Wednesday, November 26, 2008

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!

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