[Taxacom] clique analysis in texbooks (was: Evolution of, , human-ape relationships...)

[John Grehan]

I'm embarrassed to say that I did not read the CI<100. I thought I read CI=100. Must be Friday.

My view is that if plesiomorphies become subjects of analysis one is in effect doing an analysis that will represent overall similarity rather than derived similarity. That's my position now even though it seems that no one else agrees (apologies if someone has said otherwise).

"So I got it right! Finally. Then, and I've mentioned this before, the Human-Orangutan hypothesis can be viewed as a phylogenetic tree conditional only on characters which polarity can be decisively determined, often a priori."

Sergio - you deserve an award! You get it. If you were here I would give you a chocolate fish (oh darn, they don't have those where I am now). I would modify "often" to always - always before the analysis.


> I see several potential problems for a tree inferred using John Grehan's 
> method of character pre-selection:

> 1. as an explanatory hypothesis, such a tree is worse than a tree 
> resulting from a matrix also including characters which polarity cannot be 
> decisively determined because the second tree would also provide an 
> explanation for these, say bad, characters as well. Thus the second tree 
> will have a higher explanatory power than  the first one.

It's a possibility. When someone in the primate world can show that for the orangutan analysis that will be interesting.

> 2. from a testing perspective the first tree (JGs) is less thoroughly 
> tested than the second one because characters that could potentially 
> falsate (not sure how you write this word) the topology are not being 
> used, even if the analytical method can handle them without problems and 
> no cladistic textbook (unless Wiley and Brooks are "closet pheneticists" 
> which will be scary) or published work recommend to exclude them from the 
> analysis.

I cannot see how equivocal character states (those in the outgroup as well and therefore potentially plesiomorphic etc) can falsify derived states in a cladistic analysis.

> 3. because of the way the character matrix is constructed, it seems that 
> it is really hard to add new characters to the matrix, which means that 
> the conclusions of the analysis are protected against future testing: you 
> can always take characters out (those that do not fulfil JGs criterion of 
> character selection) but never, or only very rarely, you can add 
> characters to the matrix. 

Don't get that. I have had no problem adding or removing characters from the data. Its only 'hard' to add characters if it is hard to find any. Found plenty for humans and orangutans, only two or less for the chimpanzee. So far no one has produced a mass of human-chimpanzee features that are not found in a broad outgroup and well documented.


> Moreover, if you ignore JGs criterion of character selection you are 
> "muddying the phylogenetic waters" and your matrix is phenetic, therefore 
> irrelevant. If you use DNA characters you are a "molecular theorist", 
> whatever that means.

Usually it means that you theorize that molecules give the right answer and falsify morhogenetic evidence.

> I guess these problems make a tree inferred using this method a bad 
> hypothesis when compared with an hypothesis that does not require 
> excluding potentially relevant information and does not pose obstacles to 
> further testing.

Well that's a viewpoint certainly.

John Grehan

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