Publishing on human origins

John Grehan jgrehan at TPBMAIL.NET
Tue Jun 1 22:34:14 CDT 2004

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

It wouldn't surprise me if most molecular systematists would feel that way.
After all, the orangutan relationship and fossil hominid morphology would
be easier to dismiss than address.

John Grehan

>- Jason
>   A.P. Jason de Koning, Doctoral candidate      Email: apjdk at
>     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>
>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

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