19 July 2012
DNA's kitset models
A group of Lincoln University researchers led by Rupert Collins, including Rob Cruickshank, Karen Armstrong and Laura Boykin, have been messing around with models. Rupert and his colleagues are especially interested in DNA barcoding. Basically, all species should be identifiable if you look at their DNA and, in fact, if you look at one gene region in particular - COI (the ‘barcode gene’) then there is usually enough information present to confirm what species you are looking at. The main interest in DNA barcoding at Lincoln is for bioprotection. Let's say that some grapes turn up in the Port of Auckland with some insect larvae crawling around in them. There is usually no way to tell what species it is by looking at larvae - they're all small, white and wriggly. We can't tell if this is a harmless species or something that could do unspeakable harm to our fruit industry. By looking at their barcode DNA we can quickly and easily match these mysterious larvae to a species. Well, in theory at least. There are a few complications. One complication is with the models. When analysing the DNA data a model is selected to more accurately construct the tree and find the right match. The default model for DNA barcoding is known as the K2P model (which assumes that there are two basic types of nucleotides that behave differently and are present in equal proportions). Rupert has published a paper "Barcoding's next top model" in Methods in Ecology and Evolution that tests whether the K2P model really is the top model.