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December 2014
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Interstellar mystery solved by supercomputer simulations

An interstellar mystery of why stars form has been solved thanks to the most realistic supercomputer simulations of galaxies yet made. Theoretical astrophysicists found that stellar activity — like supernova explosions or even just starlight — plays a big part in the formation of other stars and the growth of galaxies.
Spiral structure emerges in Feedback in Realistic Environments (FIRE) simulation, which modeled stellar feedback on galaxy formation. Credit: Image courtesy of University of Texas at Austin, Texas Advanced Computing Center

Spiral structure emerges in Feedback in Realistic Environments (FIRE) simulation, which modeled stellar feedback on galaxy formation.
Credit: Image courtesy of University of Texas at Austin, Texas Advanced Computing Center

Theoretical astrophysicist Philip Hopkins of the California Institute of Technology (CalTech) led research that found that stellar activity — like supernova explosions or even just starlight — plays a big part in the formation of other stars and the growth of galaxies.

“Feedback from stars, the collective effects from supernovae, radiation, heating, pushing on gas, and stellar winds can regulate the growth of galaxies and explain why galaxies have turned so little of the available supply of gas that they have into stars,” Hopkins said.

Galaxy simulations were tested on the Stampede supercomputer of the Texas Advanced Computing Center (TACC), an Extreme Science and Engineering Discovery Environment-allocated (XSEDE) resource funded by the National Science Foundation.

The initial results were published September of 2014 in the Monthly Notices of the Royal Astronomical Society. Hopkins’s work was funded by the National Science Foundation, the Gordon and Betty Moore Foundation, and a NASA Einstein Postdoctoral Fellowship.

The mystery begins in interstellar space, the vast space between stars. There dwell enormous clouds of molecules, mainly hydrogen, with the mass of thousands or even millions of Suns. These molecular gas clouds condense and give birth to stars.

What’s puzzled astrophysicists since the 1970s is their observations that only a small fraction of matter in the clouds becomes a star. The best computer simulations, however, predicted nearly all of a cloud’s matter would cool and become a star.

“That’s really what we were trying to figure out and address, for the first time, by putting in the real physics of what we know stars do to the gas around them,” Hopkins said.

A multi-institution collaboration formed with members from CalTech, U.C. Berkeley, U.C. San Diego, U.C. Irvine, Northwestern, and the University of Toronto. They produced a new set of supercomputer galaxy models called FIRE or Feedback in Realistic Environments. It focused the computing power on small scales of just a few light years across.

“We started by simulating just single stars in little patches of the galaxy, where we trace every single explosion,” Hopkins explained. “That lets you build a model that you can put into a simulation of a whole galaxy at a time. And then you build that up into simulations of a chunk of the universe at a time.”

Hopkins developed the simulation code locally on a cluster at CalTech, but the Stampede supercomputer did the lion’s share of the computation.

“Almost all of these simulations were run on XSEDE resources,” Hopkins said. “In particular the Stampede supercomputer at TACC was the workhorse of these simulations…Stampede was an ideal machine — it was fast, it had large shared memory nodes with a lot of processors per node and good memory per processor. And that let us run this on a much faster timescale than we had originally anticipated. Combined with improvements we made to the parallelization of the problem, we were able to run this problem on thousands of CPUs at a time, which is record-breaking for this type of problem,” Hopkins said.

The realism achieved by the FIRE galaxy simulations surprised Hopkins. Past work with sub-grid models of how supernovae explode and how radiation interacts with gas required manually tweaking the model after each run.

“My real jaw-dropping moment,” Hopkins said, “was when we put the physics that we thought had been missing from the previous models in without giving ourselves a bunch of knobs to turn. We ran it and it actually looked like a real galaxy. And it only had a few percent of material that turned into stars, instead of all of it, as in the past.”

FIRE has mostly simulated the more typical and small galaxies, and Hopkins wants to build on its success. “We want to explore the odd balls, the galaxies that we see that are of strange sizes or masses or have unusual properties in some other way,” Hopkins said.

Hopkins also wants to model galaxies with supermassive black holes at the center, like our own Milky Way. “In the process of falling in, before matter actually gets trapped by the black hole and nothing can escape, it turns out that for the most massive galaxies, this is even more energy than released by all the stars in the galaxy. It’s almost certainly important. But it’s at the edge, and we’re just starting to think about simulating those giant galaxies,” Hopkins said.

University of Texas at Austin, Texas Advanced Computing Center

New revelations on dark matter and relic neutrinos

Satellite have been studying relic radiation (the most ancient light in the Universe). This light has been measured precisely across the entire sky for the first time, in both intensity and polarization, thereby producing the oldest image of the Universe. This primordial light lets us “see” some of the most elusive particles in the Universe: dark matter and relic neutrinos. Between 2009 and 2013, the Planck satellite observed relic radiation, sometimes called cosmic microwave background (CMB) radiation. Today, with a full analysis of the data, the quality of the map is now such that the imprints left by dark matter and relic neutrinos are clearly visible.
Temperature map of the relic radiation (bottom left), and close-ups showing, in relief, the polarisation of light in the 353 GHz channel (the colors correspond to the intensity of the thermal emission from galactic dust. Credit: © ESA - Planck collaboration

Temperature map of the relic radiation (bottom left), and close-ups showing, in relief, the polarisation of light in the 353 GHz channel (the colors correspond to the intensity of the thermal emission from galactic dust.
Credit: © ESA – Planck collaboration

Between 2009 and 2013, the Planck satellite observed relic radiation, sometimes called cosmic microwave background (CMB) radiation. Today, with a full analysis of the data, the quality of the map is now such that the imprints left by dark matter and relic neutrinos are clearly visible.

Already in 2013, the map for variations in light intensity was released, showing where matter was in the sky 380,000 years after the Big Bang. Thanks to the measurement of the polarisation of this light (in four of seven frequencies2, for the moment), Planck can now see how this material used to move. Our vision of the primordial Universe has thus become dynamic. This new dimension, and the quality of the data, allows us to test numerous aspects of the standard model of cosmology. In particular, they illuminate the most elusive of particles: dark matter and neutrinos.

New constraints on dark matter The Planck collaboration results now make it possible to rule out an entire class of models of dark matter, in which dark matter-antimatter annihilation3 is important. Annihilation is the process whereby a particle and its antiparticle jointly disappear, followed by a release in energy.

The basic existence of dark matter is becoming firmly established, but the nature of dark matter particles remains unknown. There are numerous hypotheses concerning the physical nature of this matter, and one of today’s goals is to whittle down the possibilities, for instance by searching for the effects of this mysterious matter on ordinary matter and light. Observations made by Planck show that it is not necessary to appeal to the existence of strong dark matter-antimatter annihilation to explain the dynamics of the early universe. Such events would have produced enough energy to exert an influence on the evolution of the light-matter fluid in the early universe, especially around the time relic radiation was emitted. However, the most recent observations show no hints that this actually took place.

These new results are even more interesting when compared with measurements made by other instruments. The satellites Fermi and Pamela, as well as the AMS-02 experiment aboard the International Space Station, have all observed an excess of cosmic rays, which might be interpreted as a consequence of dark matter annihilation. Given the Planck observations, however, an alternative explanation for these AMS-02 or Fermi measurements-such as radiation from undetected pulsars-has to be considered, if one is to make the reasonable hypothesis that the properties of dark matter particles are stable over time.

Additionally, the Planck collaboration has confirmed that dark matter comprises a bit more than 26% of the Universe today (figure deriving from its 2013 analysis), and has made more accurate maps of the density of matter a few billion years after the Big Bang, thanks to measurements of temperature and B-mode polarisation.

Neutrinos from the earliest instants detected

The new results from the Planck collaboration also inform us about another type of very elusive particle, the neutrino. These “ghost” particles, abundantly produced in our Sun for example, can pass through our planet with almost no interaction, which makes them very difficult to detect. It is therefore not realistic to directly detect the first neutrinos, which were created within the first second after the Big Bang, and which have very little energy. However, for the first time, Planck has unambiguously detected the effect these relic neutrinos have on relic radiation maps.

The relic neutrinos detected by Planck were released about one second after the Big Bang, when the Universe was still opaque to light but already transparent to these particles, which can freely escape from environments that are opaque to photons, such as the Sun’s core. 380,000 years later, when relic radiation was released, it bore the imprint of neutrinos because photons had gravitational4 interaction with these particles. Observing the oldest photons thus made it possible to confirm the properties of neutrinos.

Planck observations are consistent with the standard model of particle physics. They essentially exclude the existence of a fourth species of neutrinos5, previously considered a possibility based on the final data from the WMAP satellite, the US predecessor of Planck. Finally, Planck makes it possible to set an upper limit to the sum of the mass of neutrinos, currently established at 0.23 eV (electron-volt)6.

The full data set for the mission, along with associated articles that will be submitted to the journal Astronomy & Astrophysics (A&A), will be available December 22 on the ESA web site. These results are notably derived from measurements made with the High Frequency Instrument (HFI), which was conceived and assembled under the direction of the Institut d’astrophysique spatiale (CNRS/Université Paris-Sud), and utilized, under the direction of the Institut d’astrophysique de Paris (CNRS/UPMC), by different laboratories including those from the CEA, the CNRS and French universities, with funding from CNES and the CNRS.

Notes

1. Polarisation is a property of light on the same level as color or direction of travel. This property is invisible to the human eye, but remains familiar (sunglasses with polarised lenses and cinema 3D glasses, for instance).. A travelling photon is associated with an electrical field (E) and a magnetic field (B), at right angles to each other and to their direction of travel. If the electrical field remains in the same plane, the photon is said to be linearly polarised, as is the case for relic radiation.

2. In all three frequencies of the Low Frequency Instrument (LFI) and in the 353 GHz channel of the High Frequency Instrument (HFI).

3. In some models, dark matter particles are their own anti-particles.

4. According to general relativity, even if photons have no mass, they are sensitive to the gravitational force that bends space-time.

5. According to the standard model of particle physics, there are three species of neutrinos.

6. The electron volt (symbol: eV) is a unit of energy used in particle physics to express mass, since mass-energy equivalence links energy and mass (E=mc2, where c represents the speed of light). The lightest known particle after photons and neutrinos weighs 511 keV, more than 2 million times the sum of the mass of all three neutrinos.

CNRS

Genes tell story of birdsong and human speech

A massive international effort to sequence and compare the entire genomes of 48 species of birds, representing every major order of the bird family tree, reveals that vocal learning evolved twice or maybe three times among songbirds, parrots and hummingbirds. Even more striking, the set of genes employed in each of those song innovations is remarkably similar to the genes involved in human speaking ability.
The activity of genes related to singing shows a unique pattern in the brain of an Australian Budgerigar. Credit: Duke University

The activity of genes related to singing shows a unique pattern in the brain of an Australian Budgerigar.
Credit: Duke University

“We’ve known for many years that the singing behavior of birds is similar to speech in humans — not identical, but similar — and that the brain circuitry is similar, too,” said Jarvis, an associate professor of neurobiology at the Duke University Medical School and an investigator at the Howard Hughes Medical Institute. “But we didn’t know whether or not those features were the same because the genes were also the same.”

Now scientists do know, and the answer is yes — birds and humans use essentially the same genes to speak.

After a massive international effort to sequence and compare the entire genomes of 48 species of birds representing every major order of the bird family tree, Jarvis and his colleagues found that vocal learning evolved twice or maybe three times among songbirds, parrots and hummingbirds.

Even more striking is that the set of genes involved in each of those song innovations is remarkably similar to the genes involved in human speaking ability.

The findings are part of a package of eight scientific papers in a Dec. 12 special issue of Science and 21 additional papers appearing nearly simultaneously in Genome Biology, GigaScience and other journals. Jarvis’ name appears on 20 papers and he is a corresponding author for 8 of them.

Jarvis co-led the Avian Phylogenomics Consortium with Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen and M. Thomas P. Gilbert of the Natural History Museum of Denmark. His Duke lab contributed to preparing samples, sequencing and annotating the genomes, performing the analyses and coordinating the overall project.

The Jarvis lab in the Bryan Research Building prepared DNA of many of the species, pulling it from little chunks of frozen, pink bird flesh collected over the past 30 years by museums and other institutions around the world. To ensure the DNA being sequenced really belonged to the Golden-collared manakin and not an undergraduate lab assistant, the lab has been kept spotlessly clean and many of its tools are used only once, to avoid the possibility of subsequent contamination.

“We change gloves a lot,” said Carole Parent, the lab research analyst who set up a DNA isolation pipeline for the next stage of the project to sequence still more birds and supervised sample prep with a team of Duke undergrads and a student from East Chapel Hill High School.

All of this meticulous and somewhat tedious work has given Jarvis and hundreds of colleagues around the world a crack at an unprecedented amount of genomic data generated by BGI in China. The whole-genome comparison of the 48 bird species required new algorithms written at the University of Illinois and University of Texas that ran for 400 years of CPU time on three supercomputers in the U.S.

Of the 29 papers covering everything from penguin evolution to color vision, eight are devoted to bird song.

One of the Dec. 12 papers in Science found there is a consistent set of just over 50 genes that show higher or lower activity in the brains of vocal learning birds and humans. These changes were not found in the brains of birds that do not have vocal learning and of non-human primates that do not speak, according to this Duke team, which was led by Jarvis; Andreas Pfenning, a graduate of the Ph.D. program in computational biology and bioinformatics (CBB); and Alexander Hartemink, professor of computer science, statistical science and biology.

“This means that vocal learning birds and humans are more similar to each other for these genes in song and speech brain areas than other birds and primates are to them,” Jarvis said.

These genes are involved in forming new connections between neurons of the motor cortex and neurons that control the muscles that produce sound.

A companion study by another CBB doctorate, Rui Wang, looked at the specialized activity of a pair of genes involved in the regions of the brain that control song and speech. This study, appearing in the Journal of Comparative Neurology, found that these genes are down- and up-regulated in one brain region of song-learning birds during the juvenile period of their vocal learning , changes that last into adulthood. This study, and that of Pfenning, hypothesize that changes in these genes could be critical for the evolution of song in birds and speech in humans.

“You can find those same genes in the genomes of all species, but they’re active at much higher or lower levels in the specialized song or speech brain regions of vocal learning birds and humans,” Jarvis said. “What this suggests to me is that when vocal learning evolves, there may be a limited way in which the brain circuits can evolve.”

Another paper in Science from Duke, led by post-doc Osceola Whitney, Pfenning, Hartemink and Anne West, an associate professor of neurobiology, looked at gene activation in different areas of the brain during singing. This team found activation of 10 percent of the expressed genome during singing, with diverse activation patterns in different song-learning regions of the brain. The diverse gene patterns are best explained by epigenetic differences in the genomes of the different brain regions, meaning that individual cells in different brain regions can regulate genes at a moment’s notice when the birds sing.

Among the three main groups of vocal learning birds, parrots are clearly different in their ability to mimic human speech. Mukta Chakraborty, a postdoc in the Jarvis lab, led a project that used the activity of some of the specialized genes to discover that the parrot’s speech center is organized somewhat differently. It has what the researchers call a “song-system-within-a-song-system” in which the area of the brain with different gene activity for producing song has an outer ring of still more differences in gene expression.

Parrots are very social animals, Chakraborty said, and having the ability to quickly pick up “dialects” of parrot speech may account for their super-charged speech center. The “shell” or outer regions were found to be proportionally larger in the parrot species, which are believed to have the highest vocal, cognitive and social abilities. These species include Amazon parrots, the African Grey and the Blue and Gold Macaw.

Jarvis was also part of a team with Claudio Mello and his Ph.D. student Morgan Wirthlin at Oregon Health & Science University that found ten more genes that are unique to song-control regions of songbirds. This paper appears in BMC Genomics.

A paper in Science led by Zhang, Gilbert and Jarvis found the genomes of vocal learners are more rapidly evolving and have more chromosomal rearrangements compared to other bird species. This genomic comparison also found similar changes occurred independently in in the song-learning area of different birds’ brains.

Jarvis said knowing more of this history of how speech evolved in birds makes vocal learning birds even more valuable model organisms for helping to answer the questions he and other researchers are addressing about human speech.

“Speech is difficult to study in human brains,” he said. “Whales and elephants learn speech and songs, but they’re too big to house in the lab. Now that we have a deeper understanding of how similar birdsong brain regions are to human speech regions at the genetic level, I think they’ll be a better model than ever.”

Jarvis’ general exploration of the bird brain over his 16 years at Duke has also led to several unexpected discoveries unrelated to song.

In 2005, he and colleagues found a center of the brain in migratory birds that apparently enables sensing of magnetic fields through “night vision.” That year he also led a revision of the understanding of bird brain organization and vertebrate brain evolution. Last year, he led a re-drawing of the geography of the bird brain based on analysis of 52 genes that are active in 23 areas of the brains of eight species of birds. This new map shows neuron groupings in the birds’ brains to be organized in columns like the brains of humans and other mammals.

He also branched out a bit and learned about the brain structures that enable mice to “sing” in ultrasonic ranges beyond human hearing.

Jarvis said this first wave of findings from the Avian Phylogenomics Consortium is just the beginning of an exciting new era of genomic analysis. The international group is already sequencing more birds at the whole-genome level.

“This is an exciting moment,” said Jarvis, who is also a member of the Duke Institute for Brain Sciences. “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.”

References: G. Zhang, E. D. Jarvis, M. T. P. Gilbert. A flock of genomes. Science, 2014; 346 (6215): 1308 DOI: 10.1126/science.346.6215.1308 *** A. R. Pfenning, E. Hara, O. Whitney, M. V. Rivas, R. Wang, P. L. Roulhac, J. T. Howard, M. Wirthlin, P. V. Lovell, G. Ganapathy, J. Mouncastle, M. A. Moseley, J. W. Thompson, E. J. Soderblom, A. Iriki, M. Kato, M. T. P. Gilbert, G. Zhang, T. Bakken, A. Bongaarts, A. Bernard, E. Lein, C. V. Mello, A. J. Hartemink, E. D. Jarvis. Convergent transcriptional specializations in the brains of humans and song-learning birds. Science, 2014; 346 (6215): 1256846 DOI:10.1126/science.1256846

‘Big Bang’ of bird evolution mapped

The first findings of the Avian Phylogenomics Consortium are being reported nearly simultaneously in 29 papers — eight papers in a Dec. 12 special issue of Science and 21 more in Genome Biology, GigaScience and other journals. The analyses suggest some remarkable new ideas about bird evolution, including insights into vocal learning and the brain, colored plumage, sex chromosomes and the birds’ relationship to dinosaurs and crocodiles.
Crocodiles are the closest living relatives of birds, sharing a common ancestor that lived around 240 million years ago and also gave rise to the dinosaurs. Credit: Stephen J. O'Brien, Avian Phylogenomics Group

Crocodiles are the closest living relatives of birds, sharing a common ancestor that lived around 240 million years ago and also gave rise to the dinosaurs.
Credit: Stephen J. O’Brien, Avian Phylogenomics Group

Scientists already knew that the birds who 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 is barely known.

To resolve these fundamental questions, a consortium led by Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen, Erich D. 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 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 to an unprecedented scale,” said Guojie 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.”

“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,” added Tom Gilbert. “This is precisely 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 neuroscientist Erich 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 Sciencedescribe 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; ways in which singing behavior regulates genes in the brain; and a new method for phylogenic analysis with large-scale genomic data.

The Avian Phylogenomics Consortium has so far involved more than 200 scientists hailing 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 Museum, the Chinese Academy of Sciences, Louisiana State University and many others.

A Clearer Picture of the Bird Family Tree

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, the consortium authors 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.”

This new tree resolves the early branches of Neoaves (new birds) and supports conclusions about some 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 that killed off all dinosaurs except some birds. This contradicts the idea that Neoaves blossomed 10 to 80 million years earlier, as some recent studies 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.

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 say.

With about 14,000 genes per species, the size of the datasets and the complexity of analyzing them required several new approaches to computing evolutionary family trees. These were developed by computer scientists Tandy Warnow at the University of Illinois at Urbana-Champaign, Siavash Mirarab, a student at 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 (LRZ), the Texas Advanced Computing Center (TACC) and the San Diego Supercomputing center (SDSC).

“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 appearing in GigaScience.

A Genomic Perspective of Avian Evolution and Biodiversity

For all their biological intricacies, birds are surprisingly light on DNA. A study led by Zhang, Cai Li and the consortium authors found that compared to other reptile genomes, avian genomes contain fewer of the repeating sequences of DNA and lost hundreds of genes in their early evolution after birds split from other reptiles.

“Many of these genes have essential functions in humans, such as in reproduction, skeleton formation and lung systems,” Zhang said. “The loss of these key genes may have a significant effect on the evolution of many distinct phenotypes of birds. This is an exciting finding, because it is quite different from what people normally think, which is that innovation is normally created by new genetic material, not the loss of it. Sometimes, less is more.”

From the whole chromosome level to the order of genes, this group found that the genomic structure of birds has stayed remarkably the same among species for more than 100 million years. The rate of gene evolution across all bird species is also slower compared to mammals.

Yet some genomic regions display relatively faster evolution in species with similar lifestyles or phenotypes, such as involving vocal learning. This pattern of what is called convergent evolution may be the underlying mechanism that explains how distant bird species evolved similar phenotypes independently. Zhang said these analyses on particular gene families begin to explain how birds evolved a lighter skeleton, a distinct lung system, dietary specialties, color vision, as well as colorful feathers and other sex-related traits.

Important Lessons

The new studies have shed light on several other questions about birds, including:

How did vocal learning evolve?  Eight studies in the package examined the subject of vocal learning. According to new evidence in the two flagship papers, vocal learning evolved independently at least twice, and was associated with convergent evolution in many proteins. A Science study led by Andreas Pfenning, Alexander Hartemink, Jarvis and others at Duke, in collaboration with researchers at the Allen Institute for Brain Science in Seattle and the RIKEN Institute in Japan, found that the specialized song-learning brain circuitry of vocal learning birds (songbirds, parrots and hummingbirds) and human brain speech regions have convergent changes in the activity of more than 50 genes. Most of these genes are involved in forming neural connections. Osceola Whitney, Pfenning and Anne West, also of Duke, found in another Science study that singing is associated with the activation of 10 percent of the expressed genome, with diverse activation patterns in different song-learning regions of the brain, controlled by epigenetic regulation of the genome. Duke’s Mukta Chakraborty and others found in a PLoS ONE study that parrots have a song system within a song system, with the surrounding song system unique to them. This might explain their greater ability to imitate human speech. In a BMC Genomics study, Morgan Wirthlin, Peter Lovell and Claudio Mello from Oregon Health & Science University found unique genes in the song-control brain regions of songbirds.

The XYZW of sex chromosomes. Just as the sex of humans is determined by the X and Y chromosomes, the sex of birds is controlled by the Z and W chromosomes. The W makes birds female, just as the Y makes humans male. Most mammals share a similar evolutionary history of the Y chromosome, which now contains many degenerated genes that no longer function and only a few active genes related to “maleness.” A Science study led by Qi Zhou and Doris Bachtrog from the University of California, Berkeley, and Zhang found that half of bird species still contain substantial numbers of active genes in their W chromosomes. This challenges the classic view that the W chromosome is a “graveyard of genes” like the human Y.

This group also found that bird species are at drastically different states of sex chromosome evolution. For example, the ostrich and emu, which belong to one of the older branches of the bird family tree, have sex chromosomes resembling their ancestors. Yet some modern birds such as the chicken and zebra finch have sex chromosomes that contain few active genes. This opens a new set of questions on how the diversity of sex chromosomes may drive the diversity of sex differences in the outward appearance of various bird species. Peacocks and peahens are dramatically different; male and female crows are indistinguishable.

How did birds lose their teeth? In a Science study led by Robert Meredith from Montclair State University and Mark Springer from the University of California, Riverside, a comparison between the genomes of living bird species and those of vertebrate species that have teeth identified key mutations in the parts of the genome that code for enamel and dentin, the building blocks of teeth. The evidence suggests that five tooth-related genes were disabled within a short time period in the common ancestor of modern birds more than 100 million years ago.

What’s the connection between birds and dinosaurs? Unlike mammals, birds (along with reptiles, fish and amphibians) have a large number of tiny microchromosomes. These smaller packages of gene-rich material are thought to have been present in their dinosaur ancestors. A study of genome karyotype structure in BMC Genomics analyzed whole genomes of the chicken, turkey, Peking duck, zebra finch and budgerigar. It found the chicken has the most similar overall chromosome pattern to an avian ancestor, which was thought to be a feathered dinosaur. This work was led by Darren Griffin and Michael Romanov from the University of Kent, and by Dennis Larkin and Marta Farré from the Royal Veterinary College, University of London.

Another study in Science examined birds’ closest living relatives, the crocodiles. This team, led by Ed Green and Benedict Paton from the University of California, Santa Cruz, David Ray from Texas Tech University and Ed Braun from the University of Florida, found that crocodiles have one of the slowest-evolving genomes. The researchers were able to infer the genome sequence of the common ancestor of birds and crocodilians (archosaurs) and therefore all dinosaurs, including those that went extinct 66 million years ago.

Do differences in gene trees versus species trees matter? In the phylogenomics flagship study by Jarvis and others, the consortium found that no gene tree has a history exactly the same as the species tree, partly due to a process called incomplete lineage sorting. Another Science study, led by Tandy Warnow at the University of Texas and the University of Illinois, and her student Siavash Mirarab, developed a new computational approach called “statistical binning.” They used this approach to show it does not matter much that the gene trees differ from the species tree because they were able to infer the first coalescent-based, genome-scale species tree, combining gene trees with similar histories to accurately infer a species tree.

Do bird genomes carry fewer virus sequences than other species? Mammalian genomes harbor a diverse set of genomic “fossils” of past viral infections called “endogenous viral elements” (EVEs). A study published in Genome Biology led by Jie Cui of Duke-NUS Graduate Medical School in Singapore, Edward Holmes of the University of Sydney and Zhang, found that bird species had 6-13 times fewer EVE infections in their past than mammals. This finding is consistent with the fact that birds have smaller genomes than mammals. It also suggests birds may either be less susceptible to viral invasions or better able to purge viral genes.

When did colorful feathers evolve? Elaborate, colorful feathers are thought to be evolutionarily advantageous, giving a male bird in a given species an edge over his competitors when it comes to mating. Zhang’s flagship paper in Science, which is further analyzed by Matthew Greenwold and Roger Sawyer from the University of South Carolina in a companion study in BMC Evolutionary Biology, found that genes involved in feather coloration evolved more quickly than other genes in eight of 46 bird lineages. Waterbirds have the lowest number of beta keratin feather genes, landbirds have more than twice as many, and in domesticated pet and agricultural bird species, there are eight times more of these genes.

What happens to species facing extinction or recovering from near-extinction? Birds are like the proverbial canaries in the coal mine because of their sensitivity to environmental changes that cause extinction. In a Genome Biology study led by Shengbin Li, Cheng Cheng and Jun Yu from Xi’an Jiaotong University and Jarvis, researchers analyzed the genomes of species that have recently gone nearly extinct, including the crested ibis in Asia and the bald eagle in the Americas. They found genes that break down environmental toxins have a higher rate of mutations in these species and there is lower diversity of immune system genes in endangered species. In a recovering crested ibis population, genes involved in brain function and metabolism are evolving more rapidly. The researchers found more genomic diversity in the recovering population than was expected, giving greater hope for species conservation.

The Start of Something Bigger

This sweeping genome-level comparison of an entire class of life is being powered by frozen bird tissue samples collected over the past 30 years by museums and other institutions around the world. Samples are sent as fingernail-sized chunks of frozen flesh mostly to Duke University and University of Copenhagen for DNA separation. Most of the genome sequencing and critical initial analyses of the genomes have then been conducted by the BGI in China.

The avian genome consortium is now creating a database that will be made publicly available in the future for scientists to study the genetic basis of complex avian traits.

Setting up the pipeline for the large-scale study of whole genomes — collecting and organizing tissue samples, extracting the DNA, analyzing its quality, sequencing and managing torrents of new data — has been a massive undertaking. But the scientists say their work should help inform other major efforts for the comprehensive sequencing of vertebrate classes. To encourage other researchers to dig through this ‘big data’ and discover new patterns that were not seen in small-scale data before, the avian genome consortium has released the full dataset to the public in GigaScience, and in NCBI, ENSEMBL and CoGe databases.

Under the leadership of Dave Burt, the National Avian Research Facility at the Roslin Institute and Edinburgh University, UK, has created genome browser databases based on the ENSEMBL model for 48 species.

in Science at http://www.sciencemag.org/content/346/6215/1308.

 

Evolutionary reversal previously unseen in animal kingdom

The saga of the Osedax “bone-eating” worms began 12 years ago, with the first discovery of these deep-sea creatures that feast on the bones of dead animals. The Osedax story grew even stranger when researchers found that the large female worms contained harems of tiny dwarf males.

A male Osedax priapus (bone worm) attached on a seal bone (scale: 0.5 mm). Credit: Greg Rouse

A male Osedax priapus (bone worm) attached on a seal bone (scale: 0.5 mm).
Credit: Greg Rouse

Examining bone worms collected at 700 meters (2,296 feet) depth by an MBARI remotely operated vehicle, Rouse observed a surprising new type of Osedax species. Females of the new species are roughly the same size as their previously studied relatives, but males are tens of thousands of times larger than those of other Osedax worms, and are roughly the same size as the females.

“This discovery was very unexpected,” said Rouse. “It’s the first known example of such a dramatic evolutionary reversal from dwarf males.”

“Evolutionary reversals to ancestral states are very rare in the animal kingdom,” noted coauthor Vrijenhoek. “This case is exceptional because the genes for producing full-sized adult males should have deteriorated over time due to disuse. But apparently the genes are still there.”

Also surprising was the discovery that males of the new species consume bone on their own, something their dwarf relatives don’t ever do.

Adding even more peculiarity to the discovery is the mating process for the new species. Previously studied Osedax male dwarfs are permanently attached to their female hosts, and therefore do not need mobility to mate, so the scientists wondered how the newly discovered males are able to seek out a mate, given their independence.

“The evolutionary solution (the new species) found was to actually make the male’s body very extendable so he can reach far out to find females to mate with — he can extend his body ten-times its contracted state,” said Rouse.

In essence, Rouse said, the entire worm’s body has evolved as a tool for mating, “and that’s why we named it Osedax ‘priapus,’ the mythological god of fertility,” said Rouse.

The scientists speculate that less competition for space on certain animal bones allowed the evolutionary introduction of Osedax primps.

“This worm was weird enough as it was and now it’s even weirder,” said Rouse. “This shows us that there continue to be mysteries in the sea and there is still so much more to discover, especially since we only found these creatures 12 years ago.”

University of California, San Diego

Natural selection is furthering mutations that are making skin paler

Skin colour varies according to the latitude and, therefore, according to the intensity of incident ultraviolet light: individuals living at low latitudes have darker skin, whereas those living at high latitudes have pale pigmentation. One researcher has studied why this depigmentation has taken place, and has concluded that evolution is furthering mutations that are lightening the skin, probably owing to the need to synthesize vitamin D at latitudes where there is reduced solar irradiation (compared with Africa) although, in turn, this increases the probability of developing melanoma or skin cancer.
A piece of research by the UPV/EHU-University of the Basque Country has concluded that skin depigmentation in Europeans has taken place through an adaptive process furthered by natural selection. Credit: Image courtesy of University of the Basque Country

A piece of research by the UPV/EHU-University of the Basque Country has concluded that skin depigmentation in Europeans has taken place through an adaptive process furthered by natural selection.
Credit: Image courtesy of University of the Basque Country

The first hominids that appeared in Africa probably had pale skin covered with hair, like other primates. They are thought to have lost their hair when they became bipedal, and that natural selection subsequently furthered darker skins in Africa as they protect against ultraviolet (UV)light. However, when humans left Africa (about 100,000 years ago) and headed for Asia or Europe, where UV intensity was lower, they once again acquired a less pigmented skin colour. What caused the depigmentation of these populations is not clear, and two hypotheses have in fact been put forward: firstly, it could be due to a relaxing in natural selection that keeps the skin dark in Africa, since when leaving Africa, UV levels are lower; secondly, it could be due to the fact that natural selection furthers certain mutations so that individuals can have paler skin, since at these latitudes having a skin with a dark pigmentation prevents the synthesis of adequate levels of vitamin D, essential for our survival.

Saioa López, a researcher at the Department of Genetics, Physical Anthropology and Animal Physiology of the UPV/EHU’s Faculty of Science and Technology, has carried out research into this subject. The main aims of her research work were to identify the selective pressures that have guided the evolution of this trait, as well as identify new genes and genetic variants responsible for pigmentary differences between individuals. More specifically, the aim was to show that depigmentation has been an adaptive process furthered by natural selection. The methodology used covered a whole host of techniques, including those relating to molecular and cell biology and bio-computing.

Through all this two mutations that functionally cause the lightening of the skin in our population were identified. Highly significant evidence was found to suggest that natural selection is positively furthering these mutations, which are being maintained in the population to produce a paler skin colour. What is more, melanoma samples were analysed and it was observed that these same mutations lead to an increase in susceptibility towards developing melanoma, in other words, the most aggressive, deadly skin cancer.

Why does natural selection further a mutation that causes cancer?

“If natural selection is furthering these mutations that lighten the skin,” explained López, “it is because there has to be some advantage for the individuals, probably enhanced synthesis of vitamin D.” Vitamin D can be obtained through the diet but also in an indirect way through a process in the skin in which UV light intervenes. Dark skins contain a pigment (melanin) that acts as a barrier and prevents UV rays from penetrating. At high latitudes where the intensity of UV light is very low, this is a problem, as insufficient quantities of vitamin D are synthesised.

Vitamin D is essential for skeletal mineralisation and development, and the lack of this vitamin can lead to various problems in children’s health. Yet melanoma is a cancer that tends to appear in adult life following the reproductive phase. From the evolutionary point of view, as these adult individuals have by now produced offspring, they are no longer important in evolution.

Reference: S. López, O. García, I. Yurrebaso, C. Flores, M. Acosta-Herrera, H. Chen, J. Gardeazabal, J. María Careaga, MD Boyano, A. Sánchez, JA Ratón-Nieto, A. Sevilla, I. Smith-Zubiaga, A. García de Galdeano, C. Martinez-Cadenas, N. Izagirre, S. de la Rúa C and Alonso. The Interplay between Natural Selection and Susceptibility to Melanoma on Allele 374F of SLC45A2 Gene in a South European Population”. PLoS ONE, 2014; 9: e104367

Uncovering one of humankind’s most ancient lineages

Scientists have successfully discovered one of modern humans’ ancient lineages through the sequencing of genes of the Southern African Khoisan tribespeople. This is the first time that the history of humankind populations has been analyzed and matched to Earth’s climatic conditions over the last 200,000 years.

A Khoisan hunter/gatherer with his bow and arrows. Credit: Image courtesy of Nanyang Technological University

A Khoisan hunter/gatherer with his bow and arrows.
Credit: Image courtesy of Nanyang Technological University

A geneticist from NTU, Professor Stephan Christoph Schuster, who led an international research team from Singapore, United States and Brazil, said this is the first time that the history of humankind populations has been analysed and matched to Earth’s climatic conditions over the last 200,000 years.

Their breakthrough findings are published today (4 Dec) in Nature Communications.

The team has sequenced the genome of five living individuals from a hunter/gatherer tribe in Southern Africa, and compared them with 420,000 genetic variants across 1,462 genomes from 48 ethnic groups of the global population.

Through advanced computation analysis, the team found that these Southern African Khoisan tribespeople are genetically distinct not only from Europeans and Asians, but also from all other Africans.

The team also found that there are individuals of the Khoisan population whose ancestors did not interbreed with any of the other ethnic groups for the last 150,000 years and that Khoisan was the majority group of living humans for most of that time until about 20,000 years ago.

Their findings mean it is now possible to use genetic sequencing to reveal the ancestral lineage of any ethnic group even up to 200,000 years ago, if non-admixed individuals are found, like in the case of the Khoisan. This will show when in history there have been important genetic changes to an ancestral lineage due to intermarriages or geographical migrations that may have occurred over the centuries.

“Khoisan hunter/gatherers in Southern Africa have always perceived themselves as the oldest people,” said Prof Schuster, an NTU scientist at the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and a former Penn State University professor.

“Our study proves that they truly belong to one of mankind’s most ancient lineages, and these high quality genome sequences obtained from the tribesmen will help us better understand human population history, especially the understudied branch of mankind such as the Khoisan.

“The new data gathered will also enable scientists to better understand how the human genome has evolved and hopefully lead to more effective treatment options for certain genetic diseases and illnesses.”

Of the five tribesmen who were the oldest members of the Ju/’hoansi tribe and other tribes living in protected areas of northwest Namibia, two individuals were found to have a genome which had not admixed with other ethnic groups.

The Ju/’hoansi tribe was made famous in the 80s and 90s by the box-office hit movie series “The Gods Must Be Crazy.” The main character of the series was a hunter/gatherer tribesman, played by Nǃxau, a bushman.

The research paper’s first author, Dr Hie Lim Kim, a SCELSE senior research fellow, said “it was very surprising that this group apparently did not intermarry with non-Khoisan neighbours for thousands of years.” This is because the Khoisan peoples and the rest of modern humanity shared their most recent common ancestor around 150,000 years ago.

The current Khoisan culture and tradition, where marriage occurs either among Khoisan groups or results in female members leaving their tribes after marrying non-Khoisan men, appears to be long-standing.

“A key finding from this study is that even today after 150,000 years, single non-admixed individuals or descendants of those who did not interbreed with separate populations can be identified within the Ju/’hoansi population, which means there might be more of such unique individuals in other parts of the world,” added Dr Kim.

Reference: Hie Lim Kim, Aakrosh Ratan, George H. Perry, Alvaro Montenegro, Webb Miller, Stephan C. Schuster. Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history. Nature Communications, 2014; 5: 5692 DOI: 10.1038/ncomms6692

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