Publishing on human origins

[John Grehan]

At 07:34 AM 6/1/04 +1200, David Orlovich wrote:

>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.

In hominid systematics the approaches in both morphology and DNA sequencing
data are both presented as being 'cladistic'. In all the morphological
studies there is an a priori designation of the character state for the
ingroup being derived with respect to the outgroup so only characters
conforming to this pattern are analyzed for congruence/incongruence. In
molecular studies it appears that all sequences are used (i.e. there is not
a priori separation and exclusion of primitive sequences).

>  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.

This is where I differ in my understanding of cladistics in that I would
only use characters that have already been polarized as being present
within the group being analyzed and absent in the outgroup.

>These changes can go in either direction.

This is where I find matters quite wishy washy. If one has so little
understanding of characters for a group to be in total ignorance of their
'direction' it makes me wonder how any confidence can be held in the result.

>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.

The trouble I have with this is the garbage in garbage out problem.

>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.

The alignment would seem to assume homology rather than establishing homology.

>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.

A recipe is by definition objective, but the criteria seem to be at the
whim of whatever one might pose as the initial understanding of what is or
is not homologous.


>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.

Who has demonstrated that DNA sequences are a precise match phylogeny at
all (other than the rather ludicrous proposition that they match morphology
which is then cast in doubt when the two conflict)?

>Please let me know if i've made any glaring errors here - I'm thinking as
>I go.

Thanks for the input without the imputation along the way that I'm missing
brain cells! I'm thinking on the go to - hence any manner of potential
oversights.

John Grehan


>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