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

[de Queiroz, Kevin]

On 11/28/12 12:48 PM, "David Marjanovic" <david.marjanovic at gmx.at> wrote:

>Kevin de Queiroz wrote:
>
>> It counts as two lineage  segments: one from the basal node to A; the
> > other from the basal node to E.
>
>So, if it's branched, it's not a single lineage? Just trying to make
>sure I understand the concept.

That's right.  A lineage is a single line of direct ancestry and descent.
I've described the concept in more detail in several of my papers about
species.

>
>> 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.
>
>That is true given the same species concept. It's trivially true given
>different species concepts.

Of course, as I said, if people disagree about assumptions, then they
can't expect to agree about conclusions.

>
>> 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).
>
>In the latter case, however, scientific arguments can (at least) often
>be made that, given the conditions of the case, one method is less
>error-prone than the others in recovering the true phylogeny
>(reticulated as it may be). In the case of species concepts, there is
>nothing comparable to the true phylogeny; different species concepts
>aren't different approaches to describing true species*, they describe
>different kinds of entities that have nothing in common other than the
>_word_ "species".
>
>* Even though the inventors of many species concepts seem to have
>believed that that's what they were doing.

This is a matter of interpretation.  If the different species criteria are
interpreted as necessary properties of species, then their corresponding
species definitions describe different kinds of entities and disagreements
are largely semantic.  However, I have argued that that is not the most
useful way to interpret the properties--specifically, that it is more
useful to interpret them as different lines of evidence concerning the
separation of lineages.  Under that interpretation, the criteria become
very comparable to different optimality criteria for estimating
phylogenies in that we can indeed consider them in terms of how reliable
(or error-prone) they are with regard to inferences concerning the
separation of species-as-lineages.

>
>Mike Keesey wrote:
>
>> A phylogenetic hypothesis  cannot even be formulated until the
> > relevant life forms are grouped into taxonomic units (whether those
> > units are individuals, populations, species, or something else). Only
> > then can the units be related to each other in terms of descent,
> > creating a phylogenetic hypothesis. So the unit taxonomy is an
> > essential part of the hypothesis.
> >
> > I used to argue that the only type of unit should be the individual,
> > since it's objective, but a discussion with a lichenologist
> > disabused me of that notion. There's no simple, objective way to
> > mandate the composition of any type of taxonomic unit, be it species
> > or individual. The Code avoids this problem by recognizing that it is
> > a taxonomic matter, not a nomenclatural one.
>
>I think we have an easy way out: as least as far as specifiers are
>concerned, we can use specimens as opposed to individuals. That leaves
>the decision to the curators. :-)
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