Outgroup selection

James Francis Lyons-Weiler weiler at ERS.UNR.EDU
Mon Jun 30 15:58:35 CDT 1997


On Mon, 30 Jun 1997, aj49 wrote:

> Forgive my ignorance, but I am writing to ask the members of taxacom for
> help finding published papers that deal with the selection of outgroups and
> study taxa in cladistic analysis of morphological data.  Specifically, I am
> interested in whether anybody has examined the effect of outgroup choice on
> results, and the effect on tree topology of excluding taxa or sets thereof
> from analyses.
>
> I would very much appreciate any references anybody may be able to point me
> to.  Thanks!

I've spent the better part of two years on this very problem, so I have a
rather comprehensive command of this literature.  The best empirical
example of sensitivity to ingroup topology to changing which outgroup one
uses in Milinkovitch etl., 1996s reappraisal of a whale phylogeny.
Your question really is two; what is the effect of changing outgroup taxa,
and what are the effects of deleting/including various ingroup taxa?  It
is becoming better appreciated that taxon sampling has a huge effect on
the probability of getting the right tree, independent of the tree
building algorithm one favors.

I predict that we'll be seeing a flury of papers in the very near future
on taxon sampling and outgroup choice (which are intimately related
questions), as well as some new methods to test for the apparent
positive or ill effects of using particular outgroup taxa, and for
detecting problematic taxa directly...

Anyway, here's some refs to get you going...

OUTGROUP ANALYSIS

Clark, C. and D. J. Curran. 1986. Outgroup analysis, homoplasy and global
parsimony: a response to Maddison, Donoghue, and Maddison. Systematic
Zoology 35:422-426.

De Queiroz, K. 1985. The ontogenetic method for determining character
polarity and its relevance to phylogenetic reconstruction.  Systematic
Zoology 34:280-299.

Donoghue, M.J. and P.D. Cantino.  1984. The logic and limitations of the
outgroup substitution approach to cladistic analysis.  Systematic Botany
9:192-202.

Farris, J.S. 1982. Outgroups and parsimony. Systematic Zoology 31:328-334.

Hanken, J. 1993. Model systems versus outgroups: alternative approaches to
the study of head development and evolution.  American Zoologist
33:448-456.

Kellogg, E.A. 1992. Tools for studying the chloroplast genome in the
Triticeae: an ECORI map, a diagnostic deletion, and support for Bromus as
an outgroup.  American Journal of Botany 79:186-

Lyons-Weiler, J.F. 1997.  RASA 2.1  Software and Manual for the
MacintoshTM.  http://loco.biology.unr.edu/archives/rasa/rasa.html.

Maddison, W.P., M.J. Donoghue and D.R. Maddison. 1984. Outgroup analysis
and parsimony. Systematic Zoology 33:83-103.

Milinkovitch, M.C;  LeDuc, R. G.; Adachi, J.; Farnir, F.; Georges, M.  and
Hasegawa, M. 1996.  Effects of character weighting and species sampling on
phylogeny reconstruction: A case study based on DNA sequence data in
cetaceans. Genetics. 144. Pp 1817-????.

Mooi, R. 1989. The outgroup criterion revisited via naked zones and
alleles. Systematic Zoology 38:283-290.

Nixon, K.C. and J.M. Carpenter. 1993. On outgroups. Cladistics 9:413-426.

Smith, A.B. 1992. Rooting molecular trees: problems and strategies.
Biological Journal of the Linnean Society 51:279-292.

Stevens, P.F. 1980. Evolution of polarity of character states. Annual
Review of Ecology of Systematics 11:333-358.

Trueman, J. 1996. Permutations tests and outgroups.  Cladistics, in press.

Watrous, L.E. and Q.E. Wheeler. 1981. The out-group comparison method of
character analysis.  Systematic Zoology 30:1-11.

Wheeler, Q.D. 1981. The ins and outs of character analysis: a response to
Crisci and Stuessy. Systematic Botany 6:297-306.

Wheeler, W.C. 1990. Nucleic acid sequences phylogeny and random outgroups.
Cladistics 6:363-368.




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