# News this Week

Science  19 Jul 2013:
Vol. 341, Issue 6143, pp. 220
1. # Around the World

1 - Rome
Rinderpest Research Poised for a Comeback
2 - Bethesda, Maryland
U.S. Senate Panel Gives NIH $31 Billion in 2014 3 - Brussels E.C. Beefs Up Research Partnerships With Industry 4 - Rome Scientists, Stem Cell Provider Meet to Discuss Trial 5 - Okuma, Japan Contaminated Water Likely Polluting Ocean From Reactors ## Rome ### Rinderpest Research Poised for a Comeback In 2011, rinderpest, a devastating cattle illness, became the second infectious disease after smallpox that humans have eradicated from nature. In June 2012, the U.N. Food and Agricultural Organization (FAO), in Rome, and the Paris-based World Organisation for Animal Health (OIE) banned research using live rinderpest virus, fearing an accident could cause a resurgence. Now, research on the virus is set to resume following a 10 July decision by FAO and OIE to lift the moratorium. The two organizations used the hiatus to develop safety protocols and risk-versus-benefit criteria. Juan Lubroth, FAO's chief veterinarian, says that there is interest in sequencing some of the hundreds of isolates that were collected over decades to understand how the virus changed over time. They also want to see if vaccines developed for peste des petits ruminants, a closely related disease, can protect cattle from rinderpest. If so, stores of rinderpest virus used to replenish vaccines could be destroyed, eliminating another potential source of accidental release. Researchers will have to convince a joint FAO-OIE expert committee that they can meet the new safety criteria. "We want to ensure [rinderpest research] is done in the safest possible environment," Lubroth says. ## Bethesda, Maryland ### U.S. Senate Panel Gives NIH$31 Billion in 2014

A U.S. Senate spending panel last week approved a bill giving the National Institutes of Health (NIH) $31 billion in 2014, a 7% increase over this year's budget, which was depressed by the across-the-board federal budget cuts known as sequestration. The NIH funding level approved by the Senate Appropriations Committee is$147 million below the president's request for 2014, but $2 billion more than the$28.9 billion that NIH has to spend this year.

Jennifer Zeitzer, legislative relations director for the Federation of American Societies for Experimental Biology, said that her group is "thrilled" with the figure. "It's far better than the current situation and it's a move in the right direction," she says. The bill now awaits a vote by the entire Senate. The House Appropriations Committee, which has a much smaller pot of money to fund NIH and other agencies, has not yet taken up its version of the bill.

## Brussels

### E.C. Beefs Up Research Partnerships With Industry

The European Commission wants to double public money available for Joint Technology Initiatives (JTIs), five research programs that provide public support to private research and innovation, with industry matching E.U. funding. Together, the JTIs will receive €6.44 billion from the E.U. budget between 2014 and 2020, up from €3.12 billion in 2007 to 2013, research commissioner Máire Geoghegan-Quinn announced on 10 July. Industry says that it will put about €10 billion on the table for the next 7 years, up from €4.66 billion in the current period.

JTIs bring together academia, research organizations, and competing businesses in research areas considered complex or risky, such as aeronautics or pharmaceuticals. The initiatives have been slammed for having complex rules and procedures, but the funding boost is a testament to the participants' overall satisfaction with this collaborative model. Future incarnations will be more ambitious, cut down on red tape, and align disparate rules, a commission spokesman says.

The commission will release a detailed legal proposal early next week. The plans must then be signed off on by the European Parliament and member states before the programs are rolled out next year. http://scim.ag/EUJointTech

## Rome

### Scientists, Stem Cell Provider Meet to Discuss Trial

A panel of top science administrators and stem cell scientists met on 12 July with Davide Vannoni, president of the Stamina Foundation, which provides controversial stem cell treatments, to hash out details for a government-sponsored clinical trial of the therapy. Many stem cell scientists remain opposed to the study, saying there's little to suggest that the therapy—which is based on cultured mesenchymal stem cells but whose details remain unpublished—will work.

In May, the Italian Parliament ordered an 18-month clinical trial of the therapy and allocated €3 million to carry it out. But prior to the 12 July meeting, Vannoni had not yet provided the committee appointed to coordinate the study with protocols describing how his treatment works, because he says that he's still working on their standardization. The start of the trial has been delayed by at least a month. Vannoni has his own conditions, including that there can be no changes to his protocol and the cells need to be produced at one facility under the supervision of a Stamina biologist. Barring these, Vannoni says that he may move the research abroad. http://scim.ag/Staminatrial

## Okuma, Japan

### Contaminated Water Likely Polluting Ocean From Reactors

Japanese and international groups monitoring Pacific Ocean waters near the Fukushima Daiichi Nuclear Power Plant have continued to find radioactive cesium at levels higher than expected, given the effects of dilution and radioactive decay. They have claimed that this suggests contaminated cooling water is leaking from the crippled reactors, though plant operator Tokyo Electric Power has long denied this possibility. At a press briefing on 10 July, Shunichi Tanaka, chair of Japan's new Nuclear Regulation Authority (NRA), sided with the experts, saying that the evidence suggests that radiological contamination of the ocean probably "has been continuing for the last 2 years." Tanaka added that it was important to take measures to minimize the leaks.

Also last week, four Japanese electric utilities applied for approval to restart 10 nuclear power plants that have been idled since shortly after the Fukushima accident. NRA will review the applications based on new safety standards unveiled last month. The process is expected to take at least 6 months. The utilities will also need the approval of local governments.

2. # Random Sample

## Meet 'Big-Nose Horned-Face'

There's a new contender for wackiest-looking dinosaur: Nasutoceratops, which means, in Latin, "big-nose horned-face." The 5-meter-long dino had a giant schnoz and sharp, curved horns measuring nearly a meter long. Nasutoceratops, a distant relative of the famed Triceratops, was recently discovered by paleontologists digging in Utah's Grand Staircase-Escalante National Monument. As the team reports online this week in the Proceedings of the Royal Society B, the creature lived about 76 million years ago in a swampy, subtropical region that geologists call Laramidia, formed when an inland sea filled the center of North America and divided it in half. The dino's nose wasn't used for smelling; the scent organs of horned dinosaurs were further back in their heads, next to the brain. So why such a big honker? The researchers don't know, but suggest that the elaborate horns might have been used to attract females and fend off competing males.

## By the Numbers

23.82 months Average time from publication to retraction for articles published after 2002, according to a PLOS ONE analysis. Papers published between 1973 and 2002 took nearly 50 months before retraction, perhaps due in part to higher barriers to pulling papers.

64% Fraction of 455 women who experienced infertility after surviving childhood cancer and were eventually able to become pregnant, according to a report in The Lancet Oncology.

8000 years ago First known use of manure as fertilizer among Europe's first farmers—thousands of years earlier than thought—according to a study in the Proceedings of the National Academy of Sciences.

## Cool by the Numbers

When it comes to a hot, crowded room, hell really is other people. But once they exit, air-conditioning the empty room is an energy drain. The solution: a ventilation system that adjusts to the number of people in a room. Such a system could save three times as much energy as simply turning off the heat and air conditioning to empty rooms, computer models show. Installing people-counting sensors could save 18% of the energy used by a typical large office building in the United States, report researchers at the Department of Energy's (DOE's) Pacific Northwest National Laboratory (PNNL) in Richland, Washington. By comparison, turning off heating, ventilation, and air conditioning to empty rooms saves 6%, says PNNL engineer Guopeng Liu.

But building owners are likely to install such a system only if it's cheap and doesn't require rewiring the building, says Aravind Dasu, a computer scientist with the University of Southern California in Washington, D.C.: "If it's all wireless it's a game-changer." James Freihaut, chief scientist at DOE's Energy Efficient Buildings hub in Philadelphia, Pennsylvania, notes that local building codes may also present a challenge, as many of them require constant ventilation within an occupied commercial structure.

3. # Newsmakers

Two physicists who made fundamental contributions to understanding how the universe evolved into its current structure have won the 2013 Gruber Cosmology Prize. Viatcheslav Mukhanov, a professor at Ludwig Maximilians University in Munich, Germany, and Alexei Starobinsky, a researcher at the Landau Institute for Theoretical Physics in Moscow, will share the 500,000 award. Starobinsky's calculations in the late 1970s showed that the universe could have exploded in size in the first moments after the big bang. The work laid the foundations for the idea of an inflationary universe, a bedrock of modern cosmology. Mukhanov's contribution dates back to 1981, when he was a researcher at the Moscow Physical Technical Institute. Along with a fellow scientist named G. V. Chibisov, Mukhanov showed that quantum fluctuations in the dense and tiny newborn universe could have served as the seeds of modern day cosmic structure. As the universe swelled, these fluctuations gave rise to the formation of galaxies and galaxy clusters. 4. # Battle for the Americas 1. Richard Stone The formation of the Isthmus of Panama allowed the fauna of two continents to mingle, transforming biogeography. A radical new hypothesis holds that the land bridge formed millions of years earlier than scientists thought. Panama, 3 million years ago. A narrow strip of land bridging the Americas turns into a migratory highway. Heading north is an assemblage of creatures isolated for tens of millions of years: porcupines and armadillos; the elephant-sized ground sloth Megatherium; opossums and other marsupials; and bizarre life forms like the terror bird, a flightless carnivore that reached 3 meters in height and sprinted like a cheetah. Beating a southward path are more familiar animals, including horses, cougars, and saber-toothed cats. Alfred Russel Wallace, the father of biogeography, recognized the faunal melting pot created when the tip of Central America collided with South America and forged the Isthmus of Panama, and in 1876 he postulated what is now called the Great American Biotic Interchange. The story has a dark ending: South American fauna compete poorly at home and away, and many species go extinct. More intriguing is how the battle for the Americas got started. Decades ago the fossil record showed, indisputably, that intercontinental migrations exploded between 3 million to 2.5 million years ago—evidence to most scientists that the isthmus had just formed by then. Other studies have bolstered the idea, although it grew more nuanced as evidence accumulated of "herald" species moving from one continent to the other millions of years earlier. That led some to suggest that fragmentary marshes allowed some species to cross the gap early, followed by others on a sturdy land bridge that formed 4 million to 3 million years ago. A radical new model envisions a much earlier bridge, however. After dating the uplift of land masses born of volcanism in Central America and analyzing the geochemistry and magnetic alignment of rocks in the region, Camilo Montes of the University of the Andes in Bogotá; Carlos Jaramillo of the Smithsonian Tropical Research Institute (STRI) in Balboa, Panama; and colleagues argue that the land bridge was largely formed as early as 15 million years ago, with the last deep-water connection between the oceans closing at most 5 million years later. By then, "most of the modern landscape was already uplifted," Jaramillo says, although shallow links between the oceans persisted until full closure 4.2 million to 3.5 million years ago. The new model had its coming-out party at a feisty symposium at the annual meeting of the Geological Society of America last November. Their scenario poses a number of conundrums, not least of which is why it took so long—several million years—for the Great American Biotic Interchange to gain momentum. "Why did that vast diversity of land mammals stay penned up in their respective continents if there was a bridge to cross?" asks Jeremy Jackson, a STRI ecologist and paleontologist and former director of the Center for Marine Biodiversity and Conservation at the Scripps Institution of Oceanography in San Diego, California. The timing of isthmus formation matters, Jackson says. "The joining of the continents and severing of ocean contacts stands as one of the most important and best documented events in earth system evolution," he says. The new model, if correct, would force scientists to reinterpret dozens of studies—a prospect that delights Jaramillo. "We're unraveling the whole story," he says. The debate is heating up. In April, geologists Anthony Coates of STRI and Robert Stallard of the U.S. Geological Survey in Boulder published a report online in the Bulletin of Marine Science (BMS) defending the standard model of late closure and offering an analogy for the late stages of closure: the Indonesian archipelago, where a narrow but deep strait between the islands of Bali and Lombok—identified in the 19th century by Wallace—is mostly impassable to animals moving south from mainland Asia. And two more papers in press marshal data from disparate disciplines supporting late closure, while acknowledging that the prelude to closure could have been messier—and more interesting—than thought. ## Oceans of evidence While the first clues to a late closure of the isthmus came from fossils, the oceans on either side of the isthmus yielded more compelling evidence. In 1982, Lloyd Keigwin of the Woods Hole Oceanographic Institution published a seminal paper in Science comparing oxygen isotopes in the shells of bottom-dwelling foraminifera recovered from deep-sea drilling in the western Caribbean and the eastern Pacific. Keigwin found that oxygen isotopes on either side of Panama began to diverge about 4 million years ago, suggesting that the Caribbean's salinity increased around that time—"possibly in response to shoaling of the Panama isthmus," he wrote. Combined with changes in carbon-13 enrichment, the oxygen isotope data suggested that modern ocean circulation patterns in the Caribbean and eastern Pacific developed about 3 million years ago. "It's a brilliant paper," Coates says. He credits Keigwin for "launching the standard model of isthmus closure." Over the next quarter century, a string of paleoceanographic studies have supported the standard model. For example, researchers found that carbonate began to pile up in the Caribbean sea floor from about 4.6 million years ago, pointing to more sluggish deep-ocean circulation. Then, about 3.5 million years ago, new kinds of carbonate-loving foraminifera and corals appear in the Caribbean's fossil record, and molecular genetics data also back rapid diversification around this time. "It's a classic Darwinian evolutionary experiment," Coates says. Another consequence of isthmus closure in the Caribbean was the collapse of upwelling, in which deeper, colder waters rise to the surface, bringing nutrients to shallower waters. Proxies of this collapse include local extinctions—seafloor organisms "withered on the vine," Coates says—and a shift in the Caribbean from fast-growing oysters to slower-growing species about 3.5 million years ago. The bottom line, Jackson says, is that until 4 million years or so ago, deep-ocean indicators in the Caribbean looked like those in the Eastern Pacific. "The ocean core data are the killer of the new hypothesis," he says. "How could the two oceans have been so well mixed geochemically if there were a land barrier in between?" ## Putting the s in isthmus Jaramillo and Montes's journey into tectonic heresy began with a1 million grant from the Panama Canal Authority that Jaramillo landed to conduct geological studies along banks of the Panama Canal slated for obliteration to widen the waterway. "He started a fantastic project," Coates says. A companion effort in rescue paleontology has netted thousands of specimens, including 10 species new to science (see sidebar, p. 232).

As part of the projects, Montes and Jaramillo used radioisotope, geochemical, and paleomagnetic analyses to date rocks and discern relationships between rock formations. They wanted more accurate timelines for recovered fossils, and they hoped that these would lead to a better understanding of how the link between the continents was forged. "When we started our study, we didn't have any problem with 3 million years" as the date of isthmus formation, Montes says.

The gold standard for dating rock formations is a technique that relies on the radioactive decay of uranium-235 and uranium-238. The mineral zircon is chock full of these isotopes and their lead and thorium decay products. By measuring the proportions of these isotopes in a zircon crystal, researchers can determine the time since the crystal and surrounding rock hardened and cooled, as well as the exhumation, or exposure, of rock from tectonic processes. The team recovered zircon crystals, formed during the cooling of magma, from the Azuero Peninsula west of the Panama Canal and from the San Blas mountains, a range to the east that extends into Colombia. The zircons revealed that a volcanic arc began forming about 70 million years ago in the gap between the two continents, with major exhumation events lifting up blocks of the arc about 47 million, 25 million, and 11 million years ago. By measuring the direction of the ancient magnetic fields frozen into the volcanic rocks, the researchers were able to reconstruct how tectonic forces had shifted and deformed the arc.

Piecing together the evidence, the researchers, with geologist David Farris of Florida State University in Tallahassee, proposed that the collision between South America's northern Andean blocks and the Central American volcanic arc began about 25 million years ago. Panama's 'S' shape, Montes points out, betrays the tremendous strain that the arc underwent. Around that time, the arc melded with the rest of Central America to form a peninsula, allowing North American fauna to colonize it, as fossils found among the remnants of the arc testify. By then, possibly the final barrier to intercontinental movement was a deep-water gap between the peninsula and the coast of modern-day Colombia as it subducted under the arc.

"It's terrific work," Jackson says about the scenario, which Montes and Jaramillo published in the Geological Society of America Bulletin in January 2012 and in the Journal of Geophysical Research: Solid Earth that April. But he and others reject the headline-grabbing conclusion that Montes and Jaramillo arrived at: that by 10 million years ago, the geological shape-shifting they meticulously documented had squeezed away the last deep-sea connection between the oceans.

## Wallace would be proud

Coates himself accepts Montes and Jaramillo's account of the first stages of isthmus closure. "Our geological reconstructions are stunningly similar," says Coates, referring to a pair of studies in the Geological Society of America Bulletin in 2003 and 2004. However, he argues, "There's no way you can tell from their data whether parts of the arc were still submerged" in the final stages of filling in. And the spatial resolution of their data is not fine enough, he says, to rule out deep-water gaps in the arc.

Coates and Stallard think that Indonesia may offer a modern-day analog of pre-isthmus Panama. Over millennia, Asian species have readily hopped or drifted between islands in the Sunda region, west of Bali. There, the migration mostly stopped at Bali. Lombok, the next major island to the east, is only 35 kilometers away, but the strait is several hundred meters deep and has an especially swift current, thwarting purposeful or accidental migration and forming a species barrier—Wallace's Line. Several hundred kilometers to the east is a similar species barrier: Lydekker's Line, the edge of the world for marsupials and other creatures from the Sahul region, encompassing Australia and New Guinea. In between the Wallace and Lydekker lines is a collection of islands stretching from Borneo to New Guinea that biogeographers refer to as Wallacea for its unique faunal assemblage.

Coates and Stallard propose that deep-water gaps in the present-day Panama Canal Basin and between the volcanic arc and South America were equivalent to the Wallace and Lydekker lines. They argue that even as the isthmus was filling in, the path of migration was interrupted for 10 million years or more.

"Essentially, South America is a few million years ahead of Australia," in that Indonesia's volcanic arc and Australia should eventually form a contiguous land mass, says Coates, whose report with Stallard appeared online in BMS on 4 April. "It's a very elegant analog," says STRI paleobiologist Aaron O'Dea.

O'Dea and others who adhere to the late-formation thesis have also taken up the gantlet. In a paper in press at BMS, Jackson and O'Dea comprehensively review studies on the paleocean environment, dispersal of terrestrial and marine creatures, and molecular phylogeny of sea life, all pointing, they say, to closure of the isthmus about 3 million years ago.

One especially compelling find, presented at the geology meeting last November, is shark teeth and fish fossils such as otoliths recovered from 6-million-year-old sediments in the Chagres Formation in the Panama Canal Basin. The otoliths, or ear bones, are from marlins and bluefish: species that generally don't ply shallow waters. STRI's Carlos De Gracia and colleagues argue that the fossil assemblage points to waters between 100 and 700 meters deep. Coates calls the Chagres fossils a "smoking gun" for the existence of a deep-sea gap millions of years later than the closure envisioned by Jaramillo and Montes.

Yet, other pieces of the puzzle don't fit the late closure thesis. Most troubling are the so-called herald animals. Biogeographers have long recognized that the Great American Biotic Interchange was never a stampede, as if a drawbridge were lowered over a moat. About 9 million years ago, well before the surge of migrations, two sloth species descended from South American ancestors appear in Florida and Texas. One gave rise to Megalonyx, a 1-ton sloth named by Thomas Jefferson, a fossil buff, who mistook a claw of the beast for that of a gigantic meat-eater. (Sloths are vegetarians.) The first emigrant from North America appears to have been the raccoon-like carnivore Cyonasua, fossils of which show up in Argentina 7.3 million years ago. Terror birds stormed Texas 5 million years ago, with giant armadillolike pampatheriids hot on their heels.

Scientists have generally chalked up these early migrations to island-hopping or rafting. Modern sloths and raccoons are good swimmers, Jackson notes, while globally, the annals of biogeography are replete with accounts of accidental émigrés borne to distant lands on clumps of vegetation.

But some scientists find that explanation hard to swallow. And then there is the case of the stingless bees.

About 22 million years ago, ancestors of these honey bees, which were cultivated by the Maya in Central America, arose in the Amazon; they reached Central America only after the isthmus formed. In 2011, STRI ecologist David Roubik, a specialist on bees, discovered two new, closely related stingless bee species: one in Colombia and one on Coiba Island, off the Pacific coast of Panama. The forest-dwelling bees are not accomplished fliers. "They can't establish a new nest across more than a short stretch of open water," Roubik says. It's possible that rafts carried nests to Coiba, he says. But to Roubik, a simpler explanation is that a land bridge well before 3 million years ago paved the way for the bees. "My opinion is that there was something akin to a little isthmus around 6 to 12 million years ago," he says, before portions of the volcanic arc were submerged again, only to reemerge about 3 million years ago.

That concept could be gaining traction. Most scientists accept that present-day Panama rose from the sea over millions of years as the volcanic arc and South America collided. In a paper in press at Biological Reviews, O'Dea; STRI ecologist Egbert Leigh; and Geerat Vermeij of the University of California, Davis, propose that about 10 million years ago, the shoaling resulted in a land bridge that was "briefly near-complete." That would explain how key herald species, such as the sloths up north and the Cyonasua down south, pioneered new terrain long before the Great American Biota Interchange. By 7 million years ago, they propose, deep-water gaps in the emerging isthmus had disrupted the land bridge. "Multiple stages of isthmus formation are not inconsistent with the biological evidence," Farris says.

That explanation may satisfy some researchers, but at STRI, where many of the debate's antagonists are either based or spend time for research, the sparring continues. "I'll see Carlos in the hall, and flash him three fingers. He flashes back 15," says Coates, who calls Jaramillo "a very fine scientist" and says that their interactions "are always polite. This is the way science is supposed to be."

Good manners can't disguise the rift, however. "Both sides," Montes says, "have entrenched positions." For opponents in the debate, that means, for now, no closure.

5. # Salvage Paleontology on the Seaway

1. Richard Stone

Expansion of the Panama Canal has opened up sections of the seaway to salvage paleontology; fossil finds are bringing this cradle of biodiversity into sharper focus.

PARAISO, PANAMA—On an embankment hewn from the jungle during the construction of the Panama Canal a century ago, Jason Bourque sits hunched over a 19-million-year-old turtle. Under a broiling midday sun, Bourque spends a half hour patiently brushing away grit from a fractured black carapace the size of a dinner plate before covering it in a plaster bandage for removal. By the time he's finished, a dozen or so container ships, oil tankers, and other vessels steam past along the 77-kilometer-long seaway.

Bourque, a preparator at the Florida Museum of Natural History, is taking advantage of a fossil windfall. As part of a $5.5 billion expansion of the canal that will move 152 million cubic meters of earth, the canal authority has opened up sections of the seaway to salvage paleontology: collecting fossils in newly exposed rock faces. "It's a once-in-century opportunity," says Bruce MacFadden, curator of vertebrate paleontology at the museum, run by the University of Florida in Gainesville, and director of the Panama Canal Project. The project's geological studies have provided grist for a radical hypothesis that the Isthmus of Panama formed a land bridge several million years earlier than thought (see main story, p. 230). Its fossil finds are also revelatory: a menagerie of miniature horses and camels, gopherlike rodents, peccaries, and caimans, as well as weird creatures such as the giant bear-dog and the hippolike anthracothere. The assemblage recovered so far from the prehistoric rainforest suggests that the volcanic arc from which the isthmus formed was a "species pump," MacFadden says, spawning new life forms that spread through North America. The canal's construction in the early 20th century revealed a fossil trove, which scientists secured piecemeal over the years. The expansion is opening up whole new exposures. That's especially exciting because throughout the isthmus, lush forest has made it difficult for identify rich fossil sites, says Aaron Wood, a postdoc at the Florida Museum of Natural History. With the canal expansion slated for completion as early as next year, the window of opportunity for paleontologists is closing fast. Racing to gather up as many fossils as they can, MacFadden's crew over 4 years has hauled in more than 3000 specimens, among them 10 new species. A top fossil hunter on the team is Aldo Rincon, a Ph.D. student at the University of Florida, lead author on a report published in the Journal of Vertebrate Paleontology last March describing a new species of anthracothere. Rincon's favorite specimen, he says, is the fragile jawbone and teeth of a bat that he unearthed from the Cucaracha Formation, in the shadow of the Centennial Bridge, last year. "I rolled down the hill, I was so excited," he says. The bat, descended from a South American species, is a rare example of a nonswimmer to have traversed the deep-water gap that separated Colombia and Panama about 19 million years ago. (Crocodiles, turtles, and snakes crossed much earlier.) A view of life in this ancient cradle of biodiversity is coming into sharper focus. The Panama Canal, says Andrés Cárdenas, a postdoc at the Smithsonian Tropical Research Institute in Balboa, Panama, "has everything you need to tell the story." 6. Biodiversity # The Amazon in 4D 1. Lizzie Wade An interdisciplinary team is linking data from field research in the Amazon into a comprehensive digital collection, aiming to map evolution in space and time. NEW YORK CITY—In a chilly specimen storage room on the sixth floor of the American Museum of Natural History (AMNH), Joel Cracraft opens a cabinet and slides out two trays filled with delicate, palm-sized songbirds, inhabitants of the Amazon rainforest. One tray holds a jumble of red-headed manakins—eyeless, boneless, and stuffed with cotton. The other holds their close relative, golden-headed manakins. The two species seem to differ only in the color of the males' crown feathers. But they are never found in the same place. Red-headed manakins live south of the Amazon River; golden-headed manakins live north of it. How that pattern arose is a mystery, says Cracraft, the museum's curator of ornithology. Scientists don't know what drove the birds to evolve different colored crowns. They don't know when the two species began to diverge, or the precise age of the river that separates them—much less, when it became wide enough to deter birds from flying across. They don't know just how these birds, and the plants and animals living alongside them, may have adapted to the Amazonian climate, or exactly how that climate may have changed over time. In short, scientists don't know how the Amazon rainforest and its stunning biodiversity came to be. "It's one of the great questions of all time," says Thomas Lovejoy, biodiversity chair of the Heinz Center in Washington, D.C., and an ecologist who has worked in the Amazon for more than 45 years. Now, dozens of scientists from Brazil and the United States have teamed up across disciplines to try to find an answer. Called Dimensions of Amazonian Biodiversity, their project aims to create a "four-dimensional evolutionary atlas" of the Amazon. By combining data from a variety of fields such as geology, evolutionary biology, DNA analysis, and climate modeling, the team plans to track the region's biodiversity and environment through space and time to understand how they interacted and evolved. ## A volatile place For many years, biologists took the Amazon's abundance of plant and animal species to mean that its rainforest was an old, stable ecosystem—a kind of ecological "museum" that has "had more time to accumulate more species," says botanist Lúcia Lohmann of the University of São Paulo in Brazil, who is, along with Cracraft, a principal investigator for Dimensions. But geological evidence points to a much more volatile history for the region, according to Lohmann and her collaborators. From at least 17 million to 11 million years ago, in the middle of an epoch known as the Miocene, the Amazon Basin was covered in an extensive system of wetlands that scientists refer to as Lake Pebas. At some point—exactly when is still disputed—the lake's water began flowing east, eventually breaking through into the Atlantic and forming the beginnings of what is now the Amazon River. As the wetlands drained and gave way to forest, the biodiversity that we see in today's Amazon began to take shape, Lohmann says. New evidence garnered from DNA sequencing and other evolutionary data point to an image of the region not as an environmental museum but as what Lohmann calls a biological "cradle" where large numbers of species have diversified fairly recently. As a result, says Alan Graham, a paleobotanist at the Missouri Botanical Garden in St. Louis, scientists now "need a whole new suite of explanatory factors" to account for the region's biodiversity. Dimensions, launched in September 2012 with a promise of$2 million over 5 years from the U.S. government and an equivalent offer from the state of São Paulo in Brazil, aims to find them.

To untangle the Amazon's complicated history, scientists from many disciplines will need to work together, says Carina Hoorn, a geologist at the University of Amsterdam. Hoorn is involved in CLIM-AMAZON, a European-Brazilian collaboration begun in 2011 that is gleaning data on the region's climate and environmental history from sediments throughout the Amazon River Basin. It's not enough to focus on a single critical field, such as geology or evolutionary biology, she says. "You really have to see it in an integrated, interdisciplinary way."

Cracraft's manakins provide an example of how such a strategy might work. If you were studying Amazonian birds, he says, you might plot the location where each of AMNH's manakins was collected and see a sharp north-south separation between the golden-headed and red-headed species. But only if you overlaid the data on a map of the region's waterways would it be clear that the barrier separating them is the Amazon River, the formation of which may have isolated two groups that evolved into separate species. Knowing precisely how long ago the two manakins split off from their common ancestor might give a good clue as to when the river became the major waterway that it is today. "This is one of the purposes of the grant, to try to tease apart that layered history of Amazonia and [its] biota in a way that can explain it all," Cracraft says. "Or at least most of it."

The team plans to go through a similar mapping process with all the region's birds, primates, and butterflies, as well as two families of plants. "To start with, we just want to understand general patterns of diversity and see how those relate to environmental features," Lohmann explains. A project like this is "long overdue," Lovejoy says.

## Finding hidden patterns

Although museum specimens are at the heart of the Dimensions project, much of the information that they contain is not easily accessible because it's not yet online. Improving digital archives is one of the project's main objectives. The team plans to create a comprehensive, freely available database, including details on when, where, and how specimens were acquired, which anyone will be able to use to analyze the region's biodiversity. "The key will be to make this information comparable so that we can combine stuff and analyze bigger data sets," Cracraft says. If this succeeds, "suddenly it will be possible to look at patterns and questions that have been hard to actually get at before," predicts Lovejoy, who is not involved in the Dimensions project.

In this first year of their grant, Dimensions researchers have been focusing on adding precise geographical coordinates to records of museum and herbarium specimens. Location is the common factor that runs through everything, from plants to birds to primates, and even "the paleo and geological data," says Barbara Thiers, director of the New York Botanical Garden's herbarium, which is contributing to the Dimensions project. "Collectors didn't routinely record [latitude and longitude] information on the specimens" until handheld GPS devices came along, she says. So the Dimensions team is reconstructing coordinates as best they can, trying to match up places mentioned in collectors' original notes with the localities included in geographical directories called gazetteers, or by pulling out paper maps and retracing a collector's route.

Some patterns line up, like the distribution of plants and their pollinators, while others diverge in curious ways. Amazonian birds, for example, tend not to fly across rivers, meaning that scientists often find strikingly different species on either side of a waterway. Many plant species, however, "seem to cross rivers without any problems," Lohmann says. So while the formation of rivers might be a driving force behind bird evolution in the basin, researchers need to come up with other ideas about how populations of plants might have become isolated and evolved into separate species.

The atlas coordinates should reveal not just how species are distributed but also where collectors in the past focused their efforts. Most fieldwork in the Amazon has been done along major rivers or near cities. But collecting in just a few areas, no matter how extensive, does not guarantee a representative sample of diversity—especially because Amazonian species tend to be very particular about where they live, even when barriers separating one area from another aren't yet clear to scientists. "People have basically been looking at nice, cute things at eye-height … things that were easy to get at," says Alexandre Antonelli, an evolutionary biologist at the University of Gothenburg in Sweden.

This can skew conclusions and bias ongoing research, Lohmann agrees. "We often go back to the most collected areas as being the centers of diversity just because our data sets don't allow a very fair comparison throughout the area," she says. If the Dimensions atlas can reveal which places and species are already well studied, it could help scientists target future fieldwork on undercollected areas.

Coordinating such a sprawl ing, interdisciplinary effort is not easy, and often requires getting "out of your comfort zone," Lohmann admits. As the Dimensions project progresses, it's "essential" that research leaders "be very closely attuned to other specialists, and especially those that have alternate viewpoints," agrees Graham, who is not involved in the project. For example, the Dimensions and CLIM-AMAZON researchers disagree on some fundamental questions about the region, particularly the age of the Amazon River. Hoorn says that she welcomes the discussions. "The better people work together, the better the results will be," she says.

Although Dimensions focuses on Amazonia's history, it may help scientists and policymakers protect the increasingly at-risk ecosystem. The atlas, for example, may pinpoint areas where new species are likely to evolve. Preserving those hotspots of biodiversity might give Amazonia's inhabitants a leg up in the race to adapt to Earth's changing climate, says George Gilchrist, the National Science Foundation (NSF) program director in charge of the Dimensions grant. "If we can't keep the full diversity of species there, can we keep the evolutionary potential that generated [it]?" he wonders.

Ultimately, scientists and NSF officials hope that Dimensions will serve as a model for interdisciplinary studies about the evolutionary history of all kinds of ecosystems. Cracraft, for one, seems to have already taken the Dimensions' strategy to heart. Outside the room where the AMNH manakins are stored, he calls to a group of museum employees about to go bird watching in Central Park, "Tell me what you see and where!"