Counting the species: how DNA barcoding is rewriting the book of life

Guanacaste conservation area in north-west Costa Rica is the most DNA barcoded place on Earth. On its western frontier, jaguars hunt turtles from the mangrove swamps that line the Pacific coast. Endangered spider monkeys swing through dry tropical forest, the remnants of a rapidly disappearing ecosystem that once ran from northern Mexico to Panama.

Updated version of map

On the slopes of volcanoes, the last before Lake Nicaragua to the north, rainforest covers the land. High on the volcanic peaks, cool, moist air brought by the Atlantic trade winds forms cloud forests. There is a lot of life to document in this world heritage site, which is roughly the size of New York City.

As the sixth mass extinction of life on Earth gathers pace, humanity can only manage a well-informed guess about the true magnitude of the loss. We have identified around 2 million species on the planet. We know their abundance has plummeted. But with estimates for the total ranging from 8.7 million to a trillion, we are still unable to answer a fundamental question: how many species are there on Earth?

Until recently, there was little hope of a quick solution to the so-called “taxonomic impediment”, the phrase used to describe our inadequate account of the world’s library of life and the scarcity of taxonomists. Detailed species knowledge was routinely lost when experts died. Most plants and animals that went extinct slipped away unnoticed and unrecorded, anonymous casualties of human overconsumption and overpopulation.

But that was before the invention of DNA barcoding. In 2003, Canadian scientist Paul Hebert published a study claiming to have developed a technique that could identify and differentiate between all animal species on Earth. Using common moths collected in his own backyard, he successfully identified 200 closely related species using the mitochondrial gene cytochrome c oxidase I (COI), which is present in all aerobic life.

Rincon de la Vieja volcano, the highest point in Area de Conservacion Guanacaste (ACG), home to cloud forests and a variety of wildlife.

Hebert, known primarily for his expertise in water fleas at the time, had cracked it. The short genetic sequence would serve as a DNA barcode for all animals, separating species by their genetic divergence. An equivalent section of DNA could be used to discriminate between plants and fungi. Museum collections could be identified, too. Barcoding was also cheap. All he needed now was $1bn to identify the millions of animals unknown to science, a fraction of the cost of the International Space Station or the Human Genome Project, the paper concluded. But Hebert’s study was not met with universal acclaim.

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“I was surprised. I had anticipated harsh criticism from morphologists. But I had not expected critiques from my peers in evolutionary biology,” Hebert recounts. He was accused of acting like a “creationist”. Others said his findings were uninteresting.

But nearly two decades later DNA barcoding has become mainstream. In August, Hebert, a professor at the University of Guelph in Ontario, was awarded the prestigious Midori prize for creating “a research alliance which is revolutionising our understanding of planetary biodiversity”.

DNA barcoding has been used to track the illegal trade in wildlife and plants, monitor water quality and even uncover the sale of endangered sharks in fish and chips. The technique has unmasked so-called cryptic species that were identified as one animal by traditional taxonomic approaches but are in fact many distinct creatures that appear the same to the human eye.

So far the reference library of species overseen by the International Barcode of Life (iBOL), where Hebert is the scientific director, numbers around 750,000 species. Last year the group launched a $180m project to barcode two million more species around the world, approximately the total number of flora and fauna already described using traditional taxonomy. While estimates for the number of plants, animals and fungi species range from eight to 20 million, insects are believed to account for a huge number of undiscovered species. Around $60m has been raised for the project so far.

Benefits

The benefits of knowing the Earth’s library of life are not limited to understanding the extent of biodiversity loss. Discoveries in medicine, agriculture, food, engineering and even beauty products are hidden in the genomes of the species that will be barcoded. A complete library of life could underpin food distribution networks, allow a smartphone attachment to identify any piece of organic material on Earth and integrate natural history into the social, cultural and economic fabric of society.

Inside the Centre for Biodiversity Genomics' DNA extraction lab, part of the University of Guelph's International Barcode of Life Consortium.

Now Hebert has turned his attention to the creation of a global biosurveillance system underpinned by barcoding that will continuously monitor the planet and check the health of global ecosystems in near real time. A network of satellites, underwater drones and DNA sequencers would patrol Earth, alerting scientists and governments to any dangerous changes, intercepting new diseases and highlighting harmful human activity. He estimates it would cost $1bn over 20 years.

There are good reasons to create such a system. Compared with the atmospheric monitoring infrastructure and billions of research money for combating the climate crisis, the resources dedicated to measuring the ongoing biological annihilation of life on Earth are pitiful. The tale of our heating planet is based on more than 150 years of weather records, while it is not uncommon for studies on insect collapse to be based on figures compiled by amateur entomologists.

Prof Paul Hebert, the 'father of DNA barcoding'.

“It’s a million centuries between every mass extinction event and we’re living in the century that brings the next one,” Hebert says. “We’re talking about the irrevocable loss of knowledge on the largest scale ever experienced by humanity – driven by humanity. Because every one of those genomes and every one of those species: that’s a book of life, and it’s about 10 times bigger than the longest book ever written by any human. So I think history will indict us severely for allowing this erosion of knowledge on an absolutely unprecedented scale.”

Pioneers

Guanacaste conservation area World Heritage site (ACG in its Spanish acronym) exists largely thanks to a lifetime of work by University of Pennsylvania professors Daniel Janzen and Winnie Hallwachs. Dan and Winnie, as they are known to everyone, split their lives between Philadelphia and a forest cabin in Santa Rosa national park, which is part of the ACG. They immediately understood the potential of Hebert’s innovation and are the major drivers behind Costa Rica’s bid to become the most extensively barcoded country on Earth with a new project: BioAlfa.

“For me, the invention of DNA barcoding is easily as significant as the discovery of DNA,” Janzen says as we sit outside their forest home. “And you could even go further back to some bigger discovery that we’ve had – the microscope, for example.” The 81-year-old evolutionary ecologist is a generational talent in his field, recipient of the Crafoord prize and a MacArthur fellow. His peers also admire his bravery, hard work and excellent salesmanship.

BioAlfa aims to systematically record and describe all of Costa Rica’s biodiversity, with barcoding at its heart. In 2019, President Carlos Alvarado Quesada designated the scheme of national importance, but it still needs $100m to make its goals a self-sustaining reality. While temperate countries have launched similar schemes, the sheer abundance of life in the tropics makes BioAlfa a completely different challenge.

Daniel Janzen and Winnie Hallwachs in an outhouse filled with samples near their cabin in the ACG. Janzen is holding a jar of frozen insects that will be DNA barcoded in Canada.

The Central American country is home to an estimated 4% of the world’s biodiversity. Coexistence with nature is part of Costa Rica’s essence and it promotes ambitious decarbonisation plans and wields international influence in the environmental arena. Overcoming the taxonomic impediment within its borders by identifying and understanding all of its flora and flora would be an unprecedented achievement. Hebert has reserved half of his barcoding capacity for BioAlfa this year.

Janzen began documenting life in the dry tropical forests of northern Costa Rica after collecting leaves to feed Rufus, an excitable teenage tapir, in the mid-70s. The pig-like herbivore had been orphaned and entrusted to friends, surviving on scraps from the kitchen table. But Rufus was no longer welcome at dinner after he learned that a swift tug on the tablecloth would bring a feast crashing to the floor.

Daniel Janzen in regenerating rainforest in the ACG.

“When he was banished outside, I came to the question of what kinds of leaves he would eat,” Janzen says, chuckling as he recounts the tale.

Janzen drove to the forest of Santa Rosa national park, which now forms part of the ACG, and filled plastic bags with an array of leaves for Rufus. But when he returned to the corral, he realised he could not identify the leaves the grateful tapir was devouring. So he returned to Santa Rosa with a botanist and spent the next six months identifying the plants in the forests. Then he moved on to insects.

‘Butterfly factories’

A network of malaise traps, moth lamp stations and rearing barns – jokingly known as “butterfly factories” to those who work in them – has been established across the different ecosystems to record insect life. The painstaking research will help make a global biosurveillance system possible but it needs to be conducted everywhere.

A former water buffalo shed is filled with carefully organised rows of plastic bags, each containing a caterpillar feasting on leaves from the nearby rainforest. Osvaldo, a former shark fisherman and field assistant to the couple for 30 years, is holding a hungry caterpillar hidden under a leaf. The insect will be carefully reared and ultimately sent to Canada for DNA barcoding analysis in Hebert’s lab once it has completed its life cycle.

The caterpillar is a chaotic creature that writhes in the light when Osvaldo turns over the leaf, the end of its body quivering like the rattle of a poisonous snake. Its shades of brown and beige combine like a cubist artwork. Barcoding might show it is a new species.

A parataxonomist monitors the health of caterpillars in a butterfly-rearing barn in the ACG. These will eventually be DNA barcoded.

“There are much bigger ones than that,” Osvaldo tells me, disappearing back into the lines of plastic bags.

The next caterpillar is huge, covered in orange and blue spikes. It makes a low-level, muttered clicking sound as Osvaldo strokes its back. We cross to the other side of the rearing barn to inspect pupae undergoing their final stage of development. Osvaldo delights in the range of chrysalis shapes and colours.

But not all become butterflies and moths. The bags filled with dead pupae are moved to another line in the barn. From them, parasitoids emerge from eggs that were laid inside the unsuspecting hosts they have slowly devoured.

In the main building on a hill above the rearing barn, Gloria, another parataxonimist, shows me photos of how the pupae are changed by the parasitoids. Some look like they’ve been stuffed with polystyrene. Others look normal apart from small groups of black bubbles on the pupa. Sometimes flies emerge from them, sometimes wasps.

Gloria is carefully inspecting glass jars filled with the parasitoids’ pupae, inputting information about the host specimen they emerged from and taking photos. They, too, will be sent for DNA barcoding to better understand the web of life in the ACG.

Osvaldo shows a caterpillar that was collected from the nearby rainforest.

The results of this process have been astonishing. Almost 200 new parasitoid wasp species were discovered where only three had previously been described. At least 3,000 more species have been barcoded and are awaiting the attention of a taxonomist to formally introduce them to science.

While the thrill of discovery is an end in itself, the library of species that BioAlfa will help create will also be of economic importance. A DNA barcode is just a way to identify an organism but the genome – its entire sequence – can prove lucrative: the basis for new discoveries in medicine, agriculture, food and beauty.

Alongside conservation and sustainability, sharing the benefits from genetic resources is the third and often ignored pillar of the UN convention on biological diversity which will hopefully produce the “Paris agreement for nature” in 2021. Developing countries, which are normally the most biodiverse, want just payment for the riches that might hide in their ecosystems.

(Left) Gloria, a parataxonomist, holds a larva that has been killed by parasitoids. (Right) Janzen points to a box of insects collected in the ACG that have been dried and preserved.

(Left) Janzen hold insect leg samples that will be sent for DNA barcoding analysis in Canada. (Right) Boxes of insect and plant samples collected in the ACG for analysis.

Janzen and Hallwachs, alongside the Costa Rican government, are well aware of this issue and the potential economic benefits of BioAlfa. Anyone who spends long enough with Janzen will see his trusty comb emerge from his back pocket – the beginning of a story about the future of being able to identify any organism anywhere with a device that connects to an iPhone. Using a sensor the size of a comb, he says, farmers will be able to calculate the economic cost of cutting down rainforest for cattle or monoculture crops by rapidly checking areas for potential discoveries.

Costa Rica already has had early success bioprospecting. South of the ACG is the Nicoya peninsula, one of the four blue zones on Earth where humans routinely live above the age of 100. In 2017, Chanel launched its Blue Serum skincare range, which uses ingredients from here. Antioxidants from the region’s green coffee were used and the Costa Rican government received payment. BioAlfa’s library of life might bring many more paydays.

Unknown extinctions

Heading out into the dry tropical forest a short drive from Janzen and Hallwachs’ cabin, we inspect the number of moths that have emerged in the first few weeks of the rainy season.

To the untrained eye, the hundreds of insects on the white sheet in the darkness overwhelm and exhilarate in equal measure. Moths the size of birds flutter around my head, brushing my ears, legs and every uncovered body part. Geckos lurk on the corner of the sheet picking off the smaller moths. Mexican burrowing toads belch in unison in the valley below the lamp station. But the couple are quick to temper my naive exuberance.

There used to be many more, Hallwachs quietly assures me as we stand with the darkness at our backs, looking at the spectacular display. “There are all kinds of species missing,” she says.

The next day Janzen shows me a picture of the same light station in 1984 – it is barely possible to see the white linen under the layer of moths.

Daniel Janzen points to a large moth at a lamp station in the dry tropical forest in the ACG.

As Hallwachs shows me to my room on the first night of my second visit to the park, I point through stormy weather conditions to fireflies blinking around the trees. It is a species of firefly that only appears in the first few weeks of the rainy season, she says.

“Firefly numbers are going down around the world. And they’re not nearly as abundant as they used to be. But they are magical. They’re totally magical,” she says, as we crouch together in the rain admiring them.

The ACG is marked by human extraction: scar marks on the chicle trees, which were targeted in the second world war to provide chewing gum; stumps of mahogany, still rock solid decades after they were felled; the mangrove forest that was cut down for textile dye. All are indicators of the overconsumption driving biodiversity loss around the world.

On my final day with the couple, they indulge my interest in the beach on the western flank of the ACG, which might have the largest concentration of jaguars in Central America. In the middle of another rainy season storm, Janzen stops the 4×4 we are travelling in to explain why.

“When I got here in about 1971, I met an old jaguar hunter who hunted with dogs. And he said to me, not bragging, just matter-of-factly, that he normally got five to six jaguars per year out of this valley. So a few years later, I’m exploring this valley for caterpillars and all that. And I look around me as a hunter, as somebody who understands wild food. And I say to myself, ‘no way does this valley support five to six jaguars a year’.

“Years later, a biologist named Luis Fonseca started studying the nesting of sea turtles on this beach down here. And right away he discovered the jaguars were killing the sea turtles – not the eggs – but the whole adult.

A jaguar gnaws on a recently-killed freshwater turtle on Nancite Beach.

“There are four species of turtles that nest on this beach. Two are regular all year round. So there’s the food! We have endangered species eating endangered species to keep themselves going.”

There used to be more of everything, everyone is certain, but quantifying what else might be slipping away is hard when there are millions of species left to document. Maybe DNA barcoding can rectify that.

Find more age of extinction coverage here, and follow biodiversity reporters Phoebe Weston and Patrick Greenfield on Twitter for all the latest news and features

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