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.
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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.

Sophophora melanogaster hits Nature's news wire

Short of having my own article in Nature, I go for the second best with that, a news article that effectively is the result of my work. A fly by any other name reports on our effort to save Drosophila melanogaster from being renamed to Sophophora melanogaster. I reported on this before, here and here, so go there for more thought of me about this issue.

Sophophora melanogaster (part 2)

So, I am back. The meeting was fun, and it was nice to put a lot of faces by names of people I never ever had met before. It looked like most Drosophila taxonomists preferred to save the name Drosophila melanogaster but unfortunately, there was no consensus about this. About what to do with the genus was even less clear, ranging from doing nothing, lump everything together (despite the huge range if issues that would create) and splitting the genus.

Doing nothing basically leads to the conservation of the current situation, in which taxonomists can split of smaller groups if they wish. There are several good candidates to be split of, and for which it is relative easy to just examine all species and find characteristics that are unique for the new genus. Unfortunately, that is effectively just increasing the paraphyly issue in the genus Drosophila. Two people objecting to doing the split now claim that we first have to examine ALL type species of the genus and the included genera, what effectively means examining 2250+ species, especially knowing that there are at maybe as many as 1500 undescribed species in the family, many of thoise within the genus Drosophila or the embedded genera (Oriental region and Hawaii primarily). Requiring that will result in a defacto arrast of any progress with regard of thie paraphyly issue.

Lumping the genera to a single genus is maybe even worse. Besides the enormous size of the genus (~2250 describe plus undescribed -> 3000+ species), it woyuld be very heterogeneous, and that is exaclt what we don't want; it is why various genera like Hirtodrosophila and Scaptodrosophila have been removed from te genus. But worse, there will be over 100 secondary homonyms, aka, species with the same scientific species name. In all these cases, a new name has to be generated, and if someone in the future removes those species again from the genus, the renaming has to be undone because the older name has priority. So, in stead of actually dealing with the issue at hand, it is just creating a much bigger issue.

So, splitting seems the only sensible thing to do. several clades are well defined, generally recovered as well-supported monophyletic clades. Some claim that for example the saltans-willistoni clade is basal to all the other drosophilids (aka, that this clade is the first to branch off, see MP-situation). This would mean that the second main branch in the subgenus Sophophora, the obscura-melanogaster clade together with all the other subgenera and the included genera is the sisterclade of the saltans-willistoni clade.

Well, there is a substantial amount of evidence against that topology. First of all, all studies claiming such an effect are based on Maximum Parsimony (MP), notorious for many things, but in this case primarily because it is often inadequate for issues related to variation in nucleotide composition. Variation in bucleotide composition can be adequatly addressed in Maximum Likelihood and Bayesian analyses using an adequate nucleotide substitution model that can explain apparant deviations. When you do that, the result is as in the figure under "Actual situation".

But there is another reason to suspect that the figure under "Actual situation" is better, and that is that the 12 genome paper actually has species of all three branches, and that study using about 9000 genes (gasp) clearly demonstrated that the "Actual situation" figure is correct, and the MP situation is incorrect. A similar situation occurs with the virilis s.l. and repleta s.l. clades in the virilis-repleta radiation. Here again, the 12 genome project tree clearly confirms that both branches are within a single monophyletic clade, and not in a different topology as suggested by some.

So, what will happen in the future? That is inclear. We have first to wait till the commission decides about the Sophophora melanogaster problem, and if they decide to go ahead, we will submit an article proposing to split the genus. If the commission decides against us, it might take a different route, with proposals to split of various clades till be effectively have a very extreme genus Drosophila with the melanogaster-obscura group and part of the immigrans-tripunctata radiation that contains the type species, D. funebris.

I keep you all posted!

Sophophora melanogaster

Yeah, in a few days, I will go to San Diego, to a meeting where all the major names in the Drosophila systematics will come together to discuss the future of the genus Drosophila, and especially Sophophora melanogaster. The genus Drosophila as currently defined is paraphyletic, and I together with a few others are going to propose to split the genus.



Not everybody likes that, and some have decided to organise a one day workshop to address this issue and some additional issues.

A major issue with splitting the genus is that one most used model organism, Drosophila melanogaster will change its name to Sophophora melanogaster. Yes, indeed. Impossible! That is not even worth a discussion, the sheer magnitude of schoolbooks, internet pages, etc that need to be adapted to accommodate such a change is unacceptable. Fortunately, there is a small group of scientists at the International Commission on Zoological Nomenclature who can debate, vote and overrule the normal rules for naming species. So, we submitted an application (pdf) to them, in which we asked them to fix this for the community by setting asside the current type species (D. funebris), and make D. melanogaster the new type species. Problem solved. You would think. Sounds like a no-brainer to me.

Unfortunately, a bunch of people object to it. Some say that the world just has to print new books, change the texts etc, and that we do not have to be mindfull of all those schoolkids etc. Others say we do not know enough, which as fas as I am concerned is bogus, but heck, disagreement is the fuel for progress.

Anyway, in a few days, I will be defending our proposal to split the genus, and see whether we can actually agree on this. I keep you posted!