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The Magazine of the CALIFORNIA ACADEMY OF SCIENCES |
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Feature DNA Barcoding Systematists are charged with documenting and describing the history of life on Earth. They search for answers to several fundamental biological questions: What kinds of living things exist? Where do they live? How are they related? With only an estimated 10 percent of life described on this planet so far, the thought of being able to identify all or most of the world’s species might seem like an impossible, idealistic dream. In today’s era of accelerating species extinctions, the quest to identify all or most of the world’s species is even more daunting: scientists must discover and describe biodiversity before it disappears. Identifying what’s out there is key to protecting the future of these species. Taxonomy can help ensure that the wildlands that are conserved will protect the widest array of species possible. In addition, understanding the planet’s life forms will undoubtedly put humankind in a better position to understand the essential ecosystem services they provide, and foster the development of new uses for natural products. Modern technology has presented us with a new and exciting means to identify diversity on this planet. This technique, based on DNA sequencing, will complement the more traditional and painstaking work of morphological taxonomy—describing species by their physical traits. Known as DNA barcoding, it involves reading and comparing the same small segments of genetic data between species. It provides a new source of data that can easily be used to describe species. In addition, large volumes of barcoding data can be generated for relatively low cost. For all of these reasons, barcoding represents a major step forward in the race to describe and conserve biodiversity in the face of rapid species extinctions. I am now testing the utility of DNA barcoding for uncovering diversity in an ecologically important group: ants. I have teamed up with colleagues at the University of Guelph, Alex Smith and Paul Herbert, to test whether DNA barcoding can accelerate our inventory of the ants of Madagascar. Our results convince me that the union of DNA barcoding and traditional systematics mark a major advance in twenty-first century science. Madagascar is one of the world’s outstanding biodiversity hotspots. It is populated by a unique biota whose composition and origins are helping scientists piece together the course of evolution since the breakup of the ancient supercontinent Gondwana. Gondwana consisted of what are now Madagascar, India, Africa, Australia, Antarctica and South America. Madagascar and India both split away from Africa around 120 million years ago. (India then broke away from Madagascar and slammed into Asia, a collision that formed the Himalayas.) Madagascar’s long isolation has resulted in a unique set of flora and fauna. But since humans colonized Madagascar approximately 2,000 years ago, it is estimated that as much as 90 percent of Madagascar’s original habitat has been destroyed. To help stem these losses, the Malagasy government plans to more than triple the number of protected areas over the next five years. It now needs to prioritize the remaining patches of natural habitat for conservation. If we are really serious about "zero biodiversity loss" in Madagascar and elsewhere, conservation planning needs to be based more fundamentally on science. Researchers must conduct detailed inventories of what species exist and precisely where they are found, and protect the remaining habitat fragments that possess the greatest biodiversity. Yet at present, scientists have only an incomplete knowledge of the island’s patterns of diversity. What is known is based mostly on vertebrates—which represent only a small proportion of the island’s species. Vertebrate data is generally on a scale too coarse to assess habitat quality or uncover diversity differences among the remaining fragments of natural habitat. Insects, on the other hand, are generally a better gauge of a habitat’s biodiversity. They often exhibit far higher rates of spatial change than larger animals. For example, while one species of lemur might range over hundreds of square miles, different ant species might populate each small valley. Insects therefore provide a measure of biodiversity on the same spatial scale at which conservation decisions are typically made. In 1999, the Academy initiated in Madagascar one of the largest arthropod inventory programs ever undertaken in the world. From 2000-2005, a field crew of Malagasy taxonomists inventoried 85 sites across Madagascar, and processed over 3.5 million specimens. A team of 15 trained Malagasy students sorted specimens at the processing facility in the capital, Antananarivo, and sent them on to the Academy for distribution to over 100 collaborating taxonomists around the world. Processing such massive collections posed a major challenge—how to quickly recognize known species and identify new ones. In traditional, morphology-based taxonomy, discrete “forms” are tentatively recognized and hypothesized to be species. Taxonomists search for consistent differences in physical traits that might indicate reproductive isolation. Identifying and describing the species from the Madagascar arthropod inventory will take decades of work. It takes countless hours of careful observation through a dissecting microscope to measure and study morphological variations such as head width and length when describing ant species. Traditional morphological taxonomy will not provide enough data in the short term to address Madagascar’s urgent conservation needs. If nothing is done to change the slow pace of current taxonomic efforts, it will take centuries to complete even a preliminary map of the insect diversity of Madagascar. To determine whether DNA barcoding might eliminate these bottlenecks, Smith, Herbert and I began testing whether diversity patterns based on DNA barcode sequences are significantly different from patterns based on traditional morphological taxonomy. In our study, recently published in the Philosophical Transactions of the Royal Society, we tested ants collected from four critical forest patches in northeastern Madagascar. By comparing the sequence of each specimen’s cytochrome oxidase I (cox1) gene, we have been able to rapidly group specimens with similar cox1 sequences. These sequence groupings are termed Molecular Operational Taxonomic Units, and can be used to assess species richness and changes in species composition across landscapes. We found that data from DNA barcoding grouped the ants in the same way as the study of their traditional morphological traits. Both approaches discerned the same relative patterns of diversity within and between forest patches. However, DNA barcoding achieved results much faster. Our DNA analyses took only three weeks, whereas detailed morphological analyses of each specimen would have required many years. We concluded that barcoding can rapidly help create biodiversity maps—a boon for groups such as insects, where experts are scarce and identifying specimens is time-consuming. In this case, barcoding allowed the results of insect inventories to be applied immediately towards conservation. Our experience showed that DNA barcoding can speed up the description of new species as well. In Madagsacar, up to 75 percent of the insects we collected may represent new, undescribed species. Barcoding allowed us to quickly highlight specimens of particular interest, such as those with unusual sequences. Those have been culled for further morphological study to assess whether they represent variants of a single species, or a novel species altogether. Sequence data are particularly helpful for sorting through insect specimens. For example, when we set out to describe the ant species belonging to the genus Anochetus, we used both DNA barcoding and traditional morphology. The workers, queens, and soldiers had very different morphologies, but were easily ascribed to the correct species with DNA barcoding. In sum, we found that DNA barcoding works in concert with more conventional morphological approaches to taxonomy. It neither competes with nor replaces the traditional study of physical characteristics. This is a world where we cannot cherish what we do not know exists, where we cannot conserve what is of no known use. In this environment, the documenting of life will help create a bioliterate society, a society that can for the first time understand and hopefully value all of the components of life on this planet, from species to ecosystems. Armed with a new tool such as DNA barcoding, enthusiasm for the exploration of the planet will return. Little time remains to document global biodiversity. DNA barcoding—a simple, standardized data format which will eventually expand to include multiple genes—is helping to change taxonomy. Collaborating taxonomists, equipped with modern tools, have a chance to move systematics to the forefront of conservation and the public’s attention. As more taxonomic information is produced, in a more visible and accessible manner, public and political support for the conservation of life on this planet should follow. Brian L. Fisher is Associate
Curator and Chair of Entomology at the California Academy of Sciences. |