[Taxacom] Taxacom Digest, Vol 65, Issue 12

[John Grehan]

But that is my point too, one has to designate what represent features unique or derived for the ingroup taxa for the analysis to be meaningful.

John Grehan

-----Original Message-----
From: Sergio Vargas [mailto:sevragorgia at gmail.com] 
Sent: Friday, August 12, 2011 2:16 PM
To: taxacom at mailman.nhm.ku.edu; John Grehan
Subject: Re: Taxacom Digest, Vol 65, Issue 12

Hi there,

SV: Binary transformation series, whether restricted in a way that one character state is present in the ingroup and absent in the outgroup or not, contribute the same number of steps to a parsimony analysis independently of the polarity assessment so identifying polarity in this characters prior to the analysis is irrelevant."

JG: But an algorithm cannot distinguish derived states if they are not specified. If one mixes in non-derived states and codes them as such, then no problem - but then why bother including them?

Well yes, but that's precisely the point, the algorithm recognizes a change from a character state to other and adds a step to the global step counts. For the algorithm derived/non-derived means nothing. Polarity is only use afterwards for interpreting the cladogram and requires rooting the cladogram using an outgroup (but you could use an hypothetical ancestor too). All phylogenetic software available operate over unrooted trees. Trees are "rooted" only for visualization (and polarity interpretations).

sergio



-- 
Sergio Vargas R., M.Sc.
Dept. of Earth&  Environmental Sciences
Palaeontology&  Geobiology
Ludwig-Maximilians-Universität München
Richard-Wagner-Str. 10
80333 München
Germany
tel. +49 89 2180 17929
s.vargas at lrz.uni-muenchen.de
sevra at marinemolecularevolution.org

check my webpage:
http://www.marinemolecularevolution.org

check my research ID:
http://www.researcherid.com/rid/A-5678-2011