Thursday, April 8, 2010

Drosophila politics: Sophophora melanogaster

The commission has ruled, Drosophila funebris remains the type species of the genus Drosophila, opening the way a renaming of Drosophila melanogaster to Sophophora melanogaster. To understand better how we got here, I will provide some background information on the history of the genus, the history of the case, the decision and how to move forward.

The history of the genus Drosophila

The genus Drosophila was established in 1823 by Fallén, who included 12 species. Drosophila melanogaster was described in 1830 by Meigen, who placed it in the genus Drosophila. Then, in 1939, Sturtevant subdivides the genus in several subgenera, including the subgenus Sophophora, home of Drosophila melanogaster. In 1990, Grimaldi removed several subgenera from the genus Drosophila, and elevates them to the level of genus, including the subgenera Scaptodrosophila, Hirtodrosophila while several other subgenera are moved to the Hawaiian 'Drosophila' genus, Idiomyia. The latter name has only been accepted sparely, most researchers place them in the subgenus Drosophila. Over time, the genus Drosophila has been the receptacle for many species of fruit flies, especially those lacking obvious characteristics that warrant a separate genus, resulting in a genus that consists of more than 1000 species (or 1500 if the Hawaiian 'Drosophila' are included).

The history of the case

Several years ago, I was in need of a good phylogeny of the genus Drosophila for a comparative analysis. I have images of more than 21.000 fly wings spanning more than 100 species across the family Drosophilidae. However, if you want to know how those wings evolved, you have to consider that closely related species will be more similar because they share more of their evolutionary history with each other compared to more distantly related species. Six years ago, everybody was waiting for Patrick O'Grady to finally publish his comprehensive molecular phylogeny. A few years earlier, in 2002, O'Grady, together with Rob DeSalle had received a US$ 367.221 grant to study the phylogenetic relationships within the family Drosophilidae by sequencing and analysing up to 60 genes for more than 100 different species. We are still waiting, well, not for long any more as we now have our own molecular phylogeny in press with Genetics Research.

After waiting a few years on the Drosophila phylogeny, something had to happen, en I pulled together all the existing literature covering small parts of the phylogenetic tree of the genus Drosophila, and pieced them together first by hand, and later using a formal method, called the supertree analysis. That tree was published in 2008. What the analysis showed was that the genus Drosophila as currently defined is paraphyletic. Several genera, including Hirtodrosophila, Scaptomyza, Zaprionus, Mycodrosophila and several more are positioned within the genus Drosophila.

Among taxonomists, a continuing discussion is whether paraphyletic taxa are desirable/accaptable or not. However, there is one crucial aspect to consider. Homogeneity. Consider the following scenario. Take a group of species that are closely related. All species, except those in one small branch look very similar to each other. The exception is that small clade that is very different from the remaining species. In such a case, grouping the two genera in a single genus to make a monophyletic genus does not make sense. Unfortunately, this is not the case in Drosophila. The genus is very heterogeneous, and the various clades are often more alike to the included genera than to the more distantly related relatives in the genus. So, Drosophila is not a good candidate to keep as a paraphyletic genus, an option preferred by some researchers such as Patrick O'Grady.

So, what are the alternatives?

One alternative is to sink all included genera into the genus Drosophila, which would result in a very large (2250+ species) genus, that is rather heterogeneous, and it would result in more than 100 secondary homonyms (that is, two species with the same name of which the species described last needs to get a new name).

The other is to split the genus along the major clades, and elevate each of the clades to the rank of genus. That is an easy solution, and done frequently in taxonomy. Unfortunately, there is only one small problem. And that is that Drosophila melanogaster would be renamed to Sophophora melanogaster.
Yes. You read that right.

This is a situation where nomenclature, the science of how to name species and higher taxa, clashes with reality. Why? Because Drosophila melanogaster is not just your average run-of-the-mill species. Drosophila melanogaster is one of the most studied model-organisms in the world, with more than 50.000 published articles; references in almost each and every biology textbook on many many different topics; it is used in high school biology classes to teach kids the fundamentals of genetics; it is used in medical research, in neurobiology, in ecological, studies, in genetics, etc. So, renaming such a species is not feasible.

When you come to that conclusion, there is only one way to go, and that is to the International Commission on Zoological Nomenclature, effectively a small group of well-respected taxonomists who decide when overruling their own rules is better for taxonomic stability. So, we submitted an application to the commission for consideration, in which we asked them to change the type species for the genus Drosophila to Drosophila melanogaster, so that the name Drosophila melanogaster would be carved in stone. For now and for ever.

The Decision

A few days ago, the commission published their decision. In the three years between the publication of the application and the decision by the ICZN, many comments by outsiders have been published. Some of them were in favour, some against. In the end, the commission ruled 4 against 23 to reject the application. I won't go into the arguments of the individual commissioners, but they can be grouped in several broad arguments:
  1. We do not know enough.
  2. People can learn a new name.
  3. Let's not create precedent.
  4. A paraphyletic genus is not a problem.
  5. Conserving the name would require more species to be renamed.
  6. The other model species
Lets see.

1. We do not know enough.

Really? Sorry if I sound underwhelmed. There are over 20 published phylogenies covering a wide range of species, and at least a 30 more that focus on smaller groups. We summarized everything in a nice article in 2008, and there is only one conclusion that follows from that article, and that is that the genus is paraphyletic, and that most clades are well defined. A comprehensive molecular study pointing at exactly the same thing is in press. Okay, they did not have access to the latter, but the latter only confirms what we already knew from the previous publication.

2. People can learn a new name.

True. But will they accept the new name? Because if the scientists won't accept the new name, they won't learn it, and it won't trickle down to the general public. During the proceedings, various examples have been put forward on acceptance of new names. One example was hilarious, because it was presented as a perfect example on how new names were accepted. Stegomyia aegypti used to be called Aedes aegypti, until a few years ago, the genus was revised and the name changed. Unfortunately, contrary to the claim as a successful name change, it was not accepted by the community at large, to the point that several journals, including Journal of Medical Entomology, Annals of Tropical Medicine and Parasitology, Emerging Infectious Diseases, Journal of the American Mosquito Control Association, Journal of Vector Ecology, Medical and Veterinary Entomology, Transactions of the Royal Society of Tropical Medicine and Hygiene, Vector Borne and Zoonotic Diseases, and PROMED, publicly denounced the new name. Another example was the renaming of the zebrafish, Danio rerio, which was easily accepted. True, but as a colleague who works on the species explained, that name change did take place before the zebrafish became a popular model system, so hardly anything was affected by it. The situation with Drosophila melanogaster is rather different as I explained above.

3. Let's not create precedent.

First of all, the commission by design does not have to take into consideration what happened in previous cases. Each case is decided on its merits, without regard of previous rulings. But even if they did consider precedents? Would that be a problem? Unlikely because there are not that many widely used model systems, and most of them are phylogentically positioned in places that a name change is really unlikely. Unsurprisingly, no examples of other potential cases have been presented.

4. A paraphyletic genus is not a problem.

Okay, I discussed that one above already, no need for repetition.

5. Conserving the name would require more species to be renamed.

I am not sure how they came to this conclusion as we explained in the original application. When the genus is split, it will be split according to the four major clades. So, the names of the species in two of the clades will change regardless. Of the two remaining clades, the clade with Drosophila melanogaster is the largest, effectively preserving the name of the largest possible number of species.

6. The other model species

Some voiced concern about renaming the other Drosophila model species like Drosophila virilis and Drosophila grimshawii. Well, by rejecting the application, none of the species will retain the name Drosophila because none of the species is in the clade with the type species.

How to move forward

So, what is next? Good question. Several options remain:

  1. Do nothing.
  2. Accept phylocode for the genus and forget about having a nice rank-based classification.
  3. Split the genus and renames Drosophila melanogaster to Sophophora melanogaster and test the argument that it won't matter and that people will accept the new name.
  4. Elevate the clade one by one to the level of genus, slowly but surely dismantling the genus until only two relative small unrelated clades remain, one with funebris, and one with melanogaster.
At this stage, I have not made a decision what my next step will be. See my next post here.


Al Dove said...

What a fascinating drama. I had no idea the genus was so big to start with.

I have to feel in this situation its best to just accept that perhaps the accepted taxonomy doesn't entirely reflect reality, and just live with it. On some level, ALL taxonomy is subjective, so wouldnt it make more sense to just make it a special case and realise that the upside of doing so far outwieghs the "truth" benefit to be gained by rearranging the whole thing.

Unknown said...

Al, what you suggest is basically equivalent to accepting phylocode. Once you accept that, there is not a problem, because the ranks have disappeared and everything will be in the clade called Drosophila.

Christopher Taylor said...

Very much horn-grabbing time, I feel - establish Sophophora as a separate genus.

While I knew that this had been an issue for some time, I was a little surprised by László Papp's statement that it had been so for more than thirty years. If people hadn't been tiptoeing around the question so long then it could have been resolved one way or another long before now.

Andreas Johansson said...

I don't understand how adopting the Phylocode helps here. It doesn't govern species names, and it's precisely the species name Drosophila melanogaster that's the problem here.

Buddhist_Monk_Wannabe said...

While I sympathize with Drosophilologists and other biologists who specialize on the species formerly known as D. melanogaster, I can't tolerate paraphyletic groups. Something deep down in my nature, I suppose. So, either the ICZN should be offed and phylocode put in it's stead (good way to make EVERYTHING instable), OR

we can raise Sophophila to genus and understand that 'Drosophila' has become a common vernacular term for the species S. melanogaster.

I think I take the latter.