Drosophila forever?


As I've commented before on this blog, taxonomy holds an unusual position in the biological sciences in that it fills two equally significant roles. On the one hand, it is a science in its own right, investigating the best way to describe and express the relationships between organisms. On the other hand, it supplies the means for communication between biologists in all fields. For the most part, these two aims compliment each other, but sometimes they can clash. The first aim implies continual change, as our understanding of the relationships between organisms changes and (hopefully) improves. Wheeler (2007) commented in a recent editorial that "Doing taxonomy as an independent science advances simultaneously both the aims
of taxonomy and its users"
, a sentiment that I agree with fully (be warned, though, that the general tone of Wheeler's editorial is fairly incendiary). To fulfil the second aim, however, a certain amount of stability is usually desired, as researchers who are not working in taxonomy may have trouble keeping up with the changes (or, for that matter, appreciating their necessity).

All of the codes of nomenclature have a central commission to regulate taxonomy - zoology has the International Commission on Zoological Nomenclature, botany has the International Association for Plant Taxonomy. One of the main roles of these commissions is to allow suspension of the usual rules in cases where their strict application would cause more trouble for communication than otherwise. In the case of zoology, applications for rulings on such cases that are submitted to the ICZN are published in the journal Bulletin on Zoological Nomenclature, allowing researchers the opportunity to comment on submissions before the Commission decides on them. One submission that appeared in the December 2007 issue of the BZN involves a case that could affect a large number of researchers in many fields - the impending revision of the fly genus Drosophila.

Drosophila is a very large genus, containing about 1500 species. However, phylogenetic studies (e. g. Robe et al., 2005) have found that Drosophila as currently defined is significantly paraphyletic with regard to a number of other genera in the family Drosophilidae. There are two options to resolve this situation. One is to sink all the smaller genera arising from Drosophila into the larger genus. However, this is not regarded as a suitable solution - not only would it leave Drosophila with over 2000 species, but it would result in over a hundred secondary homonyms (two or more species ending up with the same name as a result of change in genus assignment) that would require correction. The other option, that seems much more likely to be used, is to divide Drosophila into a number of smaller genera. The name Drosophila would then be restricted to a smaller group of species closely related to the type species.

All this would be fairly routine, except that one of the species affected happens to be one of the most widely used model organisms in genetics - the "fruit fly" Drosophila melanogaster (the inverted commas are because Drosophila isn't really a fruit fly proper, but a vinegar fly). So familiar is this species that many people simply refer to it as Drosophila without invoking the species name. One might be forgiven for expecting D. melanogaster to be the type species of Drosophila, but it's not. That honour goes to Drosophila funebris (shown at the top of the post in a photo from here). And as it happens, the two species are not that closely related. If Drosophila is divided up, the Drosophila melanogaster everyone knows and loves becomes a far less familiar Sophophora melanogaster. How will geneticists respond to the loss of their favourite organism?

To avert an apocalypse in evolutionary biology, van der Linde et al. (2007) have made a submission to the ICZN to redefine the type species of Drosophila. They suggest that that honour be given to D. melanogaster rather than D. funebris, meaning that D. melanogaster would remain forever more Drosophila. But if this is accepted, what will become of D. funebris and its close friends and relatives? Will the ICZN exalt D. melanogaster to the position of type species? Or will the geneticists just have to learn to refer to Sophophora, and like it?

REFERENCES

Linde, K. van der, G. Bächli, M. J. Toda, W.-X. Zhang, Y.-G. Hu & G. S. Spicer. 2007. Case 3407: Drosophila Fallén, 1832 (Insecta, Diptera): proposed conservation of usage. Bulletin of Zoological Nomenclature 64 (4).

Robe, L. J., V. L. S. Valente, M. Budnik & E. L. S. Loreto. 2005. Molecular phylogeny of the subgenus Drosophila (Diptera, Drosophilidae) with an emphasis on Neotropical species and groups: a nuclear versus mitochondrial gene approach. Molecular Phylogenetics and Evolution 36: 623-640.

Wheeler, Q. D. 2007. Invertebrate systematics or spineless taxonomy? Zootaxa 1668: 11-18.

33 comments:

  1. Nice summary of one of the central conflicts of taxonomy! Interesting issue -- damned if you do and damned if you don't.

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  2. Or will the geneticists just have to learn to refer to Sophophora, and like it?

    The same geneticists that insist on calling it Drosophila, drosophila, the fruit fly or (my favourite) 'the fly' (to go with the other model organisms the mouse and the worm)? I think, no matter what happens at the ICZN, there is little chance of that

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  3. I love it! I would prefer to see Drosophila split into several small genera, as that would better preserve the family's actual diversity. So we'll have to start calling our lab flies something different...I would hope our emotional attachment to a name does not impede scientific understanding.

    It would be analogous to following Paul's (1988) taxonomy and sinking all ornithomimids into Ornithomimus. No Struthiomimus, Gallimimus, Dromiceiomimus, etc. Just various species of Ornithomimus. That's ridiciulous--they are clearly different animals. Gallimimus is very derived, while, say, Archaeornithomimus is not. Yet they're all in the family Ornithomimidae. Furthermore, Ornithomimus and Struthiomimus are closer to each other than either one is to Gallimimus!

    To call them all "Ornithomimus" underscores the diversity of the group, just as renaming everying "Drosophila" would undercut fly diversity.

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  4. I would guess that Drosophila, even sensu stricto, is a lot more diverse than Ornithomimus sensu Paul. If we used insect standards of genus-splitting for vertebrates, we'd have a lot less vertebrate genera. Things would probably be closer to Linnaeus' vertebrate taxonomy (where, e.g., all primates are in Lemur, Simia, or Homo, and Homo is only grudgingly split from Simia) than to the one we commonly use.

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  5. Personally, I could never see any difference between ornithomimid genera.

    According to Wikipedia, Drosophila subgenus Drosophila includes about 1100 species, while Sophophora includes over 300, so even in the strict senses these are not small genera. Personally I'd be all for just telling people to get used to Sophophora melanogaster, especially as probably more species names change overall if the proposal to change the type species passes, but we'll have to see what the ICZN decides.

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  6. I get the impression that many plant "genera" are even more diverse. Just look at Ficus or Euphorbia. Of course there are exceptions, but it seems that in vertebrates (especially birds), genera are much more split than anywhere else.

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  7. I could never tell the difference between ornithomimids, either.

    I think the human total group has birds beat for generic splitting. Ditto most non-avian groups of dinosaurs (with the curious exception of Psittacosaurus).

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  8. That true; Psittacosaurus is unusually lumped. I think one of the "species" recently got its own genus name, but yeah, there are like nine species.

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  9. Lars; I did look up the sizes of some plant genera when I wrote the post (I had this image in my head of a botanist scoffing Paul Hogan style, "You call that a big genus? This is a big genus!") Ficus contains about 800 species, Rubus a little less. Senecio includes about 1500 species. Euphorbia is the biggest I've found so far, with a little over 2000 species. So even by plant standards, Drosophila is a fairly respectable size.

    Zach; nine species in Psittacosaurus? (actually, it's 11 including P. sibiricus, plus five more that are currently regarded as synonyms). Read what I've just written and consider just how pathetic that is.

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  10. "You call that a big genus? This is a big genus!"

    Ahahaha!

    So if botanists or entomologists took over ornithology, we'd have about 9 genera of birds. (Even Linnaeus was not that unkind.) Tinamous would be in Struthio, woodpeckers would be in Fringilla....

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  11. Well, I know that plant systematics are handled differently than animals. STILL, I mean...2000 species in a single genus? DAMN. What the heck are the new species standards? "Well, this individual tree is ten feeet away from that one over there...I'm thinking new species!"

    (I'm sure--hopeful--that it's not handled that way)

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  12. STILL, I mean...2000 species in a single genus? DAMN. What the heck are the new species standards?

    Trust me, a lot more difference a lot of the time than between those ornithomimids. Euphorbia, for instance, contains large trees to succulents to low herbs. Compare this to this to this to this. All of them are members of the genus Euphorbia.

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  13. I think that many problems of this kind, are because codes are awfully old... :S

    By the way, at least for several insect taxa, even with their huge number of species, the 'standard' for species nomination are high!

    ;)

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  14. Under the PhyloCode, you could just let Drosophila be a more inclusive clade than Clade Sophophora. Then the species in question could be validly referred to as Drosophila melanogaster or Sophophora melanogaster. (Or even Diptera melanogaster -- how's that for "the fly"? Then again, there's probably some other dipteran species with the same trivial epithet, so that's probably not a good idea -- not that it was really a good idea, anyway.)

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  15. Chris, your pictures, which are all apparently from the same genus, have left my tetrapod taxonomy mind reeling. Are botonists even vaguely preoccupied with taxonomy? Aren't two of those plants (first and third, perhaps) more closely related to each other than either is to the second one? And why doesn't that enormous one get its own genus? LOOK AT IT! That would like calling Gigantoraptor "Oviraptor!" Wouldn't it?

    (my mind is collapsing)

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  16. Salva:
    I think that many problems of this kind, are because codes are awfully old...

    They're not that old. The ICZN only appeared in its current form in 1961 (there was a zoological code before then that appeared in 1901 or thereabouts, the Regles, but in many ways it was quite a different beast), though the botanical code is older (I don't know the dates for botany). The prokaryote code, of course, didn't make an appearance until 1985 (previously, bacteria had benn regulated by the botanical code). All of the codes have been updated since they first arrived as conditions change and problems are noted - the latest edition of the ICZN came out in 1999, and I believe a new one may appear in the not too distant future.

    The problem you're referring to, I think, is that taxonomy itself has been around for much longer than the codes have, and conditions were even more hazy before the various codes were introduced to try and drag some order out of chaos. We're pretty much stuck with this historical baggage whatever we do - even if we were to adopt a new nomenclatorial system such as the PhyloCode, we would have to decide between taking over the baggage or starting over anew, and the former would probably cause a lot less trouble in the long run.

    Zach; part of the issue is that compared to animals with their well-defined developmental pathways, plants seem to change morphology with almost embarressing ease - take two cuttings from the same plant and plant them in different environments and you'll see what I mean. I think about how the cabbages and such in the garden tend to go a little woody if you leave them too long, and I can imagine that you only need to continue the process a little longer and you've got a full tree on your hands. This is why botanists have long emphasised flowers and fruit and other such characters that are probably not so environmentally labile.

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  17. LOL, seems I hit the blogosfeer! Anyway, I am curious myself where the application is going. As for names, D. funebris is in the immigrans-tripunctata radiation, and the first available synonym is Chaetodrosophilella ;-)

    Anyway, the issue of genus size variation across various phyla is a nice one, but what would be inportant is to consider that there are many many more insect species (~3.000.000) than birds (~9.900). A better indication is to take divergence times. In general, I think that if you take that, you end up with much larger insect genera than bird genera. Large homogeneous genera are not the issue, large heterogeneous genera are.

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  18. Midnight Rambler1 February 2008 at 03:05

    That's why there would inevitably be more species per genus in insects than tetrapods, but the big problem is that mammal and bird people just like to put everything into a different genus. I mean, we've got four extant species of great apes, and three genera. Every new fossil gets a new genus, unless you can't actually tell it apart from another one, in which case it's only a new species :-) (FTR, yes I am being a little facetious, but only a little)

    As for the Drosophila renaming issue, I think the first post summed up the possible outcomes of the ICZN decision on this case perfectly: damned if you do, damned if you don't.

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  19. Actually, we have six extant species of great ape (seven if you count our own species). Each genus (except for Homo) has two extant species. But anyway, excellent point—vertebrate paleontologists are horrible splitters, and vertebrate neontologists are only slightly better.

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  20. I work on Drosophila (a couple of different species, including melanogaster) and I'd have to say a name change at this point would create a lot of headaches - just in terms of literature searches and genetic databases... D. mel is one of the most well studied organisms on the planet, and it would be a logistical nightmare for ongoing research. I would almost bet that, if the official name changed taxonomically, there'd be a long period of passive resistance to the idea in the published experimental evolution and genetics literature.

    I like the idea of making melanogaster the type species, though... It would reflect the Drosophilist reality. Who in Hubbard's name has ever even HEARD of D. funebris?

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  21. If we used insect standards of genus-splitting for vertebrates, we'd have a lot less vertebrate genera. Things would probably be closer to Linnaeus' vertebrate taxonomy ... than to the one we commonly use.

    I for one want salamanders back in Lacerta. ;)

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  22. Hehe! (Never mind that Lacerta agilis is more closely related to us than it is to salamanders. And if you include us, then I think Homo might have page precedence. :)

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  23. Ah, but page precedence is only a convention, and there's no obligation to follow it. Lacerta sapiens it is, then - there's less species names that have to change if we make Homo a synonym of Lacerta than the other way around :-P.

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  24. Ah, but far more has been written on Homo sapiens than on any species of Lacerta, so that move would actually create greater instability. Homo agilis! :)

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  25. kim van der linde wrote:
    Anyway, the issue of genus size variation across various phyla is a nice one, but what would be inportant is to consider that there are many many more insect species (~3.000.000) than birds (~9.900). A better indication is to take divergence times. In general, I think that if you take that, you end up with much larger insect genera than bird genera.

    I just read in Valentine, On the Origin of Phyla, that the split between D. melanogaster and D. pseudoobscura (both in subg. Sophophora) is estimated at 40 Ma or more. If that's the standard, there should be an good deal fewer bird genera around.

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  26. Well, you have to take into account that flies breed much faster than birds, so the difference in terms of generations is less (although probably still pretty substantial).

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  27. Wait, I'm stupid -- the difference is greater, far greater.

    Where's that coffee?

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  28. David Marjanović10 April 2008 at 18:53

    What makes taxonomy a science? What does a taxonomic hypothesis look like? Don't people here confuse it with phylogenetics, which really is a science?

    Chris, your pictures, which are all apparently from the same genus, have left my tetrapod taxonomy mind reeling. Are botonists even vaguely preoccupied with taxonomy? Aren't two of those plants (first and third, perhaps) more closely related to each other than either is to the second one? And why doesn't that enormous one get its own genus? LOOK AT IT! That would like calling Gigantoraptor "Oviraptor!" Wouldn't it?

    (my mind is collapsing)


    You have to remember, though, that the ICZN has a very unusual restriction: the number of ranks between genus and subspecies is fixed at five -- genus, subgenus, species group ("superspecies"), species, subspecies. And then it ends. In botany, you can add section and subsection below subgenus, which is done a lot, and below the subspecies there's the variety and don't ask me what else. It follows logically that zoologists might call a genus what a botanist would call a subsection. All hail the PhyloCode, where this kind of "problem" simply evaporates.

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  29. David Marjanović10 April 2008 at 18:55

    BTW, the starting date for the bacteriological code is 1980, not 1985. The latest issue of that code is from 1992, of the ICZN from 1999, and of the ICBN from 2000.

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  30. What's so bad about being paraphyletic?

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  31. Paraphlyletic defeats the main purpose of what taxonomy is all about - better phylogenetic language.

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  32. The MAIN purpose is to be able to treat life in terms of sets. (And the main purpose of nomenclature is to be able to communicate about those sets clearly.) Arguably phylogeny is the best basis for that, but it's not a necessary basis. Keep in mind that Linnaeus preceded Darwin by about a century.

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