Nature Blog Network

Thursday, May 29, 2008

Ants, DNA Barcoding and Open Access

ResearchBlogging.orgThis week, as Alex Wild put it, Brian Fisher and Alex Smith "break the PLoS taxonomy barrier". In my last post, I evangelized and pontificated on the benefits of open access publishing in PLoS for taxonomy. That in itself is a ground-breaking accomplishment, but the paper by Fisher and Smith is interesting in own right. They report on ants in the Malagasy region from 2 genera, Anochetus and Odontomachus, and describe 3 species new to science. Additionally they evaluate the efficacy of DNA Barcoding as a "tool to accelerate species identification and description".

Of Ants and Islands

Madagascar is a unique island off the eastern coast of Africa with a highly endemic fauna, meaning that many of the creatures found there are found no where else on this planet. Fisher and Smith also report the first records from the nearby islands of Seychelles and Comoros. Using 500 individuals from 6,000 leaf litter samples, 4,000 pitfall traps, and 8,000 additional hand collecting events over a 14 years period, they were able to group together worker, queen and male castes. The descriptions are fine and document the features and variation in morphology well. One criticism I have is they contain no information that I could see on the etymology of the new species. Etymology is where the author describes what the name means. For the 3 new species described in the genus Anochetus, each is given a specific epithet honoring an individual, a Mr./Ms. Bolton, Goodman and Patterson. Who these people are that should get immortalized in ants we shall never know.

DNA Barcoding and Species Assessment

While the description and discussion on the ants' distributions are important for biodiversity studies, the authors spend a good deal of the paper discussing the efficacy of DNA barcoding in helping to delineate taxa. DNA barcoding is using a standard gene, typically the mitochondrial COI gene, as a marker to identify a species. This is useful when there is a specimen voucher with a known barcoded sequence to match unknown to. There is a good deal of controversy surrounding its use in taxonomy. Many taxonomists agree that describing species based only on a short snippet of DNA is bad practice.

Fisher and Smith use DNA barcoding on their ants for two reasons. The first is group the different castes together. Ants are social insects separated into workers, queens and males. Some ant societies have even more castes, such as sanitary workers and fungal farmers. Because the different ant castes are morphologically different from one another, it is sometimes difficult to tell closely related species apart, especially if they co-occur in a similar location. The authors assert that DNA barcoding was the "principal source of data" that group together different castes, sizes and genders.

The other reason is to rapidly assess species identification. Fisher and Smith analyzed all the collections of a genus. Those showing a high degree of sequence divergence, i.e. the outliers, were "culled" from the analysis for morphological scrutiny. Traditionally, each individual would have to have measurements and notes taken on the morphological characters of interest. This is an extremely time-consuming process, but amplify that to 500 individuals of ants. The barcode method actually allowed them find the interesting individuals right away. This might not work for every taxon, but considering how affordable DNA sequencing has become this practice might take off for large collections. This will be extremely important as many biodiversity inventories are ongoing or coming to a close in the near future.

Another use for DNA barcoding brought up by Fisher and Smith is hypothesis generation. Hopefully most people will agree me (and the study's authors) that species are testable hypotheses. Like any scientific hypothesis, it is subject to refinement with new data. The barcode data helped Fisher and Smith to generate testable hypotheses regarding within-species divergence, several interesting aspects of biogeography (see page 20, last paragraph of first column for list) and female-limited dispersal capabilities in species with wingless queens.

I'll let Fisher and Smith have the final word:

"Nothing can replace the countless hours of careful observation necessary to understand variation and to delimit species boundaries. However, the addition of sequence data provides a means to create short-term results from inventories and at the same time generate data helpful to taxonomists. For taxonomists, sequencing highlights the specimens most deserving of focused study."
Disclaimer: Brian Fisher was my Evolution teaching assistant at UC-Davis. Although he is unlikely to remember me anyways, but the contents of this post are not in any way an artifact of this coincidence.
Fisher, B.L. & Smith, M.A. (2008). A Revision of Malagasy Species of Anochetus Mayr and Odontomachus Latreille (Hymenoptera: Formicidae). PLoS ONE, 3(5), e1787. DOI: 10.1371/journal.pone.0001787


  1. Fisher and Smith have employed DNA barcodes in the way that most DNA barcoding advocates intend: to complement "traditional" taxonomy in order to 1) gain information about life stages (etc.) that are recalcitrant to morphological analysis alone and 2) increase the rate and efficiency of the taxonomic process.

    While you are right that "Many taxonomists agree that describing species based only on a short snippet of DNA is bad practice", I would have added to the end of your sentence, "but this is not the intended use of DNA barcodes."

    While it is true there are advocates of DNA-only taxonomy out there, I feel it is important not to jumble this (much more controversial) proposal together with DNA barcoding.

    Besides that little nit-pick, I applaud your post!

  2. I agree with your complaint about etymology. If you name a species after somebody, you shouldn't keep it a secret. After all, aren't you honoring that person?
    Fyi. Bolton is most likely Barry bolton, the foremost ant guy, who described so many new species that he ran out of names and has had to use random character strings (see his 2000 work on Dacetine ants). Unfortunately, Bolton doesn't believe in revealing his etymology either. Most of his names are a mystery, if not downright meaningless (by design).

  3. Karen, yeah I agree

    Dave, Its amazing that (especially with insects) the taxonomist can run out of names and have to use gibberish. Makes you wonder if there is not enough characteristics to give a species a name, are we sure its a new species? At least in the Linnaean tradition of naming as a descriptive process.

    But yes, its important for a variety of reasons to know the meaning (or lack of meaning) behind a name. EVERY NAME HAS A DEFINITION!!!


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