Publishing on human origins

[A.P. Jason de Koning]

Dear David,

I totally agree with your sentiments.

Your characterization of cladistic analysis is fully in keeping with
conventional approaches used in hominoid molecular systematics.

For my part, I would really like to see this thread put to rest...

Cheers,
- Jason

__________________________________________________________________________
  A.P. Jason de Koning, Doctoral candidate      Email: apjdk at albany.edu
    Department of Biological Sciences             Lab:  (518) 442-4347
    University at Albany, SUNY                    FAX:  (518) 442-4767
    1400 Washington Ave., Albany NY 12222, USA  Mobil:  (518) 210-4504
__________________________________________________________________________



----- Original Message -----
From: "David Orlovich" <david.orlovich at BOTANY.OTAGO.AC.NZ>
To: <TAXACOM at LISTSERV.NHM.KU.EDU>
Sent: Monday, May 31, 2004 3:34 PM
Subject: Re: Publishing on human origins


> > If this were the case for molecular data then I would not have an
> > argument
> > about molecular characters not being cladistic. Please provide
> > reference to
> > a published example as this is not an approach used in hominoid
> > molecular
> > systematics so far as I can see.
> >
>
> Dear John and others.
>
> The above comment really surprised me. I haven't read a paper about
> hominoid systematics, so I can't cite published examples from that
> field. However, the a priori designation of polarity (and homology) are
> what I have come to understand is what outgroup rooting and cladistics
> are all about, so when I read that this approach is not used in
> hominoid systematics, I am at a loss to understand what these authors
> must mean if they use the word cladistics.
>
>  From my reading, I understand that in the 'old days', people used to
> look at a bunch of character states and say "this is a primitive
> character state, and this other one is derived". They could then
> construct a freehand tree with taxa having primitive character states
> branching near the bottom and those with derived character states
> diverging later. This is quite problematic as it is at the whim of what
> the worker took to be primitive and derived. Anyway, let's construct an
> unrooted tree by any method (lets say by finding the tree on to which
> the character state changes fit with the least number of steps - this
> is what I call parsimony, be they molecular or morphological
> characters). So far, I haven't had to make any decision about polarity
> of characters, I have simply fit character state changes on to a tree.
> These changes can go in either direction. Now, I want to root the tree,
> say using the outgroup method. Once the tree is rooted, it gets an
> 'evolutionary direction'. I am then polarising all the character states
> on the tree - and I haven't had to make any explicit decisions about
> polarity of characters, molecular or morphological. Occasionally this
> is problematic when the outgroup is too distantly related to the
> ingroup and the position of attachment to the tree is equivocal, but
> this simply requires working around with other outgroups etc. What I
> have described is what I call a cladistic analysis, and at no time did
> I force polarity on any characters until I actually rooted the tree,
> and rooting the tree didn't require me to make explicit decisions about
> polarity, they happen 'automagically' when the tree is rooted.
>
> In a sense what I have just described applies to homology as well. Let
> me describe a less-than-perfect scenario. We aim to compare like with
> like in constructing a character-state matrix, but with morphological
> characters at least, we have to rely on criteria (Remanes criteria I
> think they're called) to help us decide which character states are
> actually states of the same character. We hope that we might be
> choosing homologous character states in our matrix, and in case we make
> a few mistakes, we choose lots and lots of characters so we can
> minimise any misinterpretations (i.e. homoplasy). Once we have
> constructed our character-state matrix, we can try to fit those
> characters on to a tree. If we again use the criterion of parsominy, we
> try to fit those character state changes on to a tree in the shortest
> number of steps. After we root the tree, we have done again what I call
> a cladistic analysis. From this tree, we can see that some character
> states evolved once (these are interpreted to be homologous) and other
> character states evolved more than once (these are interpreted to be
> homoplasy). However, this might sound problematic as it is a circular
> argument. On the one hand we tried to chose homologous character states
> before the analysis, and on the other hand we are using the results of
> our cladistic analysis to determine which characters are homologous. I
> prefer to think of the character state matrix at the start of an
> analysis as a hypothesis of homology, and a test of that hypothesis of
> homology is where those character states came out on the tree. This can
> be done with molecular or morphological characters. I see one clear
> advantage with DNA sequence data - that the prior designation of
> homology is done by alignment algorithms and (when done by hand) by the
> conservative minimisation of character state changes. This removes some
> of the subjectivity that arises when using Remane's criteria for
> morphological characters. It's not perfect of course, but it can be
> less problematic because of fewer ambiguities with interpreting
> character states.
>
> OK, so I've just outlined what I think cladistics is. Thinking about
> groups of taxa as monophyletic, paraphyletic etc is also part of
> cladistics, but that doesn't seem to be at issue at this point. I've
> admitted that I think molecular data works better with cladistic
> analyses than morphological data, but I see both have value. In view of
> the difficulty with prior designation of homology, I prefer to use
> molecular data for analyses, and then to map morphological character
> state changes on to my cladistic tree a priori.
>
> I've outlined this above because when I read John's posts about whether
> or not molecular characters are cladistic or not, i think to myself
> "What is he talking about?" and I see lots of responses to echoing
> similar sentiments. What I have outlined above is what plant
> systematists (and the odd animal systematist I know) do when they 'do
> cladistics' - at least that's how I understand it. Whether the
> character is molecular or morphological isn't relevant to the method
> (even though it might be relevant to the outcome). I wonder sometimes
> if there a still lots of hangovers in the minds of some from the 'old
> days' when people were more concerned with prior designation of
> homology and polarity. Computer programs like MacClade and PAUP still
> allow us to do these things prior to the analysis, but whenever this
> sort of thing is done, I feel it should be assessed on a case-by-case
> basis and doesn't constitute an essential part of what I see as the
> cladistic method.
>
> Please let me know if i've made any glaring errors here - I'm thinking
> as I go.
>
> Cheers, David Orlovich.
>
> Dr David Orlovich,
> Department of Botany,
> University of Otago,
> P.O. Box 56,
> Dunedin,
> New Zealand.
>
> Phone: +643 479 9060
> Fax: +643 4769 7583