D. or S.? melanogaster

One interesting high impact dipterological discussion popping up on science news sites is the nomenclatural snafu that is Drosophila melanogaster. In a sentence, if melanogaster Meigen was not a model organism but still was part of a modern systematic revision, it would not be in the genus Drosophila. The problem is the genus. Drosophila contains about 1500-2000 described species and the earliest divergences in the genus occurred more than 60 Mya. More than half of the species in the family Drosophilidae are currently placed in Drosophila. Drosophila as currently conscribed is in the top five largest fly genera in term of described species (along with Tipula, Tabanus, Simulium, and Megaselia- future blog post topic, for sure). I would be surprised if any of those five are monophyletic. Drosophila is an ecologically diverse genus, with some generalist saprophages, some fungivores, and some phytophages, including some that are host species specific. The genus is morphologically diverse in terms of size and patterning, from classic tiny brown flies to ornate, house fly-sized Hawaiian picture winged Drosophila.

These flies are vastly popular in experimental biology. Summarizing all of the contributions to modern science from studies of these flies would be quite a task. Nobel prizes have been awarded to scientists who study Drosophila for such discoveries as homeobox genes. Most research is done on Drosophila melanogaster but a few other dozen other drosophilid species are cultured for research. Elements of the life history of Drosophila melanogaster from its behavior to its genetics are vigorously researched. Scientists have sequenced the genomes of D. melanogaster and eleven other Drosophila species in largest comparative genomics project currently available. The phylogenetic relationships of those twelve species represent one of the most certain areas on the entire tree of life. Rigorous phylogenetic hypotheses of Drosophilidae have followed suit.

Many lucid, well-written studies have concurred that Drosophila is paraphyletic with respect to at least seven other genera. If these were tiny unimportant genera, maybe they could be sunk into Drosophila and problem solved. Unfortunately, these genera, such as the speciose, cosmopolitan Scaptomyza have hundreds of species, are morphologically diverse and are easily distinguished from Drosophila. Furthermore, the type species of Drosophila, D. funebris Fabricius, is nowhere near melanogaster phylogenetically. According to common taxonomic practice, Drosophila melanogaster's subgenus Sophophora would be elevated to genus, creating Sophophora melanogaster. Indeed, only 3 of the 12 Drosophila species with sequenced genomes are Drosophila sensu stricto. The other nine are in subgenus Sophophora and the other six or seven smaller subgenera of Drosophila sensu lato are not represented by sequenced genomes. Understandably, there is a lot of backlash towards Sophophora melanogaster.

These findings leave the scientific community with three main options:

  1. leave Drosophila sprawling and paraphyletic.
  2. suck it up and accept Sophophora melanogaster.
  3. change the type species of Drosophila to melanogaster.

Here is a Nature News article about this predicament. I'll go over some of the pros and cons of each.

Drosophila melanogaster
The lowly pomace fly, Drosophila melanogaster… or is it Sophophora melanogaster. Thanks to gurkeeeee for capturing this image.

To be honest, option 1 has been the modus operandi for many years. The fact that Drosophila melanogaster belongs in a different genus than Drosophila funebris has been some combination of a migraine headache, open secret, and skeleton in the closet for fly taxonomists for at least 30 years. Leaving the genus non-monophyletic opposes a practical convention in modern systematic that every name should ideally describe a monophyletic taxon. It is obviously problematic if one wants to compare a species of Drosophila to its closest relatives, but it closest relative is in a different genus. It is possible to argue that this convention should be ignored as long it is made clear to all workers on drosophilids that Drosophila is not monophyletic. Upending this scientific convention for the sake of convenience (though some might argue that paraphyletic taxa are A-OK) is not likely to happen, at least not for long. Such phylogenetic focus on a single fly family from so many workers is rare, and we should take advantage of their findings.

The reasons for or against accepting Sophophora melanogaster are simple but coercive. This name change is the proper procedure under the ICZN. The zoological community created and should accept the decisions of the ICZN. However, this will lead to a headache-inducing upheaval in many other fields. D. melanogaster and the other Sophophora species pervade modern biological literature. “Chaos” according to Patrick O'Grady, “Genetic work could be lost. It would be hard to find things.” Andrew Polaszek for instance, claims that D. melanogaster is the most studied organism other than Homo sapiens. That seems hyperbolic to me; I would say that is the most studied organism that we don't eat, that doesn't make us sick, and that isn't us. Certainly it is the most important organism that might potentially change its name. It is often pointed out that many references to 'Drosophila' really mean 'Drosophila melanogaster.' The commonly used abbreviation 'Dmel' will also be outdated. Changing all those names will cause instability in the short term, and the ICZN was created to maintain stability.

The last option has already been submitted as a case to the ICZN by van der Linde et al. (a community ecology postdoctoral student, curiously.) The proposal will:

  1. raise all subgenera other than Drosophila and Sophophora to generic level
  2. switch the type genus of Drosophila to melanogaster, making Sophophora a junior synonym (melanogaster is conveniently the type species of Sophophora).
  3. split the old Drosophila subgenus into three genera, resurrecting already existing names.
  4. move the 78 species unplaced in Drosophila senso latu to Drosophila sensu stricto/novo.

So Sophophora goes bye-bye, and nine of the species with genomes sequenced stay Drosophila. Two other sequenced Drosophila species will be in Siphlodora and grimshawi, the sequenced Hawaiian species, will be in Idiomyia. One thing this proposal does is remove the Hawaiian Drosophila radiation from the genus Drosophila. A lot of ecological and systematic literature concerns that radiation (and calls it Drosophila). More species will change their names than would if Sophophora was accepted. The worst part of this proposal to me is what happens to the unplaced species. Sophophora is a well-defined monophyletic clade, and most of those 78 unplaced species probably have nothing to do with Sophophora, but they will all be in the same genus according to this proposal. I think that moving those species to incertae sedis within the tribe or subfamily is a better plan. Switching the type species of a genus has been done very rarely, if at all, in the history of the ICZN. Clearly, no matter which option is chosen, well-studied organisms will change genera. Synonymizing Sophophora is not a silver bullet. This proposal might create more nomenclatural stability problems than would exist in the Sophophora melanogaster scenario.

I think I agree most with the position that Chris Thompson & the other editors of the BDWD have adopted: let the name changes go the way they would with any other lucid taxonomic paper, e.g. go ahead with Sophophora melanogaster. Then, see whether the broader scientific community accepts the name or not. To further editorialize, I think that if the change happens and you call Sophophora melanogaster 'Drosophila melanogaster,' no one will slap you in the face; it will be clear what you are talking about. I don't really understand how any information will be lost. S. and D. melanogaster won't refer to different species, one name will just be more correct than the other. I think one could go as far as to consider 'Drosophila melanogaster' a common name for the fly, just as Boa constrictor is the scientific and common name for that snake. To get even more snarky, there are no rules set up by a respected international committee of geneticists and developmental biologists that have formally decided that model organisms can never have their names changed. The ICZN, on the other hand, has established proper nomenclatural protocol. Of course there are some solutions that I have not discussed (PhyloCode anyone?).

This is a difficult problem, and deserves thought and input from everyone from entomologists to medical researchers to high school teachers. I am not decided for sure, and will continue to follow the situation. It would be great for you to read the proposal and the comments on the ICZN site and voice your opinion here or elsewhere.

Also, Happy Darwin Day!

5 Responses to “D. or S.? melanogaster”

  1. Mike Sharkey says:

    Another solution to this nomenclatorial conundrum is to change the rules of zoological nomenclature, i.e., fix all species names in their present generic combinations to facilitate communication and maximize information retrieval. A new rank in the hierarchical scheme, just above the genus level, could be erected to replace the generic rank, and it would be free to float with changing information.

    Posted by Mike Sharkey on February 12, 2009 at 06:54 PM EST

  2. ardeans says:

    Epic and thought-provoking post. I was going to make a joke about how we should just refer to this species by is its ZooBank LSID, but it isn’t registered! At least not as of the time of this comment. Google Scholar, by the way, breaks down the research like this: Homo sapiens 107,000 articles, Bos taurus 28,500 articles, Plasmodium 276,000 articles, HIV 4,380,000 articles, and Arabidopsis 740,000 articles. And the lowly D. (S.) melanogaster? 240,000 articles.

    Posted by ardeans on February 12, 2009 at 07:07 PM EST

  3. kmbayles says:

    Your google scholar results are a little misleading. No way Arabidopsis beats Drosophila.
    Arabidopsis 740,000 vs. Drosophila 1,100,000
    Arabidopsis thaliana 138,000 vs. Drosophila melanogaster 240,000

    Posted by kmbayles on February 12, 2009 at 10:23 PM EST

  4. Ted C. MacRae says:

    I keep waiting to see the ‘chaos’ that results from proper application of ICZN protocol. I say proceed with the name change – people will quack for awhile but eventually get over it and move onto the next ‘threat to stability’.

    Besides, if the name becomes Sophophora melanogaster, we can change the abbreviation to ‘Smel’ – kinda poetic for a fly!

    Posted by Ted C. MacRae on February 13, 2009 at 12:36 AM EST

  5. ardeans says:

    There’s an interesting conversation about this very topic (the Drosophila situation) going on over at the Nature network.

    Posted by ardeans on February 17, 2009 at 10:01 AM EST

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