[CPN] Fwd: PLEASE VOTE on CBM-related proposals

[de Queiroz, Kevin]

>> The problem illustrated by  David's fish example is a consequence of
> > our having broadened the PhyloCode's operational definition of the
> > species category to accommodate those who do not accept the idea that
> > a species is a population lineage segment.
>
>Really? Here's my example again:
>
>--+--A
>   `--+--B
>      `--+--C
>        `--+--D
>          `--E
>
>A and E can interbreed with each other, but all other combinations don't
>work.
>
>All nodes should be considered parts of the species A + E; they were all
>able to interbreed. The species is (multiply) paraphyletic, not
>polyphyletic. Does that not count as a lineage segment?


It counts as two lineage segments:  one from the basal node to A; the
other from the basal node to E.  It could be considered a single lineage
on an unrooted tree, but such a tree is not really a phylogeny until it's
rooted (you can't identify clades on an unrooted tree).  Of course, if A
and E interbreed (actually, not only potentially), the two lineages are
incompletely separated.  On the other hand, if they are not at least
partially separated, then there is no A and E in the phylogeny (only AE).
Nonetheless, I would not argue that adopting the view that a species is a
separately evolving population lineage segment will remove all
disagreements about species boundaries and thus about the application of
clade names defined using species as specifiers.


>
>> I am not suggesting that we  revisit that decision, which I personally
> > support, but if we retain a broad operational definition of "species"
> > in the code, we may simply have to accept that differences in species
> > concepts or hypotheses of species boundaries will result in
> > occasional changes in the application of the names of low-level
> > clades whose contents coincide with or overlap the membership of
> > those species. As Kevin pointed out to me in our discussions of this
> > problem over the past couple of weeks, variability in the application
> > of clade names due to differing conceptualizations of the species
> > used as specifiers is analogous to variability in the application of
> > clade names due to differing phylogenetic hypotheses.
>
>I disagree. Disagreements about phylogenetic hypotheses are (hopefully)
>scientific disagreements -- different datasets supporting different
>topologies, that kind of thing. Disagreement about which species concept
>should be called "species" are purely semantic. That's, as I said,
>_precisely_ what the PhyloCode is supposed to stop. One of the most
>important ideas behind phylogenetic nomenclature is to turn the question
>"does organism X belong to taxon Y?" into a scientific hypothesis.


On the contrary, disagreements about phylogenetic hypotheses are often
very similar to disagreements about species circumscriptions in terms of
their scientific (or unscientific) bases.  Thus, just as different
datasets may support different topologies, different datasets may support
different inferences about species boundaries.  Moreover, just as
different species circumscriptions may result from people adopting
different species criteria (e.g., intrinsic reproductive isolation versus
fixed character state differences), different phylogenetic hypotheses may
result from people adopting different optimality criteria (e.g, parsimony
versus likelihood).

I agree that phylogenetic nomenclature makes questions about taxon
membership scientific hypotheses (rather than mere conventions); however,
scientists don't always agree about the answers to such questions
(conclusions), because they don't always agree about underlying
assumptions (premises).


>
>Consequently, I still think species shouldn't be used as specifiers.
>Phylogenetic nomenclature is about clades; mixing species in causes
>trouble.
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