Thursday, July 15, 2010

DNA Barcoding and Taxonomic Tangles

DNA barcoding is an intuitively compelling idea - since every species's DNA is unique, why not use it as a 'barcode' to identify it? In this way, we might be able to catalogue all life on Earth. It sounds so simple that it might surprise some people that such a catalogue is not already in place.

Despite some detractors - I've heard one person mutter "there's more interesting things to do with that data than just species identification" - barcoding initiatives are now well under way around the world. A new review in PLoS Biology looks at the state of barcoding today (and gives links to the major consortia carrying out barcoding projects), and some issues that surround it, including the politically sensitive problem of 'genetic resources'.

Many countries, especially developing countries with rich biodiversity, have laws protecting biological resources, including genetic information, reasoning that bioprospectors might profit from them without paying their dues to the country from which the resources are taken. This review argues that genetic barcodes must be recognized as 'non commercial' research, not least because it is a valuable tool for conservation.

Barcoding also has potential to address one problem that faces biology today: the lack of taxonomists to classify organisms. Biology programs in universities no longer produce as many students with taxonomic expertise, and the ones already out there are either retiring or dying off. As a result, there are groups of organisms for which only a handful of people might be able to identify new species or sort out existing ones. This problem is widely acknowledged, and there are some initiatives, such as the PEET program of the US National Science Foundation, for addressing it. However, the ubiquity of molecular techniques in biology labs today (most biologists now know their way around a micropipette even if they can't tell a calyx from a corolla) makes barcoding potentially an easier way to get a quick ID or to pin down an ambiguous specimen.

That all depends, of course, on the quality of barcoding databases. They're only as good as the specimens and data put into them. This means that whoever is matching scientific names to molecular sequences had better know what he or she is doing, because misidentifications can propagate themselves indefinitely if no one has the expertise to recognize the mistake. Misidentifications are definitely a problem on GenBank and other public sequence databases.

Which brings me around to the taxonomic tangle: a Yale paleontologist has found that a dinosaur specimen in the American Museum of Natural History is actually a genus new to science, but had lain undetected (despite being on public display) for decades because the partial specimen had been restored to look like an existing genus that it resembles.

Mr. Longrich has made a career out of digging through museum collections and tying up loose ends left by previous generations of paleontologists, avoiding the more glamorous but expensive work of digging up new fossils out in the field. Two of his previous discoveries were made in this way, and he said he has two more in the works.

“I’m just kind of doing mop-up work,” Mr. Longrich said.

As the molecular revolution in biology starts to move beyond well-characterized model species, we need a good mop-up crew now more than ever.


Kevin Zelnio said...

Nice post. But I think I disagree that DNA barcoding helps the taxonomic crisis (if I read you correctly). You have more people with molecular skills, which is fantastic, but they can only give evidence for splitting or combining existing species. You still have to include the morphology, ecology, behavior, etc. as part of the description. Naming new taxa of metazoans, at least, from only a snippet of mitochondrial DNA is bad idea for many reasons. Even in microbes, where DNA taxonomy is the norm, use whole genomes or multiple loci.

Taxonomy is about providing multiple evidences to support a hypothesis that a type is sufficiently different from other described types to justify dealing with as a novel evolutionary unit, which has implications down the road in medicine, ecology and conservation. So it needs to be well justified!

Brandon said...

Yay comments!

Thanks for sharing. I probably wasn't too clear on my stand, which is that DNA barcoding can never replace traditional taxonomy. I'm not saying that we should use the barcode as the sole descriptor of a species - not even people involved in barcoding projects think so. Instead, I think that it will become a useful tool to aid identification when experts may not be available, or for screening large numbers of specimens.

I agree that taxonomy needs to be well justified. That's why I raised the issue of good database curation. "Real taxonomists" have to be involved in every step of data production and quality control, because the users of these databases will probably not be taxonomic experts, and will be relying on the quality of the deposited data.

Hope this clears up the air.