Wednesday, July 31, 2013

The taxonomic impediment and DNA barcoding

Further to yesterday's conference, there was also a talk about DNA barcoding. First, what is that?

Some time ago I did a post on the taxonomic impediment, the problem that the number of taxonomists worldwide is too small (and, due to short-sighted funding policies, shrinking) to deal with the massive amount of biodiversity still to be described and classified, a situation that impedes downstream studies in ecology, evolutionary biology, conservation management etc relying on an accurate description and classification of life.

The idea behind DNA barcoding is to allow an easier determination of species by sequencing a few carefully chosen gene regions for as many species as possible and depositing that information in a searchable database. So if you found, for example, a plant in a rainforest plot and you needed to know what it is, you don't collect a specimen any more and send it to a botanist for determination, but instead you extract DNA, sequence the right gene regions, and then use the database to find out, say, that there is an 98.9% likelihood that the plant you are dealing with is Ruellia brevifolia.

Optimists could say that this is a good solution to take superfluous work off the shoulders of overtaxed taxonomists so that they can get on with describing new species. Cynics might think that the idea is ultimately to de-fund taxonomic research and to replace taxonomists with shiny DNA sequencers.

There are good reasons to believe that barcoding cannot work in principle, at least not at the species level. (Hint: the most important one starts with "i" and ends with "ncomplete lineage sorting".) But the talk I heard yesterday raised a different issue.

You see, the colleague who presented it had earlier been at a different conference dedicated specifically to barcoding, and one of the things she learned there was that the vast majority of barcode reference sequences in Genbank are what is called "level 0", meaning that nobody knows what species they are from because the people who produced them were unable to find a taxonomist who could confidently determine the specimen they got the DNA out of.

Is that not just awesome? Of course barcoding, even discounting other technical problems, can only work if there is a high quality, reliable reference database. Maybe at a minimum one should have waited with starving taxonomic expertise to death until such a high quality database was in place.

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