Thursday, November 28, 2013

Beating the dead horse Paraphyly.

I know I said I was going to cut back on the ICZNerdery. But this letter by Jaroslav Flegr to Zootaxa this week was too weird to pass up. Morgan Jackson summed it up nicely:



Summary (tl;dr): There is not one shred of anything new here. There's not even anything nomeclature related. The author is using Zootaxa to opine about paraphyletic inclusive classification, that is it, there's nothing else to this "paper" if it could even be called that. (Though, note: the link above only contains the first page and references if you don't have a subscription.)


The title, "Why Drosophila is not Drosophila anymore, why it will be worse and what can be done about it?", suggests this is going to be about the Drosophila melanogaster ICZN case last year. I never wrote a proper post about it, and given the complicated nature of the case I'd prefer not to repeat it here. So check out Kim Van Der Lin's summary in the link if you need a reminder. 

But the title is deceptive. Flegr starts off discussing the case, and he gets one thing wrong immediately. Molecular taxonomic studies have not shown that "the correct name of this species should be Sophophora melanogaster". What they have shown is that Drosophila as it stands now is a paraphyletic taxon. The actual raising of the subgenera to genus level is something that has yet to happen. And when, inevitably, someone revises the genus and raises them, the rest of us can dispute that action. That's right, you heard me correctly. Changing a taxon's rank, changing it's genus, etcetera, are subjective decisions, and unlike the fixation of types are not regulated under the Code. Someone else can come along later and challenge it without getting the Commission involved. D. melanogaster is also not "the fly that eats their fruit". Though they are often called "fruit flies", the common name is "vinegar flies" because they feed on fermenting fluids.

The rest of the "paper" is devoted to supporting a paraphyly friendly classification system, something that seems quite strange to the Cladist majority of taxonomists. Now, mind you, there's nothing in the Code prohibiting paraphyly, but the majority reject it because we've become devoted to a classification system that is descriptive, predictive, and explanatory. We've discovered that when our biological classification is based upon evolutionary descent, and in particular on monophyletic groups (groups that contain a common ancestor and all of it's descendants), it is a powerful general reference system. And when that system includes paraphyletic groups (which contain a common ancestor and only some of it's descendants), it looses predictive and explanatory power.

Flegr moves to his point in a roundabout manner, first starting with an utterly confusing explanation of paraphyly. (Note: Taxonomists are overwhelmingly visual. Reading a long list of possible relationships between Taxon A and Taxon B is about like trying to decipher one of my grandfather's differential equations.) Fer Linneaus sake, use a real life example!  He blames molecular systematics for the multiplication of paraphyletic taxa in recent years, which is a common enough theme in the literature that I don't pay it much attention. All it tells us is that the author is a traditional taxonomist who probably uses physical structures of the organism exclusively.

His statements about "inner and outer similarity" reflect a real problem in systematics, sometimes called the phenotype/genotype conflict. When we infer evolutionary relationships, often times the physical and DNA characters deliver us a differently shaped tree, and we're unable to tell whether one or either of these reflects reality better. But calling it a "conflict" is a misnomer. As one of my committee members recently told me, there is no real conflict between between the morphological and molecular characters. The conflict is in the methodology, and how we analyze the data. Flegr writes "nothing might be possible to guess from a system that would not reflect the inner similarity of the species", as if morphology is doomed to forever represent convergence and DNA is innately neutral to selection. Neither of these are right. 

The deep and real problem that he is reaching for but missing, is that many traditional classifications are based upon obvious physical characters rather than evolutionarily meaningful ones. There are, for example, many characters that place birds as a therapod lineage. But since these are not as obvious as "has feathers" and "is warm blooded", and since this uniqueness is part of a traditional classification, people continue to place them in a separate lineage from other archaeosaurs. Why? Because tradition, because, as Flegr puts it, "secondary school biology teachers are far much more numerous than theoretical taxonomists."

I'll refrain from commenting upon this except to say that allowing high school biology teachers to dictate how we should classify organisms is ridiculous.

Flegr's solution is to allow paraphyletic groups to stand. Of course. What better way to solve a problem than to ignore that it exists? Then you don't have to go through the messy route of educating people. And while we're at it, why don't we just throw out this whole evolution thing? It's so much easier to classify organisms based on obvious characters like, for example, lacking wings. The insect order "Aptera" worked out so well.

There are also some fairly ugly diagrams which are not at all convincing. 

Throughout, Flegr tries to make his case using the prevalence of punctuated equilibrium in major radiations rather than gradual change. Somehow this is evidence for rejecting reciprocal monophyly. I don't see it. There's also the opinion that these phylogenies will make our classification system inherently unstable. To which I reply: They are unstable now. Classifications that are based upon obvious similarities rather than evolutionarily relevant characters will forever be subject to the whims of authority opinions. What Flegr wants is to go back to the days of evolutionary taxonomy, where if Dr. Smith was the expert on so and so group, then whatever he said goes. NOPE NOPE NOPE. 

This is all very much a Dubois-ism, in the spirit of the last paper I wrote about. He concludes,

It is, of course, probable that most of the current theoretical taxonomists, who spent a large part of their active professional life fighting the fuzzy eclectic phylogenetics and taxonomy, would not be very enthusiastic about the recurrent more and more urgent suggestions of rehabilitating the paraphyletic taxa (Hörandl, 2006; Hörandl & Stuessy, 2010; Podani, 2010a; Zander, 2010). The change, fuelled by practical taxonomists who mostly use a ‘wrong’ eclectic taxonomy in their everyday practice anyway, will be probably slow and painful. It is, however, necessary to start the change as soon as possible. Otherwise, we might soon have to say farewell not only to drosophilas but to the whole taxonomic system.
I suspect these authors he cites are all in the same boat, a bunch of "taxonomic reactionaries" who can't cope with their authority being overturned and their traditional taxa being reshaped by evolutionary understanding. They call it "practical taxonomy"; I call it the easy way out. Flegr also shows himself to be a doomsayer by the last line. It's the end of the world as we know it, apparently.

In closing, no, wait. I don't think this mess merits a wrap up. Flegr leaves us one last gift, a tagline. 

"Australopithecus sapiens, possibly Reptilia, Pisces"
  1. Australopithecus does not have priority over Homo
  2. Reptilia is a paraphyletic group.
  3. So is Pisces.

7 comments:

Stephen Thorpe said...

Yes, this "paper" was pretty much a pointless self-indulgence on the author's part, and boo Zootaxa for publishing it (or are they a tabloid now?) Nevertheless, the actual issues involved in the D. melanogaster case are important. In this case, just about any option which avoids a name change is preferable, on pragmatic grounds, since the name Drosophila melanogaster is sooo widely known and used. The best option seems to me to make Drosophila a more inclusive genus. This would solve the problem of paraphyly, but would result in a fair few other necessary name changes due to homonymy. However, changing the names is easy, and none of the species requiring a name change are particularly significant, so the sum of the disruption to current usage would be small by comparison to the massive disruption of a name change to D. melanogaster.

ZL "Kai" Burington said...

Oh, I agree completely Stephen! And I was looking forward to reading a paper on the actual case and proposed solutions. Unfortunately this wasn't any of those things.

I also agree that making Drosophila more inclusive is the best option. On the other hand, Drosophila is such a huge genus. It would be nice to find some amiable way of breaking it up, but I guess people "need" D. melanogaster to stay with the same name. In any case, I don't actually work on the group so I await the inevitable revision.

Stephen Thorpe said...

Well, the beetle genus Agrilus has over 3000 species (see https://species.wikimedia.org/wiki/Agrilus), and this doesn't seem to cause too much of a problem.

I would however be quite happy to retain a paraphyletic Drosophila, provided that it was somehow tagged as paraphyletic (or at least made well-known to be paraphyletic). I'm not convinced by the "less predictive" argument against paraphyletic taxa. One doesn't predict anything from the name! Not really. As long as you know it is paraphyletic, you can make any predictions accordingly.

Thomas R. Holtz, Jr. said...

Actually, "Reptilia" is a monophyletic group. The standing definition for vertebrate workers was best summarized by Modesto and Anderson (http://sysbio.oxfordjournals.org/content/53/5/815.full): all taxa closer to Lacerta agilis and Crocodylus niloticus than to Homo sapiens. This definition matches the use of Reptilia by paleontologists and other vertebrate systemacists since the mid-1980s.

However, with this definition the members of Synapsida, including mammals, including Homo sapiens are NOT reptiles nor reptile descendants. And in fact the Modesto & Anderson definition explicitly excludes Homo sapiens!

ZL "Kai" Burington said...

Ah, so it's synonymous with Sauropsida. That is acceptable, as long as it includes birds. :)

Mike Keesey said...

Note that the original conversion of "Reptilia" was as the name for the sauropsid crown group. Depending on the placement of turtles, this may or may not be the same as the diapsid crown group.

Others have suggested that we just abandon it as a formal taxonomic name, like "Pisces".

Thomas Holtz said...

Yes, regardless of whether we use the branch-based or crown-based definition, "Reptilia" as currently used by vertebrate systemacists includes birds.

However, as Mike notes, it would have been nice if had been dropped back in the 1980s, and we just went with "Sauropsida" for the branch-based clade and "Eureptilia" for the crown-based one. Neither of these terms come loaded with much historical baggage.