NSF HELPS FUND RESEARCH ON GENETIC ORIGINS OF BIRDS

FROM:  NATIONAL SCIENCE FOUNDATION 
'Big bang' of bird evolution mapped by international research team
Genes reveal histories of bird origins, feathers, flight and song

The genomes of modern birds tell a story: Today's winged rulers of the skies emerged and evolved after the mass extinction that wiped out dinosaurs and almost everything else 66 million years ago.

That story is now coming to light, thanks to an international collaboration that has been underway for four years.

The first findings of the Avian Phylogenomics Consortium are being reported nearly simultaneously in 23 papers--eight papers in a special issue this week of Science, and 15 more in Genome Biology, GigaScience and other journals.

The results are funded in part by the National Science Foundation (NSF).

Scientists already knew that the birds that survived the mass extinction experienced a rapid burst of evolution.

But the family tree of modern birds has confused biologists for centuries, and the molecular details of how birds arrived at the spectacular biodiversity of more than 10,000 species was barely known.

How did birds become so diverse?

To resolve these fundamental questions, a consortium led by Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen; neuroscientist Erich Jarvis of Duke University and the Howard Hughes Medical Institute; and M. Thomas P. Gilbert of the Natural History Museum of Denmark has sequenced, assembled and compared the full genomes of 48 bird species.

The species include the crow, duck, falcon, parakeet, crane, ibis, woodpecker, eagle and others, representing all major branches of modern birds.

"BGI's strong support and four years of hard work by the entire community have enabled us to answer numerous fundamental questions on an unprecedented scale," said Zhang.

"This is the largest whole genomic study across a single vertebrate class to date. The success of this project can only be achieved with the excellent collaboration of all the consortium members."

Added Gilbert, "Although an increasing number of vertebrate genomes are being released, to date no single study has deliberately targeted the full diversity of any major vertebrate group.

"This is what our consortium set out to do. Only with this scale of sampling can scientists truly begin to fully explore the genomic diversity within a full vertebrate class."

"This is an exciting moment," said Jarvis. "Lots of fundamental questions now can be resolved with more genomic data from a broader sampling. I got into this project because of my interest in birds as a model for vocal learning and speech production in humans, and it has opened up some amazing new vistas on brain evolution."

This first round of analyses suggests some remarkable new ideas about bird evolution.

The first flagship paper published in Science presents a well-resolved new family tree for birds, based on whole-genome data.

The second flagship paper describes the big picture of genome evolution in birds.

Six other papers in the special issue of Science report how vocal learning may have independently evolved in a few bird groups and in the human brain's speech regions; how the sex chromosomes of birds came to be; how birds lost their teeth; how crocodile genomes evolved; and ways in which singing behavior regulates genes in the brain.

New ideas on bird evolution

"This project represents the biggest step forward yet in our understanding of how bird diversity is organized and in time and space," said paper co-author Scott Edwards, on leave from Harvard University and currently Director of NSF's Division of Biological Infrastructure.

"Because this information is so fundamental to our understanding of biodiversity, it will help everyone--from birdwatchers to artists to museum curators--better organize knowledge of bird diversity."

The new bird tree will change the way we think about bird diversity, said Edwards. "The fact that many birds associated with water--loons, herons, penguins, petrels and pelicans--are closely related suggests that adaptations to lakes or seas arose less frequently than we thought."

Added paper co-author David Mindell, an evolutionary biologist and program director in NSF's Division of Environmental Biology, "We found strong support for close relationships that might be surprising to many observers.

"Grebes are closely related to flamingos, but not closely related to ducks; falcons are closely related to songbirds and parrots but not closely related to hawks; and swifts are closely related to hummingbirds and not closely related to swallows."

Genome-scale datasets allowed scientists to "track the sequence of divergence events and their timing with greater precision than previously possible," said Mindell.

"Most major types of extant birds arose during a 5-10 million year interval at the end of the Cretaceous period and the extinction of non-avian dinosaurs about 66 million years ago."

It takes a consortium...of 200 scientists, 80 institutions, 20 countries

The Avian Phylogenomics Consortium has so far involved more than 200 scientists from 80 institutions in 20 countries, including the BGI in China, the University of Copenhagen, Duke University, the University of Texas at Austin, the Smithsonian Institution, the Chinese Academy of Sciences, Louisiana State University and others.

Previous attempts to reconstruct the avian family tree using partial DNA sequencing or anatomical and behavioral traits have met with contradiction and confusion.

Because modern birds split into species early and in such quick succession, they did not evolve enough distinct genetic differences at the genomic level to clearly determine their early branching order, the researchers said.

To resolve the timing and relationships of modern birds, consortium scientists used whole-genome DNA sequences to infer the bird species tree.

"In the past, people have been using 10 to 20 genes to try to infer the species relationships," Jarvis said.

"What we've learned from doing this whole-genome approach is that we can infer a somewhat different phylogeny [family tree] than what has been proposed in the past.

"We've figured out that protein-coding genes tell the wrong story for inferring the species tree. You need non-coding sequences, including the intergenic regions. The protein-coding sequences, however, tell an interesting story of proteome-wide convergence among species with similar life histories."

Where did all the birds come from?

This new tree resolves the early branches of Neoaves (new birds) and supports conclusions about relationships that have been long-debated.

For example, the findings support three independent origins of waterbirds.

They also indicate that the common ancestor of core landbirds, which include songbirds, parrots, woodpeckers, owls, eagles and falcons, was an apex predator, which also gave rise to the giant terror birds that once roamed the Americas.

The whole-genome analysis dates the evolutionary expansion of Neoaves to the time of the mass extinction event 66 million years ago.

This contradicts the idea that Neoaves blossomed 10 to 80 million years earlier, as some recent studies have suggested.

Based on this new genomic data, only a few bird lineages survived the mass extinction.

They gave rise to the more than 10,000 Neoaves species that comprise 95 percent of all bird species living with us today.

The freed-up ecological niches caused by the extinction event likely allowed rapid species radiation of birds in less than 15 million years, which explains much of modern bird biodiversity.

For answers, new computational tools needed

Increasingly sophisticated and more affordable genomic sequencing technologies, and the advent of computational tools for reconstructing and comparing whole genomes, have allowed the consortium to resolve these controversies with better clarity than ever before, the researchers said.

With about 14,000 genes per species, the size of the datasets and the complexity of analyzing them required new approaches to computing evolutionary family trees.

These were developed by computer scientists Tandy Warnow at the University of Illinois at Urbana-Champaign, funded by NSF, Siavash Mirarab of the University of Texas at Austin, and Alexis Stamatakis at the Heidelburg Institute for Theoretical Studies.

Their algorithms required the use of parallel processing supercomputers at the Munich Supercomputing Center, the Texas Advanced Computing Center, and the San Diego Supercomputing Center.

"The computational challenges in estimating the avian species tree used around 300 years of CPU time, and some analyses required supercomputers with a terabyte of memory," Warnow said.

The bird project also had support from the Genome 10K Consortium of Scientists (G10K), an international science community working toward rapidly assessing genome sequences for 10,000 vertebrate species.

"The Avian Genomics Consortium has accomplished the most ambitious and successful project that the G10K Project has joined or endorsed," said G10K co-leader Stephen O'Brien, who co-authored a commentary on the bird sequencing project in GigaScience.

-NSF-
Media Contacts
Cheryl Dybas, NSF,

THE SPECIATION OF TREES

FROM:  THE NATIONAL SCIENCE FOUNDATION 
Tracing the evolution of forest trees

Evergreen tree in Hawaii offers clues into survival of tropical ecosystems
There are at least 60,000 identified tree species in the world, "but we know next to nothing about how they got here," Elizabeth Stacy says. "Trees form the backbone of our forests, and are ecologically and economically important, yet we don't know much about how speciation happens in trees."

Speciation, the evolutionary process by which new biological species arise, fascinates Stacy, an associate professor of biology at the University of Hawaii Hilo, and forms the core of her research. The National Science Foundation (NSF)-funded scientist is focusing on the origins of the many forms of Metrosideros, a diverse genus of forest trees, and on one of its species in particular--Hawaii's M. polymorpha--as a model for studying diversification.

The Hawaiian Islands were formed and continue to be formed from volcanic activity, which makes them an ideal place to study speciation. Because the islands are so isolated, their plant and animal species almost certainly colonized for the first time millions of years ago when wind, ocean currents, birds and insects carried early specimens there.

"Hawaii is a fantastic place to study evolution and the origins of species," Stacy says. "It's like its own planet, its own evolutionary experiment."

Metrosideros comprises trees and shrubs found predominantly in the Pacific Rim region. The name means "iron heartwood," and derives from the ancient Greek metra, or "heartwood," and sideron, or "iron." Stacy is trying to discern the relationships among the many forms of this genus in Hawaii and learn how reproductive barriers arise between diverging populations.

"Over time, Metrosideros has diversified into five species," she says. "M. polymorpha is by far the most abundant. It's unusual for its huge ecological breadth. You can find it in almost every habitat in Hawaii. It's everywhere."

Insights into the evolution of such long-lived trees as these could have important implications for future conservation practices in Hawaii, and possibly elsewhere.

"Because it is so abundant and dominant, Metrosideros is a keystone species for many of Hawaii's terrestrial environments," Stacy says. "It is an important resource for native birds and insects. Insights into how the many forms of Metrosideros originated and how different they are from each other today can reveal insights into the same for the many animals that use Metrosideros. Understanding the ecological needs of species is an essential first step in their conservation.

"Conservation biology has gained an appreciation for evolution," she adds. "Over the last decade, people have grown to appreciate that we need to pay attention to the processes that give rise to species. Speciation is literally the origin of the biodiversity that we are concerned about saving. To really think about long-term conservation, we need to be aware of these evolutionary processes."

Stacy is conducting her research under an NSF Faculty Early Career Development (CAREER) award, which she received in 2010. The award supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organization. NSF is funding her work with about $750,000 over five years.

Her project uses molecular genetic methods to "try to unravel the very shrouded evolutionary history of Metrosideros in Hawaii," she says. "We're experimenting with novel molecular markers--previously inaccessible genes and gene regions--to get a clearer picture of how the forms of Metrosideros are related, both within and across islands."

Uncovering the evolutionary relationships among closely related trees is especially difficult because of their tendency to hybridize, and thus share the same genetic material, she adds.

Also, she and her team are conducting experiments in the field and in the greenhouse with seedlings of various forms, exposing them to different stresses to compare their differences.

"These experiments are revealing insights into how long-term exposure of tree populations to Hawaii's famous environmental gradients can lead to diversification, and they reveal which specific environmental factors, for example, water, light and wind are most important for causing the differences among the forms of the tree," she says.

"Lastly, we are looking at their reproductive barriers: can you two make 'babies' with each other, and how fit are your 'babies?"' she adds. "How well do your offspring survive, and reproduce compared to everyone else in your population? We do a lot of hand-crossing, or hand pollination, where you take pollen from one tree and pollinate another."

These crosses allow examination of the both prezygotic (before fertilization) and postzygotic (after fertilization) barriers that accumulate between diverging populations on the way to speciation.

"I posit that adaptation of this widespread tree to Hawaii's highly varied environments has led to the evolution of partial reproductive isolating barriers between forms that are adapted to different habitats," she says.

As part of the grant's educational component, she is encouraging her students to participate in research through field and lab projects. The team also has established Ho'oulu Lehua, a community-based organization that provides hands-on environmental education for youth with projects that address real conservation issues in the native forests of East Hawaii Island.

The goal of Ho'oulu Lehua, under the leadership of CAREER technician Jennifer Johansen, is to strengthen connections between Hawaii's young people and native forests through restoration activities based on scientific understanding and cultural traditions.

"This island has 11 of 13 climate zones," she says. "We have desert, and wet forests and bogs. Because we are in this amazing evolutionary laboratory, I think we excel in engaging our students with authentic research experiences outside. You can't do this stuff in a lab."

-- Marlene Cimons, National Science Foundation
Investigators
Elizabeth Stacy
Related Institutions/Organizations
University of Hawaii at Hilo

CLIMATE CHANGE AND MAMMALS OF THE PAST

FROM:  NATIONAL SCIENCE FOUNDATION 

Understanding how ancestors of today's mammals responded to climate change
Research provides valuable insights for future environmental challenges
About 10 million years into the current Cenozoic Era, or roughly 56 million years ago, during a climate that was hot and wet, two groups of mammals moved from land to water. These were the cetaceans, which include whales, dolphins and porpoises, and the sirenians, with its sea cows, manatees and dugongs.

Over time, their bodies began to adapt to their new environment. They lost their hind limbs, and their forelimbs began to resemble flippers. Their nostrils moved higher on their skulls. The cetaceans became carnivores, eating fish and squid, while the sirenians became herbivores, living on sea grasses and algae.

"It's an interesting example of evolution, and a natural experiment you don't normally have," says Mark T. Clementz, an associate professor of paleontology in the University of Wyoming's department of geology and geophysics. "The changes are so extreme, you can't really ignore them. By studying these groups, we can tease out the main environmental factors that affect mammalian groups as they move into a new environment, and a new ecosystem."

The National Science Foundation (NSF)-funded scientist believes that understanding how the ancient ancestors of today's mammals responded to climate change will provide valuable insights that will help in dealing with environmental challenges.

"A better understanding of how these mammals responded in the past will give us a more informed idea of how they will respond to climate change in the future," he says. "This could benefit conservation efforts down the road, for example, what to look out for, what things could benefit these groups, and what will hurt them if climate change goes as we project."

Moreover, "these mammals are like data loggers," he adds. "You can infer what the environmental conditions of the past were like, and how they changed over time, and you can say something about how marine ecosystems have changed over time."

The primary goal of his project is to compare the evolutionary ecology of these two orders, the Cetacea and the Sirenia, in the context of Cenozoic climate change.

The Cenozoic Era is made up of two time periods, the Paleogene and the Neogene, with each of those divided into epochs, which are smaller subdivisions of geologic time.

"With the appearance of whales and sea cows in the Early Eocene [the second epoch of the Paleogene], the evolution and diversification of both groups occurred across major episodes of significant climate change as the Earth moved from the greenhouse conditions of the early Paleogene and into the icehouse conditions of the Neogene, and today," he says.

Clementz is conducting his research under an NSF Faculty Early Career Development (CAREER) award, which he received in 2009. The award supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education, and the integration of education and research within the context of the mission of their organization.

In order to evaluate the impact of climate change on each group, Clementz is examining fossil specimens of these ancient whales and sea cows as part of marine food webs, analyzing the stable isotopes of calcium, carbon, oxygen and strontium, with an emphasis on, among other things, each group's ecological status, including diet and salinity tolerance.

"When we look at the sirenians, it appears that they had a relationship with sea grasses, which are found only in salt water, that extends far in the past," he says, noting that it is unusual for mammals to move from land to saltwater without first spending a transitional period in freshwater. "The isotopes suggest they were feeding in sea grass beds while still capable of walking on land, and skipped the freshwater phase."

However, these conclusions may change upon examining recently acquired additional specimens.

"We now have some new fossils that imply that some sea cows might have been living in freshwater, but we haven't been able to fully analyze them yet," he says. Should that be the case, "it might have been a really fast transition," he says. "They might have spent a very short amount of time in freshwater, then moved quickly into a marine habitat."

The cetaceans, on the other hand, "do show a freshwater phase," he says.

Interestingly, the sirenians are very sensitive to environmental temperatures, staying where the water is warm--20 degrees Celsius (about 68 degrees Fahrenheit) or warmer. Today's global warming may, in fact, support them but possibly only to a certain extent.

"They like it warm," he says. "In the past, when conditions were warm, their range was greater. They went further north and further south. So, from a temperature perspective, today's climate change warming could benefit them. There is some question about how the climate could affect sea grasses and algae. It could be worse for them if it hurts their food supply."

Cetaceans, being more diverse, are more complicated, he says.

"They have about 80 different species, compared to the sirenians' four," he says. "They have been more successful at taking advantages of changes. It could be related to their diet of fish and squid. In cooler environments, they had higher food productivity They exploited those periods and diversified. Now that things are getting hotter, we're not sure how this will affect them."

As part of the grant's educational component, Clementz is taking an integrative big-picture approach to teaching K-12 and college students the concepts of evolution, ecology and climate change.

For example, he wrote a children's play that explains what occurred during the evolution of whales. Later, with the input of a choreographer and dance instructor, the play expanded to include a dance recital. It has been performed multiple times on campus, and many outside groups of young children have seen it.

"The children studied the movement of whales, then learned about their movements through dance," he says. "They got to see how whales move, and how it affects their bodies, and they got to dance, using dance moves that simulate whale movement. Visually, it really was stunning, and the kids learned a lot this way."

-- Marlene Cimons, National Science Foundation
Investigators
Mark Clementz
Related Institutions/Organizations
University of Wyoming

THE FOX WHO GOT READY FOR AN ICE AGE

FROM:  NATIONAL SCIENCE FOUNDATION 

"Out of Tibet" hypothesis: Cradle of evolution for cold-adapted mammals is in Tibet

Extinct Tibetan fox, ancestor of today's arctic fox, used Tibet as training ground for Ice Age climate

June 11, 2014

For the last 2.5 million years, Earth has experienced millennial-long cold and warm cycles. During cold periods, continental-scale ice sheets have blanketed large tracts of the Northern Hemisphere.

As climate warmed, glaciers receded, leaving Yosemite-like valleys and similar geologic features behind.

The advance and retreat of the ice sheets also had a profound influence on the evolution and geographic distribution of many animals, including those that live in far northern regions.

New results from research conducted in the Himalayan Mountains and published this week in the journal Proceedings of the Royal Society B: Biological Sciences identify a recently discovered three to five million-year-old Tibetan fox, Vulpes qiuzhudingi, as the likely ancestor of the living arctic fox, Vulpes lagopus.

The finding lends support to the idea that the evolution of present-day animals in the Arctic traces back to ancestors that adapted to life in cold regions in the high-altitude Tibetan Plateau.

The paper's lead author is Xiaoming Wang of the Natural History Museum of Los Angeles County. Co-authors are Zhijie Jack Tseng from the University of Southern California, Qiang Li from the Chinese Academy of Sciences, Gary Takeuchi from the Page Museum at the La Brea Tar Pits and Guangpu Xie from the Gansu Provincial Museum.

The scientists, part of a team of geologists and paleontologists led by Wang, uncovered fossil specimens of the Tibetan fox in the Zanda Basin in southern Tibet.

In addition to the fox, the team also discovered extinct species of a wooly rhino (Coelodonta thibetana), three-toed horse (Hipparion), Tibetan bharal (Pseudois, known as blue sheep), chiru (Pantholops, known as Tibetan antelope), snow leopard (Uncia), badger (Meles), and 23 other mammals.

The new fossil assemblage lends credence to a scenario the scientists call the "Out of Tibet" hypothesis.

It argues that some Ice Age megafauna--which in North America include the woolly mammoth, saber-toothed cat and giant sloth--used ancient Tibet as a training ground for developing adaptations that allowed them to cope with a harsh climate.

"The concept 'Out of Tibet' is an exciting insight for the origin of cold-adapted mammals of the Pleistocene," says Rich Lane, program director in the National Science Foundation's (NSF) Division of Earth Sciences, which funded the research.

"It parallels the 'Out of Africa' theory for the evolution of hominids. Together they may be a model for wider application in biological history and geography."

Tibet, Wang says, is a rich but grueling location for paleontological fieldwork.

Fifteen summer field seasons and a great deal of luck have led to his and his colleagues' successes.

Their expeditions involve a one-week journey to Lhasa, then a four-day drive into the remote "layer cake" sediments of the Zanda Basin--a drive made in old-model Land Cruisers known for becoming mired in streambeds.

At the more than 14,000-foot elevation, it's difficult to breathe, water freezes overnight in camps, and the scientists often must walk alone in search of fossils.

They've trained their eyes to search for ancient lake margins, where megafauna are reliably found.

Despite the challenges, Wang says that it's his favorite place to look for fossils.

"It's a pristine environment, the Tibetan people are kind, and in paleontological terms," he says, "it's relatively unexplored."

-- Cheryl Dybas, NSF (703) 292-7734 cdybas@nsf.gov
-- Kristin Friedrich, L.A. County Museum of Natural History (213) 763-3532 kfriedri@nhm.org
Investigators
Xiaoming Wang

RESEARCH ON COMPETITION TO SURVIVE

FROM:  NATIONAL SCIENCE FOUNDATION 

Study suggests survival isn't always about competition

New research findings contradict one of Darwin's hypotheses, which encourages prioritizing species for conservation based on evolutionary or genetic uniqueness
May 1, 2014

One of Charles Darwin's hypotheses posits that closely related species will compete for food and other resources more strongly with one another than with distant relatives, because they occupy similar ecological niches. Most biologists have long accepted this to be true.

Thus, three researchers were more than a little shaken to find that their experiments on fresh-water green algae failed to support Darwin's hypothesis.

"It was completely unexpected," says Bradley Cardinale, an associate professor in the University of Michigan's school of natural resources and environment. "We sat there banging our heads against the wall. Darwin's hypothesis has been with us for so long, how can it not be right?"

The researchers--who also included Charles Delwiche, a professor of cell biology and molecular genetics at the University of Maryland, and Todd Oakley, a professor in the department of ecology, evolution and marine biology at the University of California, Santa Barbara--were so uncomfortable with their results that they spent the next several months trying to disprove their own work. But the research held up.

"The hypothesis is so intuitive that it was hard for us to give it up. But we are becoming more and more convinced that he wasn't right about the organisms we've been studying," Cardinale says. "It doesn't mean the hypothesis won't hold for other organisms, but it's enough that we want to get biologists to rethink the generality of Darwin's hypothesis."

Preserving species

The assumptions underlying Darwin's hypothesis are important for conservation policy, since they essentially encourage decision-makers to prioritize species preservation based on how evolutionarily or genetically unique they are. "We don't have enough time, people or resources to save everything," Cardinale says. "A large number of species will go extinct and we have to prioritize which ones we will save.

"Many biologists have argued that we should prioritize for conservation those species that are genetically unique, and focus less on those species that are genetically more similar," he adds. "The thinking is that you might be able to tolerate the loss of species that are redundant. In other words, if you lost a redundant species, you might not see a change."

But if scientists ultimately prove Darwin wrong on a larger scale, "then we need to stop using his hypothesis as a basis for conservation decisions," Cardinale says. "We risk conserving things that are the least important, and losing things that are the most important. This does bring up the question: How do we prioritize?"

The scientists did not set out to disprove Darwin, but, in fact, to learn more about the genetic and ecological uniqueness of fresh-water green algae so they could provide conservationists with useful data for decision-making. "We went into it assuming Darwin to be right, and expecting to come up with some real numbers for conservationists," Cardinale says. "When we started coming up with numbers that showed he wasn't right, we were completely baffled."

The National Science Foundation is supporting the work with $2 million over five years, awarded in 2010.

Experiments with green algae

The researchers sequenced 60 species of algae most common in North America and can describe with a high certainty their evolutionary relationships. "We know which ones are ancient and have become genetically unique, and which are new and recently diverged," he says.

Their experiments involved taking closely related species and putting them into competition, and taking evolutionarily ancient distantly related species and similarly pitting them against each other.

They also sent graduate students into natural lakes to gather samples, including one lake with "the most spectacular group of green algae," as well as something else, prompting the nickname "Leech Lake."

When the students stood in the water to collect their samples, "the entire bottom of the lake would start moving toward them," Cardinale says. "They would congregate on their boots, and start crawling up their legs. The challenge was to get the samples before the leeches got into their waders."

Samples obtained, they put species that have different evolutionary histories into bottles and measured how strongly they competed for essential resources such as nitrogen, phosphorus and light.

"If Darwin had been right, the older, more genetically unique species should have unique niches, and should compete less strongly, while the ones closely related should be ecologically similar and compete much more strongly – but that's not what happened," Cardinale says. "We didn't see any evidence of that at all.” They found this to be so in field experiments, lab experiments and surveys in 1,200 lakes in North America.

"If Darwin was right, we should've seen species that are genetically different and ecologically unique, doing unique things and not competing with other species," he adds. "But we didn't."

Traits and the quality of competition

Certain traits determine whether a species is a successful competitor or a poor competitor, he says. "Evolution does not appear to predict which species have good traits and bad traits," he says. "We should be able to look at the Tree of Life, and evolution should make it clear who will win in competition and who will lose. But the traits that regulate competition can't be predicted from the Tree of Life."

The scientists have a few ideas of what may be going on, and why Darwin's hypothesis is incorrect, at least for this group of organisms.

"Organisms like algae can be plastic. Maybe they all have the same genes that do the same things and can turn them off and on at different times," he says. "Maybe they sometimes can flip a switch for nitrogen on or off, or all at the same time. If we are correct, and they are not diverging in the genes that control competition, maybe they are diverging in other genes."

Darwin "was obsessed with competition," Cardinale says. "He assumed the whole world was composed of species competing with each other, but we found that one-third of the species of algae we studied actually like each other. They don't grow as well unless you put them with another species. It may be that nature has a heck of a lot more mutualisms than we ever expected.

"Maybe species are co-evolving," he adds. "Maybe they are evolving together so they are more productive as a team than they are individually. We found that more than one-third of the time, that they like to be together. Maybe Darwin's presumption that the world may be dominated by competition is wrong."

Cardinale's broad research goal is to gain a better understanding of how human alteration of the environment affects the biotic diversity of communities and, in turn, the impact of this loss on fluxes of energy and matter required to sustain life. "I focus on this because I believe that global loss of biodiversity ranks among the most important and dramatic environmental problems in modern history," he says.

Editor's Note: This Behind the Scenes article was first provided to LiveScience in partnership with the National Science Foundation.

-- Marlene Cimons, National Science Foundation
Investigators
Todd Oakley
Xiaoxia Lin
Phillip Savage
Bradley Cardinale
Related Institutions/Organizations
University of Michigan Ann Arbor

EARLY VENOMOUS SNAKE FOSSILS FOUND IN AFRICA

FROM:  NATIONAL SCIENCE FOUNDATION 
Snakes Alive! NSF-funded researchers find oldest fossil evidence of modern African venomous snakes

Seasonal habitats may have given rise to active hunters earlier than previously reported

National Science Foundation (NSF)-funded researchers at Ohio University have found the oldest definitive fossil evidence of modern, venomous snakes in Africa. The newly discovered fossil was unearthed in the Rukwa Rift Basin of Tanzania. The research results were published in PLOS ONE.

The lead author, Jacob McCartney, and his coauthors note that these findings demonstrate that elapid snakes, such as cobras, kraits and sea snakes--were present in Africa as early as 25 million years ago.

Elapids belong to a larger group of snakes known as colubrids--active foragers that use a variety of methods, including venom to capture and kill prey.

The team was surprised to discover higher-than-expected concentrations of colubroid snakes, suggesting the local environment was more open and seasonally dry, thus more hospitable to these types of active hunting snakes that don't require cover to ambush prey like boas and pythons do.

They say it also points to a fundamental shift toward more rapid venom delivery mechanisms to exert very different pressures on the local fauna.

-- Dena Headlee, National Science Foundation

JET PROPULSION LABORATORY USES FUEL CELLS TO INVESTIGATE ORIGINS OF LIFE

FROM:  NASA 

How Did Life Arise? Fuel Cells May Have Answers

How life arose from the toxic and inhospitable environment of our planet billions of years ago remains a deep mystery. Researchers have simulated the conditions of an early Earth in test tubes, even fashioning some of life's basic ingredients. But how those ingredients assembled into living cells, and how life was first able to generate energy, remain unknown.

A new study led by Laurie Barge of NASA's Jet Propulsion Laboratory in Pasadena, Calif., demonstrates a unique way to study the origins of life: fuel cells.
Fuel cells are found in specialized cars, planes and NASA's human spacecraft, such as the now-retired space shuttle. The cells are similar to batteries in generating electricity and power, but they require fuel, such as hydrogen gas. In the new study, the fuel cells are not used for power, but for testing chemical reactions thought to have led to the development of life.

"Something about Earth led to life, and we think one important factor was that the planet provides electrical energy at the seafloor," said Barge. "This energy could have kick-started life -- and could have sustained life after it arose. Now, we have a way of testing different materials and environments that could have helped life arise not just on Earth, but possibly on Mars, Europa and other places in the solar system."

Barge is a member of the JPL Icy Worlds team of the NASA Astrobiology Institute, based at NASA's Ames Research Center in Moffett Field, Calif. The team's paper appears online March 13 in the journal Astrobiology.
One of the basic functions of life as we know it is the ability to store and use energy. In cells, this is a form of metabolism and involves the transfer of electrons from one molecule to another. The process is at work in our own bodies, giving us energy.
Fuel cells are similar to biological cells in that electrons are also transferred to and from molecules. In both cases, this results in electricity and power. In order for a fuel cell to work, it needs fuel, such as hydrogen gas, along with electrodes and catalysts, which help transfer the electrons. Electrons are transferred from an electron donor (such as hydrogen) to an electron acceptor (such as oxygen), resulting in current. In your cells, metal-containing enzymes -- your biological catalysts -- transfer electrons and generate energy for life.

In the team’s experiments, the fuel cell electrodes and catalysts are made of primitive geological material thought to have existed on early Earth. If this material can help transfer electrons, the researchers will observe an electrical current. By testing different types of materials, these fuel cell experiments allow the scientists to narrow in on the chemistry that might have taken place when life first arose on Earth.

"What we are proposing here is to simulate energetic processes, which could bridge the gap between the geological processes of the early Earth and the emergence of biological life on this planet," said Terry Kee from the University of Leeds, England, one of the co-authors of the research paper.

"We're going back in time to test specific minerals such as those containing iron and nickel, which would have been common on the early Earth and could have led to biological metabolism," said Barge.

The researchers also tested material from little lab-grown "chimneys," simulating the huge structures that grow from the hydrothermal vents that line ocean floors. These "chemical gardens" are possible locations for pre-life chemical reactions.
When the team used material from the lab-grown chimneys in the fuel cells, electrical currents were detected. Barge said that this is a preliminary test, showing that the hydrothermal chimneys formed on early Earth can transfer electrons – and therefore, may drive some of the first energetic reactions leading to metabolism.

The experiments also showed that the fuel cells can be used to test other materials from our ancient Earth. And if life did arise on other planets, those conditions can be tested, too.

"We can just swap in an ocean and minerals that might have existed on early Mars," said Barge. "Since fuel cells are modular -- meaning, you can easily replace pieces with other pieces -- we can use these techniques to investigate any planet’s potential to kick-start life."

At JPL, fuel cells are not only for the study of life, but are also being developed for long-term human space travel. Hydrogen fuel cells can produce water, which can be recycled and used as fuel again. Researchers are experimenting with these advanced regenerative fuel cells, which are highly efficient and offer long-lasting power.

Thomas I. Valdez, who is developing regenerative fuel cells at JPL, said, "I think it is great that we can transition techniques used to study reactions in fuel cells to areas such as astrobiology."

Other authors of the paper are: Ivria J. Doloboff, Chung-Kuang Lin, Richard D. Kidd and Isik Kanik of the JPL Icy Worlds team; Joshua M. P. Hampton of the University of Leeds School of Chemistry, Mohammed Ismail and Mohamed Pourkashanian at the University of Leeds Centre for Fluid Dynamics; John Zeytounian of the University of Southern California, Los Angeles; and Marc M. Baum and John A. Moss of the Oak Crest Institute of Science, Pasadena.
JPL is managed by the California Institute of Technology in Pasadena for NASA.

FRUIT SMELLING BATS

FROM:  NATIONAL SCIENCE FOUNDATION 
By dark of night, how do bats smell their way to fruit?
Scientists find distinctive patterns of olfactory receptors in fruit-eating bats
March 3, 2014

How do we smell? The answer lies in the 1,000 or so genes that encode what's known as olfactory receptors inside our noses.

This gene superfamily constitutes 3 to 6 percent of a mammal's genes.

But scientists don't completely understand what odors bind to which receptors, and how this complex process translates into interpreting a particular smell.

In fact, little is known about how olfactory receptors function in mammals, or how this large gene family has evolved in response to different evolutionary challenges.

Specialized gene pattern in fruit-eating bats

Now scientists have identified a distinctive olfactory receptor gene pattern in fruit-eating bats, as well as the particular olfactory receptor gene families important to their fruit diets.

The findings offer new insights that link olfactory receptors with the odors they bind.

The research highlights the importance, the biologists say, of exploring diversity in nature to understand genome functions and evolutionary history in mammals.

Evolutionary biologists Liliana Davalos of Stony Brook University, Emma Teeling of University College Dublin and colleagues report their results in a paper published in this month's' issue of the journal Molecular Biology and Evolution.

"This study provides new insights into the mechanisms that have allowed bats to diversify their diets so extensively," says Simon Malcomber, a program director in the National Science Foundation's Division of Environmental Biology, which funded the research.

This research was also supported by the Science Foundation Ireland and the Irish Research Council.

"We knew that animals that live in various ecological environments--whales, bats, cows--have evolved different suites of olfactory receptors," says Davalos. "That suggests that the ability to smell different odors is important for survival."

Since these lifestyles evolved so long ago, she says, it's difficult to tell what forces have shaped the repertoire of olfactory receptors.

Bats hold key to evolution of smell receptors

Has the evolution of other sensory systems, changes in diet, or the random accumulation of changes through time driven the evolution of olfaction in mammals?

"Bats offer a prime opportunity to answer this question," says Davalos.

"They've evolved new sensory systems such as echolocation, and various bat species eat very different foods, including insects, nectar, fruit, frogs, lizards and even blood."

Two large groups of bats branched out since diverging about 64 million years ago. These groups separately evolved specialized echolocation and a diet based on fruit.

The patterns have arisen twice, once among New World leaf-nosed bats that feed primarily on figs and another among Old World fruit bats. The bats feed on variety of fruits, including figs, guavas, bananas, mangoes and other tropical fruits.

Could their evolutionary patterns help explain their olfactory receptors?

Finding fruit by dark of night

After sequencing thousands of olfactory receptors from dozens of bat species and analyzing an evolutionary tree including all the species, the researchers found distinctive patterns of olfactory receptors among bats that specialize in eating fruit.

Although the olfactory receptors are similar, the distinctive repertoires have arisen in different ways in New World and Old World bats.

That suggests, Davalos says, that independent mechanisms have shaped this part of the bat genome in response to the challenge of finding fruit by dark of night.

FINDING ENGINEERING INSIGHTS FROM ANIMAL DRINKING STUDIES

FROM:  NATIONAL SCIENCE FOUNDATION 
Scientists apply biological behavior to human engineering

Study of animals' water drinking motions could lead to better water pumps and new insights into locomotion and propulsion

Have you ever watched your cat or dog drink water?

Their lapping motions, which differ from the way humans drink--and also differ in some respects from each other--are an evolutionary marvel of nature.

Cats and dogs, many other animals, have developed survival mechanisms over time that help them adapt to their environments, in this case, figuring out a way to get water into their mouths when the location of the water is low and the animals' location is high.

The way they do it provides important information for scientists trying to apply biological behavior to human engineering, especially in the field of fluid mechanics, which studies liquids and gases and the forces upon them.

"Nature has spanned billions of years finding the best designs for its many systems," says Sunghwan Jung, an assistant professor of engineering, science and mechanics at Virginia Polytechnic Institute and State University. "Human engineering can learn much from how nature does it."

Jung and his colleagues--Jake Socha, also an assistant professor of engineering, science and mechanics at Virginia Tech, and Pavlos Vlachos, a professor of mechanical engineering--all National Science Foundation (NSF)- funded scientists, have been studying the drinking behavior of both domestic animals.

Their findings could have significant applications in the development of novel coating/dipping systems for materials engineering, as well as in designing new types of pumps to transport water, with potential uses in the military, in industry and recreation.

The cat's method relies on its instinctive ability to calculate when gravitational forces overcome inertia, causing the water to fall. A cat curves the upper side of its tongue downward so that the tip lightly touches the surface of the water, then pulls it upward at a high speed, creating a column of water behind it. At the very moment that gravity starts to pull the column down, the cat closes its jaws over the jet of water and swallows it.

The dog, on the other hand, appears to scoop water into its mouth, using its highly curled tongue. The amount of water ingested depends on the lapping frequency, and the size of the air cavity created by its tongue.

Both animals create columns of water when they do this, but only the dog's tongue uses a scooping motion.

"Cats and dogs have a mouth structure very different from us," Jung says. "They have incomplete cheeks. Humans don't have a large mouth opening, but have a complete cheek. We drink water, rather than lap. But cats and dogs have incomplete cheeks, so they can't lower the pressure inside their mouths. If they did, they would just suck air. So they developed a lapping mechanism."

Their research could influence the future design of water pumps, Jung says. There are two main types used today, pressure-driven pumps and inertia-driven pumps. The former involves sucking water up through a tube, while the latter uses a moving part--a water wheel, for example--to move water from a low place to a high place.

The water drinking methods used by dogs and cats are examples of inertia-driven pumps. "Their tongues are the moving parts," Jung says. "There may be places where you cannot use a pressure driven pump. Perhaps we can design some bio-inspired pump by learning how cats and dogs drink water."

Jung and his colleagues are conducting their research with a grant from NSF's Physics of Living Systems program, which supports theoretical and experimental research exploring the most fundamental physical processes that living systems use to perform their functions in dynamic and diverse environments. The focus is on understanding basic physical principles that underlie biological function.

As part of their experiments, the team will create artificial three-dimensional tongues of both dogs and cats and plans to "actuate these artificial tongues in rotational motion, mimicking what cats and dogs do, to understand the fluid dynamics," Jung says. "We want to see how fluids move due to the tongues' motion, and how water is transported upward."

Along with water drinking, the scientists also are studying how some animals--lizards and frogs, for example--move effortlessly across a water surface or jump from it to capture insects for food. The idea is to gain new insights about locomotion and propulsion.

"Since there are no engineered systems that operate under conditions similar to these reptiles and amphibians, we have an opportunity to learn how nature effectively uses the interaction of these forces," Jung says.

In addition to faster dipping and coating processes, their findings also could produce "water-walking robots," he says.

"Nature is very smart," he adds. "In nature, animals both move around a lot and also drink fluids. Those two are everyday essential behaviors. Most animals have evolved to optimize these behaviors, and their methods can teach us quite a bit."

-- Marlene Cimons, National Science Foundation
Investigators
John Socha
Sunghwan Jung
Pavlos Vlachos
Related Institutions/Organizations
Virginia Polytechnic Institute and State University

NSF ARTICLE ON PHYSICS OF MOVEMENT FOR DESERT DWELLERS AND ROBOTS

FROM:  NATIONAL SCIENCE FOUNDATION 

Desert dwellers and 'bots reveal physics of movement
The Georgia-Tech based 'CRAB' lab investigates how organisms navigate tricky terrain

Physicist Daniel Goldman and his fellow researchers at the Georgia Institute of Technology shed light on a relatively unexplored subject--how organisms such as sea turtles and lizards move on (or within) sand.

If you've ever struggled to walk with even a modicum of grace on a soft, sandy beach, you may appreciate the question. The answers that Goldman's CRAB lab (Complex Rheology and Biomechanics Laboratory) uncovers--with the help of living animals and biologically inspired robots--deepen our understanding not only of animal survival, evolution and ecology, but also, potentially, the evolution of complex life forms on Earth. The lab's research also assists the design and engineering of robots that must traverse unstable, uneven terrain--those used in search and rescue operations at disaster sites, for example.

Goldman first investigated the properties of sand, which can act like a solid, fluid or even a gas, when he was a doctoral student of physics at University of Texas at Austin. Later, as a postdoc in the University of California-Berkeley lab of biologist Robert J. Full (a leader in the field of nature-inspired robots), he helped investigate locomotion on complex terrain--cockroaches' climbing of vertical surfaces, for example, or spiders running over surfaces with few footholds. A fellow researcher, Wyatt Korrf, was interested in movement on a different kind of complex terrain--granular, shifting media. Goldman became hooked, and the two men started working together.

"Some of the insights and tools we developed then were incredibly helpful in my early and current research, in particular, air fluidized beds as a way to control ground properties," Goldman says.

To a student or lover of critters, Goldman's job might seem like a dream. He has worked with a large variety of desert dwellers and other animals, including geckos, zebra-tailed lizards, sidewinders , ghost crabs, sandfish, wind scorpions, funnel weaver spiders and hatchling loggerhead sea turtles.

In the lab and in the field, he and his colleagues observe these animals as they creep, crawl, walk, run, slither and otherwise transport themselves over or in granular matter. The researchers pin down precise details--the flexible spines on a spider's legs that appear to facilitate movement over a wire mesh, for example, or the way a snake flattens itself when climbing a slope. Then they design robots with the physical elements and movement patterns they want to know more about. With these tests as well as computer simulations and analyses, the team can develop, challenge and refine hypotheses related to physics principles inspired by the animals' movements.

The CRAB lab's cast of robot characters to date includes a robot modeled after baby sea turtles, as well as a sandfish robot.

Flipperbot

Recently, the team studied newly hatched sea turtles hurrying across the beach to the sea--a treacherous journey many of us have seen in nature TV shows.

"The best robots people design and build can't out-compete a hatchling sea turtle whose life consists of swimming all the time and using these appendages on land only for half an hour, running from the nest. If a female makes it to adulthood she will use flippers again, of course, to lay eggs," Goldman said.

For this study, CRAB lab researcher Nicole Mazouchova and research technician Andrei Savu traveled with a mobile lab to Jekyll Island in Georgia. They video-recorded hatchlings' movements on the beach and in a portable test bed. Analyzing the videos back at the lab, they saw that on more packed sand, the baby turtles used their flippers as rigid struts and to pivot. On looser sand, however, the turtles dug in deeper and bent their wrists.

With the help of Flipperbot (you guessed it, a robot with flippers), a poppy-seed-filled test bed, plus theoretical modeling by mechanical engineer Paul Umbanhowar of Northwestern University (who also helped make the 'bot), the team confirmed that the turtles' wrist bending helped them avoid slipping and kept their bodies above the sand, minimizing friction and drag. The model revealed how digging in deeper to more sand provided greater efficacy, keeping the substrate from yielding underfoot.

"We found [the turtle] extremely sensitive to how deep it puts its flippers into the ground and that it did better when it bends its wrists," Goldman said.

They also found the turtles (and Flipperbot) were seriously hindered when trying to navigate sand that had already been disturbed by movement.

Flipperbot--whose movements are surprisingly graceful--is the first robot modeled on sea turtles and tested on granular materials. Its work may someday help engineers make more agile robots as well as advance our understanding of evolution on Earth--especially those first walkers to emerge from the sea.

"There is a lot of speculation about the mechanics which allowed early animals to walk on land," says Goldman. "They had hand-like fins or finlike feet and nobody knows in detail how they would have interacted with flowable substrates (like mud and sand)

"We have an eye on biological questions of existing organisms but also those who could have lived in the past. If you look at gazelles, cheetahs--these animals are incredibly agile over terrestrial ground, and they came from things that had no concept of terrestrial ground."

The Flipperbot findings may be useful in other ways as well, such as informing sea turtle conservation strategies.

Sandfish robot

In various studies, Goldman's team has uncovered patterns that can help the engineering of search and rescue robots designed to move over and into debris piles and wreckage. It confirmed, for example, something scientists long suspected--that the chiseled head of the sandfish--a lizard found in north Africa--helps it dive underground. Robot tests showed that the angular head shape not only reduces drag but also generates greater lift forces.

Using x-ray imaging to reveal how the sandfish moves under the surface, the researchers found that to escape predators the little lizard tucks its limbs close to its body and undulates through the sand--looking like a true swimmer. The sandfish uses a consistent wave pattern from head to tail that pushes its body against the sand and generates forward motion. This wave pattern optimizes speed and energy use.

In a more recent study involving a six-legged robot, the team used 3-D printing technology to make legs of different shapes and physical orientations, and learned that convex robot legs made in the shape of the letter "C" worked out best.

Developing 'terradynamics'

It may be tempting to regard the CRAB lab's unique robots as the end rather than the means of research. But the machines are first a way to develop and confirm hypotheses, Goldman says. The lab, which is funded in part by National Science Foundation's (NSF) Physics of Living Systems and Dynamical Systems programs, is steadily identifying basic principles that will significantly advance understanding of how objects move on or in granular media.

"The idea is to begin to develop a terradynamics--equivalent to aero- and hydrodynamics--which will allow us to predict mobility of devices in these complex environments," Goldman says.

The lab has had recent success in terradynamics, publishing a paper in Science that describes a new approach to predicting how small-legged robots move on sand or other flowing materials. The approach uses the forces (such as drag) applied to independent elements of the robot legs to get a measure of the net force on a moving robot (or animal).

"The lizard swimming in sand gives us a broad understanding behind all animals swimming in true fluids," Goldman says. "Analyzing sandfish turns out sufficiently simple we can use as a baseline to understand other swimmers."

What specific studies are up ahead for the busy Georgia Tech lab? In the near future, the team will test and refine theoretical models as they apply to legs and wheels thrusting into flowing material. They also will be conducting experiments to learn more about wet sand versus dry. And thirdly, they will be looking at the physics involved when teams of organisms, such as fire ants, move and dig within complex terrain.

GENES BY THE NUMBERS

Photo:  DNA.  Credit:  NIH/Wikimedia.

FROM:  NATIONAL SCIENCE FOUNDATION 

Genomic and computational tools provide window to distant past

Out of the estimated 23,000 or more genes in the human genome, about 100 of them will differ--they will be present or not--between any two individuals. Genes lost or gained over time result from evolution and adaptation, as species respond through the years to their environment and other influences.

The availability of genomic sequences now allows scientists to study the presence or absence of whole genes among individuals and between species, and the impact of such changes for evolution.

Some individuals, for example, have a sharper sense of smell than others because they have more copies of olfactory receptor genes, which allow them to detect a wider range of odors. Others, especially those who live in societies with starchy diets, have more copies of the gene responsible for producing amylase, an enzyme in saliva that breaks down starch.

"There have been lots of changes, and we want to know which ones might have been involved in human adaptation," says Matthew Hahn, an associate professor of biology and informatics at Indiana University at Bloomington. "The comparison of whole genomes has revealed large and frequent changes in the size of gene families. Comparative genomic analyses allow us to identify large-scale patterns of change in gene families, and to make inferences regarding the role of natural selection in gene gain and loss."

Using computer models and available genomic data, Hahn studies the differences in genes among humans and other species, and compares them, in order to better understand the timeline of genetic changes and adaptation throughout our history. By developing computational and statistical tools to analyze whole genomes, Hahn and his team are learning new things about the evolution of gene regulation and gene families, human genomic history, and the evolution of phenotypically important genes.

"We can't go back in time, but we can use current species to get a pretty good estimate of what the ancestors looked like, and to get some ideas of what changes occurred and the order of these changes," he says.

The scientists are examining all the genes in the genome, and focusing on differences among species, such as chimpanzees and other primates compared to humans. "There's a 6 percent difference between humans and chimps in the genes they have," he says. "In the end, after 6 million years of being separate, we don't have exactly the same set of genes as chimps. How and when did those differences occur?"

Hahn is conducting his research under a National Science Foundation (NSF) Faculty Early Career Development (CAREER) award, which he received in 2009 as part of NSF's American Recovery and Reinvestment Act funding. The award supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education, and research within the context of the mission of their organization. He is receiving about $1 million over five years.

The work could have wide-ranging applications in diagnosing and treating diseases, since many illnesses and conditions arise from genetic mutations, including the duplication or loss of important genes.

"There is a lot of interest in trying to associate these changes to human diseases," Hahn says. "There are diseases that are caused when you lose or even gain a gene, not just affecting smell or the ability to digest starch. A lot of the genes that differ in copy number are genes involved in our immune response, and these are obvious candidates for the genetic changes underlying differences in disease susceptibility among individuals. By understanding normal variation in gene copy-number, we hope to be able to better recognize changes that may be detrimental to human health."

The researchers often start by examining the differences in the number of copies of different genes among individual humans.

"The 1,000 Genomes Project (an international research effort, launched in 2008, to establish the most detailed catalogue of human genetic variation) has allowed us to study the full genetic complement of genes in a wide variety of human populations, from all of the inhabited continents," he says. "We find differences between individuals within populations and among populations, largely recapitulating the known relationships among humans.

"But we also find population-specific changes in genes that have allowed us to adapt to our surroundings," he adds. "These changes have involved both the adaptive gain and adaptive loss of genes, and are associated with important phenotypic differences among individuals."

To understand the differences shared among all humans, and that distinguish us from our ancestors, the researchers then compare the full complement of genes to those of other primates, including chimpanzees, orangutans, macaques and marmosets.

"These comparisons, and similar ones to other new genomes that are being sequenced all the time, allow us to make strong inferences about what our common ancestral genome looked like, and, therefore, the changes that have occurred along the human lineage," he says.

Such genetic changes are highly likely to have been involved in human-specific adaptations, for example, humans' increased cranium size, according to Hahn.

"Having these genomic and computational tools gives us a window into the distant past that we otherwise would not have had," he says.

-- Marlene Cimons, National Science Foundation
Investigators

WHY ARE DISEASES NASTY TO THEIR HOSTS?

House Finch.  Credit:  Wikimedia.

FROM: NATIONAL SCIENCE FOUNDATION
Evolution in the Blink of an Eye
A disease in songbirds has rapidly evolved to become more harmful to its host at least twice in two decades, scientists report.

The research offers a model to help understand how diseases that threaten humans may change in virulence as they become more prevalent in a host population.

"Everybody who's had the flu has probably wondered at some point: 'Why do I feel so bad?'" said Dana Hawley of Virginia Polytechnic Institute, lead author of a paper on the results published today in the journal PLOS Biology.

"That's what we're studying: Why do pathogens cause harm to the hosts they depend upon? And, why are some life-threatening, while others only give you the sniffles?"

Disease virulence is something of a paradox.

"The jumping of a pathogen to a new host, such as bird flu jumping to humans, is just the first step of disease emergence," said Sam Scheiner, National Science Foundation (NSF) program director for the joint NSF‒National Institutes of Health Ecology and Evolution of Infectious Diseases Program, which funded the research.

"The subsequent evolution of that pathogen in its new host can be critical to determining further [pathogen] spread," Scheiner said.

"This study is the first to confirm predictions that pathogens may evolve to become more deadly. The results are important for planning responses to events such as the bird flu outbreak in China."

To spread, viruses and bacteria must reproduce in great numbers. But as their numbers increase inside a host's body, the host gets more and more ill.

So a highly virulent disease runs the risk of killing or debilitating its hosts before the hosts can transmit the bug along. But sometimes pathogens find the right balance through evolution. The new study shows that can happen in just a few years.

Hawley and co-authors studied house finch eye disease, a form of conjunctivitis, or pinkeye, caused by the bacteria Mycoplasma gallisepticum.

It first appeared around Washington, D.C., in the 1990s. The house finch is native to the Southwest but has spread to towns and backyards across North America.

The bacteria are not harmful to humans, which makes them a good model for studying the evolution of dangerous diseases such as SARS, Ebola and avian flu.

"There's an expectation that a very virulent disease will become milder over time, to improve its ability to spread," said André Dhondt, director of bird population studies at Cornell University. "Otherwise, it just kills the host and that's the end of it for the organism.

"House finch eye disease gave us an opportunity to test this--and we were surprised to see it actually become worse rather than milder."

The researchers used frozen bacterial samples taken from sick birds in California and along the Eastern Seaboard on five dates between 1994 and 2010, as the pathogen was evolving and spreading.

The samples came from an archive maintained by co-author David Ley of North Carolina State University, who first isolated and identified the causative organism.

The team experimentally infected wild-caught, house finches, then measured how sick the birds got with each sample. The researchers kept the birds in cages as they fell ill then recovered (none of the birds died from the disease).

Contrary to expectations, the biologists found that in both regions--California and the Eastern Seaboard--the disease had evolved to become more virulent over time.

Birds exposed to later disease strains developed more swollen eyes that took longer to heal.

A less-virulent strain spread westward across the continent. Once established in California, however, the bacteria again began evolving higher virulence.

In evolutionary terms, some strains of the bacteria were better adapted to spreading across the continent, while others were more suited to becoming established in a more localized area.

"For the disease to disperse westward, a sick bird has to fly farther, and survive for longer, to pass on the infection," Hawley said. "That will select for strains that make the birds less ill.

"But when it gets established in a new location, there are lots of other potential hosts, especially around bird feeders. It can evolve toward a nastier illness because it's getting transmitted more quickly."

House finch eye disease was first observed in 1994 when birdwatchers reported birds with weepy, inflamed eyes as part of Project Feederwatch at Cornell University.

Though the disease does not kill birds directly, it weakens them and makes them easy targets for predators.

The disease quickly spread south along the East Coast, then north and west across the Great Plains and down the West Coast. By 1998 the house finch population in the eastern United States had dropped by half--a loss of an estimated 40 million birds.

Birdwatchers can do their part to help house finches and other backyard birds by washing their feeders in a 10 percent bleach solution twice a month.

Along with Hawley, Dhondt and Ley, the paper's authors include Erik Osnas and Andrew Dobson of Princeton University, and Wesley Hochachka of the Cornell Lab of Ornithology.

-NSF-

SCIENTISTS FIND EARLY MONKEY-APE SPLIT

Olive Baboon.  Credit:  Wikimedia.

FROM: NATIONAL SCIENCE FOUNDATION
Scientists Discover Oldest Evidence of Split Between Old World Monkeys and Apes
Two fossil discoveries from the East African Rift reveal new information about the evolution of primates, according to a paper published this week in the journal Nature.

Findings by scientists at Ohio University's (OU) Heritage College of Osteopathic Medicine and colleagues document the oldest fossils of two major groups of primates: the group that today includes apes and humans (hominoids) and the group that includes Old World monkeys such as baboons and macaques (cercopithecoids).

The research, funded in part by the National Science Foundation (NSF), underscores the integration of paleontological and geological approaches that are essential for deciphering complex relationships in vertebrate evolutionary history, the scientists said.

Geological analyses of the study site indicate that the finds are 25 million years old, significantly older than fossils previously documented for either of the two groups.

Both fossil discoveries uncovered primate species newly recognized by scientists. The fossils were collected from a single site in the Rukwa Rift Basin of Tanzania.

Rukwapithecus fleaglei is an early hominoid represented by a fossil mandible in which several teeth were preserved. Nsungwepithecus gunnelli is an early cercopithecoid represented by a tooth and jaw fragment.

The primates lived during the Oligocene epoch, which lasted from 34 to 23 million years ago. The research documents that the two lineages were already evolving separately during this geologic period.

"The late Oligocene is among the least sampled intervals in primate evolutionary history, and the Rukwa field area provides a first glimpse of the animals that were alive at that time from Africa south of the equator," said Nancy Stevens, Ohio University paleontologist and first author of the paper.

Co-authors are Patrick O'Connor, Cornelia Krause and Eric Gorscak of Ohio University; Erik Seiffert of SUNY Stony Brook University; Eric Roberts of James Cook University in Australia; Mark Schmitz of Boise State University; Sifa Ngasala of Michigan State University; Tobin Hieronymus of Northeast Ohio Medical University and Joseph Temu of the Tanzania Antiquities Unit.

Documenting the early evolutionary history of these groups has been elusive, as there are few fossil-bearing deposits of the appropriate age, Stevens said.

"Finding monkey and ape fossils of this age in Africa has been extremely difficult, but to find both branches in a well-dated fossil layer this old is extraordinary," said Paul Filmer, program director in NSF's Division of Earth Sciences.

"These 'oldest-yet' fossils reinforce that the Old World monkey and ape branches were already separate 25 million years ago."

Using an approach that dated multiple minerals in the rocks, geologists could determine a precise age for the specimens.

"The rift setting provides an advantage in that it preserves datable materials together with these important primate fossils," said Roberts.

Prior to these finds, the oldest fossil representatives of the hominoid and cercopithecoid lineages were recorded from the early Miocene, at sites dating millions of years younger.

"The Nsungwe Formation of Tanzania is a unique site, both geographically and chronologically, with excellent potential to yield important fossils from a vitally important time period and biogeographic area of Africa," said Carolyn Ehardt, NSF program director for biological anthropology.

"To have described two highly distinctive and completely new primates, one designated the oldest known fossil 'ape' and the other the oldest 'stem' member of the Old World monkey clade, is remarkable."

The new discoveries are particularly important for helping reconcile a long-standing disagreement between divergence time estimates derived from analyses of DNA sequences from living primates versus those suggested by the primate fossil record, Stevens said.

Studies of clock-like mutations in primate DNA have indicated that the split between apes and Old World monkeys occurred between 30 million and 25 million years ago.

"Fossils from the Rukwa Rift Basin in southwestern Tanzania provide the first real test of the hypothesis that these groups diverged so early, by revealing a novel glimpse into this late Oligocene terrestrial ecosystem," Stevens said.

The new fossils are the first primate discoveries from this precise location in the Rukwa deposits, and represent two of only a handful of known primate species from the entire late Oligocene, globally.

The scientists scanned the specimens in OU's MicroCT scanner, allowing them to create detailed three-dimensional reconstructions of the ancient specimens. The reconstructions were used for comparisons with other fossils.

"This is another great example of how modern imaging and computational approaches allow us to address more refined questions about vertebrate evolutionary history," said O'Connor.

In addition to unveiling these newly discovered primates, the Rukwa field sites have produced several other fossil vertebrate and invertebrate species new to science.

The late Oligocene interval is interesting because it provides a final snapshot of the unique species inhabiting Africa prior to the large-scale faunal exchange with Eurasia that occurred later in the Cenozoic Era, Stevens said.

A key aspect of the Rukwa Rift Basin project, she said, is the interdisciplinary nature of the research team, with paleontologists and geologists working together to reconstruct vertebrate evolutionary history in the context of the developing East African Rift System.

"Since its inception, the project has employed a multi-faceted approach to addressing a series of large-scale biological and geological questions centered on the East African Rift System in Tanzania," O'Connor said.

The research was also funded by the Leakey Foundation and the National Geographic Society.

-NSF-

NSF AND THE TREE OF LIFE BRANCHES AND EVOLUTION

FROM:  NATIONAL SCIENCE FOUNDATION
June 4, 2012
A new initiative aims to build a comprehensive tree of life that brings together everything scientists know about how all species are related, from the tiniest bacteria to the tallest tree. Researchers are working to provide the infrastructure and computational tools to enable automatic updating of the tree of life, as well as develop the analytical and visualization tools to study it.

Scientists have been building evolutionary trees for more than 150 years, since Charles Darwin drew the first sketches in his notebook.

Darwin's theory of evolution explained that millions of species are related and gave biologists and paleontologists the enormous challenge of discovering the branching pattern of the tree of life.

But despite significant progress in fleshing out the major branches of the tree of life, today there is still no central place where researchers can go to visualize and analyze the entire tree.

Now, thanks to grants totaling $13 million from the National Science Foundation's (NSF) Assembling, Visualizing, and Analyzing the Tree of Life (AVAToL) program, three teams of scientists plan to make that a reality.

"The AVAToL awards are an exciting new direction for an area that's a foundation of much of biology," says Alan Townsend, director of NSF's Division of Environmental Biology. "That's critical to understanding a changing relationship between human society and Earth's biodiversity."

Figuring out how the millions of species on Earth are related to one another isn't just important for pinpointing an antelope's closest kin, or determining if tuna are more closely related to starfish or hagfish.

Information about evolutionary relationships is fundamental to comparative biology research. It helps scientists identify promising new medicines; develop hardier, higher-yielding crops; and fight infectious diseases such as HIV, anthrax and influenza.
If evolutionary trees are so widely used, why has assembling them across all life been so hard to achieve?

It's not for lack of research, or data. Advances in DNA sequencing and evolutionary analysis, discovery of pivotal early fossils, and novel methods and tools have enabled thousands of new evolutionary trees to be published in scientific journals each year.

However, most of these focus on specific, disconnected branches of the tree of life.
Part of the difficulty lies in the sheer enormity of the task. The largest evolutionary trees to date contain roughly 100,000 groups of organisms.

Assembling the branches for all species of animals, plants, fungi and microbes--and the countless more still being named or discovered--will require new computational tools for analyzing large data sets, for combining diverse kinds of data, and for connecting vast numbers of published trees into a synthetic whole.

Another difficulty lies in how scientists typically disseminate their results. A tiny fraction of all evolutionary trees have been published.  Researchers estimate a mere four percent end up in a database in a digital form.

Most of the knowledge is locked up in figures in static journal articles in file formats that may be difficult for other researchers to download, reanalyze or merge with new information.

AVAToL aims to change that.
What makes this program different from previous efforts, scientists say, is its scope: its focus on creating an open, dynamic, evolutionary framework that can be continually refined as new biodiversity data is collected, and its development of computational and visualization tools to scale up tree-based evolutionary analyses.

Researchers will be able to go online and compare their trees to others that have already been published, or download trees for further study.

They'll also be able to expand the tree, filling in the missing branches and placing newly named or discovered species among their relatives.

The goal is to incorporate new trees automatically, so the complete tree can be continuously updated.

In addition to the creation of an updatable tree of life, AVAToL scientists will create new tools for the kinds of research that rely on evolutionary trees and for the collection and analysis of important evolutionary data, including from fossils critical to the placement of many branches in the tree of life.

The three NSF-funded AVAToL projects are:
Automated and Community-Driven Synthesis of the Tree of Life
Principal Investigator: Karen Cranston, Duke University and the National Evolutionary Synthesis Center
This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientists.  Assembly of the tree will incorporate previously published results and efforts to develop, test and improve methods of data synthesis. This initial tree of life, called the Open Tree of Life, will not be static. Scientists will develop tools for researchers to update and revise the tree as new data come in.

Arbor: Comparative Analysis Workflows for the Tree of Life
Principal Investigator: Luke Harmon, University of Idaho
Scientists deal with daunting volumes of data.  One of the most basic challenges facing researchers is how to organize that information into a usable format that can inspire new scientific insights. This project team is working to develop a way to visually portray evolutionary data so scientists can see, at a glance, how organisms are related. The team will create software tools that will enable researchers to visualize and analyze data across the tree of life, enabling research in all areas of comparative biology at multiple evolutionary, space and time scales. The results have the potential to transform the way biologists test evolutionary and ecological hypotheses, enabling new research in fields from medicine to public health, from agriculture to ecology to genetics.

Next Generation Phenomics for the Tree of Life
Principal Investigator: Maureen O'Leary, SUNY-Stony Brook
This team of biologists, computer scientists and paleontologists will extend and adapt methods from computer vision, machine learning and natural language processing to enable rapid and automated study of species' phenotypes on a vast scale across the tree of life. The team's goal is to develop large phenomic datasets using new methods, and to provide the scientific community and the public with tools for future such work. Phenomics is an area of biology that measures the physical and biochemical traits of organisms as they change in response to genetic mutations and environmental influences.

Enormous phenomic datasets, many with images, will foster public interest in biodiversity and the fossil record. Phenotypic data allow scientists to reconstruct the evolutionary history of fossil species, in turn crucial for an understanding of the history of life. This project will leverage recent advances in image analysis and natural language processing to develop novel approaches to rapidly advance the collection and analysis of phenotypic data for the tree of life.

NEW FROG SPECIES FOUND IN NEW YORK CITY

The following excerpt is from the National Science Foundation website:
March 14, 2012
In the wilds of New York City--or as wild as you can get that close to skyscrapers--scientists have found a new leopard frog species.
For years, biologists mistook it for a more widespread variety of leopard frog.
While biologists regularly discover new species in remote rainforests, finding this one in ponds and marshes--sometimes within view of the Statue of Liberty--is a big surprise, said scientists from the University of California, Los Angeles; Rutgers University; the University of California, Davis and the University of Alabama.
"For a new species to go unrecognized in this area is amazing," said UCLA biologist Brad Shaffer, formerly at UC Davis.

Shaffer's research is funded by the National Science Foundation's (NSF) Division of Environmental Biology.

In recently published results in the journal Molecular Phylogenetics and Evolution, Shaffer and other scientists used DNA data to compare the new frog to all other leopard frog species in the region.

"Many amphibians are secretive and very hard to find, but these frogs are pretty obvious animals," said Shaffer.

"This shows that even in the largest city in the U.S., there are still new and important species waiting to be discovered."

The researchers determined the frog is an entirely new species. The unnamed frog joins a crowd of more than a dozen distinct leopard frog species.
The newly identified wetland species likely once lived on Manhattan. It's now only known from a few nearby locations: Yankee Stadium in the Bronx is the center of its current range.

Lead paper author Cathy Newman, now of Louisiana State University, was working with Leslie Rissler, a biologist at the University of Alabama, on an unrelated study of the southern leopard frog species when she first contacted scientist Jeremy Feinberg at Rutgers University in New Jersey.

Feinberg asked if she could help him investigate some "unusual frogs" whose weird-sounding calls were different from those of other leopard frogs.
"There are northern and southern leopard frogs in that general area, so I was expecting to find one of those that for some reason had atypical behaviors or that were hybrids of both," Newman said.

"I was really surprised and excited once I started getting data back strongly suggesting it was a new species. It's fascinating in such a heavily urbanized area."
Feinberg suspected that the leopard-frog look-alike with the peculiar croak was a new creature hiding in plain sight.

Instead of the "long snore" or "rapid chuckle" he heard from other leopard frogs, this frog had a short, repetitive croak.

As far back as the late 1800s, scientists have speculated about these "odd" frogs.
"When I first heard these frogs calling, it was so different, I knew something was very off," Feinberg said.

"It's what we call a cryptic species: one species hidden within another because we can't tell them apart on sight. Thanks to molecular genetics, people are picking out species that would otherwise be ignored."
The results were clear-cut: the DNA was distinct, no matter how much the frogs looked alike.

"If I had one of these three leopard frogs in my hand, unless I knew what area it was from, I wouldn't know which one I was holding because they all look so similar," Newman said. "But our results showed that this lineage is very clearly genetically distinct."
Mitochondrial DNA represents only a fraction of the amphibian's total DNA, so Newman knew she needed to do broader nuclear DNA tests to see the whole picture and confirm the frog as a new species. She performed the work at UC Davis.

Habitat destruction, disease, invasive species, pesticides and parasites have all taken a heavy toll on frogs and other amphibians worldwide, said Rissler, currently on leave from the University of Alabama and a program director in NSF's Division of Environmental Biology.

Amphibians, she said, are great indicators of problems in our environment--problems that could potentially impact our health.

"They are a good model to examine environmental threats or degradation because part of their life history is spent in the water and part on land," Rissler said. "They're subject to all the problems that happen to these environments."
The findings show that even in densely-populated, well-studied areas, there are still new discoveries to be made, said Shaffer.  And that the newly identified frogs appear to have a startlingly limited range.

"One of the real mantras of conservation biology is that you cannot protect what you don't recognize," Shaffer said. "If you don't know that two species are different, you can't know whether either needs protection."

The newly identified frogs have so far been found in scattered populations in northern New Jersey, southeastern mainland New York and on Staten Island.
Although they may extend into parts of Connecticut and northeastern Pennsylvania, evidence suggests they were once common on Long Island and other nearby regions.
They went extinct there in just the last few decades. "This raises conservation concerns that must be addressed," said ecologist Joanna Burger of Rutgers University.
"These frogs were probably once more widely distributed," Rissler said. "They are still able to hang on. They're still here, and that's amazing."

Until scientists settle on a name for the frog, they refer to it as "Rana sp. nov.," meaning "new frog species."