DNA Barcoding, an unwilling demonstration

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You might recall how much I dislike DNA barcoding.

So you can imagine my frustration when, in spite of my best efforts to mount an empirical demonstration of what a waste of time it is, the technique turns out to be extraordinarily useful.  I’ve been processing sequence data all day from the barcoding gene (COI) for a set of 7 Pheidole species distributed from Costa Rica to Argentina.  The results are in hand, and here are the pairwise genetic distances:

gap

See that blank spot in the middle?  That shouldn’t be there.  If barcoding didn’t work, that is.

For this sample of ants, then, any two individuals will either be genetically similar (the bars at left), or different (at right), without ambiguous intermediates.  So it is relatively easy to predict from the COI sequence whether any two ants belong to the same species.  The gap also demarcates the same divisions I’ve found using traditional morphological characters.  It’s remarkably clean.

6 thoughts on “DNA Barcoding, an unwilling demonstration”

  1. Just a tool, Alex, just another tool. Very useful tool, but just one tool.

    The way I see it being used is not on a widespread scale, but localized in individual projects, like yours. Once you’ve determined for a small group that there is some sort of difference in species between individuals based upon morphology and ecology, you can use barcoding to confirm that, and furthermore, use COI sequences for rapid assessment of any other specimens you have, knowing that it takes time to look under the microscope at these things.

    Its hardly going to take our jobs away as taxonomists, because no one is going to believe that two species are just so based upon simply a DNA sequence. Its not good science and I think all biologists realize that. One step closer to understanding what a species is.

  2. Its hardly going to take our jobs away as taxonomists, because no one is going to believe that two species are just so based upon simply a DNA sequence.

    I’ve got this nice bridge in Brooklyn, going for a song. 🙂

    1. Okay, okay, some people are that gullible, but I would hope that the vast majority of biologists are more intelligent than that.

  3. The cox1 barcoding region is pretty useful for a lot of different organisms, mine included. Most of the resistance to barcoding seems to come from the perception (or reality) of claims by some proponents, e.g. that the barcode region will work for every species; that only barcodes are needed; that barcodes make traditional taxonomy obsolete. Then there is the reality of barcoding tending to suck-up the funding. There is also the circularity of reasoning that tends to pop-up, ‘they have different barcodes, therefore they are different species’.

    The only real problem I’ve had with barcodes is the occasional ‘unambiguous result’ that seems entirely specious and eventually gets dumped as an ‘alimentary contaminent’, pseudogene, or some other ad hoc reason. If I didn’t know what the animal should have been, then then these results would have been accepted. The other ‘unambiguous results’ that split my species hypotheses are actually the most interesting bar codes so far – not that I feel any urge to split these groups into different species just because there are structural differences in their cox1 genes.

  4. As a taxonomist, I’ve always prided myself on how cheaply I do science and make progress. Its a shame that I would be judged on how much money I could bring to university instead of my scientific output and teaching capabilities! I can produce a few sequences for multiple genes and come up with a nice phylogenetic framework for my taxonomy relatively cheaply.

    But it is not frugalness and amt. of research per dollar. It is amount of dollars per research that gets you hired! DNA barcoding is a great tool for many taxa. For my work in deep sea critters it is more or less irrelevant for a variety of reasons, sample number being one and the fact that most things I bring up in a sample are not very closely related or have very obvious morphological differences. I can see its usefulness for gazillions of ants though!

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