01 March 2010

The Great PhyloCode Land Run

Sometime in the near future, the PhyloCode will be enacted. For this to happen, two things need to happen concurrently:

1. The registration database (called "RegNum") must be completed and opened to the public. This is necessary because the PhyloCode requires all names to be registered electronically.

2. Phylonyms: a Companion to the PhyloCode must be published. This is a multi-authored volume that will include the earliest definitions under the PhyloCode.

Which names will be defined in Phylonyms? The original goal was to cover the most historically important names (what Alain Dubois calls "sozonyms"). However, proponents of phylogenetic nomenclature tend to be clustered in several fields (most notably vascular plant botany and vertebrate zoology—note that the code's authorship reflects this). This means certain parts of the Tree of Life (e.g., entomology) will unfortunately be underrepresented, due to lack of interest in those fields. (The alternative, having non-specialists define such names in Phylonyms, does not bear consideration.) So Phylonyms will be less about providing coverage and more about providing sturdy, well-reasoned definitions that can serve as examples.

What about all the names that it omits? What will happen to those once the PhyloCode is enacted? That will be interesting to see.


One thing I could envision is a sort of "land run". I picture it working this way. Let's consider a field, say, anthropology, where phylogenetic nomenclature has not taken much of a hold. Currently there is debate about how to use some taxonomic names related to the field. Some workers like to use the familial name "Hominidae" to refer to a large taxon, including humans and great apes. Others prefer to restrict it to the human total clade (i.e., humans and everything closer to them than to other extant taxa). Similarly, some workers use the generic name "Homo" in a broad sense to include short, small-brained species like Homo habilis, while others prefer to restrict it to the tall, large-brained clade (relegating H. habilis to another genus, e.g., Australopithecus).

Let's say there's a researcher out there named Dr. Statler, who prefers a strict usage for "Hominidae" and a broad use for "Homo". But his colleague, Dr. Waldorf, prefers a broad usage for "Hominidae". Dr. Waldorf isn't really that interested in phylogenetic nomenclature, but when he notes that "Hominidae" is not in the registration database, he sees an opportunity. He writes a quick paper defining "Hominidae" as a node-based clade: "The clade originating with the last common ancestor of humans (Homo sapiens Linnaeus 1758), Bornean orangutans (Pongo pygmaeus Linnaeus 1760), common chimpanzees (Pan troglodytes Oken 1816, originally Simia troglodytes Blumenbach 1775), and western gorillas (Gorilla gorilla Geoffroy 1852, originally Troglodytes gorilla Savage 1847)."

Dr. Statler is, of course, outraged. Not that he cares that much about phylogenetic nomenclature, but what if anthropologists do start using it? What if someone ruins another taxonomic name? His colleagues Drs. Honeydew and Beaker prefer a strict definition of "Homo"—what if they author a paper cementing that definition under the PhyloCode?

This cannot come to pass! Dr. Statler does some reading on the code and decides that a branch-based definition would work nicely for his broader usage. He defines "Homo" as, "The clade consisting of Homo sapiens Linnaeus 1758 and all organisms that share a more recent common ancestor with H. sapiens than with Australopithecus africanus Dart 1925, Paranthropus robustus Broom 1938, Zinjanthropus boisei Leakey 1959, or Australopithecus afarensis Johanson & White 1978." This sets off another anthropologist, and soon all sorts of anthropological/primatological names are being defined under the PhyloCode, as workers struggle to assert their usages.




This is not an ideal situation. It would be much nicer if a group of anthropologists were to come together, discuss the matters rationally, and arrive at an agreement which they then publish together. But it's still not a horrible situation—at least people are defining phylogenetic names and at least interest in phylogenetic nomenclature is being spread. I can't predict the future, but I feel like this sort of "land run" is bound to occur at least in some fields—and maybe that's okay.

7 comments:

  1. I'm starting to believe the phylocode is a bad idea once again, the arguments being:
    1) if the goal is stability, then throwing out 250 years of nomenclature isn't going to aid that,
    2) it includes a priori assumptions about phylogeny before observing and investigating the physical pattern (an issue I have already with maximum likelyhood techniques),
    3) hybridization and polytomy are not things we can objectively test, a bifurcating cladogram is still more informative,
    4) if there is an issue with our phylogeny not representing the patterns of synapomophy we see, we can already change it by publishing revisions, and
    5) we don't have to name every rank; people who equate ranks with any meaning other than adding a bit of information about hierarchy to the classification system are operating under a false understanding of systematics in the first place.

    So, I'm sorry, but I don't agree with you anymore. I think phylogenetic nomenclature will go the same direction as uninomial nomenclature in a few years.

    ~Kai

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  2. "1) if the goal is stability, then throwing out 250 years of nomenclature isn't going to aid that"

    Who said anything about throwing it out? Converting a name simply clarifies its meaning under a given phylogenetic context. It throws nothing out.

    "2) it includes a priori assumptions about phylogeny before observing and investigating the physical pattern (an issue I have already with maximum likelyhood techniques)"

    It's a nomenclatural code—it does not govern phylogeny itself. It does not require any a priori assumptions except that: A) there are units (organisms, species, whatever), and B) they can be arranged according to ancestor-descendant relationships. You can't tell me that's too much to swallow.

    "3) hybridization and polytomy are not things we can objectively test, a bifurcating cladogram is still more informative"

    Why can't we test those? And who says you can't use a bifurcating cladogram?

    "4) if there is an issue with our phylogeny not representing the patterns of synapomophy we see, we can already change it by publishing revisions"

    I'm not sure what you're saying here.

    "5) we don't have to name every rank; people who equate ranks with any meaning other than adding a bit of information about hierarchy to the classification system are operating under a false understanding of systematics in the first place."

    Again, I'm not sure what you're saying. The PhyloCode allows ranks. See Article 3.

    "So, I'm sorry, but I don't agree with you anymore. I think phylogenetic nomenclature will go the same direction as uninomial nomenclature in a few years."

    Phylogenetic nomenclature is different from the PhyloCode. Phylogenetic nomenclature is doing quite well in several fields, so rumors of its demise are greatly exaggerated. As to whether the PhyloCode will take off—those who want to use it will use it and those who don't won't. It's hard to see how that will play out.

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  3. I'm all for PC, but I agree nothing but drama that dwarfs Aeto-Gate could come out of declaring open season on getting one's name permanently attached to any number of well-known taxa. Especially if the ICZN concurrently rules that ICZN publication of genera online can be allowed.

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  4. Which could very well happen.

    Fortunately the nominal author[s] is/are given primacy (they weren't in the original draft). But, yes, that could contribute to the "land run" mentality -- although, again, maybe that's not the worst thing that could happen.

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  5. proponents of phylogenetic nomenclature tend to be clustered in several fields (most notably vascular plant botany and vertebrate zoology—note that the code's authorship reflects this). This means certain parts of the Tree of Life (e.g., entomology) will unfortunately be underrepresented, due to lack of interest in those fields.

    Is there any good explanation for that lack of interest? And how serious a problem do you think the disproportion in field representation is?

    The PhyloCode allows ranks.

    Please enlighten the unenlightened... I thought getting rid of ranks was the whole raison d'être behind the PhyloCode? How exactly is 'allowing ranks' supposed to work in practise? To me, it sounds like trying to have the cake and eat it too, as well as like a near-certain recipe for considerable confusion. What am I missing?

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  6. "Is there any good explanation for that lack of interest?"

    That's a good question, and I don't really know the answer. With regard to entomology, possibly it's because Hennig (who was an entomologist) introduced the idea of cladistic classification early on, so the rank-based system was adapted to fit (more or less). Also, in many fields workers are more concerned with alpha taxonomy than with beta taxonomy, and phylogenetic nomenclature has been focused much more on beta taxonomy. (Or, in a sense, it replaces beta taxonomy with phylogeny.)

    I can think of two reasons why vertebrate zoology would be a natural candidate for phylogenetic nomenclature. 1) We ourselves are vertebrates, and because we are self-centered, we have historically named a lot of paraphyletic wastebasket taxa that include our ancestors but not ourselves (including at least certain usages of the names "Australopithecus", "Pongidae", "Prosimii", "Insectivora", "Cynodontia", "Therapsida", "Synapsida", "Reptilia", "Amphibia", "Sarcopterygii", "Osteichthyes", "Pisces", and "Agnatha", although many of these have been used for clades as well). This really exacerbates the rank problem when attempting to reinterpret names as clades. (Not that, e.g., Insecta doesn't have a lot of named paraphyletic subtaxa, but the nesting is not as bad, I think.) And 2) vertebrates have a relatively spectacular and well-studied fossil record, which means that we can see a lot more nodes on the tree. Again, this exacerbates the rank issue.

    "Please enlighten the unenlightened... I thought getting rid of ranks was the whole raison d'être behind the PhyloCode?"

    It's a bit more nuanced than that. The real raison d'être was to tie taxonomic meaning to phylogeny. This means getting rid of mandatory ranks, because you can't tell what rank a taxon should be from its phylogenetic definition alone. This doesn't mean you can't rank them, although it does mean that when a taxon changes rank, its name cannot change, contra the rank-based codes.

    The PhyloCode has allowed ranks since (I think) the first draft. (It's right there in Note 3.1.2.) It simply does not require them.

    I highly recommend de Queiroz's 2005 paper, Linnaean, rank-based, and phylogenetic nomenclature: Restoring primacy to the link between names and taxa for more on this topic.

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  7. David Marjanović12 October, 2011 19:40

    2) it includes a priori assumptions about phylogeny

    It doesn't include any assumptions about phylogeny, except that such a thing exists – that evolution happens at all.

    "Is there any good explanation for that lack of interest?"

    That's a good question, and I don't really know the answer.


    The answer is ignorance, plus inadvertent disinformation from ignorant people.

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