The mystery of the Alpine long-eared bat

                              An Alpine long-eared bat fully airborne , UPV/EHU

The alpine long-eared bat was discovered in the Austrian Alps in 2003; hence its name. Yet later on specimens were found in other milder environments as well, in Croatia, Greece and Crete, and what is more, often close to sea level. Members of the Behavioural Ecology and Evolution Group of the UPV/EHU’s Faculty of Science and Technology studied the distribution and way of life of this species, and found that it forages and reproduces in mostly alpine environments (above the treeline), a unique case among bats. As the biologist Antton Alberdi explained, “the common name of the species not only refers to the place where it came from but describes its nature, too.” Indeed, the researcher concluded that the resources used by the Alpine long-eared bat are the same as the ones used by alpine birds and rodents: in the Pyrenees, for example, it lives at an altitude of between 1,500 and 2,500 metres and hides under rocks, in crevices and on ledges.

Nevertheless, how is it possible that an animal that only lives above 1,500 metres in the Pyrenees can be found at sea level in Croatia? Alberdi was involved in seeking the answer to this question in his PhD thesis. Alberdi identified and quantified the environmental conditions that determine the distribution of the Alpine long-eared bat (Plecotus macrobullaris) to try to understand why this species is restricted to mountain environments and why it can appear at sea level at the same time. After that, in order to see whether the results obtained could be extrapolated to other species, he compared the distributions of 503 vertebrates with those of the bats, and found five vertebrates that have similar geographical distributions to that of the bat: the white-winged snowfinch, the Alpine chough or yellow-billed chough, the wallcreeper, the Alpine accentor and the European snow vole. The distribution of all of them is very broad, from Western Europe all the way to Asia, but they are restricted to the main mountainous areas. He studied their ecological features to see whether they were all following a common biogeographical pattern in order to work out whether they were following a common distribution model.

They need rugged places

The basic ecological features of these vertebrates and those of the Alpine long-eared bat are very similar: they all use rocks (crevices, ledges or crushed stones) as places to hide, and they need open spaces to forage. They have also seen that they can be found in cold mountain environments (in the Alps) as well as in hot ones (in the mountains of Iran and Syria, etc.) and that suggests that the reasons that restrict these species to mountainous areas are not climatic ones: they are linked to topography. In other words, they are not in mountainous areas because they cannot withstand a hot environment, but because high mountain habitats offer them the characteristics they need. In some cases, in Croatia, for example, these conditions can be found at lower altitudes, and that explains why the species can be found at sea level. Furthermore, as they have the capacity to withstand the cold, they can use the alpine habitats that other species cannot exploit and thus avoid competition. In any case, “it cannot be said that the climate does not exert any influence,” said the researcher. “In fact, the climate determines the altitude ranges that each species can live in.”

According to the researcher, to preserve the species it is essential to know everything about them: how they live, why they are present in the places where they are present, etc. In the case of these species, therefore, climate change will not exert such an effect in the future; “more attention will need to be devoted to other factors: human exploitation, pasture use, etc.,” he explained. The researcher believes that the rise in treelines taking place as a result of the decline in the pressure of livestock will affect these species most. Indeed, as the treelines recede, the surface area suited to the habitats of these species will be reduced, because other species will also recede and that way the pressure will increase. They are now working to quantify that effect.

Source: Elhuyar Fundazioa

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Genes tell story of birdsong and human speech

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

His office is filled with all sorts of bird books, but Duke neuroscientist Erich Jarvis didn't become an expert on the avian family tree because of any particular interest in our feathered friends. Rather, it was his fascination with how the human brain understands and reproduces speech that brought him to the birds.

"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."

Source: Duke University

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Scale of declines of UK migratory birds wintering in Africa revealed

Yellow Wagtails have declined in the UK by 43% since 1995. Credit: Andy Hay; rspb-images.com

The migration of millions of birds across the face of the planet is one of nature's greatest annual events. Every spring some species move in one direction, while every autumn those same species move in the opposite one, very often linking continents.

Although these migration patterns are as regular as the seasons, monitoring is revealing that, for some species, fewer birds are making the journey each season as the populations of these birds, including species nesting in the UK, are declining rapidly.

The latest in the annual series of State of the UK's Birds report includes a migratory birds section, including trends for 29 migrant species which nest in the UK in summer and spend the winter around the Mediterranean, or in Africa south of the Sahara Desert. For the first time the recent population trends for these migratory species have been combined into an indicator revealing some marked differences between species that winter in different areas.

Species, such as Whinchat, Common Nightingale, Tree Pipit and Spotted Flycatcher, which winter in the humid zone of Africa -- stretching across the continent from southern Senegal to Nigeria and beyond -- show the most dramatic declines: the indicator for this group of species has dropped by just over 70% since the late 1980s. This contrasts with species, such as Sand martin, Common Whitethroat and Sedge Warbler, wintering in the arid zone (just below the Sahara desert). These species have fluctuated considerably since 1970, but show a less than 20% decline overall.

One of the most dramatic declines is that of the European Turtle-dove with a decline of 88% since 1995. The following species have also declined over the same period: Wood Warbler, 66%; European Pied Flycatcher, 53%; Spotted Flycatcher, 49%; Common Cuckoo, 49%; Common Nightingale, 43%; and Yellow Wagtail, 43%.

Concern about migratory bird species is growing and future editions of the State of the UK's Birds report will contain a regular update to the migratory bird indicator. To understand the changing status of the UK's migratory birds, researchers need to understand more about what's driving these declines. Evidence is currently being gathered from a variety of sources including tracking studies and on-the-ground surveys.

Martin Harper, RSPB Conservation Director, said: 'West Africa is the winter home for many species bird species that breed in the UK. But many of these birds that cross continents are in rapid decline. Their nomadic lifestyle, requiring sites and resources spread over vast distances across the globe makes identifying and understanding the causes of decline extremely complex.

'The problems may be in the UK or in West Africa, or indeed on migration in between the two.'

David Noble, Principal Ecologist at the British Trust for Ornithology (BTO), said: 'We can accurately monitor the patterns of decline in these once-familiar summer breeders thanks to several decades of careful observations by an army of volunteer birdwatchers. More recently, tracking devices have shed light on migratory routes and key wintering areas.

'To take appropriate action, further study is needed to determine the pressures faced in sub-Saharan Africa, as well as breeding here in the UK.'

Colette Hall, Wildfowl & Wetlands Trust (WWT) Species Monitoring Officer, said: 'The length of many bird migrations -- often thousands of miles -- makes it very difficult to pinpoint where and what is causing populations to fall.

'So the more information we can get all along the migration routes -- on land use changes, new infrastructure etc -- the better we can target protection measures. It's important that we help build up the capacity of local bird organisations and volunteers across the world to provide vital information through their own long-term monitoring.'

Alan Law, Director of Biodiversity Delivery at Natural England said: 'It is self-evident that effective conservation of a migratory species requires appropriate measures to be in place at each step of the migratory cycle.

'For some species, there is growing evidence of pressure on breeding success here in England. Our focus therefore is to ensure that well-managed habitats are available in this country so that migratory species can breed here successfully; this work involves close collaboration with land managers both on designated conservation sites and across the wider farmed countryside.'

David Stroud, Senior Ornithologist with the Joint Nature Conservation Committee, said: 'Migratory birds depend on conservation actions in all the countries they move through in the course of their annual cycle.

'The UK is working with these countries to help improve the condition of their critical habitats through its participation in multi-lateral environmental agreements such as the Biodiversity Convention and the Ramsar Convention on wetlands.'

The State of the UK's Birds report also covers the UK's Overseas Territories. The latest evidence reveals mixed fortunes for two important albatross populations in the UK's Overseas Territories. Seventy per cent of the world's Black-browed Albatrosses nest in the Falkland Islands. A population increase here has allowed researchers to downgrade the extinction threat of this species from Endangered to Near Threatened. Sadly, the fortunes of the Grey-headed Albatross has deteriorated as declines have been reported in nesting colonies on South Georgia, which hosts half the world's population.

The State of the UK's Birds report is available online at: http://www.rspb.org.uk/Images/state-of-the-uks-birds_tcm9-383971.pdf

Source: BirdLife International

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'Big Bang' of bird evolution mapped: Genes reveal deep histories of bird origins, feathers, flight and song

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

The genomes of modern birds tell a story of how they 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 ambitious international collaboration that has been underway for four years.

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.

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 Science describe 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.

Source: Duke University

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