[CPN] Proposal to amend the PhyloCode

    Mike Keesey keesey at gmail.com
    Thu Oct 6 14:31:37 EDT 2011 
    (Apologies for double-sending most of this message to most of you. I
realized after I sent it the first time I should have sent it to the
mailing list.)

In response to the proposed revisions, I wrote:

> I'll offer some preliminary thoughts as well. 
>  
> I like the idea of removing the dependency on species from the code, 
> thus avoiding the "species problem". In the past I've advocated a 
> similar approach, where we deal in organisms rather than species. 
> However, since then I've realized there is also an "organism problem"! 
> That is, it's not always clear in biology what constitutes an 
> individual organism (think of slime molds, lichens, etc.). 
>  
> Now I think perhaps it is preferable to think of phylogeny in terms of 
> taxonomic units. A phylogeny is a directed, acyclic graph wherein the 
> nodes are taxonomic units and the [directed] edges are [immediate] 
> ancestor-descendant relationships. How units and relationships are 
> determined is beyond the purview of the code (just as taxonomy is 
> beyond the purview of the rank-based codes), but the code requires 
> them in order to be applied. 
>  
> So I would suggest that perhaps we use the phrase "taxonomic units" 
> (or, where clear, just "units") instead of "organisms", "populations", 
> "species", etc. 
>  
> I've written a document explaining this approach in nauseating detail: 
>  http://namesonnodes.org/ns/math/2009/index.html 
 
In response, David Marjanović wrote:

> That's true, but the organism problem is much, much smaller than the 
> species problem! Cases where it could lead to actual trouble will be, at 
> most, so rare that we (the CPN) could easily deal with them on a 
> case-to-case basis. 
Likely true, and, to be clear, I would definitely favor using
"organisms" over "species", even if my ultimate preference is
"[taxonomic] units".

> This will be misunderstood to include "higher taxa". 
If a taxonomic unit in a phylogenetic hypothesis is a "higher taxon"
then that is actually what I mean!

I see the process of phylogenetic nomenclature this way:

1) A researcher, using whatever criteria they desire, organizes the
relevant life forms into units.

2) The researcher, again using whatever criteria they desire,
hypothesizes ancestor-descendant relationships between the units. We
now have a phylogenetic hypothesis, which is a directed, acyclic graph
where the taxonomic units are the nodes (or vertices) and the
immediate ancestor-descendant relationships are the directed edges (or
arcs).

3) The researcher consults RegNum for definitions which are applicable
to the phylogenetic hypothesis. Definitions are applicable if their
specifiers indicate units or unions of units in the hypothesis. (A
specimen should generally indicate a single unit, a species is just a
proxy for its type specimen, and an apomorphy may indicate a union of
any number of units, as may the term "extant".)

4) The researcher applies these definitions. Definitions indicate
operations which yield either the empty set, an individual unit, or a
union of units, depending on the phylogenetic hypothesis.

5) The names associated with these definitions, under the PhyloCode,
may now be used to refer to the appropriate taxa yielded by the
definitions (under the phylogenetic hypothesis).

So, for example, suppose we have a phylogenetic hypothesis where one
of the units is "Aves", and we seek to apply a definition which uses
the type specimen of _Vultur gryphus_ as a specifier. (Note that, per
Note 11.1.1, "When a species is cited as a specifier, the implicit
specifier is the type of that species name (if a type has been
designated) under the appropriate rank-based code.") Then, in that
context, the taxonomic unit "Aves" is indicated by that specifier
(never mind that it's a "higher taxon").

You may ask, what happens if another specifier indicates the same
unit? E.g., how do we apply the definition of _Neognathae_ (the
branch-modified node-based clade stemming from the last common
ancestor of all extant members of the branch-based clade stemming from
the first ancestor of _Vultur gryphus_ not also ancestral to _Tinamus
major_ or _Struthio camelus_)? All three of the specifiers indicate
the same unit ("Aves"), so doesn't that definition yield the empty
set? The answer is, yes, *under that context*, _Neognathae_ is empty!
But the conclusion to be drawn from this isn't that there are no
neognathes *under any context*, rather that this particular context is
too coarse for a useful application of the definition.

-- 
T. Michael Keesey http://tmkeesey.net/
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