More on the 'cladistics' of sequences

[John Grehan]

Part 2.

I can take it another way:
your "callosities" character is a "phenetic" character according to your

highly personal use of the term "phenetic" 

No it is not. My understanding of phenetic characters are those
characters based on overall similarity where there is no separation of
primitive or derived states. I would view the absence of ischial
callosities as a apomorphic condition with respect to humans and
orangutans.

The method you are implementing is exactly what the programs do. They do
it 
for you. They root on outgroups, and prefer the optimal overall topology
in 
case of ambiguity.

I understand that already. However, I would place less emphasis on using
characters that have a variable presence in outgroup. 

The fact that you are apparently "computing" everything in your brain 
instead of using these so convenient programs changes nothing to the
logics.

Correct.

And you persist in rejecting these programs...  Fascinating...


It seems to me that you appear to persist with a misconception.

Hence, once again, plenty of outgroups indeed (species, monophyletic
groups 
of species, including their possible internal polymorphism for some 
characters I presume... don't tell me you overlook this possible
complexity).

No, just looking as broadly as possible.

This makes a lot of outgroups. Do they all fit unambiguously outside
your 
ingoup, i.e. are connected by a single branch with your ingroup? If not,

you have likely made a mistake and some outgroup species may be members
of 
the ingroup in fact. this is the interest of the "multiple outgroup"
approach.

These are certainly possibilities. I make no presumption at this time on
how stable the group is as a whole.

Nothing new, this is a classic, but long abandoned because of its too
heavy 
burden of arbitrariness

It seems to me that there can be a lot of arbitrariness in character
selection no matter what the method. 

(you "invent" an ideal taxon fitting your guesses 
instead of simply dealing with the taxa at hand), but still possible
with 
the programs (just introduce this fictitious taxon as "the" outgroup).

What will probably happen with the orangutan question is an initial
analysis with a single outgroup comprising Old World monkeys (which is
no worse than what all the traditional morphological analyses have
focused on). If I can get past the thought police that want to keep the
orangutan theory out of the picture then more detailed analyses could
follow (probably by primate systematists who will have the time and
resources to go through all species for the variable features (four
altogether).

>  I wonder whether the former is a product of degree of familiarity
and/or 
> the ability to generalize a structure (something that I have found can
be 
> a real challenge to understanding or recognizing comparability),

Homology decisions are easier for sequences when the alignment is non 
ambiguous (roughly: few and sparse changes in the sequences, so that 
changing sites are embedded in a non-ambiguous context of homologous 
features. This is like a change in a bone when the contiguous skeleton
is 
identical... classic "connexion criterion" for molecules like for 
morphology... once again. Molecules have form, you know...).

I do wonder if they are really comparable in this way since the DNA
sequence involves a replacement of items rather than an evolution of one
to another.

This is great news. But not at all a question of experience in my view.
I'd 
say rather a question of logics, 

I will agree to disagree on that.

Basic cladistic courses are free, and chewing on them is free, too.

I've been to cladistic courses so I've been exposed to the principles.
However, such courses focused on the algorithms, not the biological
(rather than logical) issue of whether a posteriori rooting of phenetic
characters is really cladistics or just a version of phenetics dressed
up in cladistic clothing.

So here's my prediction for the future - regardless of the algorithm,
the level of cladistic morphological support for the orangutan-human
relationship will prove to be greater than for a human-chimpanzee
relationship. So I've stuck my neck out for the sake of argument.

John Grehan