporting ((AC)B). I figure you have a 50/50 chance of guessing the correct tree.

If you have 0 contradictory gene trees, you need only 3 agreeing gene trees to match or exceed 95% confidence level that you have demonstrated a species tree. If you have 1 contradictory tree you need at least 5 agreeing trees. With 2 contradictory trees, you need 7 agreeing trees.

More on this at:
http://www.buffalomuseumofscience.org/botany/num/num_trees.htm

Yes, it is not easy to find decent molecular evidence of a probabilistic phylogenetic relationship through falsifying (at some confidence level) the null that the amount of support for each of the three arrangements of terminating branches on an internal branch is randomly generated and equal. It is possible, though.

---------
From:
Richard H. Zander
Emeritus Curator of Botany
Clinton Herbarium
FNA Editorial Center at Buffalo

The Buffalo Museum of Science
1020 Humboldt Pkwy
Buffalo, NY 14211 USA

email: rhzander at sciencebuff.org NEW EMAIL ADDRESS! (Note "h" infix)
voice: 716-896-5200 x 351   FAX: 716-897-6723
home: http://www.buffalomuseumofscience.org/div_botany.html
BFNA home: http://www.buffalomuseuofscience/BFNA/BFNAmenu.htm
FNA home: http://hua.huh.harvard.edu/FNA/


----- Original Message -----
From: "B.J.Tindall" <bti at DSMZ.DE>
To: <TAXACOM at USOBI.ORG>
Sent: Wednesday, January 16, 2002 9:54 AM
Subject: Re: Paraphytlly is real.


> Okay, but this assumes that the data set conforms to the assumption laid
> down in bootstrapping before I do the test. One of the problems is
> independence in the data set - do adjacent bases in a gene sequence evolve
> independant of each other?
> Perhaps you could answer a simple question - you have three gene trees
> which agree and then you have a set of 3 other genes which agree with
> eachother but disagree with the first set - so which one is correct?
> Given the rate at which microbial genomes are being sequenced the first
> indications suggest it may not be that easy to find 3 genes which agree in
> detail. Perhaps we have to live with that fact?
> Brian