Taxon structure

What kind of taxon (mono-, para-, or polyphyletic) would be created by joining the two species that share the trait "SSC" in the tree above?  Before we consider this question, let us examine various ways of dealing with the problem.

The most widespread view
, almost always given in textbooks and strongly advocated by Wiley and others disciples of Hennig, is whether or not a taxon contains (1) the most recent common ancestor itself and (2) all its descendents.

In the example above, a taxon that includes humans, chimps, and bonobos is monophyletic because it meets both criteria.  On the other hand, a taxon that would include gorillas, orangutans, and gibbons would only fulfill the first criterion, inclusion of the common ancestor, but not the second, as some descendents (Homo and Pan) are excluded, and thus would be regarded as paraphyletic.

Last, a taxon that includes only gorillas and the Bornean orangutan fulfills neither criterion as it does not include the common ancestor to the two species and is therefore considered polyphyletic.

Easy enough, and in a conceptual context, these definitions of mono-, para-, and polyphyly are clear and straightforward.  The problem arises when one leaves the Platonic world of concepts and instead attempts to deal with the
practical reality of  systematics.  The many advocates of the ancestor membership criterion nearly always fail to mention the small but non-trivial detail that common ancestors are in practice never available.  Even the most recent common ancestors in our ape tree, those of the two Pan species or those of the two Pongo species, are extinct and may not have left any fossils; even if fossils do exist, there is no way to demonstrate that a given fossil truly represents the ancestor of a particular extant species.  Lenski's frozen bacteria or Hillis's frozen bacteriophage are rare exceptions where the common ancestor of a population (not a collection of species) is known and available; but such situations are not expected to occur in the natural world.

In other words, a definition of taxon structure that involves membership of ancestor species is completely unworkable in real biology.  Practising systematists must use a different approach based on set structure.

Inferred phylogenies impose onto taxa a nested set structure, based on presumed ancestry.  Members of nested sets constitute a clade.  Taxa that belong to an incomplete nested set form a grade.  This ontology is entirely consistent with that proposed by Hennig.  For some unknown reason, he added the stipulation that taxa must include the common ancestor.  It is possible that Hennig's thought was distorted by translation and that he meant something else (share a common ancestor?).  This said, E.O. Wiley and many other theorists continue explicitly and emphatically to perpetuate this idea, which, if adhered to, would effectively seem to preclude the description of most taxa above the species level.

Summing up:

    - A taxon that includes all members of a nested set (clade) is monophyletic.

    - A grade, or taxon whose members are nearest neighbours but from which a nested set is missing, is a paraphyletic taxon.
    - A taxon that consists of members of two or more incomplete sets is polyphyletic.


Hennig also used character mapping as a means of defining taxa in terms of phylogenetic structure. 

A taxon that is defined by a ___

        ___ synapomorphy is monophyletic;

        ___ sympleisomorphy is paraphyletic;

        ___ homoplasy is polyphyletic.

But things are never simple.  In our ape example, one might argue that SSC-positive species acquired this trait independently, in which case a taxon defined on the basis of SSC would be polyphyletic.  However, topologically, the two SSC-positive species form a paraphyletic taxon because they share a recent common ancestor but exclude one of its descents.  This would receive further support if one had evidence that SSC was present in the common ancestor but was subsequently lost in the lineage that led to chimps.  So, nothing is black-and-white...  Likewise, there is no reason why we should not include, in our polyphyletic taxon that contains gorilla and Bornean orangutan, their common ancestor.

Note that the current taxonomy of taxon structure has never been universally accepted and is still the object of some contention.  Some authors have argued that paraphyletic taxa do share a single evolutionary origin and so should be regarded as a kind of monophyletic taxa.  The term holophyletic would then distinguish complete sets (clades) from incomplete sets (grades).  For further discussion of these matters, see Envall (2008).


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