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Tooth wear sheds light on the feeding habits of ancient elephant relatives

How can we ever know what ancient animals ate? For the first time, the changing diets of elephants in the last two million years in China have been reconstructed, using a technique based on analysis of the surface textures of their teeth.

The work was carried out by a University of Bristol student, working with an international team of researchers. The research was published online in Quaternary International.

Today, elephants live only in remote, tropical parts of Africa and southern Asia, but before the Ice Ages they were widespread.

As his undergraduate research project, Zhang Hanwen, MSci Palaeontology and Evolution graduate and now PhD student at the University of Bristol, undertook cutting-edge analysis of fossilised elephant teeth from China.

In a collaboration with the University of Leicester, and the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, where the fossilised teeth are curated, Hanwen sampled 27 teeth for tiny wear patterns called microwear.

“We are talking huge, brick-sized molars here — the largest of any animal,” said Hanwen, “but the signs of tooth wear are tiny, down to thousandths of a millimetre. However, these microscopic surface textures can tell us whether they were eating grass or leaves.”

Hanwen took peels of the fossilised teeth in China, using high-grade dental moulding materials, and captured the 3D surface textures under a digital microscope at the University of Leicester. The textures were quantified and analysed to identify what the elephants were eating in the days and weeks before they died.

By comparing the results with information from modern ruminants (deer, antelopes and oxen) of known diet, the study concluded two extinct elephants from Southern China — Sinomastodon and Stegodon — were primarily browsing on leaves. The third, Elephas, which includes the modern Asian elephants, shows much more catholic feeding habit, incorporating both grazing and browsing.

“It’s wonderful that we can identify diets of any fossil mammal with confidence now,” said Professor Christine Janis, from the University of Bristol, one of Hanwen’s PhD supervisors and a leading expert on the evolution of herbivorous mammals.

“This is based on the fact that the microwear textures produced by different kinds of plant material are comparable across unrelated animals.”

“This method for identifying diet relies on high-quality 3D surface data and analysis,” said Professor Mark Purnell, of the University of Leicester, another co-supervisor of Hanwen’s.

“It removes the subjectivity of trying to quantify microwear textures by identifying and counting scratches and pits in 2D microscopic images.”

Sinomastodon and Stegodon coexisted in Southern China between 2.6 and one million years ago, but Sinomastodon then became extinct and left Stegodon to become the dominant elephant of Southern China for the remainder of the Pleistocene, the time of the great Ice Ages.

“The fossil pollen record, and recently-excavated mammal fossil assemblages from various karst cave sites near the Chinese-Vietnamese border, suggest a prolonged, fluctuating period of environmental deterioration around this time,” Hanwen explained.

He added: “Forests were on the decline, alongside many of the more archaic mammal species that inhabited them. The highly evolved molars of Stegodon, with multiple enamel ridges, might have allowed it to browse on its preferred foliage in a more efficient way, thus outcompeting Sinomastodon, which preferred the same diet, but had less sophisticated molars consisting of large, blunt, conical cusps.”

On the other hand, the new study also suggests that Stegodon and Elephas subsequently coexisted for long periods in Southern China by eating different things. Stegodon remained a specialist foliage feeder whereas Elephas was more of a generalist, consuming a wider variety of vegetation.

Stegodon became extinct at around 11,000 years ago, at the end of the Pleistocene, coinciding with the worldwide disappearance of large mammal species at this time, including the iconic woolly mammoths, giant deers and sabretoothed cats. The Asian elephant survived in Southern China into historical times.

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https://www.sciencedaily.com/releases/2016/07/160728101924.htm Original web page at Science Daily

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* Desert elephants pass on knowledge — not mutations — to survive

Despite reported differences in appearance and behavior, DNA evidence finds that Namibian desert elephants share the same DNA as African savanna elephants. However, Namibian desert-dwelling elephants should be protected so they can continue to pass on their unique knowledge and survival skills to future generations.

“The ability of species such as elephants to learn and change their behavior means that genetic changes are not critical for them to adapt to a new environment,” said lead author Alfred Roca, a professor of animal sciences and member of the Carl R. Woese Institute for Genomic Biology at the University of Illinois. “The behavioral changes can allow species to expand their range to novel marginal habitats that differ sharply from the core habitat.”

Namibian desert-dwelling elephants have figured out how to prevent overheating in triple-digit temperatures by covering their bodies with sand wetted by their urine or regurgitated water from a specialized pouch beneath their tongue that holds many gallons of water. They also remember the location of scarce water and food resources across their home ranges, which are unusually large compared to those of other elephants. They play a critical role in this arid ecosystem by creating paths and digging watering holes.

Published in Ecology and Evolution, this study evaluated the nuclear DNA and mitochondrial DNA (mtDNA) of both desert-dwelling and non-desert-dwelling elephant populations throughout Namibia. Researchers found the desert-dwelling elephant DNA was not significantly different from the DNA of other savanna elephant populations in Namibia, except from those of the Caprivi Strip.

Female elephants live in tight-knit matrilineal family groups so mutations in mtDNA, which is passed from mothers to offspring, are closely tied to geographic populations. Not surprisingly, mitochondrial DNA from savanna elephants in Namibia’s Caprivi Strip — a small region analogous to Oklahoma’s panhandle — was more similar to mitochondrial DNA of elephants in Botswana and Zimbabwe, which border the Caprivi Strip.

“Our results and the historical record suggest that a high learning capacity and long distance migrations enabled Namibian elephants to shift their ranges to survive against high variability in climate and in hunting pressure,” said first author Yasuko Ishida, a research scientist in animal sciences at Illinois.

The lack of genetic differentiation (aside from the Caprivi Strip) is consistent with historical evidence of elephant movements during the Namibian War of Independence, which increased hunting pressures. Using mtDNA, the researchers identified other Namibian elephant migration patterns; for example, elephants from the Ugab River catchment shared mtDNA with elephants from the Huab River catchment, from where they are said to have migrated.

The lack of genetic differences in Namibian elephants could also be attributed to their long distance migrations; large home ranges; recent increases in population size and range; or gene flow provided by male elephants breeding with different groups of female elephants.

“Regardless, these elephants should be conserved,” said Roca. “Their knowledge of how to live in the desert is crucial to the survival of future generations of elephants in the arid habitat, and pressure from hunting and climate change may only increase in the coming decades.

“The desert elephants are also rumored to be larger, which may put them at greater risk for trophy game hunting,” he added. “Animals that live in these marginal environments are vulnerable, and their numbers do not bounce back very quickly. ”

https://www.sciencedaily.com/  Science Daily

https://www.sciencedaily.com/releases/2016/08/160803161607.htm  Original web page at Science Daily

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Ridiculously cute mouse lemurs hold key to Madagascar’s past

“For a long time, scientists weren’t sure how or why Madagascar’s biogeography changed in very recent geological time, specifically at the key period around when humans arrived on the island a few thousand years ago. It has been proposed they heavily impacted the Central Highland forests,” says Steve Goodman, MacArthur Field Biologist at The Field Museum in Chicago, who co-authored the study and has been studying Malagasy animals for thirty years. “This study shows the landscape was changing thousands of years before humans arrived.”

So scientists wanted to learn about the history of Madagascar’s landscape — why study mouse lemurs? The tiny primates are the perfect combination of fast-breeding, hardy, and unique to the island. “They reach reproductive maturity within a year, and that means that a lot of generations are produced very quickly,” explains Goodman. “That enables us to see evolution at work faster than we would in an animal that took, say, five years to first reproduce.” The lemurs, which are found only on Madagascar, live across much of the island, even forested areas that have been damaged by humans. That means that for scientists studying how the island changed over time, mouse lemurs are a jackpot. “The mouse lemurs are forest dependent — as the forest changes, they change. By studying how mouse lemurs evolved in different areas of the island, we’re able to glimpse how the island itself changed and learn whether those changes were caused by humans,” says Goodman.

By analyzing DNA from five different mouse lemur species, the scientists were able to tell when the different kinds of lemurs branched out from each other. “We were able to characterize tens of thousands of changes in the genomes of mouse lemurs that are now isolated and form separate species. By analyzing these DNA changes, we were able to understand when the species diverged from each other, and by inference, identify the ecological forces that might have driven them apart,” says Anne Yoder, Director of the Duke University Lemur Center and lead author on the paper.

“When we analyzed the mouse lemurs’ DNA, we were able to see genetic similarities between lemur species that are closely related but today live far apart from each other. That suggests that their ancestors were able to disperse across forested habitat that no longer exists — portions of the Central Highlands that formed the bridge between the eastern and western parts of the island today,” explains Goodman. Instead, the scientists believe, Madagascar was covered by a patchwork of forests, enabling the mouse lemurs to slowly disperse over tens of thousands of years between different areas. Then, once those bridges did not exist anymore, the populations became isolated.

The DNA analysis allowed the scientists to infer the timeline for the habitat changes of the Central Highlands — it happened thousands of years before humans arrived on the island. “At least at first, the changes to this region of the island were almost certainly the result of natural climate change over the past approximately 50,000 years,” says Goodman.

The study also indicates that the former forested areas of the Central Highlands may have been an important zone of ecological transition between the extremes of eastern humid forests and western dry forests. This has important implications for understanding how the mid-section of the island served as a zone of dispersal for animals, such as mouse lemurs and many others. “We’ve learned that it’s probably incorrect to talk about Madagascar’s humid east and dry west like they’re two completely separate habitats,” says Goodman. “The eastern and western parts of the island are just different extremes on the continuum.”

“Madagascar is one of the top conservation priorities in the world,” says Goodman. “All of the native land mammals on Madagascar occur nowhere else in the world. This study is important because it sheds light upon the long-term life history of Madagascar, before human colonization. It helps us understand change.”

https://www.sciencedaily.com/  Science Daily

https://www.sciencedaily.com/releases/2016/07/160718160927.htm Original web page at Science Daily

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* Monkeys in Brazil ‘have used stone tools for hundreds of years at least’

New archaeological evidence suggests that Brazilian capuchins have been using stone tools to crack open cashew nuts for at least 700 years. Researchers say, to date, they have found the earliest archaeological examples of monkey tool use outside of Africa. In their paper, published in Current Biology, they suggest it raises questions about the origins and spread of tool use in New World monkeys and, controversially perhaps, prompts us to look at whether early human behaviour was influenced by their observations of monkeys using stones as tools. The research was led by Dr Michael Haslam of the University of Oxford, who in previous papers presents archaeological evidence showing that wild macaques in coastal Thailand used stone tools for decades at least to open shellfish and nuts.

This latest paper involved a team from Oxford and the University of São Paulo in Brazil, who observed groups of modern capuchins at Serra da Capivara National Park in northeast Brazil, and combined this with archaeological data from the same site. Researchers watched wild capuchins use stones as hand-held hammers and anvils to pound open hard foods such as seeds and cashew nuts, with young monkeys learning from older ones how to do the same. The capuchins created what the researchers describe as ‘recognisable cashew processing sites’, leaving stone tools in piles at specific places like the base of cashew trees or on tree branches after use. They found that capuchins picked their favourite tools from stones lying around, selecting those most suitable for the task. Stones used as anvils were over four times heavier than hammer stones, and hammers four times heavier than average natural stones. The capuchins also chose particular materials, using smooth, hard quartzite stones as hammers, while flat sandstones became anvils

Using archaeological methods, the researchers excavated a total of 69 stones to see if this tool technology had developed at all over time. They dug to a depth of 0.7 metres at a site close to cashew trees where they had seen modern capuchins frequently using their stone tools. They identified the tools from inspecting the size and shape of the stones, as well as the distinctive damage on the stone surface caused by capuchin pounding. Through mass spectrometry, the researchers were able to confirm that dark-coloured residues on the tools were specifically from cashew nuts. They also carbon dated small pieces of charcoal discovered with the stones to establish the oldest were least 600 to 700 years old — meaning the tools predate the arrival of Europeans in the New World.

In the paper, the researchers estimate that around 100 generations of capuchins have used this tradition of stone tools. They compared tools used by modern capuchins with the oldest excavated examples, finding they are similar in terms of weight and materials chosen. This apparent lack of change over hundreds of years suggests monkeys are ‘conservative’, preferring not to change the technology used, unlike humans living in the same region, says the paper.

Lead author Dr Michael Haslam, from the School of Archaeology at the University of Oxford, said: ‘Until now, the only archaeological record of pre-modern, non-human animal tool use comes from a study of three chimpanzee sites in Cote d’Ivoire in Africa, where tools were dated to between 4,300 and 1,300 years old. Here, we have new evidence that suggests monkeys and other primates out of Africa were also using tools for hundreds, possibly thousands of years. This is an exciting, unexplored area of scientific study that may even tell us about the possible influence of monkeys’ tool use on human behaviour. For example, cashew nuts are native to this area of Brazil, and it is possible that the first humans to arrive here learned about this unknown food through watching the monkeys and their primate cashew-processing industry.’

Tool use by monkeys has featured in other research led by Dr Haslam in recently published papers. In a study in the Journal of Human Evolution (published in June 2016), the team noted how groups of macaques in the marine national park on Piak Nam Yai Island, Thailand, selected stones as tools to crush marine snails, nuts and crabs. They also identified 10 tools in excavations at the site, which they dated as between 10 and 50 years old. In another research paper detailing fieldwork at the same site, they say the modern macaques typically moved their tools a metre or less from where they picked them up, but the longest distance they observed was around 87m. The macaques ate nine oysters at a time, on average, and generally carried the same tool over short distances. In one case, however, the researchers saw a hungry macaque eat 63 oysters one after the other, using the same stone tool to open all the shells, says the paper.

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https://www.sciencedaily.com/releases/2016/07/160711150920.htm  Original web page at Science Daily

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* New veterinary research helps distinguish accidents from abuse

A veterinarian sees a canine patient with severe rib and head injuries whose cause of injury is unknown. Without having witnessed the incident, how can the veterinary professional distinguish an accident from abuse?

Using data from criminal cases of animal abuse, researchers from Cummings School of Veterinary Medicine at Tufts University and the American Society for the Prevention of Cruelty to Animals (ASPCA) have demonstrated that motor vehicle accidents and non-accidental blunt force trauma cases in dogs and cats present with different types of injuries. The research, which appears online in advance of the September 2016 print edition of the Journal of Forensic Sciences, can help in the effort to uncover and address animal abuse.

While the veterinary community, health professionals and public officials have acknowledged the need to address animal cruelty and have developed general guidelines for identifying suspicious behavior, clinicians face many difficulties in identifying specific injuries caused by abuse.

In cases of injury caused by animal abuse, commonly referred to as non-accidental, the cause reported by the abuser typically differs from the actual cause. Motor vehicle accidents are often falsely cited when an animal presents with skeletal injuries.

The new study compared records from 50 criminal cases of abuse provided by the ASPCA’s Humane Law Enforcement Division with a sample of 426 motor vehicle accident cases from the Foster Hospital for Small Animals at Cummings School. It is the first study of its kind to look at two populations of animals with known causes of injuries.

“Our research has found that non-accidental injury and motor vehicle accidents cause different patterns of skeletal and soft tissue injury,” says one of the study’s lead authors, Nida Intarapanich, fourth-year veterinary student at Cummings School.

The researchers found that abused animals generally had more head injuries and rib fractures, as well as tooth fractures and claw damage. Pets involved in motor vehicle accidents tended to suffer skin abrasions or injuries in which the skin is torn from tissue, lung collapse and bruising, and hind end injury, which the researchers suggest could be a result of running away from a moving vehicle.

“To date there has been very little documentation in veterinary literature regarding the patterns of injury caused by humans harming an animal intentionally, and there is a need for greater awareness and knowledge,” says another author on the study, Emily McCobb, D.V.M, M.S., DACVAA, clinical assistant professor and director of the Shelter Medicine Program at Cummings School of Veterinary Medicine at Tufts University.

A clear difference in rib fracture patterns was demonstrated, with abuse injuries generally causing fractures on both sides of the body, while rib fractures caused by motor vehicle accidents tended to appear on only one side of the body, with the ribs closer to the head more likely to fracture.

Researchers also found that victims of non-accidental injury were more likely to have evidence of older fractures, a pattern that is similarly seen in human abuse cases.

“The forensic veterinarian’s job is to use scientific evidence to tell the story of an animal victim of cruelty. This study serves as a valuable tool in that process,” says Robert Reisman, D.V.M., supervisor of forensic sciences, ASPCA Anti-Cruelty Group, who also collaborated on this research. “This study contributes to the expanding body of research in the growing field of veterinary forensic medicine and will help forensic veterinarians continue to give a voice to the voiceless.”

https://www.sciencedaily.com/ Science Daily

https://www.sciencedaily.com/releases/2016/05/160525101720.htm Original web page at Science Daily

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30 years after Chernobyl, camera study reveals wildlife abundance in Chernobyl

Thirty years ago, the Chernobyl Nuclear Power Plant in Pripyat, Ukraine, became the site of the world’s largest nuclear accident. While humans are now scarce in the Chernobyl Exclusion Zone, continued studies–including a just-published camera study conducted by researchers from the University of Georgia’s Savannah River Ecology Laboratory–validate findings that wildlife populations are abundant at the site.

The camera study, published in the journal Frontiers in Ecology and the Environment and led by UGA’s James Beasley, is the first remote-camera scent-station survey conducted within the Chernobyl Exclusion Zone, or CEZ. The study’s results document species prevalent in the zone and support earlier findings that animal distribution is not influenced by radiation levels.

The restricted CEZ encompasses the bordering lands of Ukraine and Belarus impacted by radiation fallout from the accident, which occurred April 26, 1986.

Within the southern portion of Belarus is the Polessye, or Polesie State Radiation Ecological Reserve, with over 834 square miles of diverse landscape including forests and deserted developed lands. The levels of radiation vary significantly across this landscape.

The previous study, published in fall 2015, determined populations were thriving in the CEZ by counting animal tracks. Beasley and his research team used a more contemporary research method–remote camera stations–to substantiate previous findings.

“The earlier study shed light on the status of wildlife populations in the CEZ, but we still needed to back that up,” said Beasley, an assistant professor with UGA’s Savannah River Ecology Laboratory and the Warnell School of Forestry and Natural Resources and the senior author on the study. “For this study we deployed cameras in a systematic way across the entire Belarus section of the CEZ and captured photographic evidence–strong evidence–because these are pictures that everyone can see.”

The study was conducted over a five-week period at 94 sites using 30 cameras. A remote camera was set up on a tree or tree-like structure for seven days at each location. Each station was equipped with a fatty acid scent to attract the animals.

Sarah Webster, a graduate student at SREL and Warnell working with Beasley, set up the stations approximately 2 miles apart to prevent animals from visiting more than one station during a 24-hour period.

The team documented every species captured on the cameras and the frequency of their visits, specifically focusing on carnivores, Webster said, because of their hierarchy on the food chain.

At the top of the food chain, carnivores have an increased opportunity to receive contamination. In addition to ingesting it from prey that have foraged on the landscape, they receive it directly from the environment–through the soil, water and air.

“Carnivores are often in higher trophic levels of ecosystem food webs, so they are susceptible to bioaccumulation of contaminants,” Webster said. “Few studies in Chernobyl have investigated effects of contamination level on populations of species in high trophic levels.”

Beasley and his research team saw 14 species of mammals on the camera footage. The most frequently seen were the gray wolf, wild or Eurasian boar, red fox and raccoon dog, a canid species found in East Asia and Europe. Beasley said all of these species were sighted at stations close to or within the most highly contaminated areas.

“We didn’t find any evidence to support the idea that populations are suppressed in highly contaminated areas,” Beasley said. “What we did find was these animals were more likely to be found in areas of preferred habitat that have the things they need–food and water.”

Webster said locations were chosen to ensure habitat variance and to incorporate the diverse levels of radiation in the zone.

The study provides much needed verification, Beasley said, but further studies are needed “to determine the density of wildlife and provide quantitative survival rates.”

https://www.sciencedaily.com/  Science Daily

https://www.sciencedaily.com/releases/2016/04/160418161400.htm  Original web page at Science Daily

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DNA proves mammoths mated beyond species boundaries

Several species of mammoth are thought to have roamed across the North American continent. A new study in the open-access journal Frontiers in Ecology and Evolution, provides DNA evidence to show that these mammoths, which should only mate within their species boundaries, were in fact likely to be interbreeding.

A species can be defined as a group of similar animals that can successfully breed and produce fertile offspring. By using differences in the size and shape of their fossilized teeth, a number of North American mammoth species have been identified. But, some scientists are not confident this method of species categorization tells the whole story.

“Species boundaries can be very blurry. We might find differences in features of the teeth or skeleton that closely correspond to what we think are real species boundaries. But other features may not correspond to those boundaries, suggesting that what we formerly regarded as separate species are in fact not at all,” explains Hendrik Poinar, a Professor at McMaster University in Canada, who co-led the new study with his former graduate student Jake Enk and collaborator Ross MacPhee, a Professor at the American Museum of Natural History.

Professor Poinar and his co-authors used cutting-edge methods to distinguish species of North American mammoths. Tiny samples of fossilized mammoth bone, teeth and faeces, were generously donated by a number of museums across America and Canada. DNA was extracted from these samples in a specialized laboratory of the Ancient DNA centre at the McMaster University, and used to create a family tree of their evolution. The results proved to be very interesting.

North American mammoths such as the Columbian and Woolly Mammoths were historically thought to originate from two separate primitive species. However, this latest DNA analysis agrees with a more recent idea that all North American mammoths originated from a single primitive species, the Steppe Mammoth.

“Individuals of the Woolly and Columbian mammoths look like they represent different species in terms of their molar teeth, but their genetics say that they were not completely separate in the evolutionary sense and could successfully interbreed,” says Professor MacPhee.

Professor Poinar continues, “Mammoths were much better at adapting to new habitats than we first thought — we suspect that subgroups of mammoths evolved to deal with local conditions, but maintained genetic continuity by encountering and potentially interbreeding with each other where their two different habitats met, such as at the edge of glaciers and ice sheets.”

So, while mammoths clearly evolved differences in their physical appearance to deal with different environments, it did not prohibit them from cross-breeding and producing healthy offspring.

Despite this apparent adaptability, which should surely be a recipe for success, mammoths disappeared from the face of Earth 10,000 years ago. “Humans are suspected to be the cause, but this is not by any means proven. Explaining the loss of mammoths and a host of other Ice Age creatures continues to be a fascinating conundrum in paleobiology,” concludes Professor MacPhee.

As well as challenging the classic method of defining a species, the authors believe the findings of this study are just the start of understanding mammoth evolutionary history. Techniques to extract and analyse ancient DNA have undergone a tremendous improvement in recent years and as these technologies continue to improve we can expect further breakthroughs.

https://www.sciencedaily.com/  Science Daily

https://www.sciencedaily.com/releases/2016/04/160421100815.htm  Original web page at Science Daily

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Mammal-like reptile survived much longer than thought

Teeth can reveal a lot, such as how the earliest mammals lived with their neighbors. Researchers have uncovered dozens of fossilized teeth in Kuwajima, Japan and identified this as a new species of tritylodontid, an animal family that links the evolution of mammals from reptiles. This finding suggests that tritylodontids co-existed with some of the earliest mammal species for millions of years, overturning beliefs that mammals wiped out mammal-like reptiles soon after they emerged.

Tritylodontids are the last known family of near-mammalian reptiles, before mammals with features such as advanced hearing evolved.

“Tritylodontids were herbivores with unique sets of teeth which intersect when they bite,” explains study author Hiroshige Matsuoka, based at Kyoto University. “They had pretty much the same features as mammals — for instance they were most likely warm-blooded — but taxonomically speaking they were reptiles, because in their jaws they still had a bone that in mammals is used for hearing.”

While excavating a geologic layer from the Cretaceous era in Kuwajima, researchers found fossils of dinosaurs, turtles, lizards, fish, many types of plants, and Mesozoic mammals. Among these were more than 250 tritylodontid teeth, the first to be found in Japan.

Tritylodontids lived in the Jurassic era and proliferated worldwide, but were thought to have died out as herbivorous mammals took over their ecological role in the late Jurassic. “This made sense, because otherwise tritylodontids and the herbivorous mammals would have competed for the same niche,” says Matsuoka.

But according to the team’s finding, trytylodontids seem to have survived at least 30 million years longer than what paleontologists had believed.

“This raises new questions about how tritylodontids and their mammalian neighbors shared or separated ecological roles,” says Matsuoka.

The study is also the first of its kind to depend solely on details from teeth to determine whether the species is new, and also where it sits on the evolutionary tree.

“Usually fossils are identified as a new species only when a relatively complete set of structures like a jaw bone are found. In these cases, characteristics of teeth tend to be described only briefly,” adds Matsuoka. “Tritylodontid teeth have three rows of 2-3 cusps. This time we paid attention to fine details like the size and shape of each cusp. By using this method it should be possible to characterize other species on the evolutionary tree as well.”

“Because fossils of so many diverse families of animals are to be found in Kuwajima, we’d like to keep investigating the site to uncover things not just about individual species, but also about entire ecological dynamics.”

https://www.sciencedaily.com/  Science Daily

https://www.sciencedaily.com/releases/2016/04/160425112655.htm  Original web page at Science Daily

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Scientists discover how the brain repurposes itself to learn scientific concepts

The human brain was initially used for basic survival tasks, such as staying safe and hunting and gathering. Yet, 200,000 years later, the same human brain is able to learn abstract concepts, like momentum, energy and gravity, which have only been formally defined in the last few centuries.

New research from Carnegie Mellon University has now uncovered how the brain is able to acquire brand new types of ideas. Published in Psychological Science, scientists Robert Mason and Marcel Just used neural-decoding techniques developed at CMU to identify specific physics concepts that advanced students recalled when prompted. The brain activation patterns while thinking about the physics concepts indicated that all of the students’ brains used the ancient brain systems the same way, and the patterns revealed how the new knowledge was formed — by repurposing existing neural systems.

The findings could be used to improve science instruction. “If science teachers know how the brain is going to encode a new science concept, then they can define and elaborate that concept in ways that match the encoding. They can teach to the brain by using the brain’s language,” said Mason, a senior research associate in the Dietrich College of Humanities and Social Sciences’ Department of Psychology.

Mason and Just, the D. O. Hebb University Professor of Psychology, recruited nine advanced physics and engineering students to participate in the study. Each student’s brain was scanned at CMU’s Scientific Imaging and Brain Research (SIBR) Center while they were shown a set of 30 familiar concepts, such as gravity, entropy, inertia, refraction and velocity.

Using a machine learning program, Mason and Just were able to identify which of the 30 concepts a student was thinking about because the thought of each concept created its own brain activation pattern. They also could break down the patterns into the different neural pieces used to build the full concepts.

The research showed for the first time how learning physics concepts is accomplished by repurposing neural structures that were originally used for general everyday purposes. More specifically, the brain is able to learn physics concepts because of its ability to understand the four fundamental concepts of causal motion, periodicity, energy flow and algebraic (sentence-like) representations.

Brain systems that process rhythmic periodicity when hearing a horse gallop also support the understanding of wave concepts in physics. Similarly, understanding gravity involves visualizing causal motion, like an apple falling from a tree; energy flow uses the same system as sensing warmth from a fire or the sun; and understanding how one concept relates to others in an equation uses the same brain systems that are used to comprehend sentences describing quantities.

“This is why humans have been able to move ahead and innovate — because we can use our brain for new purposes,” Just said. “Human brains haven’t changed much over a few thousand years, but new fields like aeronautics, genetics, medicine and computer science have been developed and continuously change. Our findings explain how the brain is able to learn and discover new types of concepts.”

These findings are examples of the many brain research breakthroughs at Carnegie Mellon. CMU has created some of the first cognitive tutors, helped to develop the Jeopardy-winning Watson, founded a groundbreaking doctoral program in neural computation, and is the birthplace of artificial intelligence and cognitive psychology. Building on its strengths in biology, computer science, psychology, statistics and engineering, CMU launched BrainHub, an initiative that focuses on how the structure and activity of the brain give rise to complex behaviors.

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https://www.sciencedaily.com/releases/2016/04/160412132608.htm Original web page at Science Daily

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New basal bird from China reveals the morphological diversity in early birds

Over the past three decades, representatives of all major Mesozoic bird groups have been reported from the Early Cretaceous Jehol Biota of northeastern China. A new species, Chongmingia zhengi, reported in the journal of Scientific Reports on 25 January 2016, sheds light on the early evolution of birds. Phylogenetic analyses indicate that it is basal to the dominant Mesozoic avian clades Enantiornithes and Ornithuromorpha, and represents a new basal avialan lineage. This new discovery adds to our knowledge regarding the phylogenetic differentiation and morphological diversity in early avian evolution.

This new species, represented by a single new skeleton from the Early Cretaceous Jiufotang Formation of the Jehol Group in Dapingfang, Liaoning Province, China. The generic name is from the Mandarin word Chongming, referring to a Chinese mythological bird. The specific epithet is in honour of Mr. ZHENG Xiaoting for his generous contribution in the establishment of the Shandong Tianyu Museum of Nature.

The new specimen is a partial skeleton with associated soft tissues and gastroliths, missing the skull and most of the caudal vertebrae. Comparative studies indicate that it is a large non-ornithothoracine bird distinguishable from the known basal avialans by a combination of features.

The furcula of Chongmingia is rigid (reducing its efficiency), consequently requiring more power for flight. However, the elongated forelimb and the large deltopectoral crest on the humerus might indicate that the power was available. The unique combination of features present in this species demonstrates that numerous evolutionary experimentations took place in the early evolution of powered flight.

Histological studies indicate Chongmingia had a moderately elevated growth rate relative to the long-tailed Archaeopteryx and Jeholornis. Furthermore, other morphological features, along with the evolutionary pattern drawn from other basal birds, reveal mosaic evolution and numerous evolutionary experiments relating to powered flight early in the evolution of birds.

The occurrence of gastroliths further confirms that herbivory was common among basal birds. The Jehol birds faced competition with pterosaurs, and occupied sympatric habitats with nonavian theropods, some of which consumed birds. Thus, avialan herbivory may have reduced ecological competition from carnivorous close relatives and other volant vertebrates early in their evolutionary history.

“Although our analysis suggests that the new specimen may represent the most phylogenetically basal Cretaceous bird known to date, this phylogenetic hypothesis should be treated with caution given the incomplete preservation of the skeleton and low phylogenetic support values,” said lead author Dr. WANG Min, Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of the Chinese Academy of Sciences.

https://www.sciencedaily.com/  Science Daily

https://www.sciencedaily.com/releases/2016/03/160302121331.htm  Original web page at Science Daily

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New species couldn’t hop, but outlived its fanged kangaroo contemporaries

A University of Queensland (UQ)-led study has discovered a new genus and two new species of extinct kangaroos which couldn’t hop, but may have been ancestral to all kangaroos and wallabies living today.

Lead author Kaylene Butler of UQ’s School of Earth Sciences said the new kangaroo species were discovered in ancient fossil deposits at the Riversleigh World Heritage Area in north-western Queensland, Australia.

“They lived around 15-23 million years ago and were the size of very small wallabies or pademelons,” she said.

“They moved on all fours, scurrying across a densely forested landscape quite different from the dry outback we see in western Queensland today.

“It also appears that our new species were direct competitors with a second group of kangaroos at Riversleigh, the even weirder ‘balbarid’ or fanged kangaroos.

“It seems likely that the fanged cousins were out-competed by our new species and their descendants.”

The new species may have been better adapted than their fanged cousins to the environmental change from rainforest to more open forest and woodland environments. They are described in the Journal of Vertebrate Paleontology.

Ms Butler worked on fossil material as part of her PhD research supervised by study co-authors former UQ Robert Day Fellow, Dr Kenny Travouillon, now of Western Australian Museum, and Dr Gilbert Price of UQ.

Riversleigh research leaders Professors Michael Archer and Suzanne Hand, of the University of New South Wales, are also study authors.

She said that by taking measurements and comparing skulls and teeth with known species, it was discovered that they were looking at both a new genus (taxonomic rank) and two new species within the genus.

She said the new genus was named Cookeroo, in honour of Dr Bernard Cooke, a distinguished Queensland Museum researcher who led much of the research program focused on the evolution of Riversleigh’s ancient kangaroos.

The two new species within the genus are Cookeroo bulwidarri, which lived about 23 million years ago, and Cookeroo hortusensis which lived 20 million to 18 million years ago.

Bulwidarri means “white” in the Aboriginal Waanyi language, and is named for White Hunter Site at the Riversleigh World Heritage Area where specimens of this species were obtained. Hortusensis is Latin for “belonging to the garden,” in reference to Neville’s Garden Site at Riversleigh where specimens of this species were found.

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https://www.sciencedaily.com/releases/2016/02/160222111230.htm  Original web page at Science Daily

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An ancestor of the rabbit connects Europe and Asia

The species Amphilagus tomidai was recently discovered — an ancestor of the rabbit which lived in present-day Siberia during the Miocene, about 14 million years ago. The discovery of this mammal, belonging to a family which was thought to only exist in Europe, reveals that the two continents were connected ‑free of natural barriers‑ due to the disappearance of the ancient Paratethys Sea.

A study led by the Institute of Geology of the Russian Academy of Sciences presents a new species, the Amphilagus tomidai, found in south-eastern Siberia (Russia) and dating back to the Middle Miocene, about 14 million years ago. The discovery of this mammal, an ancestor of the present-day rabbit, represents an important biogeographic link that confirms the widespread distribution of this group as well as the relationship between Asia and Europe during this period.

Amphilagus is a genus that was traditionally thought to only exist in Europe, but remains of this mammal were recently located in Asia. The discovery of this mammal on the continent of Asia indicates that there were some paleogeographic and environmental conditions that favoured the expansion of this species towards the east,” explains Chiara Angelone, a researcher at the Catalan Institute of Palaeontology Miquel Crusafont and co-author of the study published in the journal Historical Biology.

According to the study, the Miocene -which began 23 million years ago and ended 5.3 million years ago- gave rise to the barrier-free linking of Europe and Asia which would have allowed for the spread of this animal.

An ancestor of the present-day rabbit -which was located to the south of Europe and spanned from the northern Alps to the Aral Sea in western Asia- had disappeared, and a lack of high mountains here meant that there were no barriers to hinder this animal’s expansion. This situation favoured the spread of the mammal among open landscapes, aided by a cool, dry climate.

“These ancient animals help us to better understand the climatic and paleogeographic conditions of that period in time. Some discoveries add new insight into what we already know. Others, such as this one, uncover remarkable stories,” explains Angelone.

The mammal that was unearthed is the northern — most Eurasian specimen of the Amphilagus genus ‑- a large lagomorph with primitive features. Its teeth have roots and do not continuously grow as do the teeth of present-day lagomorphs, an animal order that includes the families of rabbits, hares and pikas.

This newly discovered animal also possesses a simple, lower third premolar and a hypoconulid -an additional cusp at the back of the mouth- among the lower molariform teeth.

The Amphilagus genus, which appeared in Europe during the Upper Oligocene, is not free from controversy. According to the authors of the study, all European lagomorphs whose teeth had roots are considered part of the Amphilagus genus, thus making it necessary to re-evaluate this genus.

http://www.sciencedaily.com/  Science Daily

http://www.sciencedaily.com/releases/2016/01/160126111525.htm  Original web page at Science Daily

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Ancient rodent’s brain was big … but not necessarily ‘smart’

If new U of T research on the brains of an ancient rodent tells us anything, it’s that bigger does not necessarily mean better.

U of T Scarborough PhD candidate Ornella Bertrand along with Associate Professor Mary Silcox and undergraduate student Farrah Amador-Mughal recently reconstructed two endocasts of Paramys, the oldest and best-preserved rodent skulls on record. What they found was surprising.

“The brain was certainly larger than we expected considering the time period,” says Bertrand. “Even more surprising is that it was almost as large, and in some cases larger, than primitive primates of the same time period.”

The key difference is that Paramys was relatively smaller than even the most primitive primates in the neocortex region, the part of the brain that deals with “higher” brain functions like sight and hearing.

“This tells us that something is going on in the neocortex of early primates that is not observable in early rodents. ” says Bertrand. “The changes in the neocortex of rodents occurred later in time and with less intensity than in primates.”

“It also sheds some light on what’s unique about primate brains — they were not always exceptionally large, but they were certainly ‘smart’,'” adds Silcox.

One of the specimens of Paramys was a large rodent by modern standards — about three kilograms, roughly the size of a small cat — that lived during the mid-Eocene, some 47 to 49 million years ago. Bertrand and Silcox also examined the skull of another with a body mass of about one kilogram that lived around 50 to 52 million years ago.

The goal of the research was to better understand brain evolution in early rodents. While there’s been some research looking at how the neocortical surface of primates has increased over time, practically nothing prior to this has been done on rodents.

What fascinates both Bertrand and Silcox is that Paramys‘s brain was larger than some later occurring rodents, which contradicts the idea that brains generally increase in size over time.

“It’s been assumed for a while that mammal brain size increases over time. The idea is that it’s probably an evolutionary arms race because if prey become smarter predators have to adapt. But these animals were already pretty smart prey items to begin with,” says Silcox.

The research also shows that the obsession with brain size, especially in the human paleontological literature, makes little sense since size is not the only indicator of intelligence.

“Size is certainly important, but we’re starting to look at different measures that give us a more nuanced understanding of how brains, especially in primates, evolved over time,” says Silcox. The research is available online in the journal Royal Society B.

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http://www.sciencedaily.com/releases/2016/01/160127121549.htm  Original web page at Science Daily

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Ancient wildebeest-like animal shared ‘bizarre’ feature with dinosaur

By poring over the fossilized skulls of ancient wildebeest-like animals (Rusingoryx atopocranion) unearthed on Kenya’s Rusinga Island, researchers have discovered that the little-known hoofed mammals had a very unusual, trumpet-like nasal passage similar only to the nasal crests of lambeosaurine hadrosaur dinosaurs. The findings reported in the Cell Press journal Current Biology on February 4 offer “a spectacular example” of convergent evolution between two very distantly related taxa and across tens of millions of years, the researchers say.

“The nasal dome is a completely new structure for mammals– it doesn’t look like anything you could see in an animal that’s alive today,” says Haley O’Brien of Ohio University, Athens. “The closest example would be hadrosaur dinosaurs with half-circle shaped crests that enclose the nasal passages themselves.”

This evolutionary convergence may be explained by similarities in the way Rusingoryx and hadrosaurs lived. In fact, hadrosaurs are sometimes referred to as the “cows of the Cretaceous.”

For Tyler Faith of the University of Queensland, one of the study’s corresponding authors, it all started in 2009. He and his colleagues were working on a field program in the Lake Victoria region when other scientists directed them to a site they called Bovid Hill. The hill had been so named because of an abundance of fossil Bovidae, the group including antelopes and buffaloes, eroding from its surface.

“After several years of collecting fossils from Bovid Hill, it became very clear that most of the fossils belonged to the poorly known species Rusingoryx atopocranion, described from the same site in 1983, and that we may be dealing with an entire herd that was somehow wiped out and buried at the site,” Faith says.

The researchers also uncovered stone tools and butchered bone, raising the possibility that early modern humans had something to do with the peculiar concentration of Rusingoryx skeletons. In 2011, study co-author Kirsten Jenkins of the University of Minnesota took charge of excavations, hoping to find more complete fossils and to establish why so many skeletons had ended up in that spot. Along the way, she found several intact skulls.

“I was astonished to see that the skulls looked unlike any antelope that I had ever seen–the only thing more surprising would have been fossil zebras with horns growing from their heads!” Faith says. “The anatomy was clearly remarkable.”

Faith and O’Brien later decided to explore the anatomy further in six skulls representing Rusingoryx juveniles and adults. The similarity to hadrosaurs was immediately clear to the researchers when they opened CT scan files revealing the inner structures of those bones.

“We were expecting the inside of the dome to have something closer to normal mammalian anatomy, but once we took a look at the CT scans, we were pretty shocked,” O’Brien says.

At first, the researchers thought the hollow nasal dome might have had something to do with thermoregulation. Now, based on their anatomical investigations together with acoustical modeling, they think the trumpet-like nasal tube may have allowed Rusingoryx to deepen its normal vocal calls. In fact, their calculations suggest that the animals might have been able to call at levels very close to infrasound, such that other animals may not have been able to hear individuals in the herd calling back and forth to each other.

Both Rusingoryx and hadrosaur dinosaurs are thought to have been highly social, O’Brien explains. They might have communicated with each other across fairly large distances.

“Vocalizations can alert predators, and moving their calls into a new frequency could have made communication safer,” she says. “On top of this, we know that both Rusingoryx and hadrosaurs were consummate herbivores, each having their own highly specialized teeth. Their respective, remarkable dental specializations may have initiated changes in the lower jaw and cheek bones that ultimately led to the type of modification we see in the derived, crest-bearing forms.”

The researchers say they will continue to explore the developmental shifts required to produce the animals’ bizarre morphology. They’d also like to understand what ultimately led the once-thriving Rusingoryx to disappear.

http://www.sciencedaily.com/   Science Daily

http://www.sciencedaily.com/releases/2016/02/160204150559.htm  Original web page at Science Daily

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* Dog domestication may have increased harmful genetic changes, biologists report

The domestication of dogs may have inadvertently caused harmful  genetic changes, a UCLA-led study suggests. Domesticating dogs from gray wolves more than 15,000 years ago involved artificial selection and inbreeding, but the effects of these processes on dog genomes have been little-studied.

UCLA researchers analyzed the complete genome sequences of 19 wolves; 25 wild dogs from 10 different countries; and 46 domesticated dogs from 34 different breeds. They found that domestication may have led to a rise in the number of harmful genetic changes in dogs, likely as a result of temporary reductions in population size known as bottlenecks.

“Population bottlenecks tied to domestication, rather than recent inbreeding, likely led to an increased frequency of deleterious genetic variations in dogs,” said Kirk Lohmueller, senior author of the research and assistant professor of ecology and evolutionary biology in the UCLA College.

“Our research suggests that such variants may have piggybacked onto positively selected regions, which were also enriched in disease-related genes,” Lohmueller said. “Thus, the use of small populations artificially bred for desired traits, such as smaller body size or coat color, may have led to an accumulation of harmful genetic variations in dogs.”

Such variations, Lohmueller said, could potentially lead to a number of different developmental disorders and other health risks.

Selective breeding programs, particularly those aimed at conserving rare and endangered species, may need to include and maintain large populations to minimize the inadvertent enrichment of harmful genetic changes, he said.

The research was published recently in the journal Proceedings of the National Academy of Sciences.

http://www.sciencedaily.com/  Science Daily

http://www.sciencedaily.com/releases/2016/01/160111162701.htm  Original web page at Science Daily

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Extinct 3-horned palaeomerycid ruminant found in Spain

The extinct three-horned palaeomerycid ruminant, Xenokeryx amidalae, found in Spain, may be from the same clade as giraffes, according to a study published December 2, 2015 in the open-access journal PLOS ONE by Israel M. Sánchez from the Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain, and colleagues.

Palaeomerycids, now extinct, were strange three-horned Eurasian Miocene ruminants known through fossils from Spain to China. In this article, the authors classify the palaeomerycid to their clade based on shared characteristics with the best-known species of the group and reassess their phylogenetic position among ruminants, which is currently disputed. The authors use well-preserved remains of a new palaeomerycid, Xenokeryx amidalae, which included a complete sample of cranial–including both frontal and supra-occipital ‘t-shaped’ cranial appendages–dental, and postcranial remains, from middle Miocene deposits of Spain.

The authors found that despite their apparent external similarities, Eurasian palaeomerycids are not closely related to North American dromomerycids, distant relatives to deer, as some scientists have thought. Instead, palaeomerycids are in the clade Giraffomorpha, the least inclusive clade containing Giraffa and Triceromeryx. The authors conclude that future ruminant research will benefit from more in-depth analysis, such as phylogenetic analysis combining fossil and living taxa, morphological and molecular datasets, and fossil ages.

Israel Sánchez adds: “Establishing the place of palaeomerycids in the ruminant tree gives us insights into the evolutionary history of the large clade of pecoran ruminants that include giraffes (Giraffa and Okapia) as its only extant survivors, and shows us the amazing diversity of an ancient lineage that inhabited both Eurasia and Africa.”

http://www.sciencedaily.com/  Science Daily

http://www.sciencedaily.com/releases/2015/12/151202155705.htm  Original web page at Science Daily

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* Cheetahs migrated from North America

The cheetah (Acinonyx jubatus) is now at home on the African plains, but it started a migration 100, 000 years ago from North America towards its current habitat. The research, published in the open access journal Genome Biology, found that the migration from North America was costly for the species, triggering the first major reduction in their gene pool.

The modern African cheetah is found across eastern and southern Africa, but it is highly endangered because of their small free ranging population and inbreeding. Researchers from St. Petersburg State University, Russia, in collaboration with BGI, China and CCF, Namibia, sequenced the genome from a male Namibian cheetah, called ‘Chewbaaka’, and six other wild cheetahs from Tanzania and Namibia. This gave further insight into the species evolutionary history and the breadth of genome impoverishment, which elevates juvenile mortality, causes extreme abnormalities in sperm development and increases vulnerability to infectious disease outbreaks.

A total of 18 cheetah genes showed damaging mutations and one gene in particular, AKAP4, showed a large number of mutations, which could harm sperm development and may explain why cheetah have a large proportion of defective sperm, and hence their low reproductive success.

The cheetah is descended from a relative of American pumas and their fossil record extends across the Americas, Europe and Asia. The species has suffered two population bottlenecks — an event whereby the population is rapidly reduced due to environmental factors.

The first of these took place 100, 000 years ago, around the late Pleistocene — a geological period shaped by repeated glaciations, when cheetahs started to move towards Asia across the Beringian landbridge and then travelled south to Africa. This migration was punctuated with dwindling populations and limited gene flow due to the individuals’ own vast territory boundaries, measuring 300-800 square miles, thereby increasing incestuous mating.

The second bottleneck around 10- 12, 000 years ago, further reduced numbers, leading to further loss of endemic variability observed in modern cheetahs. This is because cheetahs disappeared from North America, when the last glacial retreat caused an abrupt extinction resulting in the loss of many large mammals, including cheetahs and pumas, from North America.

Cheetahs accept skin grafts from unrelated cheetahs as if they were clones. The genome analysis suggests that this is partly due to the loss of a few immune related genes and dramatic loss of diversity in the cheetahs’ flagella genes. The variation is so limited that it is far below that observed in inbred dogs and cats. Tests carried out by the researchers show that the cheetah has lost 90-99% of the genetic variation typically seen in outbred mammals.

The researchers conclude that this latest insight into the history and adaptation of the endangered cheetah should be useful in efforts to sustain and increase cheetah population numbers in their present and former range habitats.

http://www.sciencedaily.com/ Science Daily

http://www.sciencedaily.com/releases/2015/12/151208204222.htm  Original web page at Science Daily

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* Scientists peg Anthropocene to first farmers

A new analysis of the fossil record shows that a deep pattern in nature remained the same for 300 million years. Then, 6,000 years ago, the pattern was disrupted — at about the same time that agriculture spread across North America.

“When early humans started farming and became dominant in the terrestrial landscape, we see this dramatic restructuring of plant and animal communities,” said University of Vermont biologist Nicholas Gotelli, an expert on statistics and the senior author on the new study.

In the hunt for the beginning of the much-debated “Anthropocene” — a supposed new geologic era defined by human influence of the planet — the new research suggests a need to look back farther in time than the arrival of human-caused climate change, atomic weapons, urbanization or the industrial revolution.

“This tells us that humans have been having a massive effect on the environment for a very long time,” said S. Kathleen Lyons, a paleobiologist at the Smithsonian’s National Museum of Natural History who led the new research. The study was published Dec. 16 in the journal Nature.

Gotelli and Lyons were part of a team of 29 scientists, supported by the National Science Foundation, who studied plant and animal datasets from both modern ecosystems and the fossil record stretching back to the Carboniferous Period, well before the emergence of the dinosaurs.

Examining thousands of pairs of species, the scientists looked to see how often a particular pair of plant or animal species was found within the same community. Analyses of modern communities of plants and animals have shown that, for most pairs of species, the presence of one species within a community does not influence whether the other is present or absent. “We don’t expect much interaction between, say, a woodpecker and an earthworm,” Gotelli explains.

But some pairs of species appear to be “aggregated,” meaning they tend to appear together in nature more often than one would expect by chance — like cheetahs and giraffes who both depend on savannah habitats. Other species are “segregated,” meaning that when one is found, it’s unlikely to find the other there too — “say two species of woodpecker that compete for insect prey,” Gotelli says — being driven apart by, perhaps, different habitat needs or fierce competition, so that they occur together less often than would be expected by chance.

For modern communities of plants and animals, recent studies show that segregated species pairs are more common than aggregated ones. But when the team investigated the composition of ancient communities using data from fossils, they were surprised to find the opposite pattern: from 307 million years ago to about 6,000 years ago, there was a higher frequency of aggregated species pairs. Then, from 6,000 years ago to the present, the pattern shifted to a predominance of segregated species pairs. An ancient rule had changed.

“We don’t have direct evidence to show that this pattern change was caused by humans,” Gotelli cautions, but the indirect evidence is compelling. The team’s statistical analyses considered nearly 358,896 pairs of organisms in 80 plant or mammal communities on different continents, with data sets that collectively covered the last 300 million years of earth history — including data sets that spanned the huge Permian-Triassic extinction (the “Great Dying” 252 million years ago), the Cretaceous-Paleogene extinction of the dinosaurs (66 million years ago), and a period of rapid global climate change around 56 million years ago.

The pattern of aggregated species occurrences remained the same across these massive disturbances and time spans, but then a dramatically new pattern started emerging about 6,000 years ago, during the great Neolithic revolution when humans developed agriculture and their populations grew and spread globally. From this time until the present, plant and animal communities exhibit less co-occurrence and a greater frequency of segregated species pairs.

The scientists explored — and eliminated — many possible reasons for why this new pattern appeared, including several kinds of statistical and sampling artifacts that might explain the shift they saw in the data. For example, Earth’s climate became much more variable during modern times, and the team wondered whether this might explain the shift. But when they tracked climactic trends that occurred during the periods represented by their fossils, using data obtained from ancient ice and deep-sea cores, they found no evidence that ancient climate variability was responsible for the change in co-occurrence patterns.

“So we’re left with human impacts,” Lyons said. “We think it’s something that humans do that causes barriers to dispersal for both plant and animal species.” That idea is supported by data from modern island communities of plants and animals, which show even fewer co-occurring pairs than modern mainland communities. Island data sets, the authors note, are an extreme example of this phenomenon.

“If human activity has caused the terrestrial landscape to become more island-like, more fragmented,” Gotelli said, “that would be consistent with this pattern of more segregated species pairs.”

Around the time these patterns changed, humans were becoming increasingly dependent on agriculture — a cultural shift that physically altered the environment and would have introduced new barriers to dispersal of plants and animals. Even during the initial development of agriculture and expansion of human populations, the scientists could detect a shift in the structure of species co-occurrence, perhaps suggesting that species were not able to migrate as easily as they did for the previous 300 million years.

“The pattern of co-occurring species remained stable through the evolution of land organisms from the earliest tetrapods through dinosaurs, flowering plants and mammals,” said Anna K. Behrensmeyer, a paleobiologist with the Smithsonian’s Museum of Natural History and a co-author of the study. “This pattern didn’t change because of previous mass extinctions or ancient climate variability, but instead, early human activities 6,000 years ago suddenly began resetting a basic property of natural communities.”

And this change in an ancient natural pattern may have implications for modern conservation. “Isolating species has consequences — it can catalyze evolutionary change over hundreds of thousands to millions of years,” Behrensmeyer said, “but it also makes species more vulnerable to extinction.

“We humans have influenced the landscape, but perhaps for a lot longer than we had previously recognized,” says Gotelli, a professor in UVM’s biology department. “When we look at landscapes and say, ‘this is pristine or unaltered,’ that’s not necessarily true. We may have changed the rules over a much larger scale than we appreciate.”

Modern human-driven forces, like climate change and pollution, are “orders of magnitude more destructive than what early humans were doing,” Lyons said, but even at the dawn of human civilizations, people were certainly having major — and unprecedented — ecological impacts, she said. “If we are thinking about how we’re going to restore ecosystems, or how they’re going to respond to climate change,” UVM’s Gotelli said, “we need to understand how they were organized before humans ever came on the scene.”

http://www.sciencedaily.com/  Science Daily

http://www.sciencedaily.com/releases/2015/12/151217143546.htm  Original web page at Science Daily

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Missing link between dinosaur nests and bird nests

The links between dinosaurs and birds keep getting stronger: skeletal structures, feathers—and now nests. Whereas some dinosaurs buried their eggs crocodile-style, a new analysis suggests that other dinosaurs built open nests on the ground, foreshadowing the nests of birds.

Interpreting the fossil record is always tough, but analyzing trace fossils such as nests is especially daunting. Those structures, and the materials used to make them, usually aren’t preserved, says Darla Zelenitsky, a paleobiologist at the University of Calgary in Canada. When paleontologists do find a nestlike structure that includes material such as sticks or other vegetation, the question arises: Was this stuff part of the original nest, or just carried there with the sediment that buried the nest and helped preserve it?

To gain insight into dinosaur nesting habits, Zelenitsky and her colleagues studied the most durable parts of nests—the eggs themselves. (Being largely made of the mineral calcium carbonate, they’ve got a head start on fossilization and are sometimes incredibly well preserved.) In particular, the team looked at the size and arrangement of small pores in the ancient shells, because those details are telling in modern creatures.

In crocodiles’ buried nests, the heat needed to incubate the eggs comes from decomposition of overlying organic matter or the sunlight absorbed by the soil. Plus, in buried nests airflow is somewhat limited, thus requiring eggs to be relatively porous to help increase the flow of oxygen into and carbon dioxide out of the eggs. But birds that brood in open nests can get by laying eggs with fewer or smaller pores.

So the team compared the porosity of eggshells from 29 species of dinosaurs (including large, long-necked herbivores called sauropods; bipedal meat-eaters called theropods; and duck-billed dinosaurs) with that of shells from 127 living species of birds and crocodiles

Most of the dinosaur eggs were highly porous, suggesting that they buried their eggs to incubate them, the researchers report online today in PLOS ONE. But some of the dinosaur species in one group—a subset of well-evolved theropods considered to be the closest relatives of modern-day birds—laid low-porosity eggs, which suggests they incubated their eggs in open nests.

“This is a well done paper; the results make a lot of sense,” says Luis Chiappe, a vertebrate paleontologist at the Natural History Museum of Los Angeles County in California. The findings, he says, line up other studies suggesting that some birdlike dinosaurs were warm-blooded, which would have enabled them to incubate eggs in an open nest rather than depend on rotting vegetation or sunlight. Chiappe adds that the trend toward open nests could have allowed some dinosaurs to take another step toward birdlike nesting by moving their nests into the trees.

But considering only two types of nests—open versus buried—may be too simplistic, suggests Anthony Martin, a paleontologist at Emory University in Atlanta. Some dinosaurs—like a few of today’s birds—may have nested in burrows, which could have offered the stable temperature and protection from predators of a buried nest but resulted in low-porosity shells. Also, covered nests come in different types: Loose vegetation piled atop a buried nest can have a lot of airflow through it, allowing eggs to have relatively small pores, whereas eggs buried in soil or similar materials might not breathe as well and thus require larger pores, he notes. Nevertheless, Martin adds, the team’s study “is a good first start toward answering the question about what early dinosaur nests looked like.”

http://www.sciencemag.org/  Science Magazine

http://news.sciencemag.org/paleontology/2015/11/missing-link-between-dinosaur-nests-and-bird-nests?rss=1  Original web page at Science Magazine

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* Odd creature was ancient ancestor of today’s giraffes

A distant relative of today’s giraffes was a bit of an odd creature: It was about the size of a bull moose, but it had a long neck that could stretch both up to eat tree leaves and down to eat grass. That’s the conclusion of the first comprehensive analysis of a complete set of fossilized neck bones from the animal, known as Samotherium major. Samotherium, which lived in the open woodlands of Eurasia about 7 million years ago, had a neck about 1 meter long—about half the length of that of today’s giraffes. (And like the vast majority of mammals, from tiny mice to towering giraffes, it had seven neck vertebrae.) Some scientists have long presumed today’s giraffe (Giraffa camelopardalis), which includes a handful of subspecies scattered throughout sub-Saharan Africa, evolved from an animal that looked like its close cousin the okapi (Okapia johnstoni), which lives in the tropical forests of central Africa. The team’s analyses of bones from all three animals bolster that notion—and not just because the neck bones are of a length between the giraffe’s and the okapi’s. For example, ridges and other features that are prominent on the okapi’s neck bones and missing entirely on the giraffe’s are typically present but smaller on Samotherium’s, the researchers report online today in Royal Society Open Science.

Science| DOI: 10.1126/science.aad7483

http://www.sciencemag.org/  Science Magazine

http://news.sciencemag.org/evolution/2015/11/odd-creature-was-ancient-ancestor-today-s-giraffes  Original web page at Science Magazine

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Researchers analyzed fossil teeth to identify Apidium zuetina as a species new to science

During upheaval in Libya in 2013, a window of opportunity opened for scientists from the University of Kansas to perform research at the Zallah Oasis, a promising site for unearthing fossils from the Oligocene period, roughly 30 million years ago.

From that work, the KU-led team last week published a description of a previously unknown anthropoid primate — a forerunner of today’s monkeys, apes and humans — in the Journal of Human Evolution. They’ve dubbed their new find Apidium zuetina. Significantly, it’s the first example of Apidium to be found outside of Egypt.

Apidium is interesting because it was the first early anthropoid primate ever to be found and described, in 1908,” said K. Christopher Beard, Distinguished Foundation Professor of Ecology and Evolutionary Biology and senior curator with KU’s Biodiversity Institute, who headed the research. “The oldest known Apidium fossils are about 31 million years old, while the youngest are 29 million. Before our discovery in Libya, only three species of Apidium were ever recovered in Egypt. People had come up with the idea that these primates had evolved locally in Egypt.

Beard said evidence that Apidium had dispersed across North Africa was the key facet of the find. He believes shifting climatic and environmental conditions shaped the distribution of species of Apidium, which affected their evolution.

“We’ve found evidence that climate change — not warming, but cooling and drying — across the Eocene-Oligocene boundary probably is the root cause in kicking anthropoid evolution into overdrive,” he said. “All of these anthropoids, which were our distant relatives, were living up in the trees — none of them were coming down. When the world became cooler and dryer in this period, what was previously a continuous belt of forest became more fragmented. This created barriers to gene flow and movement of animals from one part of forest to what used to be adjacent forest.” With a forest broken up, there was an inhibition of gene flow that through time resulted in speciation, or the creation of new species, according to the KU researcher.

“Animals that are sequestered become different species over millions of years,” Beard said. “As the climate oscillates again, you’ve got different species of Apidium. As forests expand and contract, now you’ve got competition between species of Apidium that have never seen each other before. One species outcompetes the other, the other goes extinct, and we think that’s what we’re picking up with this Libyan Apidium, which is related to the youngest and largest species of Apidium known from Egypt.”

Beard said that Apidium zuetina would have been physically similar to modern-day squirrel monkeys from South America, but with smaller brains, and would have dined on fruits, nuts and seeds.

“We know that Apidium was a very active arboreal monkey, a really good leaper,” he said. We know they actually had fused lower-leg bones just above the ankle joint. That’s really unusual for anthropoid primates, and the only reason for it to happen is because you like to jump a lot, as it stabilized the join between those bones and the ankle.” The team identified Apidium zuetina through detailed analysis of its teeth.

“All of the fossils we have so far are just teeth, not even jaw bones — but fortunately, the teeth of these anthropoids are so distinct and diagnostic that they function like fingerprints at a crime scene,” Beard said. “Studying details of cusps and crests on teeth, we can determine evolutionary relationships. It might sound like thin evidence, but I suspect even with whole skeletons we’d still be focused on teeth to determine relationships. This is because teeth evolve rapidly in response to shifting diets, while an animal’s skull and skeleton typically evolves more slowly. Fortunately for paleontologists, teeth are well-documented in the fossil record because tooth enamel is the hardest part of a mammal body, durable and easy to fossilize.” Yet, the researchers chose to name Apidium zuetina not after any of its physical characteristics, but after the Zuetina Oil Company that made the dangerous Libyan fieldwork possible.

http://www.sciencedaily.com/  Science Daily

http://www.sciencedaily.com/releases/2015/11/151123203116.htm  Original web page at Science Daily

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Ancient viral molecules essential for human development

Genetic material from ancient viral infections is critical to human development, according to researchers at the Stanford University School of Medicine.

They’ve identified several noncoding RNA molecules of viral origins that are necessary for a fertilized human egg to acquire the ability in early development to become all the cells and tissues of the body. Blocking the production of this RNA molecule stops development in its tracks, they found.

The discovery comes on the heels of a Stanford study earlier this year showing that early human embryos are packed full of what appear to be viral particles arising from similar left-behind genetic material.

“We’re starting to accumulate evidence that these viral sequences, which originally may have threatened the survival of our species, were co-opted by our genomes for their own benefit,” said Vittorio Sebastiano, PhD, an assistant professor of obstetrics and gynecology. “In this manner, they may even have contributed species-specific characteristics and fundamental cell processes, even in humans.”

Sebastiano is a co-lead and co-senior author of the study, which will be published online Nov. 23 in Nature Genetics. Postdoctoral scholar Jens Durruthy-Durruthy, PhD, is the other lead author. The other senior author of the paper is Renee Reijo Pera, PhD, a former professor of obstetrics and gynecology at Stanford who is now on the faculty of Montana State University.

Sebastiano and his colleagues were interested in learning how cells become pluripotent, or able to become any tissue in the body. A human egg becomes pluripotent after fertilization, for example. And scientists have learned how to induce other, fully developed human cells to become pluripotent by exposing them to proteins known to be present in the very early human embryo. But the nitty-gritty molecular details of this transformative process are not well understood in either case.

The researchers knew that a type of RNA molecules called long-intergenic noncoding, or lincRNAs, have been implicated in many important biological processes, including the acquisition of pluripotency. These molecules are made from DNA in the genome, but they don’t go on to make proteins. Instead they function as RNA molecules to affect the expression of other genes.

Sebastiano and Durruthy-Durruthy used recently developed RNA sequencing techniques to examine which lincRNAs are highly expressed in human embryonic stem cells. Previously, this type of analysis was stymied by the fact that many of the molecules contain highly similar, very repetitive regions that are difficult to sequence accurately.

They identified more than 2,000 previously unknown RNA sequences, and found that 146 are specifically expressed in embryonic stem cells. They homed in on the 23 most highly expressed sequences, which they termed HPAT1-23, for further study. Thirteen of these, they found, were made up almost entirely of genetic material left behind after an eons-ago infection by a virus called HERV-H.

HERV-H is what’s known as a retrovirus. These viruses spread by inserting their genetic material into the genome of an infected cell. In this way, the virus can use the cell’s protein-making machinery to generate viral proteins for assembly into a new viral particle. That particle then goes on to infect other cells. If the infected cell is a sperm or an egg, the retroviral sequence can also be passed to future generations.

HIV is one common retrovirus that currently causes disease in humans. But our genomes are also littered with sequences left behind from long-ago retroviral infections. Unlike HIV, which can go on to infect new cells, these retroviral sequences are thought to be relatively inert; millions of years of evolution and accumulated mutations mean that few maintain the capacity to give instructions for functional proteins.

After identifying HPAT1-23 in embryonic stem cells, Sebastiano and his colleagues studied their expression in human blastocysts — the hollow clump of cells that arises from the egg in the first days after fertilization. They found that HPAT2, HPAT3 and HPAT5 were expressed only in the inner cell mass of the blastocyst, which becomes the developing fetus. Blocking their expression in one cell of a two-celled embryo stopped the affected cell from contributing to the embryo’s inner cell mass. Further studies showed that the expression of the three genes is also required for efficient reprogramming of adult cells into induced pluripotent stem cells.

“This is the first time that these virally derived RNA molecules have been shown to be directly involved with and necessary for vital steps of human development,” Sebastiano said. “What’s really interesting is that these sequences are found only in primates, raising the possibility that their function may have contributed to unique characteristics that distinguish humans from other animals.”

The researchers are continuing their studies of all the HPAT molecules. They’ve learned that HPAT-5 specifically affects pluripotency by interacting with and sequestering members of another family of RNAs involved in pluripotency called let-7.

“Previously retroviral elements were considered to be a class that all functioned in basically the same way,” said Durruthy-Durruthy. “Now we’re learning that they function as individual elements with very specific and important roles in our cells. It’s fascinating to imagine how, during the course of evolution, primates began to recycle these viral leftovers into something that’s beneficial and necessary to our development.”

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http://www.sciencedaily.com/releases/2015/11/151123202505.htm  Original web page at Science Daily

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* Ancient wild ox genome reveals complex cow ancestry

The ancestry of domesticated cattle proves more complex than previously thought, reports a paper published in the open access journal Genome Biology. The first nuclear genome sequence from an ancient wild ox reveals that some modern domestic cow breeds, including the Scottish Highland and Irish Kerry, had wild ancestors that were British, as well as Asian.

The aurochs, Bos primigenius, is an extinct wild ox species that ranged across the grasslands of Eurasia and North Africa 11,000 years ago. Domestication of aurochs gave rise to two major groups of cattle; Bos taurus and Bos indicus.

Previous studies have shown that European B. taurus are descended from western Asian populations of aurochs. However, little was known about the relationship between domesticated cattle and wild aurochs in Europe, and how wild populations contributed to the evolutionary history of the cows that graze our fields today.

To build a clearer picture of the ancestry of European cattle breeds, scientists from University College Dublin extracted genetic material from a bone of a 6,750 year old wild British aurochs discovered in a cave in Derbyshire, England. They then sequenced its complete genome — its genetic blueprint — and compared it with the genomes of 81 domesticated B. taurus and B. indicus animals, and DNA marker information from more than 1,200 modern cows.

The team of researchers discovered clear evidence of breeding between wild British aurochs and early domesticated cattle. David MacHugh, senior author on the study from the School of Agriculture and Food Science at University College Dublin, said: “Our results show the ancestors of modern British and Irish breeds share more genetic similarities with this ancient specimen than other European cattle. This suggests that early British farmers may have restocked their domesticated herds with wild aurochs.”

Genes linked to neurobiology and muscle development were also found to be associated with domestication of the ancestors of European cattle, indicating that a key part of the domestication process was the selection of cattle based on behavioural and meat traits.

David MacHugh added: “This is the first complete nuclear genome sequence from the extinct Eurasian aurochs. Our new study contradicts earlier simple models of cattle domestication and evolution that we and others proposed based on mitochondrial DNA or Y chromosomes. What now emerges from high-resolution studies of the nuclear genome is a more nuanced picture of crossbreeding and gene flow between domestic cattle and wild aurochs as early European farmers moved into new habitats such as Britain during the Neolithic.”

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http://www.sciencedaily.com/releases/2015/10/151026092912.htm  Original web page at Science Daily

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Meet the first Iberian lynx on the Iberian Peninsula

The remains of an Iberian lynx specimen which lived 1.6 million years ago — the oldest ever discovered — were found resting in a cave in Barcelona (Spain). This discovery not only allows us to shed light on the origins of one of the world’s most endangered feline species, but it also means that the emergence of this species on the Iberian Peninsula dates back half a million years earlier than what was originally believed.

This newly discovered specimen was 10 to 20 centimetres larger and around 10 kilograms heavier than the Iberian lynx that currently inhabits Doñana National Park in Spain. Its coat was also longer than it is today in order to withstand continuous near-freezing temperatures. This description of the feline was formulated after a study was carried out on one of the first Iberian lynxes that ever lived in Spain.

Part of a cranial fossil belonging to an Iberian lynx (Lynx pardinus) was uncovered among the horse, goat, deer, woolly mammoth, fox and wolf bones preserved in the Avenc Marcel Cave located in the Garraf massif of Barcelona. This is the oldest Iberian lynx that has been found on the Iberian Peninsula to date and it was discovered by the scientist Manel Llenas in 2003.

The fossil remains of this feline are proof of its presence on the Iberian Peninsula as early as 1.6 to 1.7 million years ago. Up until now scientists had dated the appearance of the Iberian lynx to between 1 and 1.1 million years ago. Thus, this discovery means that the emergence of this feline on the Iberian Peninsula actually dates back 500,000 years earlier than what scientists originally thought.

“We have confirmed this earlier appearance of the Iberian lynx based on initial molecular studies that estimate the emergence of this feline during the Early Pleistocene in the Iberian Peninsula,” asserts Alberto Boscaini, a researcher at the Miquel Crusafont Catalan Institute of Palaeontology (ICP) and the main author of this study published by Quaternary Science Reviews.

In order to understand the origins of the Iberian Peninsula’s most emblematic species and one of the world’s most endangered felines according to the International Union for Conservation of Nature (UICN), we must first go back in time.

The common ancestor of all the species belonging to the Lynx genus, Lynx issiodorensis, first appeared in North America about four million years ago before spreading to the continents of Asia and Europe where it persisted throughout time. These species underwent few changes, with the most evident being a decrease in size.

The first species of lynx to evolve was Lynx rufus about 2.5 million years ago when it scattered across North America. In Asia Lynx lynx emerged, the species that would later spread across Europe. This feline also spread across North America about 200,000 years ago, thus giving rise to Lynx canadensis which displaced Lynx rufus towards the south.

The European population of L. issiodorensis led to the appearance of Lynx pardinus one and half million years ago. Since then, this species has endured few changes to its genetics and continues to inhabit the Iberian Peninsula today. According to scientists, this evolution may have taken place when the Iberian Peninsula became isolated due to one or several consecutive glacial periods.

The new date provided by the study -1.6 million years ago- lines up with the period of time when all of southern Europe, especially the Iberian Peninsula, became a refuge from the Quaternary glaciation.

Glacial periods alternated with interglacial periods that “greatly influenced wildlife, especially mammals, in that habitat,” the expert adds.

This refuge was also home to the European rabbit (Oryctolagus cunilus), the Iberian lynx’s primary prey more than 75% of the time. The morphological analyses carried out on the cranium found in Catalonia confirm the type of diet consumed by this feline.

“Other cranial features — such as those related to this carnivore’s diet — are proof that the Iberian lynx hunted small-sized prey such as lagomorphs and rodents which had a great presence during that time period,” the researcher states.

According to the study, speciation of the Iberian lynx could therefore be related to the special diet still followed by these specimens inhabiting our planet today, including the rabbit as their primary prey.

http://www.sciencedaily.com/  Science Daily

http://www.sciencedaily.com/releases/2015/10/151028130851.htm Original web page at Science Daily

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Ancient human ear-orienting system could yield clues to hearing deficits in infants

Vestigial organs, such as the wisdom teeth in humans, are those that have become functionless through the course of evolution. Now, a psychologist at the University of Missouri studying vestigial muscles behind the ears in humans has determined that ancient neural circuits responsible for moving the ears, still may be responsive to sounds that attract our attention. Neuroscientists studying auditory function could use these ancient muscles to study positive emotions and infant hearing deficits.

“Everyone has noticed cats or dogs orienting their ears toward a surprising or otherwise interesting sound; we as humans, of course, don’t make ear movements when we focus our attention” said Steven Hackley, an associate professor of psychological sciences in the MU College of Arts and Science. “However, there is a ‘cognitive fossil’ that lies more or less intact in the human brain and could be more than 25 million years old. Significant changes in the human auditory system began soon after the evolution of dry-nosed primates more than 30 million years ago. Ear size decreased and the associated musculature changed.”

Hackley reviewed more than 60 published studies on vestigial ear muscles and noted that research on the muscles dates back more than a century. Scientists discovered that human subjects who shifted their gaze to the left or right weakly activated a muscle within the posterior wall of the outer ear, or pinna. Later studies measured the weak electrical activity triggered within vestigial muscles when either interesting or intense sounds were introduced.

Although nonfunctional, pinna musculature activates during standard laboratory tests of attention and that makes it useful to psychologists and neuroscientists studying evolution and the brain. When subjects were presented with novel or task-relevant sounds, reflexes moved the eyes and attempted to move the ears toward the sounds they wanted to hear and see. The reflexes were too weak to cause actual movement of the ears.

“Understanding pinna orientation and the ancient muscles that caused it could help researchers who study auditory attention in humans,” Hackley said. “Additionally, the complete isolation of a nonworking motor system offers a new perspective on nature and nurture theories by shedding light on neural development and how this relates to genetic factors. Finally, gaining insight into how the relevant vestigial systems work may assist ongoing efforts to develop tests of hearing deficits in infants and, perhaps surprisingly, objective measures of positive emotions in adults.”

The study, “Evidence for a vestigial pinna-orienting system in humans,” recently was published in Psychophysiology.

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http://www.sciencedaily.com/releases/2015/10/151013112128.htm  Original web page at Science Daily

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After 100 years in captivity, a look at the world’s last truly wild horses

In the 1870s, the world’s last truly wild horses, known as Przewalski’s horses, lived in the Asian steppes of Mongolia and China. But by the 1960s, those wild horses were no longer free. Only one captive population remained, descended from about a dozen wild-caught individuals and perhaps four domesticated horses. Thanks to major conservation efforts, the current population of Przewalski’s horses numbers over 2,000 individuals, with about a quarter living in reintroduction reserves.

Now, researchers reporting in the Cell Press journal Current Biology on September 24 have sequenced the complete genomes of eleven Przewalski’s horses, including all of the founding lineages and five historical, museum specimens dating back more than a century, and compared them to the genomes of 28 domesticated horses to provide a detailed look at the endangered animals, both past and present.

“The novelty of our approach is to have not only surveyed the present-day genomic diversity of Przewalski’s horses, but also to monitor their past genomic diversity, leveraging on museum specimens,” says Ludovic Orlando of the University of Copenhagen’s Natural History Museum of Denmark. “That way we could assess the genetic impact of more than 100 years of captivity in what used to be a critically endangered animal.”

The genomic evidence helps to solve a long-standing debate in horse evolution, regarding the relationships between wild and domestic horses. The ancestors of Przewalski’s horses and domesticated horses remained connected by gene flow for a long time after their divergence, some 45,000 years ago, the researchers report. Their populations continued to mix even after humans started to domesticate the horse about 5,500 years ago.

“As a matter of fact, we also show that very early in captivity–in the early 1900s–domestic horses contributed significantly to some lineages of the Przewalski’s horse pedigree,” Orlando says. “It implies that not all of the surviving Przewalski’s lineages represent the gene pool of wild horses equally.”

Orlando and his colleagues found the greatest genetic differences between domesticated and wild horses in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways.

The findings also show that the last 110 years of captivity have left a mark on the Przewalski’s horses, in the form of lower genetic diversity, increased inbreeding, and, in some cases, the significant introduction of genes from domesticated individuals. In the most extreme cases, about a quarter of the genomes of Przewalski’s horses consisted of gene variants inherited from domesticated horses.

But there is some good news: “Even though Przewalski’s horses went through an extreme demographic collapse, the population seems to recover, and is still genetically diverse,” Orlando says. “There is, thus, hope for [other] endangered populations, fighting similar demographic issues.”

The findings also serve as evidence of the importance of ancient DNA evidence in understanding domestication. The researchers say they plan to screen many more ancient horses–both wild and domestic–over time, with the goal of reconstructing the history of horses’ 5,500 years of domestication.

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http://www.sciencedaily.com/releases/2015/09/150924142520.htm  Original web page at Science

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Return on investment slipping in biomedical research

In a report published Aug. 17 in the Proceedings of the National Academy of Sciences, the researchers found that while the number of scientists has increased more than nine-fold since 1965 and the National Institutes of Health’s budget has increased four-fold, the number of new drugs approved by the Food and Drug Administration has only increased a little more than two-fold. Meanwhile, life expectancy gains have remained constant at roughly two months per year.

“The idea of public support for biomedical research is to make lives better. But there is increasing friction in the system,” says co-author Arturo Casadevall, MD, PhD, professor and chair of the W. Harry Feinstone Department of Molecular Microbiology and Immunology at the Bloomberg School. “We are spending more money now just to get the same results we always have and this is going to keep happening if we don’t fix things.”

Casadevall, who did the research with Anthony Bowen, a visiting scholar at the Johns Hopkins Bloomberg School of Public Health and an MD/PhD student at Albert Einstein College of Medicine in New York, says that understanding the issues that are making the scientific process less efficient is a key to remedying the underlying problems.

“There is something wrong in the process, but there are no simple answers,” Bowen says. “It may be a confluence of factors that are causing us not to be getting more bang for our buck.”

Among the factors, they suggest, is that increased regulations on researchers –everything from the lengthy process of gaining consent to take blood samples for a study to cataloguing every trip to a conference for government oversight — add to the non-scientific burdens on scientists who could otherwise spend more time at the bench. Some have argued that the “easy” cures have been found and that to tackle Alzheimer’s disease, most cancers and autoimmune diseases, for example, is inherently more complex.

Casadevall and Bowen also cite “perverse” incentives for researchers to cut corners or oversimplify their studies to gain acceptance into top-tier medical journals, something that has led to what they call an epidemic of retractions and findings that cannot be reproduced and are therefore worthless. “The medical literature isn’t as good as it used to be,” Casadevall says. “The culture of science appears to be changing. Less important work is being hyped, when the quality of work may not be clear until decades later when someone builds on your success to find a cure.”

One recent study estimated that more than $28 billion, from both public and private sources, is spent each year in the United States on preclinical research that can’t be reproduced and that the prevalence of these studies in the literature is 50 percent.

“We have more journals and more papers than ever,” Bowen says, “but the number of biomedical publications has dramatically outpaced the production of new drugs, which are a key to improving people’s lives, especially in areas for which we have no good treatments.”

For the study, the researchers searched through public databases for published medical literature, looked at NIH investment data, FDA new drug approvals, data on life expectancy gains and other similar data.

The authors acknowledge that new drug approvals and life expectancy rates are not the only measures by which to judge the efficiency of biomedical research. But, they argue, when it comes down to it, when someone is sick, they either need medicine or surgery to save their lives and many times the medicines haven’t been developed. Also, they say, life expectancy is a good measure of the overall system, because gains have been made due to research into seat belts and pedestrian safety as well as due to medical therapies.

Casadevall says that many of the best drugs being used to treat conditions today were developed many decades ago, including insulin for diabetes and beta-blockers for cardiac conditions. From 1965 to 1999, the NIH budget grew exponentially. Over the next four years, the budget doubled before a steady decrease from 2003 to 2014, which is larger than apparent because of the rapidly rising costs of scientific experiments. The cost per new drug, in millions of dollars of NIH budget, has grown rapidly since the 1980s, they say.

He doesn’t doubt that more cures are out there to be found and that a more efficient system of biomedical research could help push along scientific discovery. “Scientists, regulators and citizens need to take a hard look at the scientific enterprise and see which are problems that can be resolved,” he says. “We need a system with rigor, reproducibility and integrity and we need to find a way to get there as soon as we can.”

http://www.sciencedaily.com/  Science Daily

http://www.sciencedaily.com/releases/2015/08/150817160617.htm  Original web page at Science Daily

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Four million years at Africa’s salad bar

As grasses grew more common in Africa, most major mammal groups tried grazing on them at times during the past 4 million years, but some of the animals went extinct or switched back to browsing on trees and shrubs, according to a study led by the University of Utah

“It’s as if in a city, there was a whole new genre of restaurant to try,” says geochemist Thure Cerling, first and senior author of the study published by the journal Proceedings of the National Academy of Sciences. “This is a record of how different mammals responded. And almost all of the mammals did an experiment in eating this new resource: grass.”

The experiment peaked about 2 million years ago, says Cerling, a distinguished professor of geology and geophysics. The only major group that still mostly grazes grass is the bovids: cattle, buffalo, sheep, wildebeest, hartebeest and some antelopes such as oryx and waterbucks.

The study also revealed that the present isn’t necessarily the key to the past in terms of what animals eat. Today, elephants and spiral-horned antelope (elands, kudus and bushbuck) browse on trees and shrubs, but the study showed that 2 million years ago, African elephants grazed on grass and the antelopes had mixed diets with a lot of grass. Asian elephants, which ate grass and were abundant in Africa 2 million years ago, went extinct in Africa but survive in Asia, where they graze but also browse trees and shrubs.

“That the diet of some of these animals is different from that of the present was a surprise, and shows the importance of challenging one’s assumptions when making ecological reconstructions,” says study co-author and geologist Frank Brown, dean of the University of Utah’s College of Mines and Earth Sciences.

Overall, Cerling and colleagues wrote that the assemblages of grazing, browsing and mixed-diet animals during the past 4 million years “are different from any modern ecosystem in East or Central Africa.”

They found the Turkana Basin of Kenya and Ethiopia had a much greater diversity of mixed feeders — they browsed and grazed — from 4.1 million to 2.35 million years ago. From 2.35 million to 1 million years ago, there were many more grazers than there are today. In the past 1 million years, many grass grazers either switched to browsing trees and shrubs or went extinct, leaving mostly bovids as grazers today.

In a study spanning 30 years of field work by Cerling into how grasses and the animals that eat them evolved together, he and other scientists analyzed:

— Hair keratin, tooth enamel or bone collagen from 1,800 animals of more than 50 modern herbivore species in East and Central Africa. Samples came from museum collections or from animals killed previously in 30 national parks and reserves.

— Tooth enamel from more than 900 fossil herbivores that lived 4.1 million to 1 million years ago in the Turkana Basin.

They measured the samples’ ratios of uncommon carbon-13 to common carbon-12. The ratios reveal if the animals browsed primarily on plants that use C3 photosynthesis (trees, shrubs, forbs and herbs), grazed mainly on C4 photosynthesis plants (dry-season or tropical grasses and sedges) or ate a mixed diet.

Low carbon dioxide levels in the atmosphere are believed responsible for a global expansion of tropical grasslands between 10 million and 5 million years ago. C4 photosynthesis used by tropical grasses is more efficient in hot climates, giving them an advantage over trees and shrubs.

“Over the past 10 million years, grasses went from perhaps 1 percent of productivity of the tropical landscape to 50 percent today,” Cerling says. “All the large mammal groups tried experiments in eating grasses, and a lot of those experiments didn’t work in the long run,” he says. “Animals became extinct or they switched to other diets. There was even a grazing giraffe, but that became extinct. There were three major lineages of pigs that were grazers, and only one has survived: the warthog.”

Other grazers that became extinct included a three-toed horse and the Asian elephant, which survives in Asia but went extinct in Africa 1 million years ago. Grazers that switched to browsing included forest hogs and African elephants. Browsers in the past that still browse at least 75 percent trees and shrubs today include most giraffes, black rhinos, tiny antelope and forest antelope. One-toed horses, warthogs, zebras, white rhinos and bovids — cattle, buffalo, goats, wildebeest, hartebeest and antelopes like waterbuck and oryx — stuck with grass.

“The successful grazers appear to be the bovids,” Cerling says, although even some bovids — gazelles and elands — once were mixed grazers-browsers, but today have returned to mostly browsing on trees and shrubs. Impalas, which also are bovids, shifted from mostly grazing in the past to both grazing and browsing today.

Modern herbivores with mixed browsing-grazing diets include hippos and impalas. Why did the grass craze fade? Why did some animals keep eating grass while others stopped or went extinct? “Perhaps they were much more efficient at eating grass and outcompeted some of the other animals,” Cerling says. For example, perhaps African elephants switched to browsing when they could no longer grab grass cut too short by grazers.

“It looks like there is as much grass available now as anytime in the past,” Cerling says. “It could be that the quality of grass varies enormously between the dry season and the wet season.” He also notes that during the past 1 million years, “we have been going through strong cycles with and without glaciers, and much bigger changes in atmospheric carbon dioxide.” Grasses using C4 photosynthesis not only have an advantage in hot weather, but also during glacial periods when carbon dioxide levels were low.

But there are no fossils of grasses for the past 10 million years, which makes it difficult to unveil the evolution of grasses, and whether they changed in digestibility, palatability, toxin levels and nutrient content, Cerling says.

In a 2013 study, Cerling found that early human relatives who turned to grazing, such as Paranthropus boisei, went extinct. Modern humans eat more grass than ever before — but not by grazing. Instead, we eat the meat of animals fed grass and C4 grains, as well as cultivated C4 plants such as corn and sorghum.

http://www.sciencedaily.com/  Science Daily

http://www.sciencedaily.com/releases/2015/08/150803154848.htm  Original web page at Science Daily

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Shifting winds, ocean currents doubled endangered Galápagos penguin population

Shifts in trade winds and ocean currents powered a resurgence of endangered Galápagos penguins over the past 30 years, according to a new study. These changes enlarged a cold pool of water the penguins rely on for food and breeding — an expansion that could continue as the climate changes over the coming decades, the study’s authors said.

The Galápagos Islands, a chain of islands 1,000 kilometers (600 miles) west of mainland Ecuador, are home to the only penguins in the Northern Hemisphere. The 48-centimeter (19-inch) tall black and white Galápagos penguins landed on the endangered species list in 2000 after the population plummeted to only a few hundred individuals and are now considered the rarest penguins in the world.

Most of the penguins live on the archipelago’s westernmost islands, Isabela and Fernandina, where they feed on fish that live in a cold pool of water on the islands’ southwestern coasts. The cold pool is fed by an ocean current, the Equatorial Undercurrent, which flows toward the islands from the west. When the current runs into Isabela and Fernandina, water surges upward, bringing cold, nutrient-rich water to the surface.

New research suggests shifts in wind currents over the past three decades, possibly due to climate change and natural variability, have nudged the Equatorial Undercurrent north. The changing current expanded the nutrient-rich, cold water farther north along the coasts of the two islands, likely bolstering algae and fish numbers in the cold pool. This allowed the penguin population to double over the past 30 years, swelling to more than 1,000 birds by 2014, according to the new study.

Climate change could further shift wind patterns and ocean currents, expanding cold water further north along the coasts of Isabela and Fernandina and driving fish populations higher, according to the new study.

Penguins, as well as other animals like fur seals and marine iguanas that feed and reproduce near the cold waters, may increase in numbers as the northwestern coasts of the islands become more habitable, said the study’s authors. They noted that wind and ocean currents could also return to earlier conditions, leading to a decline in penguin populations.

“The penguins are the innocent bystanders experiencing feast or famine depending on what the Equatorial Undercurrent is doing from year to year,” said Kristopher Karnauskas, a climate scientist who performed the research while at Woods Hole Oceanographic Institution in Cape Cod, Massachusetts, and lead author of the new study recently accepted in Geophysical Research Letters, an American Geophysical Union journal.

The new findings could help inform conservation efforts to save the endangered penguins, said the study’s authors. Increasing efforts on the northern coasts of the islands and expanding marine-protected areas north to where the penguins are now feeding and breeding could support population growth, the study’s authors said.

Karnauskas notes that the vast majority of marine organisms will be negatively affected by the rise in ocean temperatures and acidification that are expected to occur across the globe as a result of climate change. “With climate change, there are a lot of new and increasing stresses on ecosystems, but biology sometimes surprises us,” said Karnauskas. “There might be places–little outposts–where ecosystems might thrive just by coincidence.”

The Galápagos penguin population tenuously hangs onto the islands that so enthralled Charles Darwin during his visit in 1835. The penguins once numbered around 2,000 individuals, but in the early 1980s a strong El Niño — a time when sea surface temperatures in the tropical Pacific are unusually warm — brought their numbers down to less than 500 birds. Dogs, cats and rats introduced to the islands also stymied the penguin population by attacking the birds, disturbing their nests, and introducing new diseases, according to previous research.

Despite these setbacks, the penguins gradually increased in number in the following decades, according to local bird counts. Researchers, interested by the increase in penguins, noted that the birds remained near the coldest stretches of water. Nearly all of the Galápagos penguins live on the western coasts of Isabela and Fernandina, and two-thirds of them huddled near the coldest waters at the southern tips of the islands, according to previous research.

The study’s authors wanted to know whether the growing numbers of penguins were related to local changes in ocean temperature. They combined previously-collected penguin population data from 1982 to 2014 with sea surface temperature data from satellites, ships and buoys for the same time period.

They found that the cold pool, where sea surface temperatures are below 22 degrees Celsius (71 degrees Fahrenheit), expanded 35 kilometers (22 miles) farther north than where it was located at the beginning of the study period. In the 1980s the cold water pocket reached only the southern halves of the western coasts of Isabela and Fernandina. By 2014, the cold water pocket extended across the entire western coasts of the islands.

A shift in trade winds and underwater ocean currents likely caused the Galápagos cold pool expansion, propose the authors. Trade winds blow surface ocean waters from the southern side of the equator to the northern side of the equator. As surface waters pile up in the north, the water at the bottom of the pile is squished south, nudging the Equatorial Undercurrent — a cold current that flows roughly 50 meters (160 feet) under the ocean surface — south of the equator.

Likely due to a combination of natural variation and human-caused climate change, trade winds west of the Galápagos slackened during the study period, lessening the pressure pushing the Equatorial Undercurrent south, according to the new study. Consequently, the ocean current gradually shifted north, increasing the amount of cold water coming to the Galápagos Islands, according to the study’s authors.

Satellite images showed that this expanded pool of cold water likely encouraged the growth of phytoplankton, according to the new study. This increase in ocean algae attracted fish to the area — the main entrée for Galápagos penguins, suggest the authors. The largest pulses of cold water reached the islands from July through December, coinciding with the penguins’ breeding season. The bountiful fish helped the birds successfully reproduce and feed their young, according to the new study.

Models indicate trade winds will continue to abate in the future as the climate warms, Karnauskas said. This could cause the undercurrent to continue to move north, expanding the Galápagos cold pool and possibly further raising penguin populations, he said. Other animal populations like the endangered Galápagos fur seal and the marine iguana also may profit from the prolific amount of food in the Galápagos cold pool, according to the study’s authors.

Wind and ocean currents could also possibly return to where they were in the 1980s, compressing the cold pool and possibly leading to a decline in penguins, Karnauskas added.

The new study shows how large-scale changes in the climate can act locally, said Michelle L’Heureux, a climate scientist with the National Oceanic and Atmospheric Administration’s Climate Prediction Center in College Park, Maryland, and not an author on the new paper. “While it is important that we focus on the big picture with climate change, it’s really the small scale that matters to the animals and plants that are impacted,” she said.

http://www.sciencedaily.com/  Science Daily

http://www.sciencedaily.com/releases/2015/08/150803155108.htm  Original web page at Science Daily

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Competition from cats drove extinction of many species of ancient dogs

Competition played a more important role in the evolution of the dog family (wolves, foxes, and their relatives) than climate change, shows a new international study published in PNAS.

An international team including scientists from the Universities of Gothenburg (Sweden), São Paulo (Brazil) and Lausanne (Switzerland) analyzed over 2000 fossils and revealed that the arrival of felids to North America from Asia had a deadly impact on the diversity of the dog family, contributing to the extinction of as many as 40 of their species.

“We usually expect climate changes to play an overwhelming role in the evolution of biodiversity. Instead, competition among different carnivore species proved to be even more important for canids” says leading author Daniele Silvestro at the Department of Biological and Environmental Sciences, University of Gothenburg.

The dog family originated in North America about 40 million of years ago and reached a maximum diversity around 22 million of years ago, when more than 30 species inhabited the continent. Today, only 9 species of the dog family live in North America. They progressively increased in body size and specialized into becoming large predators. Some of them exceeded 30 Kg (66 pounds) and were among the largest carnivores on the North American continent. Although several large carnivores today face a higher extinction risk than smaller species, the authors of the study found no evidence of a similar pattern in ancient canid species.

The evolutionary success of carnivorous animals is inevitably linked to their ability to obtain food. The limited amount of resources (preys) imposes strong competition among carnivores sharing the same geographic range. For instance African carnivores such as wild dogs, hyenas, lions and other felids are constantly competing with each other for food. North American carnivores in the past might have followed similar dynamics and much of the competition is found among species of the dog family and from ancient felids and dogs. Interestingly, while felids appeared to have a strongly negative impact on the survival of ancient dogs, the opposite is not true. This suggests that felids must have been more efficient predators than most of the extinct species in the dog family.

http://www.sciencedaily.com/  Science Daily

http://www.sciencedaily.com/releases/2015/08/150812103827.htm  Original web page at Science Daily