Traits and/or states

Gianluca Polgar polgar at ALFANET.IT
Sat Nov 1 09:14:43 CST 2003

I would like to express some ideas on the character/states concepts.

1) When we speak of phylogenetic inference, we should speak of inheritance,
i.e. of vertical transmission of genes.
This is a first hypothesis.
We know that widespread and iterative events of horizontal transmission
(i.e. via retrotransposons or transposable elements in eukariotes) lead to
impressive evolutionary changes. Maybe the same explosive radiation of
eukaryotes and their extraordinary evolutionary versatility with respect to
the prokaryotes, could take place only due to continuous and iterated
genetic duplicative mechanisms mediated by transposition or retrotransposition.

2) But even assuming that horizontal transmission could be treated as a
background noise at the scale of microevolution, speaking of inheritance
when observing a phenotype (i.e. a morphological structure), implies a
biunivocal correlation between shared phenotypic similarities and shared
genetic traits.
This is a second, strong hypothesis.
We know that the morphological structure and related function of an
organism is the result of the continuous interaction between the organism
itself and its "environment", during embriogenesis and ontogenesis
(reaction norms, ecotypes...). Shared similarities could only show a
similar "interactive history" of the organism.

3) But what is a "character" and its "states" from the point of view of
The only reasonable explanation for these concepts that I find, taking into
consideration points 1) and 2), is that the "character" is an abstraction:
it is the hypothetical "type of stable structural plan" which is the
ecological and genetic stable interaction that controls the differentiation
and development of a complex morphological structure through generations.
(Note that intended so, the "character" is then linked not only to genetic
flux, but also to the environmental conditions in which this flux have
occurred through generations... but let's follow the second hypothesis).
Thus the structural genetic plan could be the "high-level construct"...
 From this point of view then, states would be the expression of a
particular structural plan, or the interaction between particular alleles
(i.e. genetic variants).
(Note that this is an oversimplification: for each allele, SEVERAL reaction
norms will be possible in different environmental conditions...)

But how could we infer that two particular morphological features of two
different species (here more problems arise, but we'd like to arrest the
haemorrhage...) which apparently share similarities... ARE actually the
outcome of a common (in the sense of a recent common ancestry) "structural
genetic plan"?
We may study their anatomy, physiology, autoecology, eco-ethology (which
most often we don't), correlate their observed characteristics with their
observed functions inside and outside of the organism, and deduce their
homology, i.e. propose a parsimonious model of their evolution. This is how
for instance, comparate anatomy seems to work.
We thus recognise in that observed, complex, reasoned cluster of
morphological details a "structure" and a "function": an identity of its own.
(In an ideal condition, we would analyse the genetic control of the
expression and differentiation of that particular phenotypic feature, and
then compare the genetic distance on the basis of targeted markers...)
Thus we may describe a "morphological trait", assuming that its
characteristics correspond to an inheritable "structural plan", and we may
call it a "character".

This is a third, very strong hypothesis.

Up to this point, seeing that in most cases taxonomists never have the
possibility to go through the long and complex experimental and theoretical
processes needed to support the mentioned hypotheses, isn't it more honest
and scientifically correct to limit the phylogenetic inference to the
subject/predicate constructs directly derived from observations? Nothing
more, nothing less of that: a phylogenetic inference based on shared
OBSERVED similarities... The subjective (and psychological) arbitrariness
of this process can be actually limited by a number of considerations, and
the taxonomist will with no doubt reasonably explain his choice of the
characters and of the states... that's all.


Gianluca Polgar
c/o Prof L. Bullini
Dip. di Gen. e Biol. Mol. "Charles Darwin"
Univ. of Roma La Sapienza
Rome Italy

>At 10:42 AM 10/31/03 +0100, you wrote:
>>The character/state distinction seems to be (to me, at least) reasonable
>>not only from the purely practical point of view.
>>What we call 'character' and 'state' in the phylogenetic analysis are
>>indeed both high-level constructs, not observations (not speaking about
>>all the problems with the process of "observation"). The character/state
>>distinction is a way how to hierarchize such constructs; we can treat this
>>hierarchic relation as a subject/predicate, variable/value or whatever but
>>the language we are using can hardly change the merit. I have personally
>>found nothing in your message (nor in your presentation referenced below)
>>what would contradict this generally accepted opinion. Perhaps you could
>>explain your position in more detail?
>My thanks to Drs. Skala and Deleporte for their thoughtful comments. I will
>try to respond here to both.
>I'm not entirely sure I understand what is meant by "high-level
>constructs." If descriptions of organisms, or the cells of a data matrix,
>do not represent our observations, then it would be difficult to claim that
>a phylogenetic hypothesis is an explanation of shared similarities.
>The concern I have had with the "character" and "state" distinction is that
>it is not consistent with the nature of observation. What we observe are
>objects by way of their properties (= character, attribute, trait), and
>these are communicated by subject-predicate relations. For instance, I
>cannot observe "number of digits." But I can observe that the distal ends
>of some set of appendages (subject) have five digits (predicate). The
>"character," "number of digits," and the "state," "five," cannot represent
>subject-predicate relations denoting observations since "number of digits"
>does not represent the subject observed. What are observed are subjects
>called appendages with the property (= character, attribute, trait) of five
>digits. The cell of a data matrix for species X must code the observation
>that individuals in this class have appendages with five digits. The cell
>is not simply a "state;" the cell summarizes observations.
>I don't find any hierarchic relation here, and such a relation would not be
>expected for objects and their properties. On the other hand, an object can
>be composed of subsidiary objects, in which case hierarchic relations can
>be stated. But, this hierarchic relation of a part composed of parts is not
>equivalent to the observations which allow us to speak of the relation itself.
>I hope this helps clarify what I said earlier.
>J. Kirk Fitzhugh, Ph.D.
>Associate Curator of Polychaetes
>Invertebrate Zoology Section
>Research & Collections Branch
>Los Angeles County Museum of Natural History
>900 Exposition Blvd
>Los Angeles CA 90007
>Phone:   213-763-3233
>FAX:     213-746-2999
>e-mail:  kfitzhug at

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