Top 10 PhyloCode Misconceptions

[keesey]

I'd like to put together a list of the top 10 misconceptions about the PhyloCode (or more, perhaps). Here's a couple to get us started:

The PhyloCode will rename all organisms.
This one is reflecting in the subtitle of this essay: "What if we decide to rename every living thing on Earth?" While the PhyloCode allows for new names, it also allows for the use of old names, and even encourages their use under most situations. It is likely that the vast majority of PhyloCode-governed names are already in existence.

The PhyloCode is intended as a replacement for the rank-based codes.
It's right there in the Preamble: "This code may be used concurrently with the rank-based codes." In fact, since the PhyloCode uses species names as specifiers but does not govern them, it actually requires the rank-based codes.

[Daniel Madzia]

I'm unable to tell which misconception would be among the top ten, but I can start with examples I heard.

First of all - there is one misconception that is also widespread among the users of phylogenetic nomenclature (though none of them is probably working on the PhyloCode). It's the belief/opinion/conviction that clades are defined, which is untrue. This statement has been advocated by Stuessy (2000, 2001) who wrote that “individuals can be described or if you like defined (my preference would be ‘characterized’), but not their names” (Stuessy, 2001: 185). As de Queiroz & Cantino (2001) replied to this, “individuals can be described or characterized, but not defined; only their names can be defined” (p. 821), because “definitions apply only to words, not to the things to which the words correspond” (Ghiselin, 1966: 127).

Species are also clades.
I heard that only once but I think that it is important to mention it. Of course, Species are not clades in the sense they are always monophyletic. They are different kind of biological entity which form clades (monophyletic groups), but we cannot require their monophyly.

The PhyloCode must introduce a lot of new names to name all clades.
That's what I heard several times. It's, of course, nonsense! It's totally impossible to name all clades (and it would be even if we had perfectly recovered tree of life).

The PhyloCode needs perfectly preserved remains.
Also untrue. It doesn't need it. People think that, because they are convinced that the PhyloCode is unable to work with more than one phylogenetic hypothesis, which is incorrect. As I already wrote to Mike, I had a presentation about the PhyloCode and phylogenetic nomenclature at Charles University. It was great experience for me but arguments were based mostly on misconceptions and misunderstandings. In one of my slides I had this picture:



It was used as an analogy to phylogenetic nomenclature (taxon name ~ the t-shirt, phylogenetic definition ~ the text, and taxon ~ beautiful girl who wears the T-Shirt). Taxon names are just like this T-Shirt. The only woman who will wear the T-Shirt is the one who loves Dan (assuming that there is only one Dan in the world). And what happens when there isn't such a girl? It's simple, no-one will wear it. So, the PhyloCode doesn't need perfectly preserved remains because it knows how to work with weak phylogenetic hypotheses (it permits qualifying clauses).

However, the most sad thing isn't the fact that they were convinced about it. It's the fact that I SAID that SEVERAL TIMES during my presentation but they didn't hear me (although they invited me).

ICZN and ICBN use phylogenetic definitions.
It's funny but I heard this as an argument against the PhyloCode: “why do you want the PhyloCode while the rank-based codes also use phylogenetic definitions?” Rank-based codes DON'T use phylogenetic definitions. Well, we can define taxon names without the PhyloCode, but people would use whatever they want, which is AGIANST the approach of phylogenetic nomenclature because one of the main points is universality (all scientists should use the same names for the same taxa).

References
de Queiroz, K. & Cantino, P. D. 2001. Taxon names, not taxa, are defined. Taxon 50: 821–826.

Ghiselin, M. T. 1966. An application of the theory of definitions to systematic principles. Systematic Zoology 15: 207-215.

Stuessy, T. F. 2000. Taxon names are not defined. Taxon 49: 231–233.

Stuessy, T. F. 2001. Taxon names are still not defined. Taxon 50: 185–186.

[mattmart]

The PhyloCode is intended as a replacement for the rank-based codes.
It's right there in the Preamble: "This code may be used concurrently with the rank-based codes." In fact, since the PhyloCode uses species names as specifiers but does not govern them, it actually requires the rank-based codes.

I think this one might be a little misleading. Didn't we already establish that there could be instances where the two codes are contradictory? Especially wrt priority of "family-level" names.

PC will rest on the part of existing codes governing species but may be incompatible with the rest, because while both codes treat species as non-clades, one set of codes also treats families and genera as non-clades and another does.

Anyway, how about:

The PhyloCode is relationship-based, never character-based.
I've encountered a few people who think all apomorphy-based clades will become character-based and destabilize everything. They're unaware apomorphy-based definitions are possible, so you don't necessarily have to exclude animals with an amnion from Amniota.

[David Marjanović]

Of course, Species are not clades in the sense they are always monophyletic.

That depends on the species concept; under some (rarely used) concepts, they are clades.

But 1) this is nitpicking, and 2) the PhyloCode should not, and does not, choose people's species concepts for them.

Still smiling at the T shirt

[David Marjanović]

That smiley is horrible. It looks outright sad. It's supposed to be smiling!

[Daniel Madzia]

That smiley is horrible.

I agree. This one is stupid. The other are fine...