DUCK LAKE is really little more than a pond. Perched on top of a scrub-studded hill in Amazonia’s remote north-western corner, it seems an unpromising place from which to try to kill off one of the 20th century’s major biological ideas. But it may be that beneath its water lies the true history of the Amazon basin, disproving a long-held explanation for the region’s extraordinary biological richness.
This explanation, known as the Pleistocene refugia hypothesis, has dominated thinking on Amazonian evolution for more than three decades. It has provided explanations for the complex species distributions and lavish diversity across Amazonia: an evolutionary “theory of everything” that actually worked. No wonder Ernst Mayr, one of the giants of modern biology, considered it “one of the few truly beautiful theories in biology”.
In its earliest and simplest form, the hypothesis proposed that several times during the Pleistocene epoch – between about 1.8 million and 12,000 years ago – glaciers forming outside Amazonia sucked up moisture, leading to a drier climate across the globe. In Amazonia, forests shrank and huddled in scattered still-wet areas known as refugia. Forest-loving plants and animals found themselves isolated for millennia in these habitat islands, surrounded by vast seas of grassland and shrubs. When the glaciers melted and wetter weather returned, the forests expanded to join up again. The forest-loving species spread out with the trees, but as they intermingled some would find they no longer recognised their long-lost cousins as mates. Separation had led to speciation. Repeated over the dozen or so glacial events known to have occurred in the Pleistocene, this process acted a powerful “pump”, creating waves of new species every few millennia.
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The idea was formulated in the late 1960s by Jurgen Haffer, a professional petroleum geologist and avid amateur ornithologist. Published in Science in 1969, it was originally designed to explain the distribution of various Amazonian birds. Support for the idea spread rapidly, however, as specialist talked to specialist, and soon frogs, lizards, snakes, butterflies and a whole variety of forest trees joined the list of organisms that seemed to fit the pattern. What’s more, when ecologists superimposed maps of the current distribution of these groups they found something extraordinary and unexpected: species congregated in certain areas while apparently shunning others. It looked as if these species-rich areas were old refugia, ancient speciation centres from which modern species were still spreading out.
“The refugia hypothesis is so beautiful nobody wants it to be wrong”
Conservationists quickly took on board the practical implications of the refugia hypothesis, arguing that it allowed reserves to be sited where they gave maximum bang for every precious conservation buck. Many parks and protected areas were created, including Jaú National Park in Brazil, which at over 2 million hectares is the second largest rainforest park in the world. “It was an exciting time,” recalls Ghillean Prance, veteran Amazonian botanist and one of the first to recognise the ideas’s full potential.
Still, the refugia hypothesis has always had its naysayers. Detractors highlighted holes in the data and inconvenient exceptions. One serious charge was that refugia are artefacts of the collection process. Sceptics pointed out that many refugia were suspiciously near Amazonia’s few big towns. “Ah, but many are not,” came the defenders’ reply – and besides, whatever concatenation made a place suitable for high-density human habitation may have been the very things that promoted refugia. So it went, back and forth, protracted academic sniping rather than a full intellectual siege – until now.
In the vanguard of the new attack is Paul Colinvaux from Woods Hole Marine Biological Laboratory, Massachusetts. In the 1960s, while at Ohio State University, he started sampling fossil pollen from South America and using it to recreate the glacial climate. “Then Haffer’s paper came out. I was very excited,” he recalls. “He had no real geological or palynological [fossil pollen] data, but made predictions that I was already set up to test.” This is exactly what Colinvaux has been doing ever since, with help from colleagues including Mark Bush from the Florida Institute of Technology. In recent years the pair have published a series of damning papers, including one in Science (vol 303, p 827), concluding that the hypothesis has failed nearly every test. Colinvaux will expand his thesis in a book to be published next year (Amazon Paradigm Lost, Yale University Press).
Endless forest
Their proving ground has been predictions that the refugia hypothesis made about the geology and palaeobotany of Pleistocene Amazonia. “If it were true then we should be able to find soils and rock types that had formed under arid conditions,” says Colinvaux. Yet when geologists Georg Irion from the Senckenberg Institute in Wilhelmshaven, Germany, and Matti Räsänen of the University of Turku, Finland, looked, they couldn’t find any. Instead they found soils that could only have formed if the region had had continuous forest cover for many millennia. More telling still, according to Colinvaux and Bush, is the evidence they themselves have amassed about Amazonia’s past flora, based on ancient pollen.
Pollen is abundant in lake-bed sediments, which can contain up to 200,000 grains per cubic centimetre. It can be dated using accelerator mass spectroscopy to measure levels of carbon-14 and can be easily assigned to a genus, sometimes even a species, because the grains have characteristic shapes. Provided you know the habitat preferences of several of these species, you can begin constructing past climates. The big problem in Amazonia was finding suitable sediments. Rivers meander across an almost flat plain, reworking deposits and leaving very few lakes with sediments that can give a reliable picture beyond about 5000 years ago. Colinvaux has made it his mission to discover these exceptions, which is what brought him to Lago da Pata – Duck Lake.
Ancient lakes
Situated atop an ancient body of rock, 300 metres above the forest, this 400-by-200-metre pool is fed only by a tiny stream, run-off and rainfall. Together with five nearby lakes it contains sediments that have never been reworked by rivers. Extracted cores go back 180,000 years and so provide the truest possible record of Amazonian pollen. This, Colinvaux points out, is rare evidence indeed. In three decades of looking he has found just two other similar sites in lowland Amazonia. Cores from lakes in these three locations – plus others from an ancient lake bed in Ecuador and deep drilling in the undersea sediment fan spreading out from the Amazon estuary – provide the pollen evidence from which Colinvaux has developed his radical reconstruction of the region’s climatic history.
With immense patience, Colinvaux and colleagues analysed their glacial-epoch sediment cores. To their initial surprise they did not find increases in pollen from plants adapted to arid conditions. Instead there were upsurges in pollen from cool-zone magnolias, alders, aspens and the conifer relative Podocarpus. These, not grasses, had supplanted areas of tropical rainforest in the ice ages. Colinvaux believes that other studies reporting widespread grasses result from “over-enthusiastic interpretation of the data”. “The refugia hypothesis was so beautiful, no one wanted it to be wrong,” he says. His own findings suggest quite a different picture. “The Amazon basin has all been continually under forest since the Miocene [at least 5 million years ago], maybe longer. It was never drier, just cooler.”
“Grasslands never dominated,” adds Bush. Instead, the make-up of the forest just changed so that there were greater numbers of cool-loving trees. “Some animals probably migrated with their host trees, but others probably just sat tight as climate and plant community changed around them. After all, to a marmoset, a liana tangle is just something to hide in – they don’t care what species it is.”
Without grassland barriers to provide isolation, Amazonian biodiversity is suddenly harder to explain. If there was no Pleistocene species pump, how to account for the incredible biological richness we see today? Some answers are suggested by a tool for studying evolutionary history that was not available to Haffer when he formulated his idea back in the 1960s. It turns out that one of the best ways to get the big picture is to think small – to zoom in on the genes.
Several recent molecular-genetic studies provide big clues to why there is such diversity in Amazonia. Analysis of mitochondrial DNA from nine different species groups of butterflies, for example, has revealed evidence of multiple speciation dates. “There was no simple pattern”, says James Mallet from University College London, who led the research team. Some pairs, like those in the tiger-stripe-winged Melinaea, had evolved only in the last few hundred thousand years. For others, like the clear-winged butterflies Oleria, no new species had been produced in tens of millions of years. “Clearly the situation is far more complex than the refugia hypothesis predicts. Much will be influenced by idiosyncrasies in the biology of individual species, not external factors like changes in the palaeoclimate,” says Mallet (see “In the neighbourhood”).
Similar analysis of vertebrates also refutes the idea that the Pleistocene was a uniquely prolific time for Amazonian speciation. When Jim Patton from the University of California, Berkeley, examined mitochondrial DNA from 31 species of small mammal, he found that many probably first appeared in the Miocene, which ended 5.3 million years ago. A similar pattern has been uncovered in trees. Toby Pennington from the Royal Botanic Garden Edinburgh, UK, discovered that while a few Amazonian tree genera did speciate in the last several thousand years, the majority did not. Even molecular analyses of birds, the very group on which the refugia hypothesis was founded, tell the same story. “Some, like the white-crowned antwren, evolved comparatively recently,” says John Bates of Chicago’s Field Museum. “But for many others, including Amazonian parrots and toucans, molecular data indicates their species differentiated well before the last ice age.” Some, including the scale-backed antbird, are at least 5 million years old.
Andes rising
These older speciation dates indicate that landscape evolution may have had at least as much influence on Amazonia’s denizens as has climate. A surge in the rise of the Andes some 11 to 9 million years ago not only changed the climate and the course of the Amazon river, but also raised a series of wrinkles in the crust under the western part of the Amazon basin. Though today almost completely concealed by sediments, these compression-arc ridges dammed some of the region’s rivers, forming substantial lakes and swamps that blocked the spread of the region’s animals and plants. Even before that, between 17 and 10 million years ago – during the Miocene – it appears that there was a wide, shallow estuarine or freshwater lake extending over 1000 kilometres inland to the east. This would have formed, dried out and reformed several times as the Andes rose, the Amazon altered course, sea levels changed and the continent dipped, submerging several hundred thousand square kilometres of land for tens of thousands of years at a time.
It seems that by focusing on the Pleistocene, many Amazonian ecologists have marginalised the extended evolutionary history of the region. Sure, there was speciation during the ice ages too, but the genetic evidence suggests this was not the biodiversity “big bang” that was previously assumed. Indeed, Bates’s research indicates that the number of species probably declined towards the end of the Pleistocene. This same pattern of species loss has also been found in the rainforests of the Great Dividing Range in north-eastern Australia. There Craig Moritz, director of the University of California, Berkeley’s Museum of Vertebrate Zoology, has been testing the refugia model by looking at everything from birds and frogs to beetles, earthworms and snails. “We’ve found nothing to support a simple species-pump model,” he says.
For Colinvaux and his supporters, all this places the original Pleistocene refugia hypothesis on the chopping block. “The refugia theory, as was, is dead,” he says. “It’s time to admit that and focus on the new challenges offered by new data.”
Others, however, are not prepared to accept its demise. “The original hypothesis made predictions. Some were wrong. So we re-vision,” says Prance. “That’s progress, not failure.” Haffer himself agrees. “When I first proposed the model, I was thinking only of such small differences as might occur between recently evolved subspecies of Ramphastos toucans, for example,” he says. “But as the evidence built, it became obvious that there had been many speciation cycles. Refugia still have value.”
“Areas of rich diversity are real, and are important to conserve”
Haffer, Prance and others now envisage a far more complex scenario that embraces the new data from molecular genetics and fossil pollen studies. This synthesis makes room for more types of barrier generating speciation over a broader swathe of time, including Miocene seaways and lakes from rivers impounded by compression arcs. Though much modified, this new model still gives Pleistocene forest distributions a key role in fostering current diversity. “In the western Amazon, near the moisture-trapping influence of the Andes, there would have been continuous forest cover. Exactly what Colinvaux has shown,” says Prance. But, in common with many Amazon experts, he maintains that pollen and species distribution data support a drier eastern Amazonia, dotted with wetter islands of forest.
So where does all this wrangling leave Amazonian conservation? If there is one aspect of the refugia hypothesis that everyone can agree on, it’s that Amazonia does contain areas of extremely rich biodiversity, which, for whatever reason, overlap with the sites of the classical refugia. “Those areas are real and important to conserve,” says Anthony Rylands, Conservation International’s director of conservation biology. He points out that before the refugia hypothesis everyone thought that Amazonian biodiversity was uniform. The prospect of conserving biodiversity spread over such a vast area seemed daunting. The discovery of super-rich sites was a major impetus to do something constructive. “Haffer’s hypothesis catalysed biological survey work and the creation of nearly a dozen reserves protecting almost 9 million hectares,” says Rylands.
Given the ongoing threats to the region, the limited resources available to conservationists and the concomitant need for informed planning, that may be the refugia idea’s best and most enduring legacy.
In the neighbourhood
Like many of the most influential ideas in science, the Pleistocene refugia hypothesis reflected the biases of its day. In the 1960s, it was thought that animals would only evolve into separate species if geographical barriers such as mountain ranges, seas, rivers and islands separated different populations. Not any longer. Earlier this year, two papers in Nature (vol 439, p 719, vol 441, p 210) described studies of speciation without physical separation – so-called sympatric speciation. The first used genetic analysis to show that a fish called the arrow cichlid evolved less than 10,000 years ago from the Midas cichlid in an isolated 5-kilometre-wide volcanic lake in Nicaragua. The researchers suspect that competition for food pushed the two down separate evolutionary tracks, with the former adapting to dine on insects at the water’s surface and the latter eating algae from the depths. The other paper revealed how, despite isolation on the tiny Lord Howe Island, nearly 600 kilometres east of Australia, one kind of palm has speciated into two. It seems that by adapting to one or other of the island’s two different soil types, the palms became reproductively isolated, since the genes for soil tolerance are linked to those for flowering time.
Despite these and several other examples of speciation without isolation, the idea of sympatric speciation has been surprisingly slow to gain acceptance. At last its time seems to have come – and not a moment too soon for ecologists looking for new explanations for Amazonia’s rich biodiversity.
