Message 2000-09-0001: Why does the PhyloCode use a hierarchy?

Fri, 22 Sep 2000 09:57:55 -0700 (PDT)

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Date: Fri, 22 Sep 2000 09:57:55 -0700 (PDT)
From: Nathan Wilson <>
Subject: Why does the PhyloCode use a hierarchy?


I just joined this mailing list at the suggestion of Philip Cantino after
asking him the following questions.

By way of introduction, I'm a computer scientist with a strong interest in
taxonomy and biological nomenclature particularly for the "higher" Fungi. 
I have been following the development of the Phylocode and have a great
deal of respect and enthusiasm for the goals of the project.  However, I
also have some serious concerns about it.

My most fundamental concern is that the Phylocode makes the implicit
assumption that you are classifying entities (clades) that are arranged in
a strict hierarchy.  It does this by relying on the vaguely defined
concept of species and the implicit assumption that clades do not exchange
genetic information.  Current research in genetic engineering is
demonstrating that we cannot make this assumption.  Furthermore, most of
the hypotheses I've heard about the evolution of eucaryotic cells also
violate this assumption.

My primary question is why assume a strict hierarchy made rather than
using the actual structure which is a directed acyclic graph?  More
simply, why does the code rely on the concept a single most recent
ancestor for defining a clade?  Expanding the definitions of clade to
allow for the possibility of multiple most recent ancestors not only
removes the assumption that clades do not exchange genetic information,
but also removes the reliance on the concept of species from the Phylocode
since now it is perfectly reasonable to talk about intra-species clades.
Are there other people thinking along these lines?  Are there strong
arguments why this approach is not feasible?  As far as I can tell there
are some fairly simple extensions to the node-based clade definition that
allow for this change.  I believe the stem-based and apomorphy definitions
can be left unchanged since they require the existence of a unique most
recent ancestor.

-Nathan Wilson


Feedback to <> is welcome!