Cladistic theory

[Bryan Simon]

I am relatively new to using cladistics to assist in the systematic study of
grasses, using morphological characters.  This has led me into chasing up a
lot of literature concerning cladistic theory, from which I have come to
realize just how much diversity there is in this field, as recent postings
on "Farewell to species" has revealed and at looking at past issues of
Cladistics and Systematic Zoology.

Two basic concerns I have at present are
a)the recognition and nomenclature of lineages following dichotomy and
b) the treatment of lineages that arise at the tokogenetic level within a
species.
Both topics are well covered in the literature and on previous Taxacom
threads, but it is proving difficult to discover some sort of uniform
treatment in dealing with them.   As an herbarium botanist I feel it vital
that I am able to explain the classifications I produce (using cladistic
methods) to the users of these classifications in the real world.

a. Recognition of lineages.  Some clarification on this issue has been
presented in the recent thread, but I still not clear exactly which path to
take.  Much has been written in recent times about the recognition or not of
paraphyletic groups. Adherents of both philosophies have presented
persuasive arguments.   It appears to all hinge on what happens at the point
of lineage splitting, be it of a dichotomous nature or budding off from an
existing lineage.  The cladistic purists would say that at the point of
lineage splitting two new entities "evolve", whether they be recognizable or
not. A good example on Taxacom a few months ago was the example of a
population of Homo sapiens becoming  isolated on Mars into a new species H.
ares.  From the instant this happens the purists say, the extant Earth
species H. sapiens has also changed (although there is no autapomorphic
character present) to H. terrestris, say.  This is a very difficult concept
to put across to practically minded people, let alone the fact that the
different populations of H. terrestris (or extant H. sapiens) are now
paraphyletic.

b. Treatment of intra-species lineages.  This essential concerns the
phylogenetic species concept and the necessity of recognising infra-specific
taxa.  Some recent postings on Taxacom have suggested 1) that if the PSC
(more recently called the diagnosability sc) is strictly adhered to there is
no need to recognize infra-specific ranks at all.  Other workers have
suggested 2) that where fixation of one or more character states has not
become complete, there are grounds for recognising the peaks of variation
that may be detected phenetically at infra-specific rank  (subspecies in
preference to var.).  Yet other workers think 3) there is no essential
difference  between species and lineages within species, and that terminal
taxa on a cladogram may be represented by a genus, section, species,
subspecies or population.  The second choice seems preferable to me as a
practical herbarium taxonomist.  The idea of working with clades at a rank
lower than species would surely lead to all sorts of problems, including the
recognition of possible paraphyletic populations within the borders of a
species.