9 April 2008

A barcode for life

Cosmos Online
Species scanners? An ambitious project to catalogue all life on Earth using DNA could revolutionise taxonomy.
A barcode for life

Pieces of the puzzle: While today's taxonomists rely on entire adult specimens, DNA barcoding can identify species using only a hair or an insect wing. Credit: iStockphoto

Deep in the Amazonian jungle a biologist sits confounded, clipboard in hand. Everywhere he looks something new and strange is staring back at him; an unfamiliar tree, a perplexing flower, an insect he prays isn’t carrying an unknown disease. He’s meant to be making a list of species in a four-square-metre area. And he can’t do it. Not without the help of a conga line of taxonomists from every corner of the globe. He sighs. If only there were an easier way.

Well, soon there might be. Enter the International Barcode of Life (iBOL) Project, which aims to establish a comprehensive library of eukaryotic life based on a new form of analysis called ‘DNA barcoding’. This technology allows for rapid species identification, today in the lab, one day in the field, using just a short sequence of DNA – a standardised ‘barcode’ region, common across an entire phylogenetic kingdom.

Species catalogue

Hoped to be up and running by February of 2009, the iBOL Project will be the first highly coordinated, worldwide effort to expand the use of barcoding. Within the initiative’s first five years, the technique will be used to catalogue some five million specimens of life; representing 500,000 species from across the globe. This is a sizeable chunk of the total 1.7 million species currently known to man, and will hopefully speed the unearthing of some countless species yet to be discovered.

“It’s a bit of a task … but we know we’re going to do it,” says Paul Hebert, a biologist from the University of Guelph in Ontario, Canada, and the driving force behind iBOL. “And we can do it all relatively quickly,” he adds, “providing the proper investments are there”.

This must be why Hebert is grinning so widely. Just weeks ago, in late February, the official fundraising campaign for the iBOL Project was kicked off at the Australian Museum in Sydney. It’s a fairly spectacular endeavour and, fittingly, carries an impressive price tag: over A$163 million (US$152 million).

While one third of this funding will come from within Canada, headquarters of the project, the remainder will be sought from international contributors. And things are off to a good start, Hebert says, with the first commitments of funding and support coming from a variety of Australian organisations, including the national science agency (the CSIRO), the NSW Department of Primary Industries, the Royal Botanic Gardens Trust and the Australian Museum itself.

So what exactly is it that has people across the world so eager to be involved? Perhaps the most intriguing (and widely promoted) aspect of barcoding is one that takes us into the future. The DNA barcode records collected by the project, when coupled with future advances in DNA sequencing and gadget technology, will one day lead to a device straight from the world of science fiction, say those involved. This hand-held gizmo will allow anyone, anywhere, to take a barcode analysis of a given sample – the leaf of a weird Amazonian plant, for example – and be linked within minutes to a host of information, including the species to which it belongs.

But barcoding already has an impressive list of proven and potential applications; from the quick and easy identification of species in the lab to the rapid unmasking of mysterious foodstuffs. It may soon even help in bolstering national security.

Mitochondrial gene

Hebert himself is considered the father of DNA barcoding, having proposed the idea just five years ago. “Back in 2003 we were pretty much barefoot and in the kitchen,” he says of the concept’s humble beginnings. It was at this time he first suggested that a portion of the mitochondrial gene, cytochrome c oxidase I (COI), could be used “as the core of a global bioidentification system for animals”.

It’s like the way supermarkets use a conserved panel of stripes and numbers to keep track of their different products. In order to be useful, the standardised DNA barcode needs to be conserved enough between a kingdom’s species to allow for its routine identification (just as the supermarket barcode must be recognisable by scanners). Yet each species must play host to enough variation in the sequence’s base pairs in order to tell them apart.

On top of this, the sequence can’t vary too much within a given species, as this could lead to accidental misclassifications. Two Amazonian squirrel monkeys, for example, could end up being assigned to different species if their barcode regions differ in base pair sequence by any great amount.

An ark of information

It’s is a boatload to consider, but Hebert appears to have hit the nail on the head in nominating COI for the most suitable animal barcode. Since his proposition, things have progressed amazingly fast, he says. Barcode records for 35,000 species have been collected so far, and most of these have been identified using COI.

The accuracy of this barcode sequence has also been established over time, says Les Christidis, Assistant Director of Research and Collections at the Australian Museum in Sydney, and chair of the Australian Barcode Network.

“For 95 per cent of the time it’s perfect,” he says, adding that “we have to remember that nothing in biology, nothing in science, is ever perfect.” Rather than seeing an elusive five per cent as a failure of the technique, Christidis sees an exciting challenge for researchers. “Knock yourselves out,” he says, “let’s find out why it isn’t working.”

But others are less optimistic about DNA barcoding’s potential shortcomings. James Mallet, a biologist at University College London in the U.K., says that while the barcoding method is useful, it is probably best used as an “approximate guide” to species identification. He suggests that the technique might be prone to mistakes “because mitochondrial DNA sometimes lies … [for example] we know that mitochondrial DNA can be transferred between species”.

Ecologist Martin Wiemers, from the University of Vienna in Austria, is also cautious. Though he thinks barcoding might be a useful tool, he suggests that the small portion of COI used might ultimately be too short to show enough variability, particularly between closely related species. “The use of even longer sections, such as the complete 1535-base-pair COI, might be necessary,” he says. In addition, he believes the use of nuclear genes would be helpful in improving the technique’s accuracy.

Nevertheless, the iBOL team is confident they will achieve great things with DNA barcoding, whose benefits, they believe, are soon to be enjoyed across the world.

Express aisle

Chief among these benefits is the fact that DNA barcoding allows for both the rapid identification of species and the flagging of specimens as yet unknown to science.

With its speedy service, barcoding will likely become a useful on-site tool across a range of operations. Quarantine ports will use it to detect the movement of prohibited cargo. National security will use it while on the look out for biological warfare agents. Scientists in remote jungles will use it to complete otherwise torturous biodiversity surveys.

The speed and ease of barcoding will be handy not only for those needing rapid answers, but will also ease the strain on the world’s few specialist taxonomists. The time of these experts is typically spread thin, challenged by a constant stream of requests for help in classifying specimens not readily identifiable by untrained eyes.

“With DNA barcoding [taxonomists] will very rapidly and automatically be able to identify the majority of specimens being presented to them,” says Christian Burks, president and CEO of the Ontario Genomics Institute in Toronto, Canada.

“It’s a great shift of focus,” he says. Rather than being asked to spend huge amounts of time attending to queries easily solved by barcoding, “they can instead be getting on with things… [for example] teasing out an interesting cul-de-sac in evolution in a remote corner of the world”.

DNA barcoding is also critically important in areas where traditional taxonomy falls flat, for instance in differentiating between species with near-identical morphologies.

It wasn’t until a variety of bats were barcoded in Guyana in 2007, for example, that six new species were identified. They were previously lumped in with doppelgangers including the fringe-lipped bat, and without barcoding we may have never known they existed.

Chloroplast gene

Numerous discoveries of previously overlooked animals are occurring in this way, including the unmasking of new species of birds, fish and insects. This is because the barcoding sequence for animals is one that is well documented and used.

But it was only in February of this year that a useable barcode for plant life was identified – DNA from the chloroplast gene, matK. Though the usefulness of this sequence was suggested early on in barcoding research, it wasn’t until new findings were published in the Proceedings of the National Academy of Sciences journal, that it was officially proven viable.

So far matK has been used to catalogue a vast number of species, including 1,600 types of orchid from Costa Rica alone. And new discoveries are already being made; for example, what was once assumed to be just one orchid species has now been teased out into two distinct flowers.

This new plant barcode discovery not only raises the possibility of uncovering a treasure trove of new vegetation, but will also lead to the broadening of the technique’s practical applications.

But wait, there’s more!

Traditional morphological taxonomy also has a fixation on whole, adult specimens. This means that if you’ve been left to contemplate just the wing of a bug, the fur of an animal or the roots of a plant, you’re out of luck. You also won’t get very far if you’ve got a specimen in its larval stage, and even a whole beetle won’t do you any good if it’s female, says Christidis.

Thankfully DNA barcoding can step in here, too, because the barcode sequence is the same whether it comes from a single hair or complete organism; male or female; larva or adult.

This is a great tool for monitoring and combating invasive species, says Christidis. He points out that here “we need to be able to respond very quickly to something that is new”, but this is a near impossibility when many critical specimens – egg-carrying female beetles, for example – can’t be identified with a traditional once-over. The ability to make an identification with just a tiny portion of a suspect specimen will be of great importance in this context too.

And in more peculiar situations, being able to identify random bits of animals and plants is already coming in handy. “We can do really cool, CSI sort of things,” says Hebert, referring to the popular American television series, Crime Scene Investigation, “like probing the origins of nasties in your food.”

Hebert points to a recent example where a severed mouse head was found in a Canadian TV dinner. Unsurprisingly, many customers were put off by the gruesome find, and the manufacturer found itself in a spot of bother. But DNA barcoding saved the day, Hebert says.

Barcoding the head revealed that the mouse was in fact a regular house mouse, but one only known to South East Asia. The Canadian production line was blissfully secure after all: the furry surprise had come in with some chicken from overseas.

So what does this mean for the curious Aussie? Might we finally discover what’s really in our meat pies? “Maybe that’s something it’s best we didn’t know,” jokes Christidis.

Whether used to reveal the origins of mystery meat, or to help a biologist unlock the secrets of deepest Amazonia, it’s clear that DNA barcoding and the International Barcode of Life Project have a lot to offer.

Even putting their intriguing promises and fancy devices aside, by generating worldwide interest, these endeavours are doing something useful: helping to keep us excited when it comes to learning about, and protecting, all life on Earth.

Lauren Monaghan is a science writer based in Sydney, Australia.

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