Sunday, October 18, 2015

DNA barcoding: a road map

I went to a DNA barcoding meeting a few months ago and I've been more inspired to integrate this technique into my own research. I've been working on a food web project but I could also use this to identify parts of birds and the bits in a bird's diet. 

The first application would be to identify the invertebrates we've been catching for our grassland food web project. My idea was that we just needed to get a bit of tissue, amplify the DNA using PCR, send it off, get the sequence, ID the species, and DONE.

If I have gone through with this I could get our critters identified but with lower confidence and the work with be of little use for other researchers. A shame and near waste of work.

At the barcoding meeting, we met up with a Smithsonian scientist, Caroline, that agreed to come up and discuss with us barcoding issues. So, last week, she came up and gave a two day workshop for Ned and I and a number of students. It was incredibly enlightening. We found (many) issues with our protocols and we were pointed to a number of resources to help us with technical issues. More importantly, we were given a work flow that greatly expands on the flow I outlined above. The biggest missing piece is building a library of local organisms that are identified independently of DNA barcodes. These organisms you barcode and then use a reference. This seems a bit circular (and it is) but you can use your reference collection to identify bits of organisms or organisms in other stages, such as larvae and eggs. This sounds simple but it means getting specimens and organizing them. Organizing them. That is completely new to our lab and will be a challenge. But it's a challenge I'm willing to take up. One of the first things to do is to create an outline for the whole project and I'm doing it here

So, the workflow is this, get specimens (mostly, go out and collect insects), give them a number, get them identified, pin them in an organized way (presumably by order), bar code a small bit of them, link the barcode to the specimen. Now unknowns can either be ID'ed through the vouchers are barcoded. Everything is organized through BOLD Systems.

It was a hugely useful workshop and Caroline was a blast. She stayed at the Hillard House, which has an awesome breakfast menu. Students enjoyed the workshop as well and I hope they're inspired as well. 

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