Taxonomy: Vital art that's disappearing

Straits Times 6 Jun 09;

A CRITICAL discipline in biology could well be as endangered as some of the animals it studies.

American life science magazine The Scientist ran an article this month, A Fading Field, on the disappearing art of taxonomy - the collecting, describing, naming and sorting of organisms based on their physical attributes.

The article mentioned that skills were being lost as older taxonomists retired and fewer students picked up the discipline. Scientists say the lack of funding and the growing popularity of molecular tools such as DNA sequencing, which can be used to tell different species apart, compound the problem, as does a shift towards other life sciences disciplines.

Dr Tan Heok Hui, of the Raffles Museum of Biodiversity Research, said: 'The educational system is leaning towards bio-medical sciences and applied life sciences for human, pharmaceutical and biochemical uses.'

The trained taxonomist was among the first to describe and classify the world's smallest fish.

Taxonomy is back-breaking work. For instance, National University of Singapore student Martin Chew, 25, spent hours dissecting dung-fly parts at the micro-metre scale, where an object is 100 times thinner than a human hair.

'At least with surgery, you can see something. With this, you can't see anything,' he said.

Yet, in an age of increasing-rapid habitat loss, being able to tell organisms apart from one another is more important than ever.

Scientists have catalogued just 6 per cent of the world's up to 30 million species, according to The Scientist article. They must race to find, name and classify the rest before they disappear.

Swedish biologist Carolus Linnaeus, the 'father of classification', developed the system of classifying organisms in the 18th century, founding modern taxonomy. The discipline still has a place in modern science, particularly in remote places where DNA tests and other complicated lab procedures are impossible.

For example, in the 1980s, researchers from Harvard University's Arnold Arboretum found a plant in Borneo whose extracts had anti-HIV properties.

On a second collection expedition, however, they returned with a lookalike plant of the wrong species.

It took botanist Peter Stevens, examining the plant, to inform them of the mistake.

GRACE CHUA

A Fading Field
The Scientist Volume 23, Issue 6 | Jun 09

Traditional taxonomists are an endangered species. Could their unique brand of knowledge disappear, too?

Anthony Cognato, an entomologist at Michigan State University, is a bark beetle expert. He's made a career out of collecting, identifying, and classifying the insects—members of the subfamily Scolytinae—that make a living by cultivating fungal gardens in tunnels they bore in dead trees. Even though he's an expert in bark beetles, Cognato can still be surprised by the organisms he's devoted his career to studying.

A few years ago, Cognato's graduate student, Jiri Hulcr, spent 18 months in the rainforests of Papua New Guinea, surveying the island's bark beetle fauna across a 1,000-kilometer transect. Hulcr set up three sampling sites, each 500 kilometers apart, by felling trees and waiting for bark beetles to inhabit the dead wood and establish their fungal gardens, called galleries. As he collected beetles, Hulcr began to notice a pattern that he showed to his advisor during Cognato's visit to the field sites. "When you collected this one smaller species, it was always associated with this other larger species," Cognato recalls. "Their galleries were always located right next to each other."

Cognato encouraged Hulcr to collect data on the frequency of this phenomenon, in which the smaller, yellowish species of beetle seemed to bore its tunnel within a centimeter of the larger, long-legged species. "He had the data and it was pretty obvious," Cognato says. "Basically you always found these species together."

With the pattern established, the researchers next sought to get to the bottom of the two beetles' relationship. They hypothesized that the smaller species was somehow leaching off of the larger species by stealing fungi rather than collecting and seeding their own spores. To test their hypothesis, they needed to look at the insects' morphology, so they temporarily set aside the molecular tools that are de rigueur among most biologists, rolled up their sleeves, and used some of the microscopes and dissection tools that have sat in the taxonomic toolbox for centuries.

Back in Cognato's Michigan State University lab, Hulcr dissected hundreds of specimens of the smaller beetle species that he had collected in the field. He dipped their heads in paraffin and made multiple histological slices, looking for specialized fungal spore-carrying structures, called mycangia, that virtually every species of bark beetle harbors in their mandibles. He found none, demonstrating that the smaller species did, in fact, depend on another source for its fungi. To confirm, Hulcr sequenced the DNA of the fungal communities he sampled from the tunnels of both the larger and smaller beetles, and showed they matched. The two taxonomists had identified a completely new ecological phenomenon that they dubbed "mycocleptism," or fungi-stealing. While comparing the DNA of the fungi was an important confirmation of mycocleptism, the scientists would never have spotted the behavior if they hadn't observed it in the field and taken a close look at the insects' morphology.

"You get more out of your systematic studies if you can actually go and collect your organism of interest," Cognato says. "It allows you to observe so much more that you can't observe in a DNA sequence." The subfamily to which these bark beetles belong contains the most commonly imported exotic beetles into the United States, and some species are currently contributing to the decimation of tree populations in the coastal southeast. There is no known control method at the moment, but knowing more about how the beetles make their livings may provide key insights into how to control the pest.

However, there are fewer and fewer biologists who practice traditional taxonomy, or the collection, description, naming and categorization of organisms through intense study of their physical attributes. In general, the field of taxonomy, or systematics as it is often called, has been leaning towards the molecular end of the spectrum since genetic technology matured in the late 1970s and 1980s, and traditional taxonomic skills have been dwindling as older taxonomic experts retire. Many taxonomists blend traditional methods, such as morphological and behavioral study, with modern molecular techniques, such as DNA sequencing, to fully characterize their pet taxa. But taxonomists like Cognato and Hulcr, who rely on fieldwork and morphological study as core aspects of their taxonomic work, appear to be slowly going extinct.

Most children are born taxonomists. Exploring, discovering, and naming the living things in one's environment, whether it's a backyard or a city block, seem to come naturally. Some of the first scientists, such as Aristotle, focused intense efforts on exploring and cataloging the living world around them, and at the height of global exploration from the 15th to 19th centuries, taxonomists were in great demand, as new lands and species were discovered. Other notable Western taxonomists include Ernst Haeckel, Carolus Linnaeus, and Charles Darwin.

Describing, naming, and preserving new taxonomic groups—specifically using the morphological skills that are traditionally central to the discipline's methodology—is just as important today, as researchers continue to uncover new genera and species in the unexplored corners of the globe. "Taxonomy provides the language of biodiversity," says Quentin Wheeler, an Arizona State University insect taxonomist and dean of that university's college of liberal arts and sciences.

By some estimates, scientists have discovered, described, and named only 6 percent of the planet's species—less than 2 million of the 30 million that exist, at most.

That remaining 94% of species tend to reside in rapidly vanishing ecosystems—biodiversity hotspots—where scores of species likely slip into extinction without ever attracting scientific attention. Research published in 2004 estimated that certain areas on Earth will lose up to 37% of their species by 2050 due to climate change alone.

The danger is that our planet's biodiversity is disappearing quicker than our accumulated mass of taxonomic expertise can catalog it. And in order to stop these extinctions, scientists have to understand how the species within each ecosystem live and relate. To fix a clock, you have to know how the individual parts work and interact, says Wheeler—and the same is true for ecosystems.

Despite the importance of taxonomic expertise in the face of such a precarious situation, children these days with an interest in the natural world typically don't grow up to be taxonomists like Haeckel and Linnaeus, but instead study life using PCR, mass spectrometers, and DNA sequencers.

Montgomery Wood, the world's foremost taxonomic expert in a family of globally distributed black flies, spent idle summer days turning over rocks, fording creeks, collecting bird nests, and catching insects. "I had nothing to do in the summer time, and I just chased things," says Wood, 76.

Growing up on the fringes of London, Ontario, in the 1930s and 40s, Wood's peregrinations were not unusual, but his eye was perhaps keener, his curiosity sharper. Though he may not have realized it then, the young Wood was embarking on a scientific career that would span nearly five decades. He can identify many of family Tachinidae's approximately 10,000 named black fly species by sight. "I'm weak in [the black fly species of] Africa and China," he concedes.

Wood honed expertise in identifying thousands of species of flies the old-fashioned way: through exhaustive examination of the organisms' morphology and natural history. "What made me an expert in Tachinidae was to stay at them for an entire lifetime," he says.

Perhaps Wood should have seen the demise of his chosen profession coming. He recalls that when he was starting his PhD work on the taxonomy of Ontario's tachinids in the early 1960s, a fellow biologist at the University of Toronto questioned his decision to enter the field, with the promise of new and exciting technologies and methodologies—namely DNA analysis—poised to revolutionize modern biology. "He didn't say I was wasting my time," Wood remembers, "but he implied that."

Just like the organisms taxonomists study, the discipline of systematics and biology as a whole was evolving. By the 1980s, the field of systematics, like many other fields, became entranced by the promise of DNA analysis and its ability to decipher genetic codes, enabling taxonomists to look past an animal's skin and into its cells. Walter Judd, a University of Florida botanist, had a front row seat for this evolution in taxonomy. "When the excitement of molecular analyses hit, people started spending a lot of time in the lab," and less in the field, he says. As younger botanists sought to validate molecular analyses as taxonomic tools, they necessarily focused their study on more well-studied plant species, such as Arabidopsis, rather than seeking out undiscovered taxa in the field, according to Judd.

Now older taxonomists like Wood and Judd are retiring from museum and university positions, with institutions tending not to replace them with more taxonomists. The United Kingdom's Royal Botanic Gardens Kew, for example, has not had a gymnosperm taxonomist since the last one there retired in 2006, and has not replaced its last fern specialist, who retired in 2007.

Judd, whose work centers largely on the morphology of tropical flowering plants, says that taxonomic expertise could slip through our fingers in alarmingly short order. "I'm worried that in perhaps a generation or two we'll be in rough shape because there won't be people who know how to use the morphological features" to identify a species.

The primary federal funder of systematic research in the United States is the National Science Foundation. This year, the agency put $2.5 million (0.04% of its total budget) towards a program designed to help experts train young students in taxonomy.

Through the Partnerships for Enhancing Expertise in Taxonomy (PEET) program, graduate students and postdocs of Gustavo Hormiga, a George Washington University spider systematist, learn to observe, measure, and draw their spiders while at the same time studying them with scanning electron microscopy and taking genetic samples to be analyzed for key diagnostic markers. Hormiga strongly encourages his students to complete taxonomic monographs—detailed publications that describe the taxonomy of organismal groups—and compile taxonomic keys, which give other researchers a map to identifying organisms. In this way, Hormiga says, his students are grounded in the traditional methods of taxonomy while utilizing modern methods to extract as much useful information from their specimens as possible. "This is not about being modern or crusty or anything," Hormiga says. "It's about having data."

The PEET program doled out its first round of grants in 1995 in the face of a rapid decline of experts in the field. An NSF survey conducted in the mid-1990s found only 940 systematic biologists working at doctorate-granting institutions, and one quarter of those were only adjunct faculty members. More than 80% of the institutions that responded to the NSF survey said that they would not hire systematists in the future if new positions opened up.2 "There was a strong perception in the scientific community that many of the folks that were doing taxonomics and systematics were getting old and retiring and weren't being replaced by their institutions," according to Scott Snyder, a PEET program officer at NSF. Since its inception, PEET, a biennial program that awards 5-year grants of $750,000 to successful applicants, has helped train hundreds of graduate students and postdoctoral fellows in taxonomic science. However, there are indications that the dwindling of taxonomy has reached a point of no return, and even this influx of funding may not be enough to reverse the trend.

When Pricila Chaverri arrived at the University of Maryland about a year ago with a PEET grant in hand, she advertised on campus for undergraduate students to work on revising the taxonomy of fungi in the order Hypocreales, which she studies. Herself a graduate of the PEET program, she waited for the expressions of interest to roll in. None came. Frustrated, she changed her advertisement to highlight the fact that students would also learn molecular techniques, such as PCR and DNA sequence analysis, as they sought to fully characterize fungal specimens in her lab. "I got, like, a hundred applications," Chaverri recalls. "And they all wanted to learn molecular biology."

Chaverri realizes that emphasizing the modernity of her research is a surefire way to attract attention from students and funding agencies alike. She's used the tactic so many times that she's begun to wonder about how she herself conducts research. "Sometimes I worry that I'm wasting my time looking at the morphology of fungi," Chaverri sighs, standing in her lab this spring as graduate students peer through microscopes at dead twigs harboring her fungal quarry. "But I like my fungi, so I'm going to keep looking at them."

Looking at her fungi, in fact, led Chaverri to an unprecedented insight into a group of neotropical species that infect scale insects and other agricultural pests. Last year, Chaverri was studying genus Hypocrella, which contained several brightly colored species grouped together based on DNA sequence data. But Chaverri decided to look more closely at the morphology of the sprawling genus, and when she trained her microscope on the ascospores—long, sexual reproductive structures—of the species, she noticed some interesting differences. Some of the species in the genus had large ascospores that could disarticulate into many smaller parts, while others had smaller ascospores that did not disarticulate. Her study of the fungi resulted in the creation of two new genera, Moelleriella (the species with the large, disarticulating ascosporse) and Samuelsia (the species with the smaller ascospores).3

Far from being an arcane taxonomic revision, Chaverri's research may help to improve the way that researchers use particular species of fungi to control agricultural insect pests. For example, using fungi of genus Moelleriella may lead to more effective control of the scale insects or whiteflies that plague citrus growers in Florida, Chaverri says. "One can hypothesize that [Moelleriella] would be more successful on spreading to new trees or insects."

Though Chaverri has managed to continue her taxonomic work, a 2007 survey by PEET graduates Ingi Agnarsson and Matja Kuntner found that 47% of PEET alumni no longer worked in taxonomy, and a further 9% had positions where taxonomy played only a minor role. In addition, 6% of the PEET program alumni were unemployed when contacted by Agnarsson and Kuntner. And the authors stress that the survey findings are likely overly rosy, because their ability to find and survey PEET graduates in part relied on their closeness to the field of taxonomy—in other words, some of the graduates they couldn't track down are likely so far removed from the field they couldn't be found. Some of the comments recorded by the two authors convey the disconcerting realities facing taxonomists today. "As it is now," one survey respondent wrote, "[PEET] trains students in skills absolutely not required by the job market."

Nearly all the classically trained taxonomists with whom I spoke echoed this sentiment.

Ralph Holzenthal, a University of Minnesota entomologist and caddisfly expert, says that he's been fighting to fund his lab for 3 years, ever since his last round of PEET funding ran out. He once supported six graduate students with two overlapping NSF grants, but now can support only one with money from the NSF. Holzenthal adds that he's in his fourth round of revisions of an NSF grant application to update the taxonomy of caddisflies in Brazil, which are severely understudied. Fewer than 350 species have been recorded in a country that spans 8.5 million square kilometers, and Holzenthal estimates that as many as 850 species await discovery and description in the southeastern corner of Brazil. He says that cataloging these species could ultimately benefit the health of tropical streams and rivers, which are intimately tied to the health and life history of caddisflies in the area.

Jerome Regier, an NSF-funded systematist at the University of Maryland, says that some classical taxonomists need to do a better job of convincing the scientific and funding communities of the importance of cataloguing the world's species before they disappear. "[Taxonomists have] got to interest graduate students in the [scientific] problems that they have. Species descriptions aren't problems as such," Regier says. "It's species loss that's a problem. It's habitat destruction that's a problem. You have to relate your species drawings to those bigger questions. The fact is you've got to get funding to carry this out."

In some sense, administrators are justified in shunning taxonomists when it comes time to hire new faculty. A taxonomist has access to essentially a fraction of a percentage of the NSF budget, while a molecular biologist has at her fingertips the budget from the National Institutes of Health, typically four times larger than the NSF's. "If your objective is just to get a job, you probably shouldn't be in taxonomy at all, molecular or descriptive," said Holzenthal.

James Rodman, a botanist and former NSF program director who was instrumental in creating the PEET program in the mid-1990s, says that the disappearance of traditional taxonomy is only part of a larger problem. "More broadly speaking, organismal biology is dying out," Rodman says, now in semi-retirement as museum research associate at the University of Washington's Burke Museum. He says that colleagues tell him all the time that even in high schools, biology field trips are seldom, if ever, taken—a trend that ripples up through the university level as survey courses in entomology, mycology, and other organismal disciplines cease to exist. "We're no longer interested in knowing about the organisms of the world. That's the sadder tragedy."

Some taxonomists feel that their legacies will live on even though they are retiring and leaving the lifelong studies that often began with an organic fascination in the natural world around them. Ralph Holzenthal's mentor and PhD advisor in the 1980s was Oliver Flint, a curator emeritus at the Smithsonian Institution and a world-class caddisfly expert. Flint says that his lasting appreciation for the field assuages any feelings of loss for the lack of jobs available to traditional taxonomists. "I think [taxonomy and systematics are] healthy enough in terms of how they're executed. The sickness is that there are no jobs anymore."

Monty Wood echoes Flint's sentiment. He says that he has no desire to lament the downfall of the type of taxonomy in which he was trained. "I have thought about it," Wood admits. "But I don't lose any sleep over it. There's nothing I can do about it."

Instead, Wood says that he focuses on studying and preserving as many specimens as possible. Quentin Wheeler, the Arizona State University entomologist who is also director of the newly-created International Institute for Species Exploration, says that he hopes to create a "cyber-infrastructure," including digital images and virtual networks, that will give researchers around the world access to all of the nearly 3 billion biological specimens currently housed at natural history museums. He says that if modern technologies and more funding are successfully combined with continued taxonomic work, taxonomists have a good chance of describing and naming 8 million new species in the next 50 years.

Ironically, the demise of taxonomy and systematics might be attributable to its most fervent champions. "I think in the past there's been a tradition in classical taxonomy that it's OK to isolate yourself from the world to work in the museum," says Regier. "There has to be somewhat of a shift in culture." Indeed, because it formed the bedrock of biology for centuries, taxonomy carries with it a lot of perceptual baggage. "It's hard to get over this image of the systematist being just a stamp collector," says Cognato. But nothing could be further from the truth, he says. "Properly done, [traditional taxonomy] gets you out in the field and discovering many new things that wouldn't have been found without them."

Correction (June 4): The original version of this story mistakenly listed Michigan State University as Ralph Holzenthal's affiliation. Holzenthal is a faculty member at the University of Minnesota. The mistake has been corrected, and The Scientist regrets the error.

References
1. C. Thomas et al., "Extinction risk from climate change," Nature, 427:145–48, 2004.
2. M. Claridge, "Introducing systematics agenda 2000," Biodivers. Conserv., 4:451–54, 1995.
3. P. Chaverri et al., Studies in Mycology 60: Neotropical Hypocrella (anamorph Aschersonia), Moelleriella, and Samuelsia, Utrecht: Centraalbureau voor Schimmelcultures (CBS), 2008, 68 pp.