Measures of phylogenetic signal (fwd)

[James Lyons-Weiler]

Date: Sat, 30 Mar 1996 07:59:51 -0800 (PST)
From: James Lyons-Weiler <weiler at ers.unr.edu>
To: "Classification, clustering,              and phylogeny estimation"
     <CLASS-L at ccvm.sunysb.edu>
Subject: Measures of phylogenetic signal



Systematists can now seriously ask whether their data are tree-like, or
are nested, or if they contain phylogenetic signal.

I am working on a comparison study of three measures of phylogenetic
signal (g1, PTP, and RASA).  If you have published or unpublished discrete
character state data that you have analyzed using the permutation tail
probability test (PTP; Archie, 1990; Faith, 1991; Faith and Cranston, 1991;
see also Trueman, 1995) or the tree length distribution central moment g1
(a measure of skewness; Hillis, 1991; Hillis and Huelsenbeck, 1991), and
would like to have your data included in this comparative study, just
send (to the addresses below), via email or post

1) any references to publications resulting from the data,
2) the data matrix (in any electronic format; e.g., BinHex, or text),
3) a short description of the type of data (e.g., morphological DNA, RNA,
protein), and the organisms studied,
4) the values of g1 or PTP that you have determined.

If you have data that you have not analyzed for signal content, the
references are given below.

(Please do not respond with 1-4 to the list, or everyone will receive your
information, and most will then have to take time to delete messages.)

Here are the references to the three measures, for general edification:

        PTP:
Archie, J.W. 1989. A randomization test for phylogenetic information in
systematic data. Systematic Zoology 38:219-252.

Faith, 1989. Homoplasy as pattern: multivariate analysis of morphological
convergence in Anseriformes.  Cladistics 5:235-258.

Faith, D.P. and P.S. Cranston. 1991. Could a cladogram this short have
arisen by chance alone? On permutation tests for cladistic structure.
Cladistics 7:1-28.

        g1:
Hillis, D.M. Discriminating between phylogenetic signal and random noise
in DNA sequences. Pp. 278-294 in M.M. Miyamoto and J. Cracraft, eds.
Phylogenetic analysis of DNA sequences. Oxford University Press, New York.

Huelsenbeck, J.P. 1991. Tree length distribution skewness: an indicator of
phylogenetic information.  J. Heredity 88:189-195.

Trueman, J.W.H. 1995. Sponges, plants and T-PTP. Systematic Biology.
44:429-434.


        RASA:
Lyons-Weiler, J., R.J. Tausch, and G.A. Hoelzer. 1996. Relative apparent
synapomorphy analysis (RASA) I: the statistical measurement of
phylogenetic signal. Molecular Biology and Evolution, in press.

PTP and g1 can be implemented with some versions of PAUP.  They are
also described in

Hillis, D.M. C. Moritz and B.K. Mable 1996. Molecular
Systematics, 2nd ed.Sinauer Associates, Sunderland, Mass.



_________________________________________________________________
JAMES LYONS-WEILER                PH:    (702) 359-6391
ECOLOGY, EVOLUTION AND            FAX:   (702) 784-4583
CONSERVATION BIOLOGY/186          eMAIL: weiler at grass.ers.unr.edu
1000 VALLEY ROAD
THE UNIVERSITY OF NEVADA, RENO
RENO, NEVADA 89512-0013
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