I’ve been interacting with DNA barcoding a lot lately. In the decade since Paul Hebert and colleagues first promoted the use of a single, short gene sequence as a rapid identification tool for animals, a huge body of literature has accumulated, some enthusiastically in support of the idea of barcoding, some vociferously opposed, but most of it just using a new tool to get down to the huge job of unraveling the biodiversity of life on earth.
As originally envisioned, and most commonly used, DNA barcodes are a powerful (although not perfect!) tool for species identification and discovery. But both those applications require an established library of DNA barcodes of known specimens that the unknown specimens can be compared against. That barcode library (BOLD) has been growing by leaps and bounds over the past ten years, but there’s still a long way to go. Last week, we hosted a crew from the Biodiversity Institute of Ontario (including ex-Lyman grad student Valérie Lévesque-Beaudin) who were at the Lyman to work through parts of our large collection for some insect and arachnid groups that are not well-represented in BOLD. After a frenzied few days with the BIO team working almost non-stop through the days, and some of the Lyman students pitching in here and there, more than 50 boxes loaded with almost 5000 specimens in total were packed up, and on their way back to Guelph where the specimens will be photographed, databased and sampled for DNA extraction and barcoding. And eventually the specimens will make their way back into our collection where they’ll continue to be available for study by future researchers. This process benefits BOLD, as well as future users of the resource, by expanding the barcode library, but it also benefits us here at the Lyman in that it unlocks some more of the valuable data in our pinned specimens that we wouldn’t easily be able to access. So this visit was a win-win-win proposition.
But the DNA barcode (a segment of the mitochondrial CO1 gene, for animals; there are other barcode markers for non-animal groups) can be used for more than just identifying species. There is enough variation within species that we can also use it as one marker for exploring population-level differences over space and time within species. My M.Sc. student Anna Solecki has been working with our colleagues Jeff Skevington and Scott Kelso at the Canadian National Collection of Insects in Ottawa to explore the genetic footprint of Pleistocene glaciation on flies in northern Canada. Anna is wrapping up her genetic work and the barcode gene has been a pretty useful tool, along with some other lines of evidence, in unravelling some interesting geographic and historical patterns.
If we scale up again, and if we accumulate enough barcode data on enough species, we can then use that data to start addressing some really big questions in ecology. At a workshop last year sponsored by the Quebec Centre for Biodiversity Science, several of us spent a very productive day brainstorming on the potential uses of DNA barcodes to address a wide range of ecological questions. The outcome of that workshop was a paper on the potential uses, and challenges, of DNA barcoding in ecology, which has just been published on-line in the journal Molecular Ecology Resources (see Joly et al. 2013 under Publications). I could summarize the paper in text form, but a picture is probably worth at least a couple hundred words. So, the diagram below, from the paper, shows a few of the ways in which DNA barcodes can be used in different approaches to assessing diversity and, in turn, some of the applications of those approaches to an array of research questions.
Is DNA barcoding 100% accurate in identifying specimens? No; no method is. Is DNA barcoding the answer to all the big questions in ecology and evolution? No. Does it have limitations? Sure; every method does. But if it’s used correctly, with an awareness of the strengths and weaknesses, it’s a really powerful tool to have in the Big Toolbox of Biology.