Mass animal die-offs may be increasing, new research shows

Large numbers of dead sunfish and largemouth bass in April 2014 following a severe winter on Wintergreen Lake, Kalamazoo County, Michigan. (Photo courtesy of G. Mittelbach)

Mass die-offs of animals may be increasing in frequency and — for birds, fishes, and marine invertebrates — in severity as well, according to a study of 727 mass mortality events since 1940.

Despite the ecological importance of individual mass mortality events, in which a larger than normal number of individuals die within a population, little research has been conducted on patterns across mass mortality events. The new study will help researchers better assess trends in mass mortality events and their causes, according to the authors of the paper in the Jan. 12 issue of the Proceedings of the National Academy of Sciences.

“The initial patterns are surprising, in terms of the documented changes to frequencies of occurrences, magnitudes of each event, and the causes of mass mortality,” said Samuel Fey, a postdoctoral fellow in the Department of Ecology and Evolutionary Biology at Yale and co-lead author of the paper. “These data also show that we have a lot of room to improve how we document and study these types of rare events.”

Fey, along with fellow researchers at the University of San Diego and University of California-Berkeley, report that the magnitude of the die-offs has increased in birds, fishes, and marine invertebrates, held steady among mammals, and decreased in frogs and amphibians. The authors recognized that more scientific research has been done on mass mortality events in the last few decades but said even accounting for this “discovery bias” does not explain all of the increase in such events. The increase in mass mortality events appears to be associated with a rise in disease emergence, biotoxicity, and multiple interacting stressors, they note.

Overall, disease was the primary culprit, accounting for 26% of the mass die-offs. The impacts of direct human activity, primarily from environmental contamination, caused 19% of such events. Another major cause was biotoxicity triggered by events such as algae blooms, rapid increases of algae in water systems. Processes directly influenced by climate — such as weather extremes, thermal stress, oxygen stress, or starvation — also contributed accounted collectively for about 25% of mass mortality events.

The most severe events were those with multiple causes, the paper shows.

“This study should improve our understanding of the continuum of mortality patterns and processes that exist between background mortality levels and species-level extinctions,” Fey said.

Adam M. Siepielski of the University of San Diego was co-lead author of the paper. Stephanie M. Carlson of the University of California-Berkeley was senior author. Fey began working on this research while a graduate student at Dartmouth College.

Source: Yale University

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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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No 'bird brains'? Crows exhibit advanced relational thinking, study suggests

Study finds crows spontaneously solve higher-order relational-matching tasks. Credit: Photo courtesy of Lomonosov Moscow University.

Crows have long been heralded for their high intelligence -- they can remember faces, use tools and communicate in sophisticated ways.

But a newly published study finds crows also have the brain power to solve higher-order, relational-matching tasks, and they can do so spontaneously. That means crows join humans, apes and monkeys in exhibiting advanced relational thinking, according to the research.

Russian researcher Anna Smirnova studies a crow making the correct selection during a relational matching trial.

"What the crows have done is a phenomenal feat," says Ed Wasserman, a psychology professor at the University of Iowa and corresponding author of the study. "That's the marvel of the results. It's been done before with apes and monkeys, but now we're dealing with a bird; but not just any bird, a bird with a brain as special to birds as the brain of an apes is special to mammals."

"Crows Spontaneously Exhibit Analogical Reasoning," which was published December 18 in Current Biology, was written by Wasserman and Anna Smirnova, Zoya Zorina and Tanya Obozova, researchers with the Department of Biology at Lomonosov Moscow State University in Moscow, Russia, where the study was conducted.

Wasserman said the Russian researchers have studied bird species for decades and that a main theme of their work is cognition. He credits his counterparts with a thoughtful and well-planned study.

"This was a very artful experiment," Wasserman says. "I was just bowled over by how innovative it was."

The study involved two hooded crows that were at least 2 years old. First, the birds were trained and tested to identify items by color, shape and number of single samples.

Here is how it worked: the birds were placed into a wire mesh cage into which a plastic tray containing three small cups was occasionally inserted. The sample cup in the middle was covered with a small card on which was pictured a color, shape or number of items. The other two cups were also covered with cards -- one that matched the sample and one that did not. During this initial training period, the cup with the matching card contained two mealworms; the crows were rewarded with these food items when they chose the matching card, but they received no food when they chose the other card.

Once the crows has been trained on identity matching-to-sample, the researchers moved to the second phase of the experiment. This time, the birds were assessed with relational matching pairs of items.

These relational matching trials were arranged in such a way that neither test pairs precisely matched the sample pair, thereby eliminating control by physical identity. For example, the crows might have to choose two same-sized circles rather than two different-sized circles when the sample card displayed two same-sized squares.

What surprised the researchers was not only that the crows could correctly perform the relational matches, but that they did so spontaneously--without explicit training.

"That is the crux of the discovery," Wasserman says. "Honestly, if it was only by brute force that the crows showed this learning, then it would have been an impressive result. But this feat was spontaneous."

Still the researchers acknowledge that the crows' relational matching behavior did not come without some background knowledge.

"Indeed, we believe that their earlier IMTS (identity matching-to-sample) training is likely to have enabled them to grasp a broadly applicable concept of sameness that could apply to novel two-item samples and test stimuli involving only relational sameness," the researchers wrote. "Just how that remarkable transfer is accomplished represents an intriguing matter for future study."

Anthony Wright, neurobiology and anatomy professor at the University of Texas-Houston Medical School, says the discovery ranks on par with demonstrations of tool use by some birds, including crows.

"Analogical reasoning, matching relations to relations, has been considered to be among the more so-called 'higher order' abstract reasoning processes," he says. "For decades such reasoning has been thought to be limited to humans and some great apes. The apparent spontaneity of this finding makes it all the more remarkable."

Joel Fagot, director of research at the University of Aix-Marseille in France, agrees the results shatter the notion that "sophisticated forms of cognition can only be found in our 'smart' human species. Accumulated evidence suggests that animals can do more than expected."

Wasserman concedes there will be skeptics and hopes the experiment will be repeated with more crows as well as other species. He suspects researchers will have more such surprises in store for science.

"We have always sold animals short," he says. "That human arrogance still permeates contemporary cognitive science."

Source: University of Iowa

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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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