Wednesday, March 4, 2015

Adventures in DNA barcoding

I'm not a molecular biologist but I have molecular biologist envy - badly. I appreciate the ability to answer interesting ecological questions using all the tools available. I have some field skills, I can make some great blood smears, and I know stats OK.

Ned Fetcher and I have been spearheading a state funded project looking at grassland diversity. At 16 sites, we have been sampling birds, insects, and plants and looking at the effects of plot size, area-perimeter ratio, and management technique (mowing, fire, nada). At 5 of the 16 sites, we are constructing food webs based on stable isotopes (carbon and nitrogen). 

One issue we can into very quickly is the fact that we have issues identifying arthropods and, to a lesser extent, plants. Lacking taxonomic skills and lab skills. Yikes.

So far we've been keying out plants and insects using stacks of books. It's slow and tedious and I know students don't enjoy it. 

I know students don't care about grasslands and they come to work in the lab because I send kids to great meetings and we try to get them published. If I could teach them some useful skills I would feel like we have the perfect project and would get much more student involvement. So we're going to try DNA barcoding. The upshot of DNA barcoding is to extract a cytochrome, in the case of animals, or chloroplast, in the case of plants, gene. Then the gene is sequenced and compared to known sequences. These genes are specific to species and constant within a species. 

We just need to figure out how to do it. 

On the upside, my labmate moved and left all his labware and some relevant chemicals. We have specimens - lots of them. We're meeting tomorrow and making a list of all the gear we'll need. 

The best recourse I've found for getting started is this

And there's a video to accompany:

Let's see how it goes... 

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