More on the 'cladistics' of sequences

[John Grehan]

I'm responding in two parts as I am not sure if this is over the word
limit.

-----Original Message-----
From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
Behalf Of pierre deleporte

You need not several outgroups. It's simply better, because if all 
outgroups don't root in the same place into your ingroup, then this is
an 
indication that you have made a mistake. Your analysis tells you that
all 
your putative outgroups cannot be "out" altogether. See PAUP's manual,
and 
also Farris 1972 as hinted off list by Jan de Laet.

I'll keep that in mind.

>  if one chooses a sufficiently broad single outgroup.

By "single", you mean a monophyletic group, or a possibly paraphyletic 
arrangement of taxa?

I see your point about the two different possibilities. If it makes a
difference to the ingroup arrangement its worth considering.

>Thus for the orangutan-human synapomorphies the context I am looking at

A "context", or a "single group", and what do you mean by "group"?

Context referred to the breadth of comparison.

>is ALL other primate species collectively and that is quite a lot of
species.

Indeed, but likely not a monophyletic group, rather a paraphyletic 
arrangement, thus simply a series of "out" species or groups of species,

hence you have not a single monophyletic outgroup but a lot of primate 
groups putatively outside your ingroup.

It's certainly a possibility, but regardless it's my starting point for
evaluating the hominoid characters.

>  Most of the characters stand up pretty well in that regard,

"Stand up"???! Trying to figure out your method from your other posts I
now 
presume that you mean "their state in the outgroups is uniform"?

Meaning that most of the characters for orangutans and humans do not
occur at all in the same state in any other primates.

>and even those of lesser distribution

Ha-ha !  Interesting... Hence, some of your characters have not a
uniform 
character state in all putatively outgroup taxa? Hence your method would

finally be the standard cladistic one as implemented in current
programs? 
But in this case, why do you reject these programs by calling them 
"phenetic"?... Very, very puzzling indeed...

I don't have any strong opinion on whether 'cladistic' programs are of
themselves phenetic or not although at least one cladist has suggested
to me his view that parsimony analysis is just a version of phenetics. 

Yes there are three characters that may be apomorphic with respect to
humans and orangutans, but also have representation in outgroup species.
One involves thick dental enamel which is found in a couple of monkeys,
the other two is the lack of estrus and the lack genital swelling during
the menstrual cycle. I agree with your point that one could include
these taxa to see what influence it has on the ingroup analysis - the
latter two characters in particular if one could get an accurate enough
documentation of the feature for outgroup species.

>  may be supportable (e.g. lack of ischial callosities which is unique
to 
> orangutans and humans among Old World monkeys and the apes could be 
> reasonably treated as an apomorphy rather than as a plesiomorphy 
> inherited all the way from the split with New World monkeys which lack

> the callosities).
You now are describing what all cladistic programs do!!! Astonishing...
Do 
you really know what the programs do? I must assume that you simply
don't 
know (or you inadvertently forgot). But you reject them?

No I realize that programs can sort out possibilities like this
according to the criteria set for character matching. However, one could
also establish an argument for characters in the first place. 

>  This is just an observation, not necessarily a criticism of using 
> several outgroups.

Your "observation" consists in describing your method, and I must 
aknowledge that your method is the one implemented by the programs. I
can't 
figure out the slightest reason why you reject these programs...

As before, I do not reject the programs. Sorry if I gave that
impression. I think all I was saying is that the programs are just
recipes and what they do follows from the assumptions about the
characters in the first place so if the characters are not already
limited to apomorphic features then the result may be just a 'cladistic'
analysis of phenetic characters.

Part 2 follows.

John Grehan