THE DEBATE over integrating genetics and ecology in conservation biology
Snails on a certain hillside in Utah have a ridge on their shells not found on the shells of snails on neighboring hillsides—do the ridged snails represent a distinct subspecies? Northern and southern populations of an endangered Brazilian parrot have different calls—do these vocal differences reflect a more fundamental genetic split within the species?
Such questions are more than mere taxonomic arcana—the answers have real-world conservation implications. For example, the answers might determine whether the snail with the ridged shell receives protection under the U.S. Endangered Species Act (ESA). They might affect whether a breeding program for the Brazilian parrot is designed to keep birds with northern and southern vocal dialects separate or to interbreed them to maximize genetic diversity in the species as a whole.
Such questions are increasingly common. Today’s conservation biologist, it seems, is both Adam and Noah—charged with naming the world’s various forms of life as well as saving them from disaster. At the center of both tasks over the past decade and a half has been the concept of the evolutionarily significant unit (ESU)—roughly speaking, an important chunk of a species.
Almost since the term first appeared in the scientific literature, an intense debate has raged over how, exactly, to define this basic unit of conservation—especially with reference to the ESA in the United States. The debate was fueled in part by the rapid development of molecular analysis techniques that took place over the same period, which forced a constant rethinking of the ESU definition and the assumptions behind it.
About a year ago, four of the debate’s most vocal participants met for a two-day session at the National Center for Ecological Analysis and Synthesis (NCEAS) in Santa Barbara, CA, to try to come to a consensus on the ESU question. What they agreed on goes beyond a simple wrap-up of the ESU debate and instead suggests a new, more holistic approach to species management that integrates the contributions of both genetics and ecology. That is, it takes into account both the history of populations as revealed by cutting-edge molecular analysis and adaptive differences as revealed by life history and other ecological information.
The Debate Begins
The term “ESU” first came into the limelight at a conference of zoo biologists in July 1985. Participants struggled with how to determine which of the world’s forms of life to preserve in their modern-day arks, given that space in zoos is limited and that taking two of every kind of beast is no longer considered a reliable species survival strategy.
The question was further complicated by the recognition that many species in need of protection were composed of multiple subspecies. Biologists might decide to save the tiger or the black rhino, but which of the 5 subspecies of tiger should be preserved? Which of the 7 subspecies of black rhino? “It emerged that zoos ought properly to address the conservation of evolutionarily significant units (ESUs) within species,” wrote Oliver Ryder, of the Zoological Society of San Diego, in a 1986 article reporting on the conference in Trends in Ecology and Evolution.
By reluctantly advocating the adoption of a new bit of jargon, the conference participants acknowledged that all subspecies—in fact, all species—are not created equal. In one case, Ryder pointed out, two different subspecies had been named and described from littermates. At the other extreme, Indian and Chinese populations of muntjacs, or barking deer, have been considered the same species by some taxonomists, yet produce sterile hybrids.
“Existing taxonomy misses a substantial portion of the biological diversity that’s out there,” agrees Craig Moritz, a geneticist at the extniversity of California, Berkeley, and Director of the University’s Museum of Vertebrate Zoology. “The problem of how you identify and protect diversity within species is what we’re grappling with.”
Among the first to grapple with applying the ESU concept in the real world was Robin Waples, a geneticist at the National Marine Fisheries Service (NMFS) Northwest Fisheries Science Center in Seattle. In 1990, NMFS received petitions for listing five stocks of salmon on the Snake and lower Columbia Rivers as threatened or endangered “distinct population segments” under the U.S. Endangered Species Act.
The 1978 amendment to the ESA that permits the listing of “distinct population segments” as well as entire species had already been applied to a wide variety of species—from grizzly bears to desert tortoises—but using an equally wide variety of criteria. There was “no guidance in the ESA about how to define distinct population segments,” Waples says.
Asked by NMFS to provide such guidance, Waples decided to employ the concept of the ESU and created a two-part test for defining these units. First, he said, to qualify as an ESU, a group of organisms should be “substantially reproductively isolated.” Yet this criterion could have unwanted effects if taken to its logical extreme. “Technically, squirrels in Central Park are reproductively isolated from other squirrel populations, but do they merit protection?” Waples asks, rhetorically. So he added a second criterion: an ESU should also represent “an important component in the evolutionary legacy of the species.”
The two-part test worked well for NMFS. Using a combination of geographic, ecological, and genetic data, NMFS biologists later conducted status reviews of all 7 species of anadromous Pacific salmonids, which clustered rather neatly into 51 ESUs. But in the meantime, a number of other researchers, particularly in the U.S., where management decisions often are made with an eye to the ESA, had begun developing and applying their own ESU criteria.
Genetics: A Wrench in the Works or a Working Wrench?
Moritz, then at the University of Queensland in Australia, was troubled by this proliferation of definitions. Most of the criteria included some genetic component, but the degree of genetic difference required for ESU status varied widely. Other researchers classified populations that were genetically identical but had some small phenotypic differences as different ESUs. “Part of the problem is the word ‘significant’—what does that mean?” he asks.
To solve the quandary of how much genetic difference is enough, Moritz offered an ESU definition based not on counting the number of genetic differences but on showing that a certain kind of genetic difference exists. In a 1994 paper in Trends in Ecology and Evolution, he wrote that ESUs should be reciprocally monophyletic—that is, all of the individuals in the ESU should have a common ancestor not shared by any individuals outside the group.
Moritz suggested that the determination of reciprocal monophyly be based on an analysis of the DNA found in mitochondria, structures inside of cells that produce energy. Mitochondrial DNA (mtDNA), which is passed only from mother to offspring rather than from both parents, tends to show reciprocal monophyly sooner than nuclear DNA, which is the main portion of an organism’s genetic material. Moritz thought that ESUs should also show “significant divergence” in their nuclear DNA.
Many researchers welcomed this ESU definition that was based exclusively on molecular analysis. Not only was genetic research high-tech and cutting-edge, and therefore exciting, it also seemed to give clear, simple, objective answers about population relationships—unlike “the murky world of ecological divergence,” as Robert Wayne, of the University of California, Los Angeles, puts it.
Reciprocal monophyly is evaluated with neutral markers, DNA sequence differences thought not to affect an organism’s characteristics. In the mid-1990s, most of the molecular information available on wild species was based on analysis of neutral markers. “Neutral markers provide us with a direct view of evolutionary history,” Wayne says. But they don’t say anything about the ecological or adaptive differences between populations.
Wayne felt that Moritz’s definition was missing that ecological component and also that the definition itself was not being applied rigorously. Many researchers cited Moritz’s paper but defined as ESUs populations that failed the reciprocal monophyly test. Conversely, researchers also used miniscule genetic differences as evidence that populations should be preserved and managed separately. He says, “I never saw anyone arguing the opposite”—that small genetic differences might mean a population is not very important from a conservation point of view. “In the end, we all love our organism,” sighs Keith Crandall, of Brigham Young University.
Moreover, by the late 1990s it was possible for researchers to find differences almost anywhere they looked. “With the increasing resolution of molecular techniques, significant differentiation can be found at very small scales, even down to the individual, and this can lead to inappropriate diagnosis of ESUs . . .” wrote Crandall, Wayne, and two coauthors in a 2000 paper in Trends in Ecology and Evolution.
In the paper, they suggested basing management decisions on a rather complex system in which populations were categorized based on their genetic and ecological “exchangeability” and on whether their distinctiveness was a historical or recent development.
Meanwhile, many other researchers had chimed into the debate. At the 2000 meeting of the Society for Conservation Biology (SCB) in Missoula, Montana, Waples and U.S. Geological Survey biologist Sue Haig organized a get-together at a local restaurant for an informal discussion about ESUs over pizza and beer.
More than 100 people attended, and the discussion lasted four hours. “We went until the place closed and we had drunk the keg,” Waples says, implying they could have kept talking a lot longer.
After the SCB meeting, Crandall approached Waples and suggested organizing an NCEAS workshop to discuss the ESU question and to try to reach a consensus. Waples readily agreed. “All of us were getting tired of the debate being unfocused,” he says. “People were talking across each other.”
So last February, Crandall, Waples, Moritz, and Wayne met to hammer out the ideas they hold in common. Since then, they’ve been working on several scientific papers detailing various aspects of that shared vision.
Towards a Consensus
“You can’t really decide what’s the best strategy for defining conservation units unless you have a stated objective,” Waples says. This was perhaps the easiest principle for the four to agree on—and something they felt had been missing from the debate in the past. “People a lot of times didn’t have the same goals in mind or didn’t even articulate their goals,” Waples continues. “There was no reference point.”
As Crandall puts it, the overall goal of conservation should be “to maintain species and the genetic variation within them.” Moritz elaborates, “We also agree that we’re trying to protect not just the products of evolution but the processes.”
In other words, it’s important to preserve not just—or even primarily—the biological world as it exists now but rather to safeguard evolution itself and the qualities that contribute to it: genetic variation within species, intact habitats, distinctive adaptations, connections between populations, and so on.
“Biological diversity is not something fixed in time and space,” Moritz explains. The living world today is only a snapshot, but conservation biology should aim to preserve the whole unfolding saga of evolution—a goal that’s particularly important in a world rapidly changing due to the effects of our own species. “There will be substantial evolution needed to catch up with recent anthropogenic change and also with coming climate change,” Moritz says.
The group also agreed that species and populations should be evaluated along two axes of diversity, which might be described as molecular genetic and adaptive diversity.
Molecular genetic diversity reflects the evolutionary history of a population—the molecular differences that arise through historical isolation and the molecular similarities that are maintained by gene flow. Analysis of neutral markers remains the primary method of evaluating this type of diversity.
Adaptive diversity, meanwhile, reflects the present-day ecological differences between populations and represents the raw material for future evolution. Traditionally, scientists have evaluated adaptive diversity through geographic, life history, and phenotypic data—a much more difficult task than the assessment of molecular genetic diversity.
But the most recent advances in molecular technology are now casting some light on adaptive differences as well. “At a molecular level, we can now look at differences in functional genes,” not just neutral markers, says Wayne. The genetic basis of adaptive traits such as growth rate, size, and number of offspring is now coming within reach. “It still takes a lot of work to get one story for one organism,” says Waples, “but progress is being made.”
Often, molecular genetic diversity is correlated with adaptive diversity. But not always—and this can make management decisions more complicated. Two populations of a skink that live in rainforests on either side of Australia’s Black Mountain Barrier, a large area of dry forest that formed during the last Ice Age, are genetically quite distinct, reflecting their long isolation from one another. Yet the lizards on either side of the barrier appear to be ecologically equivalent—they look the same and are adapted to identical habitats.
By contrast, the skinks in the rainforest on one side of the barrier are significantly larger than their conspecifics in scrub grassland just 200 meters away. Adaptation is at work here: in the grassland, larger skinks are more vulnerable to predation by birds. Yet genetically, the grassland and rainforest skinks form a single, continuous population.
Wayne, Waples, Moritz, and Crandall would agree that both of these types of diversity—the molecular diversity between rainforest skinks on either side of the Black Mountain Barrier and the adaptive diversity between rainforest and grassland skinks on one side of the barrier—are important to preserve. And, in fact, this is beginning to happen. These communities are slated for protection, and the idea of protecting habitat diversity has been well accepted.
Some of the group might, however, disagree on which type of diversity is most important. “There are different perspectives on some details,” Moritz allows. “At the moment it’s different emphases.”
Wayne and Crandall view adaptive variation as most important, an “investment strategy,” as Wayne puts it, in an age of global environmental change. “The environment is unpredictable, and this [adaptive diversity] therefore maximizes the options of the species,” he says.
Moritz, by contrast, emphasizes evolutionary history because it is irreplaceable. “To what extent can you recover through evolution certain adaptive characters if you’ve lost them?” he asks. “I think that if you look at past evolution, things can re-evolve.” But once history is gone, it’s gone forever.
Wayne sees little evidence that such re-evolution can occur, or at least, little evidence that it is very common. “So we disagree on that,” says Moritz, “but that’s a research question. We need to design some experiments.”
To Moritz, research questions also underlie the debate as a whole: “The reason different perspectives are appearing in the literature is not because the science is flawed but because there’s not yet enough information to answer some questions.”
A Whole Species Approach
At first glance, these two axes of diversity sound a lot like some of the earliest definitions of ESUs, such as the two-part test of Waples. But the group has not simply come full circle to the beginning of the ESU debate. They have a different agenda in mind.
In the past, researchers looked at these two types of diversity to draw boundaries between ESUs—or, often, to decide whether or not a certain group of organisms constituted an ESU and was therefore worthy of protection.
Instead, the four suggest, conservation biologists should seek to understand the molecular and adaptive differences between populations to draw a better picture of the species as a whole. “Instead of looking at individual populations… We need to look at all populations and see what’s meaningful across the whole species,” Wayne says.
One of the most important tasks is to pay more attention to the connections between populations, rather than just population isolation, which the four say, has been the primary emphasis of conservation biology in the past. “Instead of just finding out which populations are distinct we should find out the historical levels of gene flow between different populations and think about how to preserve them,” Wayne argues.
Or sometimes, managers will need to think about how to restore historical levels of gene flow. On the Australian mainland, an endangered rat-like marsupial known as the quokka is currently restricted to a number of isolated populations of fewer than 25 individuals each, scattered throughout the southwestern part of the country. But genetic analysis shows that the mainland population once had a fairly continuous distribution.
Elizabeth Sinclair, a postdoctoral researcher at Brigham Young University in Utah who has investigated the genetics of the quokka, suggests that the species should be managed with historical connectedness, not present isolation, in mind. “The populations are only fragmented because [Europeans] came along and started chopping down bush and introduced foxes,” she points out.
In real life, species are often divided up for the convenience of human managers. Yet biological diversity is actually a continuum—although less continuous in some species than in others. “It’s not that evolutionary significance starts at a certain point. Your mother probably thinks you’re an evolutionarily significant unit,” Waples likes to quip.
“In practice, you need things on a list that you can tick off, not a dimensionless continuum,” says Moritz. “We’re slicing up something that’s continuous, and that’s where the debate arises.”
And where the consensus begins, it seems, is that conservation biologists should place less emphasis on slicing things up in the first place. “We want to down-play the idea of identifying ESUs and instead come up with species-wide management plans that might or might not involve defining ESUs but would involve evaluating populations on these two axes” of molecular and adaptive diversity, Waples explains. “We need to get out of this mindset of ‘Is it an ESU or not?’” agrees Wayne.
The Global Context
“The problem is that in the U.S. everything comes back to the Endangered Species Act. You’re in a legal conundrum,” Crandall says. Biologists are forced to ask whether a certain group of organisms is an ESU or not, “because that’s what affords it protection.”
Indeed, the laws and policies related to conservation in the U.S. have driven much of the ESU debate. “This issue is at the interface of science and law, which varies across countries,” Moritz points out. How to define an ESU is partly a biological question but one that is receiving a great deal of attention because of a specific U.S. law that focuses on single species protection.
In Europe, where conservation legislation focuses on protection of habitat rather than individual species or populations, the question of what qualifies as an ESU has less urgency. And in Australia, Sinclair reports, managers are “not as obsessed with the question of boundaries between populations.”
Yet Wayne suggests that the ESA’s focus on individual species or parts of species could also become an asset. “The Act is very vague—it just says ‘distinct population segments,’” he points out. Managers and agencies could define this term in a way that reflects the emerging science of molecular and adaptive variability.
Even so, the parsing of genetic and ecological detail may not be the most urgent conservation question worldwide. “The ESU debate is a bit of a distraction from the main game of conservation,” Moritz admits. “Most of the action in international conservation is aimed at identifying high-biodiversity areas and protecting those.”
Many of the efforts to analyze the ESUs within species have involved relatively well-known taxonomic groups, such as carnivores and birds, in relatively species-poor temperate areas, that is, a rather small proportion of the world’s biodiversity. “If we wait till it’s sorted out, there’ll be nothing left to save. It’s like fiddling while Rome burns,” says Tom Brooks, an ornithologist at Conservation International’s Center for Applied Biodiversity Science.
Brooks is involved in an initiative to map the world’s vertebrate species and identify biodiversity “hotspots.” That task requires a comprehensive system of measuring diversity that is comparable worldwide. “The only comprehensive taxonomic system we have is the traditional biological species concept,” says Brooks.
But Brooks does not reject altogether the idea of trying to sort out ESUs. “The ESU concept does work in practice. It can be very successfully applied in places like the U.S. where we have the information “necessary to define these units,” he says.
That’s true in the case of Pacific salmon, where the ESU effort has permitted a more targeted application of the ESA. Of the 55 ESUs representing 7 species of salmonids, 5 are currently listed as endangered, 21 are classified as threatened, and several more have been proposed for listing. Most of the listed ESUs are in California and the Pacific Northwest, allowing fishing of healthy Alaskan runs to continue.
A Call for Collaboration
Genetic analysis is also expensive. But where resources permit such analysis, genetic information is useful for much more than just drawing ESU boundaries, yielding insight into such diverse questions as past population bottlenecks and the movements of individual animals.
But not by itself. The four geneticists also agree that molecular information must be put in ecological context to be truly meaningful. “We have to reach out to people studying the ecology of these species and collaborate with them,” says Wayne. “They have a feeling for meaningful variation in life history traits.”
Such collaborations do in fact exist. Steve Blatt, a U.S. Forest Service (USFS) biologist in Utah, is working with Crandall and his colleagues at Brigham Young University to investigate the genetics of the Ogden Mountain snail, the ridged snail on the Utah hillside.
“We’re trying to figure out what we truly have out there. That’s where genetics comes in,” Blatt says. The snail was originally described as a subspecies about a century ago; but there is some controversy regarding that early literature, and very little taxonomic work on the snail and its relatives has been done since. Thus, biologists today are unsure whether the snail is truly a subspecies, is not different from the rest of the species, or deserves outright species status.
The question has taken on urgency because the ridged snail is currently a candidate for ESA listing. “We just knew that we had to get some answers before we got too far into developing a conservation strategy,” Blatt says. So the USFS and Brigham Young University have recently worked out a cost- and work-sharing agreement for a genetic study.
Yet the university geneticists are worried because, particularly with their new, holistic emphasis on understanding variation throughout species, they know that a proper genetic analysis takes time and money—two things that resource management agencies generally have little of.
“What we really need to do is sample over the whole range of the species before we can tell the relationships between populations,” says Sinclair. The USFS biologists “have a very specific question, but actually you have to do a broader study in order to answer the question properly.”
But longer-standing collaborations suggest that geneticists and ecologists might learn how to bridge these gaps. Cristina Miyaki of the University of São Paulo in Brazil has studied the genetics of nearly half of Brazil’s 70 parrot species, including the red-tailed parrot, the endangered parrot with the two vocal dialects.
Field studies recently indicated that red-tailed parrots moved from one population to another pick up the new dialect, and Miyaki’s nuclear and mtDNA studies confirmed that genetically, the species represents a single population. “From a conservation point of view this result is good because the population is bigger than we thought,” Miyaki says.
Miyaki collaborates with a number of parrot ecologists who collect blood samples for her laboratory’s genetic work and provide ecological data that help the geneticists interpret their results. “What’s difficult for both sides is that we in the lab don’t always know how difficult it is to be in the field, to find nests and so on,” says Miyaki. “And people in the field don’t always recognize the troubles we have in the lab—some techniques take months to complete.”
So recently, Miyaki has been encouraging the parrot ecologists to come to her lab and learn genetic techniques, while she and other geneticists have been accompanying ecologists into the field to learn what their work is like.
Such collaborations are shaping conservation biology’s future. Each person contributes his or her own bit of the puzzle: genetics or ecology, wrestling with the theoretical concepts of population subdivision or struggling to apply those concepts on the ground. No one can accomplish both Adam’s task and Noah’s task alone.
Crandall, K.A., et al. 2000. Considering evolutionary processes in conservation biology. Trends in Ecology and Evolution 15(7):290-5.
Moritz, C. 1994. Defining “Evolutionarily Significant Units” for conservation. Trends in Ecology and Evolution 9(10):373-5.
Moritz, C. 2002. Strategies to protect biological diversity and the processes that sustain it. Systematic Biology. In press.
Ryder O.A. 1995. Species conservation and systematics: the dilemma of subspecies. Trends in Ecology and Evolution 1(1):9-10.
Waples, R.S., et al. 2001. Characterizing diversity in Pacific salmon. Journal of Fisheries Biology (59) (Supplement A). In press.
The salmon status reviews provide examples of application of the ESU concept to real populations. www.nwfsc.noaa.gov/pubs/nwfscpubs.html.