This is the third story in a multi-part series on taxonomy and speciation. It’s meant to help you as you participate in Armchair Taxonomist — a challenge from the Encyclopedia of Life to bring scientific descriptions of animals, plants, and other living things out from behind paywalls and onto the Internet. Participants can earn cool prizes, so be sure to check it out! The deadline is May 20th
As depicted on Star Trek: The Original Series, the tricorder is a device that looks like the bastard love child of a Polaroid camera and a 1970s-era portable cassette deck. It was worn around the neck on a strap. It was black and clunky and definitely not what we would, today, call a sexy piece of electronics.
What made the tricorder a great piece of fictional technology wasn’t its looks, but what it did. “Mr. Spock could use it to identify any organism, plant or animal, anywhere in the galaxy,” said Carlos Garcia-Robledo, postdoctoral fellow in the department of botany at the Smithsonian’s National Museum of Natural History. A portable tool that could quickly identify any species anywhere would be a game changer for science. Eventually, according to Garcia-Robledo and others, we’ll have just that — put a piece of leaf or fur or insect leg into a machine and out pops its taxonomic information.
But what makes this really awesome is that — aside from the portable part — this is something we can actually do already. Garcia-Robledo does it regularly in his lab. The real-world tricorder isn’t just something that’s going to transform science someday. It’s already doing that, right now.
The non-fictional tricorder is based on an idea called DNA barcoding, which originated in 2003 with Canadian biologist Paul Hebert. He thought there might be an easy way to quickly identify species using short DNA sequences that are unique to one species or another. If you had a database of these sequences, then all you’d have to do would be to match a sample to a sequence and you’d know what species you were looking at. It’s similar to the way we store fingerprints, and then use those to match prints from a crime scene with an individual person.
Of course, like fingerprinting, DNA barcoding turns out to be more complicated than it sounds. The sequence most commonly used to barcode animals is a gene called CO1. It’s a piece of mtDNA. This DNA is found inside the mitochondria — organelles within a cell that produce energy. It’s there because, once upon a time, those mitochondria were independent bacteria, doing their own thing as single celled organisms. MtDNA doesn’t create you, it creates parts of your cells.
The mitochondria, and their DNA, get passed down from generation to generation in egg cells — sperm don’t usually have them. So you carry your mother’s mtDNA. And she carries her mother’s. But that mtDNA doesn’t travel through the generations intact. Over time, it picks up little errors and changes to the sequence. This is where DNA barcoding — and its complications — come in.
Image: A room full of DNA sequencers, a Creative Commons Attribution (2.0) image from jurvetson’s photostream
The idea is that the changes that happen to CO1 should be able to serve as a marker between species. In order for that to work, though, the mutation rate has to hit a sweet spot, said Karen James, a staff scientist at Mount Desert Island Biological Laboratory. She does a lot of work with DNA barcoding and described the ideal amount of variation in the DNA sequence as being a Goldilocks sort of problem. If you have too little variation (i.e., if the mtDNA doesn’t change fast enough) then you’ll have too many different species that share the same barcode. But if the mutations happen too quickly and you have too much variation, then you could get a bunch different barcodes within the same species. Either way, the barcode would be useless — just as if lots of people shared the same set of fingerprints.
The good news is that, for many animal species, CO1 hits that sweet spot. The bad news is that it doesn’t work for everything. In fact, it doesn’t work for plants at all. Their mtDNA changes too slowly. In 2009, James was part of a team that identified alternative DNA sequences that can be used to barcode plants.
CO1 also varies in how well it works for different kinds of animals. Like plants, mtDNA changes slowly in cnidarians — a phylum made up of more than 10,000 species, including many kinds of jellyfish. The plant sequences won’t work for them, either, so cnidarians are notoriously difficult to barcode.
All of this explains part of why DNA barcoding can’t really be used to identify new species. If you don’t know the organism well enough to know how quickly its mtDNA are mutating, than you have no idea whether the changes you see represent a new species, or just variation within an old one. But that’s okay, say researchers like Garcia and James. It doesn’t mean DNA barcoding is useless. Think back to the tricorder, and what Mr. Spock actually did with it. He wasn’t identifying new species. Instead, he was figuring out which previously-identified species lived on which planet.
Rolled leaf beetles. Carlos Garcia-Robledo pulled half-digested plant bits out of their stomachs and used the DNA from those samples to find out what the beetles were eating. Photo by Charles Staines.
DNA barcoding can be used, along with traditional taxonomy, to help identify new species. Paul Hebert demonstrated this in 2004, when he figured out that a single species of tropical butterfly was actually 10 species of tropical butterfly, cleverly masquerading as one. But naming new species and pinning them to a board really isn’t what the tool is best at — and it’s not the most interesting way to use it, either. Even though the tricorder of today currently takes up a space the size of a room, it’s already being used to study the world far outside the lab.
For example, Carlos Garcia-Robledo uses DNA barcoding to study the relationships between beetles and the plants they eat. His team figured out how to extract plant DNA from a beetle’s stomach. Compare that DNA to a barcode library, and you start to get a good idea of what different beetles in different places are chowing down on. That matters, because the beetle’s diets are changing along with the climate. As habitats get hotter, some plants can’t survive. So what happens to the beetles that eat them? Garcia-Robledo uses DNA barcoding to track those patterns of adaptation and extinction.
Turns out, DNA barcoding is very good at helping us answer questions of sustainability and environmental change. It’s especially important in places where it would be really hard to understand biodiversity and species interaction simply by collecting and counting — like the oceans, for instance.
We know that things people do can affect ocean ecosystems. And we know that some parts of the ocean bear more of the brunt of this than others. In order to understand what those differences really mean for wildlife, Smithsonian invertebrate zoologist Allen Collins has started collecting samples of all the biodiversity in a plot of ocean — from bacteria to charismatic megafauna. DNA barcodes tell him exactly what species live there. He can go back and sample the same spot over time to see how the mix of species has changed. And he can compare those changes in places relatively untouched by humans to what’s happening in areas that have a lot of human impact. What, exactly, does “human impact” mean for ocean animals? That’s what he’s going to find out.
There are even consumer applications. Earlier this year, the ocean advocacy group Oceana released a report showing that restaurants and grocery stores have a habit of selling customers one fish, but labeling it as another. In fact, 33% of the 1200 samples they took over two years were mislabeled. When you think you’re buying red snapper, you’re often actually buying much cheaper tilapia. The secret swaps can affect your health and they can also affect fish populations. All Oceana’s data came from DNA barcoding, Karen James said.
So far, all of this relies on bringing the world back to the laboratory for testing. But the real, portable tricorder is inching closer. We often talk about the $1000 genome, in terms of being able to sequence the entire thing cheaply. But the same technology that’s making that dream a reality also applies to the much easier and faster task of sequencing a small strand of genome — you just have to adapt the tools to the purpose of barcoding.
Last year, a company called Oxford Nanopore announced that it had developed a miniature genome sequencer that could plug into a laptop’s USB port. The device, called the MinION, isn’t the real-world portable tricorder. It’s designed to sequence entire genomes, for one thing, which isn’t really what DNA barcoders want. It’s also a one-time-use tool that’s expected to cost $900 a pop — if it ever makes it to the marketplace. But the MinION is a step in the right direction. Someday (and probably someday soon), scientists will be able to study changing ecosystems instantly, while they’re standing in that ecosystem — just like Mr. Spock.
Samples of organisms that Allen Collins brought back to the laboratory from a research trip to Bali. Someday, he’ll be able to skip this step.
PREVIOUSLY:
• What leeches and ligers can teach us about evolution
• In the leech library: Behind the scenes at the American Museum of Natural History
• Be an Armchair Taxonomist!: A challenge from The Encyclopedia of Life