We are writing in opposition to the van der Linde et al. proposal to set aside Drosophila funebris (Fabricius, 1787) as the type of the genus Drosophila Fallén, 1823 and replace it with Drosophila melanogaster Meigen, 1830. Van der Linde and colleagues’ case makes the argument that the paraphyletic nature of the genus Drosophila necessitates a nomenclatural change. This confuses classification, in this case phylogenetic classification, with nomenclature. It essentially asks the commission to rule in support of an unpublished classification without nomenclatural necessity. We disagree with this case on the grounds that: (1) this is not a nomenclatural issue and even if it were, there isn’t a nomenclatural or taxonomic need to make this change at this time, and (2) the phylogenetic argument that van der Linde and colleagues make is based on unpublished methods and, when examined in detail, the supporting literature does not statistically support their case.
While phylogenetic systematics is an important tool for taxonomists interested in delimiting species boundaries (e.g. Savolainen et al., 2005) and testing monophyly of higher-level taxonomic groups (APG II 2003), this field of science is quite distinct 142 Bulletin of Zoological Nomenclature 65(2) June 2008 from nomenclature. Cases submitted to the commission requesting an exception to the rules of priority generally follow a formal taxonomic revision in which species are moved from one genus to another, creating a nomenclatural problem. Case 3407 is quite different in that there has been no published study prompting such a revision, nor would a nomenclatural problem arise were such a revision to occur.
When using phylogenetic trees to justify taxonomic or nomenclatural changes, care must be taken to ensure that those phylogenies are generated by established and reproducible methods and are, in fact, strongly supporting the taxonomic assertions being made. The van der Linde et al. case fails to meet either of these criteria. While we agree that evidence is mounting that the genus Drosophila is not monophyletic, and we strongly agree that the name D. melanogaster should be preserved in the literature, we also believe that the designation of a new type species for the genus Drosophila is premature because of issues with the methodology that van der Linde and colleagues are using to justify their case.
They make their argument on the basis of phylogenetic analyses that, while outside the scope of a nomenclatural comment, should be addressed briefly here. First, the phylogenetic methods used by van der Linde et al. to justify their case are unpublished, meaning that there is no opportunity to assess whether the analytical criteria are biased or even repeatable. Second, while several studies have been published suggesting that the genus Drosophila is not monophyletic, methodological rigour has not been applied evenly across studies. The works cited in the van der Linde et al.’s proposal are based upon heterogeneous data and may individually suffer from issues of non-independence, insufficient taxon sampling, inadequate character sampling, or lack of statistical support. Although we are unable to go into detail in the current comment, we feel that these issues should be considered when weighing the merits of the van der Linde et al. proposal.
Taxonomic hypotheses, like those proposed in other scientific disciplines, must be based upon well-supported, repeatable analyses of primary data using philosophically rigorous and published methods. Taxonomic progress, in the sense of creating stable, natural groupings of monophyletic taxa, is not served by revisions of existing nomenclature based on poorly executed or incomplete studies, particularly when these do not add any new data relevant to the problem. Given the status of the current data, there is no question that a comprehensive taxonomic revision of the genus Drosophila will be necessary in the future if the taxonomy is to reflect phylogenetic relationships. However such a major reorganization based on an unpublished phylogeny is premature, at best. Such a step will only lead to confusion and instability within the Drosophila literature, which is extensive with nearly 3,000 primary publications a year. Hundreds of ecological and evolutionary studies conducted on the repleta, virilis, and immigrans species groups, as well as the work focusing on the Hawaiian Drosophila, the premiere example of adaptive radiation in nature, would be dissociated were the genus names of over 1500 species to change repeatedly as monophyletic groups are proposed and overturned as new evidence from research accumulates. A taxonomic change with such wide effect should be well supported and robust to subsequent revision as evolutionary relationships of individual species and groups are reassigned. The current proposal is neither good taxonomy, good nomenclature, nor good phylogenetic analysis. Instead, it attempts to replace thorough nomenclatural, taxonomic, and phylogenetic study by proposing a classification that is not resolved sufficiently to warrant consideration of the Commission.
A.P.G. (Angiosperm Phylogeny Group) II. 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnean Society, 141: 399–436.
Savolainen, V., Cowan, R.S., Vogler, A.P., Roderick, G. K. & Lane, R. 2005. Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society, B: Biological Sciences, 360(1462): 1805–1811.