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-
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Cheryl Dybas, NSF,

GETTING INTO THE GUTS OF BEES

FROM:  NATIONAL SCIENCE FOUNDATION 

Bees from the inside out

Researchers work to save bees by studying the diversity of microbes that live in their guts and the impacts on these microbes of exposure to antibiotics

It is 1,825 miles from New Haven, Conn., to Austin, Tex., which typically means 30 hours of driving and three nights in motels, not an easy trip for anyone. But for researchers moving from Yale University to a new lab at the University of Texas last August, it proved especially challenging. They made the journey in a minivan with a pet cat and 100,000 bees.

"That was probably the most heroic event in our beekeeping saga to date," says evolutionary biologist Nancy Moran, a professor at the University of Texas at Austin, who studies symbiosis, particularly among multi-cellular hosts and microbes. "We didn't want to be without bees upon arrival in Texas, and it wasn't a good time of year to start new colonies."

The bees--chauffeured by graduate student Waldan Kwong and postdoctoral fellow Gordon Bennett--traveled in boxes nailed shut, with duct tape over the cracks between the boxes, so they couldn't fly around in the minivan, and wire mesh over the front, so they could cool themselves, but not escape. They also received wet sponges at regular intervals to keep them hydrated.

"They [Kwong and Bennett] just turned up the air conditioning all the way, and wore sweaters," Moran says. "Bees are less excitable when it's cooler. At night, they waited to park the minivan until after dark, and then opened the windows so the bees didn't overheat in the closed space. It seemed unlikely that anyone would try to steal something from a van full of bees."

The bees arrived in Austin with no problems, and now live on top of a building on campus, "where their main forage might be drops of soda on discarded cans around campus," says Moran, who for many years studied the maternally transmitted symbionts of aphids and other sap-feeding insects, but has expanded in recent years to bees. Symbionts are organisms that co-exist and depend on each other for survival.

"I've worked for many years on genomic evolution in bacteria, but also love insects and insect biology," she says. "So this is a system that has both."

Understanding the gut microbes in bees

Today, the broad aim of her research is to understand the diversity and function of the gut microbiota in honeybees and bumblebees, emphasizing genomic approaches, not unlike the current research interest in the human microbiome.

"It has a number of parallels with the gut microbiota of humans and other mammals, because it is a long co-evolved and specialized bacterial community, and because it impacts the health of the hosts," she says.

The gut microbiota is another dimension of animal biodiversity, particularly when the animals have distinctive and co-evolved bacterial species in their guts, Moran says.

"In insects, this doesn't always appear to be true--many seem to have a selected set of bacteria taken up from the environment, and the bacteria can live in a range of habitats outside the gut," she says. "But in honeybees and bumblebees, the gut is dominated by a small number of tightly related groups.

"Why? The primary reason seems to be that sociality--social interactions--gives a route for dependable transmission between individuals. Interactions within the bee colonies are the basis for transfer of the symbionts to newly emerged adult bees. This is where the system parallels that of humans and other mammals, all of which are social at least to the extent of having extended maternal care. Gut symbionts of mammals are specialized and transmitted via these social interactions."

Microbial gut symbionts are essential for the life of most animal species, but their diversity and functions in hosts and their responses to ecological disturbance are poorly understood, she says. Apis mellifera, the honeybee, has a distinctive set of about eight symbiotic bacterial species, some of which occur in other Apis species and in the related genus Bombus--bumblebees.

Bees, of course, are critically important ecologically and economically, particularly in agriculture, where honeybees pollinate an estimated $15 billion worth of agricultural products in the United States, including more than 130 fruits, according to the U.S. Department of Agriculture. In recent years, however, there has been increasing concern over rampant bee colony losses, dubbed "Colony Collapse Disorder," and the overall health of bees in general. [Colony Collapse Disorder ]

While Moran and her colleagues are primarily trying to gain a basic understanding of biodiversity and function in the bee gut microbial community system, "some bumblebees are becoming rare and have shrunken ranges. Are we also losing diversity of their gut microbiota, and will this be a factor in trying to conserve these species?" she asks. "Are problems with gut microbiota part of the problem of honeybee health, or could microbiota be preserved in a way that helps bees thrive?

"A big part of the problem with bee health is undoubtedly the decreasing availability of diverse floral resources, and possibly nesting sites in the case of bumblebees," she adds. "But exposure to toxins and to diseases also play a part, based on numerous studies. Gut microbes very plausibly play a role in host resistance to these things, and also in improving nutrition. So we hope that we find something useful for bees."

The National Science Foundation (NSF) is funding her work with $2,006,416 over five years, awarded in 2010.

Antibiotic resistance

Moran's research has revealed that bacteria in the guts of honeybees are highly resistant to the preventive antibiotic tetracycline--probably the result of decades of exposure to it because of its use by beekeepers to prevent bacterial diseases. Moran's team identified eight different tetracycline resistance genes among U.S. honeybees that were exposed to the antibiotic, but the genes were largely absent in bees from countries where such antibiotic use is banned.

"In the bee system, even though transmission is mostly within colonies, the symbionts are much more likely to undergo horizontal transmission," she says, meaning transmission among members of the same species that are not parent and child. "This has massive consequences for patterns of genome evolution in the symbionts. Because they are undergoing recombination, and have larger genetic population sizes, they retain normal genome sizes, and have far more dynamic genomes.

"The antibiotic resistance study was an early hint about the dynamic nature of these genomes," she adds. "It turns out that in the United States, antibiotics have been used widely in beekeeping since the 1950s, mostly tetracycline. And the gut microbiota of U.S. honeybees is a treasure trove of tetracycline resistance genes that have been horizontally transferred from other bacteria. Now we are finding that strains of the bee gut microbiota show a large set of 'accessory' genes and functions. A given strain can have hundreds of genes that are not present in another strain of the same species, and that affect functions such as sugar metabolism, or ability to break down components of pollen cell walls."

Until recently, none of these bacterial species had been cultured in the lab, "but now all of them can be," she says, crediting the work of Kwong, and Philipp Engel, a postdoctoral fellow now in Switzerland.

"In fact, we have given official names to the bacterial species that are our main focus: Snodgrassella alvi, Gilliamella apical, and Frischella perrara," named after three biologists who made major contributions in honeybee biology, Robert Snodgrass, Martha Gilliam and Karl von Frisch.

"These three live together in one part of the honeybee ileum (part of the digestive tract), and two of them also live in bumblebees," she says. "But we are finding that there are diverse strains within each species, and that different bee species and different colonies within a species seem to have different strains of symbionts."

Another postdoctoral fellow in her lab, Hauke Koch, was the first to find that gut symbionts of bumblebees protect against protozoan parasites, "so we are trying to see if the same is true in honeybees, and also to extend the findings in bumblebees," she says.

She and her collaborators also conducted a survey of gut symbionts in three bumblebee species to determine whether environmental factors--especially agricultural management or geographic location--affected symbiont communities.

"And it turns out that different bumblebee species all have some of the same symbionts, particularlySnodgrassella and Gilliamella, but one bumble bee species seemed to sometimes miss being inoculated," she says. "The 'right' symbionts are simply absent from some individuals. This is very different from honeybees, where every worker bee has the main symbionts, and we think it might relate to their different life cycles and social lives."

This work provides a baseline for understanding how the gut microbiota of honeybees and bumblebees varies among colonies, and how this variation might affect colony health.

"By establishing methods for culturing and type strains that can be studied by different laboratories, we can start to untangle the mechanistic basis for colonizing hosts," she says. "And we can start to understand how the normal microbiota interacts with disease agents that infect bees."

The temperament of bees

When it's time to start new colonies, Moran's lab orders bees from different places around the country, but favors northern California bees because of their "very sweet personalities," meaning they stay calm when the hive is opened, and don't line up in an aggressive manner, preparing to attack, she says. "One can approach the hives without alarming them," she says. "Feisty bees are touchy and prone to attack when someone just gets close to the hive. We had some Texas bees, but they were a bit feisty, perhaps they did not like being plopped down in New England," before she moved to Austin.

Lab technician Kim Hammond cares for the bees and has developed into a master beekeeper, Moran says. "In fact, maybe she's too good –we can't recover the disease organisms that most beekeepers complain about, even when we would like to sample them in our colonies. She keeps the bee colonies very healthy, and we sometimes cannot detect pathogens that are generally common.

"The main ones are Nosema species, which are eukaryotic pathogens related to fungi, and RNA viruses, such as `Deformed Wing Virus,"' she adds. "In some of our experiments we want to infect bees with pathogens, to see if the microbiota protects against pathogens. In those cases we have to go to other beekeepers to try and find the disease organisms."

New to bee research and wanting to learn the basics of beekeeping, Moran actually kept several colonies in her own yard for several years.

"But I have to admit I am afraid of stings," she says. "Yes I did get stung a few times. In working directly with the colonies, it is usual to occasionally be stung. Of course we wear bee suits. In the lab, we mostly work with young worker bees, which do not sting much, plus we have them contained. If a student researcher is worried about stings, we just have them work on aspects that have no risk. But we do keep an epinephrine kit around for possible cases of a sting of someone allergic who might not realize the risk. So far we haven't had anything at all serious."

And, of course, there is at least one sweet fringe benefit of the research. "We get honey, which is very helpful as gifts to make people worry less about being stung," she says.

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

-- Marlene Cimons
Investigators
Nancy Moran
Related Institutions/Organizations
University of Texas at Austin

NSF REPORTS ON ENDANGERED LEMURS' GENOME SEQUENCING

Photo:  Aye-Aye Lemur.  Credit:  Wikimedia Commons.

FROM: NATIONAL SCIENCE FOUNDATION
Endangered Lemurs' Genomes Sequenced
 For the first time, the complete genomes of three populations of aye-ayes--a type of lemur--have been sequenced and analyzed.

The results of the genome-sequence analyses are published this week in the journal Proceedings of the National Academy of Sciences (PNAS).

The research was led by George Perry, an anthropologist and biologist at Penn State University; Webb Miller, a biologist and computer scientist and engineer at Penn State; and Edward Louis of the Henry Doorly Zoo and Aquarium in Omaha, Neb., and Director of the Madagascar Biodiversity Partnership.

The aye-aye--a lemur that is found only on the island of Madagascar in the Indian Ocean--was recently re-classified as "Endangered" by the International Union for the Conservation of Nature.

"The biodiversity of Madagascar is like nowhere else on Earth, with all 88 described lemur species restricted to the island, but with less than 3 percent of its original forest remaining," said Simon Malcomber, program director in the National Science Foundation's (NSF) Division of Environmental Biology, which in part funded the research.

"It's essential to preserve as much of this unique diversity as possible," Malcomber said.

Added Perry, "The aye-aye is one of the world's most unusual and fascinating animals."

"Aye-ayes use continuously growing incisors to gnaw through the bark of dead trees. They have long, thin, flexible middle fingers to extract insect larvae, filling the ecological niche of a woodpecker.

"Aye-ayes are nocturnal, solitary and have very low population densities, making them difficult to study and sample in the wild."

Perry and other scientists are concerned about the long-term viability of aye-ayes as a species, given the loss and fragmentation of forest habitats in Madagascar.

"Aye-aye population densities are very low, and individual aye-ayes have huge home-range requirements," said Perry.

"As forest patches become smaller, there's a risk that there won't be sufficient numbers of aye-ayes in an area to maintain a population over multiple generations.

"We were looking to make use of new genomic-sequencing technologies to characterize patterns of genetic diversity among some of the surviving aye-aye populations, with an eye toward the prioritization of conservation efforts."

The researchers located aye-ayes and collected DNA samples from the animals in three regions of Madagascar: the northern, eastern and western regions.

To discover the extent of the genetic diversity in present-day aye-ayes, the scientists generated the complete genome sequences of 12 individual aye-ayes.

They then analyzed and compared the genomes of the three populations.

They found that, while Eastern and Western aye-ayes are somewhat genetically distinct, aye-ayes in the northern part of the island and those in the east show a more significant genetic distance, suggesting an extensive period during which interbreeding has not occurred between the populations in these regions.

"Our next step was to compare aye-aye genetic diversity to present-day human genetic diversity," said Miller.

"This analysis can help us gauge how long the aye-aye populations have been geographically separated and unable to interbreed."

To make the comparison, the team gathered 12 complete human DNA sequences--the same number as the individually generated aye-aye sequences--from publicly available databases for three distinct human populations: African agriculturalists, individuals of European descent, and Southeast Asian individuals.

Using Galaxy--an open-source, web-based computer platform designed at Penn State for data-intensive biomedical and genetic research--the scientists developed software to compare the two species' genetic distances.

The researchers found that present-day African and European human populations have a smaller amount of genetic distance than that between northern and eastern aye-aye populations, suggesting that the aye-aye populations were separated for a lengthy period of time by geographic barriers.

"We believe that northern aye-ayes have not been able to interbreed with other populations for some time," said Miller. "Although they are separated by a distance of only about 160 miles, high plateaus and major rivers may have made intermingling relatively infrequent."

The results suggest that the separation of the aye-aye populations stretches back longer than 2,300 years, when human settlers first arrived on Madagascar and started burning the aye-ayes' forest habitat and hunting lemurs.

"This work highlights an important region of aye-aye biodiversity in northern Madagascar, and this unique biodiversity is not preserved anywhere except in the wild," said Louis.

"There is tremendous historical loss of habitat in northern Madagascar that's continuing at an unsustainable rate today."

In future research, the scientists would like to sequence the genomes of other lemur species--more than 70 percent of which are considered endangered or critically endangered--as well as aye-ayes from the southern reaches of Madagascar.

In addition to Perry, Miller and Louis, scientists who contributed to the research include Stephan Schuster, Aakrosh Ratan, Oscar Bedoya-Reina and Richard Burhans of Penn State; Runhua Lei of the Henry Doorly Zoo and Aquarium and Steig Johnson of the University of Calgary in Alberta, Canada.

Funding for aye-aye sample collection was provided by Conservation International, the Primate Action Fund and the Margot Marsh Biodiversity Foundation, along with logistical support from the Ahmanson Foundation and the Theodore F. and Claire M. Hubbard Family Foundation.

Additional support came from the National Institutes of Health, the Pennsylvania Department of Health and the College of the Liberal Arts at Penn State University.

-NSF-