Researchers sequence complete genomes of extinct and living elephants

An international team of researchers has produced one of the most comprehensive evolutionary pictures to date by looking at one of the world's most iconic animal families - namely elephants, and their relatives mammoths and mastodons-spanning millions of years.

Crushed dentine from a Woolly Mammoth for DNA extraction [Credit: JD Howell, McMaster University]

The team of scientists-which included researchers from McMaster, the Broad Institute of MIT and Harvard, Harvard Medical School, Uppsala University, and the University of Potsdam-meticulously sequenced 14 genomes from several species: both living and extinct species from Asia and Africa, two American mastodons, a 120,000-year-old straight-tusked elephant, and a Columbian mammoth.

The study, published in the Proceedings of the National Academy of Science, sheds light on what scientists call a very complicated history, characterized by widespread interbreeding. They caution, however, the behaviour has virtually stopped among living elephants, adding to growing fears about the future of the few species that remain on earth.

"Interbreeding may help explain why mammoths were so successful over such diverse environments and for such a long time, importantly this genomic data also tells us that biology is messy and that evolution doesn't happen in an organized, linear fashion," says evolutionary geneticist Hendrik Poinar, one of the senior authors on the paper and Director of the McMaster Ancient DNA Centre and principal investigator at the Michael G. DeGroote Institute for Infectious Research.

"The combined analysis of genome-wide data from all these ancient elephants and mastodons has raised the curtain on elephant population history, revealing complexity that we were simply not aware of before," he says.

Graduate student Emil Karpinski holds a tibial cross section from a Siberian Woolly Mammoth. This permafrost
preserved sample still contains fat entombed marrow [Credit: JD Howell, McMaster University]

A detailed DNA analysis of the ancient straight-tusked elephant, for example, showed that it was a hybrid with portions of its genetic makeup stemming from an ancient African elephant, the woolly mammoth and present-day forest elephants.

"This is one of the oldest high-quality genomes that currently exists for any species," said Michael Hofreiter at the University of Potsdam in Germany, a co-senior author who led the work on the straight-tusked elephant.

Researchers also found further evidence of interbreeding among the Columbian and woolly mammoths, which was first reported by Poinar and his team in 2011. Despite their vastly different habitats and sizes, researchers believe the woolly mammoths, encountered Columbians mammoths at the boundary of glacial and in the more temperate ecotones of North America.

Strikingly, scientists found no genetic evidence of interbreeding among two of the world's three remaining species, the forest and savanna elephants, suggesting they have lived in near-complete isolation for the past 500,000 years, despite living in neighbouring habitats.

These are African savanna elephants in the San Diego Zoo. In the middle is Swazi, the female elephant from
which the reference genome was sequenced [Credit: San Diego Zoo Global]

"There's been a simmering debate in the conservation communities about whether African savannah and forest elephants are two different species," said David Reich, another co-senior author at the Broad Institute who is also a professor at the Department of Genetics at Harvard Medical School (HMS) and a Howard Hughes Medical Institute Investigator. "Our data show that these two species have been isolated for long periods of time - making each worthy of independent conservation status."

Interbreeding among closely related mammals is fairly common, say researchers, who point to examples of brown and polar bears, Sumatran and Bornean orangutans, and the Eurasian gold jackal and grey wolves. A species can be defined as a group of similar animals that can successfully breed and produce fertile offspring.

"This paper, the product of a grand initiative we started more than a decade ago, is far more than just the formal report of the elephant genome. It will be a reference point for understanding how diverse elephants are related to each other and it will be a model for how similar studies can be done in other species groups," said co-senior author Kerstin Lindblad-Toh, a senior associate member of the Broad Institute and Director of the Science for Life Laboratory at Uppsala University in Sweden.

"The findings were extremely surprising to us," says Eleftheria Palkopoulou, a post-doctoral scientist in at HMS. "The elephant population relationships could not be explained by simple splits, providing clues for understanding the evolution of these iconic species."

Researchers suggest that future work should explore whether the introduction of new genetic lineages into elephant populations-both living and ancient-played an important role in their evolution, allowing them to adapt to new habitats and fluctuating climates.

Source: McMaster University [February 26, 2018]

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King penguins may be on the move very soon

More than 70 percent of the global King penguin population, currently forming colonies in Crozet, Kerguelen and Marion sub-Antarctic islands, may be nothing more than a memory in a matter of decades, as global warming will soon force the birds to move south, or disappear. This is the conclusion of a study published in the journal Nature Climate Change and performed by an international team of researchers.

More than 70 percent of the global King penguin population may be nothing more than a memory in a matter of decades,
 as global warming will soon force the birds to move south, or disappear [Credit: Robin Cristofari]

"The main issue is that there is only a handful of islands in the Southern Ocean and not all of them are suitable to sustain large breeding colonies" says Robin Cristofari, first author of the study, from the Institut Pluridisciplinaire Hubert Curien (IPHC/CNRS/University of Strasbourg) and the Centre Scientifique de Monaco (CSM).

King penguins are in fact picky animals: in order to form a colony where they can mate, lay eggs and rear chicks over a year, they need tolerable temperature all year round, no winter sea ice around the island, and smooth beach of sand or pebbles. But, above all, they need an abundant and reliable source of food close by to feed their chicks. For millennia, this seabird has relied on the Antarctic Polar Front, an upwelling front in the Southern Ocean concentrating enormous amounts of fish on a relatively small area.

Yet, due to climate change, this area is drifting south, away from the islands where most King penguins currently live. Parents are then forced to swim farther to find food, while their progeny is waiting, fasting longer and longer on the shore. This study predicts that, for most colonies, the length of the parents' trips to get food will soon exceed the resistance to starvation of their offspring, leading to massive King penguin crashes in population size, or, hopefully, relocation.

King penguins are picky animals [Credit: Celine LeBohec]

Using the information hidden away in the penguin's genome, the research team has reconstructed the changes in the worldwide King penguin population throughout the last 50,000 years, and discovered that past climatic changes, causing shifts in marine currents, sea-ice distribution and Antarctic Polar Front location, have always been linked to critical episodes for the King penguins. However, hope is not lost yet: King penguins have already survived such crises several times (the last time was 20 thousand years ago), and they may be particularly good at it.

"Extremely low values in indices of genetic differentiation told us that all colonies are connected by a continuous exchange of individuals," says Emiliano Trucchi formerly at the University of Vienna and now at the University of Ferrara, one of the coordinator of the study. "In other words, King penguins seem to be able to move around quite a lot to find the safest breeding locations when things turn grim."

But there is a major difference this time: for the first time in the history of penguins, human activities are leading to rapid and/or irreversible changes in the Earth system, and remote areas are no exception. In addition to the strongest impact of climate change in Polar Regions, Southern Ocean is now subject to industrial fishing, and penguins may soon have a very hard time fighting for their food.

Penguins form colonies in Crozet, Kerguelen and Marion sub-Antarctic islands [Credit: Celine LeBohec]

"There are still some islands further south where King penguins may retreat," notes Celine Le Bohec (IPHC/CNRS/University of Strasbourg and CSM), leader of the programme 137 of the French Polar Institut Paul-Emile Victor within which the study was initiated, "but the competition for breeding sites and for food will be harsh, especially with the other penguin species like the Chinstrap, Gentoo or Adelie penguins, even without the fisheries. It is difficult to predict the outcome, but there will surely be losses on the way. If we want to save anything, proactive and efficient conservation efforts but, above all, coordinated global action against global warming should start now."

Source: University of Vienna [February 26, 2018]

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Playing both ends: Amphibian adapted to varied evolutionary pressures

Caecilians are serpent-like creatures, but they're not snakes or giant worms. The limbless amphibians, related to frogs and salamanders, favor tropical climates of Africa, Asia and the Americas. Most live in burrows of their own making; some are aquatic.

A limbless amphibian, known as Caecilian, Siphonops annulatus, widely distributed in Brazil. Scientists from Utah State
University in the United States and Brazil’s Butantan Institute report skin gland concentrations adapted
to different evolutionary pressures in the head and posterior regions of the amphibian
[Credit: Carlos Jared, Butantan Institute]

With colleagues from Brazil, Utah State University ecologist Edmund "Butch" Brodie, Jr. reports caecilians feature greatly enlarged poison glands at each end of their bodies, which appear to have evolved from different selective pressures - the ability to tunnel into the ground and to defend oneself from predators.

Brodie, along with Carlos Jared, Pedro Luiz Mailho-Fontana, Rafael Marques-Porto, Juliana Mozer Sciani, Daniel Carvalho Pimenta, and Marta Maria Antoniazzi of São Paulo's Butantan Institute, published the findings in Scientific Reports.

The team's research, supported by the Brazilian National Council for Scientific and Technological Development, focuses on Siphonops annulatus, a caecilian species found throughout Brazil.

"My Brazilian colleagues noticed the burrows made by this species were lined with a shiny, slick substance," says Brodie, professor in USU's Department of Biology and the USU Ecology Center. "We didn't think it was a secretion from the poison glands, so we decided to investigate."

The Brazilian caecilian, grayish in color and measuring about 18 inches in length, is a surprisingly rapid burrower, he says.

Magnified image of connective tissue matrix forming honeycomb structure surrounding glands on the head of Caecilian,
Siphonops annulatus. Scientists from Utah State University in the United States and Brazil’s Butantan Institute report skin
gland concentrations adapted to different evolutionary pressures in the head and posterior regions of the amphibian
[Credit: Carlos Jared, Butantan Institute]

"When caecilians burrow, they force their snouts into the ground and essentially dive into the soil," Brodie says.

As suspected, the team discovered all the skin glands in the serpentine creatures' head region were greatly enlarged, tightly packed mucous glands - not poison ones. The slippery lubrication enables the caecilians' rapid, subterranean escape from predators, especially coral snakes.

"We know of no other amphibian with this high concentration of mucous glands," Brodie says. "In other terrestrial amphibians, mucous is mainly related to the uptake of oxygen. Here, in caecilians, it's obviously used in locomotion."

Examination of the caecilians revealed further information. The mucous glands extend throughout the amphibians' body, in gradually reduced concentration, and give way to poison glands concentrated in the tail.

"The poison glands, resulting from a different selective pressure, provide another defense from predators," Brodie says. "In addition to chemical defense, the tail acts as a 'plug,' blocking the tunnel and further deterring predators."

The eccentric amphibian, Brodie and colleagues write, is "really a box of surprises."

Author: Mary-Ann Muffoletto | Source: Utah State University [February 23, 2018]

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Surprising new study redraws family tree of domesticated and 'wild' horses

There are no such things as "wild" horses anymore. Research published in Science overturns a long-held assumption that Przewalski's horses, native to the Eurasian steppes, are the last wild horse species on Earth. Instead, phylogenetic analysis shows Przewalski's horses are feral, descended from the earliest-known instance of horse domestication by the Botai people of northern Kazakhstan some 5,500 years ago.

Thought to be the world's last-remaining 'wild' horse, Przewalski's horses actually descend from horses domesticated
by the Botai people about 5,500 years ago [Credit: Lee Boyd]

Further, the new paper finds that modern domesticated horses didn't descend from the Botai horses, an assumption previously held by many scientists.

"This was a big surprise," said co-author Sandra Olsen, curator-in-charge of the archaeology division of the Biodiversity Institute and Natural History Museum at the University of Kansas, who led archaeological work at known Botai villages. "I was confident soon after we started excavating Botai sites in 1993 that we had found the earliest domesticated horses. We went about trying to prove it, but based on DNA results Botai horses didn't give rise to today's modern domesticated horses -- they gave rise to the Przewalski's horse."

The findings signify there are no longer true "wild" horses left, only feral horses that descend from horses once domesticated by humans, including Przewalski's horses and mustangs that descend from horses brought to North America by the Spanish.

"This means there are no living wild horses on Earth -- that's the sad part," said Olsen. "There are a lot of equine biologists who have been studying Przewalskis, and this will be a big shock to them. They thought they were studying the last wild horses. It's not a real loss of biodiversity -- but in our minds, it is. We thought there was one last wild species, and we're only just now aware that all wild horses went extinct."

Some of the Botai horses were found to carry genetic variants causing white and leopard coat spotting patterns
[Credit: Ludovic Orlando, reworked by Sean Goddard and Alan Outram]

Many of the horse bones and teeth Olsen excavated at two Botai sites in Kazakhstan, called Botai and Krasnyi Yar, were used in the phylogenetic analysis. The international team of researchers behind the paper sequenced the genomes of 20 horses from the Botai and 22 horses from across Eurasia that spanned the last 5,500 years. They compared these ancient horse genomes with already published genomes of 18 ancient and 28 modern horses.

"Phylogenetic reconstruction confirmed that domestic horses do not form a single monophyletic group as expected if descending from Botai," the authors wrote. "Earliest herded horses were the ancestors of feral Przewalski's horses but not of modern domesticates."

Olsen said the findings give rise to a new scientific quest: locating the real origins of today's domesticated horses.

"What's interesting is that we have two different domestication events from slightly different species, or separate sub-species," she said. (The Przewalski's horse's taxonomic position is still debated.) "It's thought that modern-day domesticated horses came from Equus ferus, the extinct European wild horse. The problem is they were thought to have existed until the early 1900s. But, the remains of two individuals in St. Petersburg, Russia, are probably feral, too, or at least probably had some domesticated genes."

Olsen led excavation of Botai sites associated with the earliest-known domestication of horses
[Credit: Sandra Olsen]

Olsen began excavating Botai village sites in Kazakhstan in 1993 after the fall of the Soviet Union made the region accessible to western scientists. Some of the horse remains collected by Olsen were tested as part of the new study showing their ancestry of modern-day Przewalskis.

The Botai's ancestors were nomadic hunters until they became the first-known culture to domesticate horses around 5,500 years ago, using horses for meat, milk, work and likely transportation.

"Once they domesticated horses they became sedentary, with large villages of up to 150 or more houses," said Olsen, who specializes in zooarchaeology, or the study of animal remains from ancient human occupation sites. "They lived primarily on horse meat, and they had no agriculture. We had several lines of evidence that supported domestication. The fact the Botai were sedentary must have meant they had domesticated animals, or plants, which they didn't have. More than 95 percent of the bones from the Botai sites were from horses -- they were in a sense mono-cropping one species with an incredible focus. If they were hunting horses on foot, they would have quickly depleted bands of horses in the vicinity of the villages and would have had to go farther afield to hunt -- it wouldn't have been feasible or supported that large human population."

The KU researcher also cited bone artifacts from Botai sites used to make rawhide thongs that might have been fashioned into bridles, lassos, whips, riding crops and hobbles, as further evidence of horse domestication. Moreover, the Botai village sites include horse corrals.

The Botai buried horses with their snouts pointing southeast toward the rising sun
[Credit: Sandra Olsen]

"We found a corral that contained high levels of nitrogen and sodium from manure and urine," said Olsen. "It was very concentrated within that corral. The final smoking gun was finding residues of mares' milk in the pottery. It's commonplace today in Mongolia and Kazakhstan to milk horses -- when it's fermented it has considerable nutritional value and is very high in vitamins."

Interestingly, Olsen found that after slaughtering horses, the Botai buried some horse skulls and necks in pits with their snouts facing the southeast, toward where the sun rose in the morning in autumn. Mongols and Kazakhs slaughter most of their horses at that time of year because that is when they retain the most amount of nutritious fat in their bodies.

"It's interesting because throughout the Indo-European diaspora there's a strong connection between the sun god and the horse," she said. "It may be that Botai people spoke an early proto-Indo-European language, and they also connected the horse to the sun god. Later in time, and this idea is in the historical record for the Indo-European diaspora, it was believed the sun god was born in the east and rode across the sky in a chariot, pulled by white horses. According to the belief, he would then die in the west and be reborn every day."

The team behind the paper believe Przewalski's horses likely escaped from domestic Botai herds in eastern Kazakhstan or western Mongolia.

Excavation at the Botai site, Northern Kazakhstan, 2017
[Credit: Alan Outram/University of Exeter]

"They started developing a semi-wild lifestyle like our mustangs, but they still have a wild appearance," Olsen said. "This is partly why biologists assumed they were genuinely wild animals. They have an upright mane, something associated with wild equids. They also have a dun coat, like the ones you see in the Ice Age cave paintings in France and Spain made when horses were wild. Their size, however, is very similar to what you see at Botai and other sites."

By 1969, Przewalski's horses were declared extinct in the wild, and all living today originated from just 15 individuals captured around 1900. Today, there are approximately 2,000 Przewalski's horses, all descended from those captured horses, and they have been reintroduced on the Eurasian steppes. In a sense, the horses have fared better than the peoples who once domesticated them.

"The Botai people seem to have vanished from their homeland in northern Kazakhstan," said Olsen. "Perhaps they migrated eastward to Mongolia since the later Bronze Age people there shared the practice of ritually burying the horse's head and neck pointing toward the rising sun in the autumn, the time of year they were slaughtered. That's a very specific shared trait."

Source: University of Kansas [February 22, 2018]

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First 3D models reveal development of Tasmanian tiger from joey to adulthood

Researchers from the University of Melbourne and Museums Victoria have CT scanned all 13 known Tasmanian tiger joey specimens to create 3D digital models, allowing them to study their skeletons and internal organs, and reconstruct their growth and development.

Internal structures of Thylacine joeys [Credit: University of Melbourne]

This has revealed important new information about how this unique extinct marsupial evolved to look so similar to the dingo, despite being very distantly related.

The digital scans show that when first born the Tasmanian tiger or thylacine (Thylacinus cynocephalus) looked like any other marsupial. But three months later, when they left the pouch, they had taken on the appearance of a puppy and continued to grow with a dog-like appearance.

The research, led by the University of Melbourne and Museums Victoria and in conjunction with an international team of scientists, is published in Royal Society Open Science.

The Tasmanian tiger was a marsupial, which raised its young in a pouch. Its resemblance to the dingo is one of the best examples of convergent evolution in mammals. This is where two species, despite not being closely related, evolve to look very similar. The Tasmanian tiger would have last shared a common ancestor with the canids (dogs and wolves) around 160 million years ago.

The specimens cover ages from two to 12 weeks. The white scalebar is 10mm [Credit: University of Melbourne]

Dr Christy Hipsley, Research Associate at the University of Melbourne and Museums Victoria, said after sequencing the Tasmanian tiger genome in 2017, this research fills one more piece of the puzzle on why they have evolved to look so similar to dogs. 

"This is the first digital development series of the Tasmanian tiger, Australia’s most iconic extinct marsupial predator.

"Using CT technology we have been able to garner new information on the biology of this iconic species, and its growth and development."

These scans show in incredible detail how the Tasmanian tiger started its journey in life as a joey that looked very much like any other marsupial, with robust forearms so that it could climb into its mothers pouch. But by the time it left the pouch around 12 weeks to start independent life, it looked more like a dog or wolf, with longer hind limbs than forelimbs.

Once ranging throughout Australian and New Guinea, the Tasmanian tiger disappeared from the mainland around 3000 years ago, likely due to competition with humans and dingos.

The remaining Tasmanian tiger population, isolated on Tasmania, was hunted to extinction in the early 20th century, with the last known individual dying at Hobart Zoo in 1936.

Axel Newton, PhD student and Lead Author on the paper notes, until now there have only been limited details on its growth and development. For the very first time we have been able to look inside these remarkably rare and precious specimens.

Unable to study the living species, the team had to look to the 13 Tasmanian tiger joey specimens that exist in museum collections worldwide, including three from the collection of Museums Victoria. These joey specimens, representing five stages of postnatal development, were scanned using non-invasive X-ray micro-CT scanning technology to create high resolution 3D digital models, in which all their internal structures such as skeleton and organs could be studied.

Associate Professor Andrew Pask from the University of Melbourne explains this was an incredibly effective technique to study the skeletal anatomy of the specimens without causing any damage to them.

"This research clearly demonstrates the power of CT technology. It has allowed us to scan all the known Thylacine joey specimens in the world, and study their internal structures in high resolution without having to dissect or cause damage to the specimen. By examining their bone development, we’ve been able to illustrate how the Tasmanian tiger matured and identify when they took on the appearance of a dog."

The study has also revealed the incorrect classification of two specimens held in the collection of the Tasmanian Museums and Art Gallery (TMAG). Instead, they are most likely to be quolls or Tasmanian devils, based on the number of vertebrate and presence of large epipubic bones (specialised bones that support the pouch in modern marsupials).

Tasmanian tiger [Credit: Tasmanian Museum and Art Gallery, Hobart, Tasmania]

Senior Curator of Vertebrate Zoology at TMAG, Ms Kathryn Medlock, said that the museum had received many requests to dissect its pouch young over the years but requests were always refused.

"One of the major advantages of this new technology is that it has enabled us to do research and answer many questions without destruction of the sample specimens. This is a significant advancement that also has an additional benefit of helping us to learn more about the identity of these specimens that have been in the TMAG collection for many years."

An exciting outcome of the research is that the 3D digital Tasmanian tiger models are to be made publicly available as a resource for current and future researchers.

Source: The University of Melbourne [February 21, 2018]

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Biodiversity loss raises risk of 'extinction cascades'

New research shows that the loss of biodiversity can increase the risk of "extinction cascades," where an initial species loss leads to a domino effect of further extinctions.

Credit: Andreas Haselböck/Senckenberg

The researchers, from the University of Exeter, showed there is a higher risk of extinction cascades when other species are not present to fill the "gap" created by the loss of a species.

Even if the loss of one species does not directly cause knock-on extinctions, the study shows that this leads to simpler ecological communities that are at greater risk of "run-away extinction cascades" with the potential loss of many species.

With extinction rates at their highest levels ever and numerous species under threat due to human activity, the findings are a further warning about the consequences of eroding biodiversity.

"Interactions between species are important for ecosystem (a community of interacting species) stability," said Dr Dirk Sanders, of the Centre for Ecology and Conservation at the University of Exeter's Penryn Campus in Cornwall. "And because species are interconnected through multiple interactions, an impact on one species can affect others as well.

"It has been predicted that more complex food webs will be less vulnerable to extinction cascades because there is a greater chance that other species can step in and buffer against the effects of species loss.

"In our experiment, we used communities of plants and insects to test this prediction."

The researchers removed one species of wasp and found that it led to secondary extinctions of other, indirectly linked, species at the same level of the food web.

This effect was much stronger in simple communities than for the same species within a more complex food web.

Dr Sanders added: "Our results demonstrate that biodiversity loss can increase the vulnerability of ecosystems to secondary extinctions which, when they occur, can then lead to further simplification causing run-away extinction cascades."

The study, supported by France's Sorbonne Université, is published in the journal Proceedings of the National Academy of Sciences.

How extinction cascades work

The loss of a predator can initiate a cascade, such as in the case of wolves, where their extinction on one mountain can cause a large rise in the number of deer. This larger number of deer then eats more plant material than they would have before. This reduction in vegetation can cause extinctions in any species that also relies on the plants, but are potentially less competitive, such as rabbits or insects.

Source: University of Exeter [February 19, 2018]

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In 16 years, Borneo lost more than 100,000 orangutans

Over a 16-year period, about half of the orangutans living on the island of Borneo were lost as a result of changes in land cover. That's according to estimates reported in Current Biology showing that more than 100,000 of the island's orangutans disappeared between 1999 and 2015.

A Bornean orangutan [Credit: Marc Ancrenaz]

Many of those losses were apparently driven by the demand for logging, oil palm, mining, paper, and associated deforestation. However, many orangutans have also disappeared from more intact, forested areas, the researchers say. Those findings suggest that hunting and other direct conflicts between orangutans and people remain a major threat to the species.

"The decline in population density was most severe in areas that were deforested or transformed for industrial agriculture, as orangutans struggle to live outside forest areas," says Maria Voigt of the Max Planck Institute for Evolutionary Anthropology in Germany. "Worryingly, however, the largest number of orangutans were lost from areas that remained forested during the study period. This implies a large role of killing."

To estimate changes in the size of the orangutan population over time, Voigt, along with Serge Wich from Liverpool John Moores University in the UK and their colleagues representing 38 international institutions, compiled field surveys conducted from 1999 to 2015. They extrapolated the overall size of the island's population from the number of orangutan nests observed throughout the species' range in Borneo.

This photograph shows where Bornean forest was cleared for road development 
[Credit: Marc Ancrenaz]

All told, the team observed 36,555 nests. They estimated a loss of 148,500 Bornean orangutans between 1999 and 2015.The data also suggest that only 38 of the 64 identified spatially separated groups of orangutans (known as metapopulations) now include more than 100 individuals, which is the accepted lower limit to be considered viable.

In order to identify the likely causes of those losses, the researchers relied on maps of estimated land-cover change over the same period that have been made possible by advances in remote sensing technology. The comparison of orangutan and habitat losses suggests that land clearance caused the most dramatic rates of decline. However, a much larger number of orangutans were lost in selectively logged and primary forests. That's because while the rates of decline were less precipitous in those areas, that's also where far more orangutans are found, the researchers explain.

By 2015, they report, about half of the orangutans estimated to live on Borneo in 1999 were found in areas in which resource use has since caused significant changes to the environment. Based on predicted future losses of forest cover and the assumption that orangutans ultimately cannot survive outside forest areas, the researchers predict that over 45,000 more orangutans will be lost over the next 35 years.

This photograph shows where Bornean forest was cleared for a factory 
[Credit: Marc Ancrenaz]

They say that effective partnerships with logging companies and other industries are now essential to the Bornean orangutan's survival. Public education and awareness will also be key.

"Orangutans are flexible and can survive to some extent in a mosaic of forests, plantations, and logged forest, but only when they are not killed," Wich says. "So, in addition to protection of forests, we need to focus on addressing the underlying causes of orangutan killing. The latter requires public awareness and education, more effective law enforcement, and also more studies as to why people kill orangutans in the first place."

They note that Indonesia and Malaysia are both currently developing long-term action plans for orangutan conservation. By taking into account past failures, the hope is that new strategies to protect orangutans can be developed and implemented.

Source: Cell Press [February 15, 2018]

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Action plan released to conserve one of Africa's richest sites for biodiversity

A team of scientists led by WCS (Wildlife Conservation Society) has developed a conservation blueprint to protect one of the most biodiverse regions in Africa: the Albertine Rift, home to mountain and Grauer's gorillas, golden monkeys, chimpanzees, elephants, and 162 vertebrate, and 350 plant species unique to this region.

Grauer's gorilla. A team of scientists led by WCS (Wildlife Conservation Society) has developed a conservation blueprint
 to protect one of the most biodiverse regions in Africa: the Albertine Rift, home to mountain and Grauer's gorillas,
golden monkeys, chimpanzees, elephants, and 162 vertebrate, and 350 plant species unique to this region
[Credit: A.J. Plumptre]

Based on work by WCS and participants from five countries in the region, the "Conservation Action Plan for the Albertine Rift" summarizes the results of 16 years of research and commitment to the conservation of six key landscapes within the Albertine Rift, which runs through five countries (Uganda, Democratic Republic of Congo, Rwanda, Burundi, and Tanzania) and stretches from the southern tip of Lake Tanganyika to the northern tip of Lake Albert

Building on an initial framework plan developed in 2004, the new plan highlights the importance of the region for global biodiversity and goes further to outline the main steps required for the conservation of each landscape. The plan assesses where within each landscape is most important for the conservation of the many unique and threatened species, both now and under projected climate change, and identifies which species remain unprotected.

"The Albertine Rift is the most important site for vertebrate conservation in Africa, with more endemic and globally threatened vertebrates than any other region of the continent," said Dr. Andy Plumptre, Senior Scientist for WCS's Africa program. "We know of 163 terrestrial vertebrates that are unique to this region and we keep discovering new species. We also know the lakes in this region have incredible fish diversity and that at least 350 species of plant are unique to the region."

WCS has conducted surveys of the biodiversity of the Albertine Rift over decades, supporting surveys of some species and specific sites as early as 1959 in the case of eastern gorillas (one of the endemic species). A more comprehensive program started by WCS in 2000 compiled region-wide data on mammals, birds, reptiles, amphibians and plants. WCS worked with other NGO partners and the environmental protection authorities of Burundi, the Democratic Republic of Congo, Rwanda, Tanzania, and Uganda to identify six key landscapes and to establish cooperative protection at ground-level in each.

Based on work by WCS and participants from five countries in the region, the 'Conservation Action Plan for
the Albertine Rift' summarizes the results of 16 years of research and commitment to the conservation of six key
 landscapes within the Albertine Rift, which runs through five countries (Uganda, Democratic Republic of Congo,
Rwanda, Burundi, and Tanzania) and stretches from the southern tip of Lake Tanganyika
to the northern tip of Lake Albert [Credit: WCS]

Threats to the landscapes are substantial because this part of Africa also contains some of the highest human population densities on the continent. Habitat loss is the most critical threat for most of the species. Modeling work described in the report showed that the endemic and threatened species have already lost on average 40 percent of suitable habitat to agriculture. Climate change is likely to drastically reduce the remaining suitable habitat.

"We predict that by the end of this century, endemic species will further decline in response to climate change as many of these species will need to move to higher elevations as the climate warms. These up-slope movements will result in a dramatic 75 percent reduction in suitable habitat," said Sam Ayebare, a conservationist for WCS Uganda.

Many of the areas currently under protection are essential for the conservation of these species. Three additional areas, totaling over 10,000 square kilometers, that were gazetted in 2016, Itombwe, Ngandja and Kabobo Reserves, were critical for protecting many additional endemic species, both now and under future climate change. The report assesses the optimum ways to conserve these endemic and globally threatened species, and identifies which areas not currently under protection remain important for the conservation of some of the species.

"These critical sites outside of the existing protected areas mostly occur in DR Congo," said Deo Kujirakwinja, Technical Advisor for WCS in DR Congo. "We need to focus our attention on these sites before they, and the unique species they contain, are lost."

Supporting the conservation and management of the six landscapes within the Albertine Rift will require a dedicated effort from governments and from the conservation community. However, investment in conservation in this region yields tremendous value because of its incredible species richness.

Available at: www.albertinerift.org

Source: Wildlife Conservation Society [February 15, 2018]

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Hunting is changing forests, but not as expected

When it comes to spreading their seeds, many trees in the rainforest rely on animals, clinging to their fur or hitching a ride within their digestive tract. As the seeds are spread around, the plants' prospects for survival and germination are increased.

Researchers from UConn and the San Diego Zoo Institute for Conservation and Research examined how the overhunting
of seed dispersing animals is changing tree communities in Western Amazonia, such as those in Manu National Park
[Credit: Varun Swamy]

But in many tropical forests, over-hunting is diminishing the populations of those animals, and, as a result, changing the make-up of the forests themselves.

A new study of the Amazon rainforest by researchers at UConn and the San Diego Zoo Institute for Conservation and Research, published in the Journal of Ecology, examines what happens to plants if their seed dispersers are no longer present. They found that theoretical models predicting a dire impact on plant communities and huge decreases in the amount of carbon stored in tropical forests are not supported by the facts. Instead, the effects on the ecosystem are less straightforward and less immediately devastating.

"Yes, there is a negative effect, but there isn't 100 percent mortality," says Robert Bagchi, assistant professor of ecology and evolutionary biology at UConn. "The story is more complex and much more subtle."

Whereas the models used in the previous studies did not use actual data on items such as mortality, survival, growth, and spatial distribution, Bagchi and his fellow researchers explored the question in greater detail, using a statistical technique they recently developed with extensive data collected on tree communities in the 80,000 km2 Madre de Dios river basin, located in the southeastern corner of Peru's Amazon rainforest.

In Western Amazonia, as many as two-thirds of all tree species rely on native, fruit-eating mammals such as spider monkeys and tapirs, or birds like guans, trumpeters and toucans, who are able to travel fairly large distances and carry any ingested seeds far from their parent trees.

Dispersal is advantageous for seeds because spreading out will give seedlings an edge over specialized natural predators who might otherwise wipe out aggregations of undispersed plants.

"The idea is that the seeds escape," says Bagchi. "A lot of pathogens and insects are quite specific about which plants they will eat, and if there is no dispersal and their desired plants are densely aggregated, those plants will be clobbered."

In tropical rain forests, as many as two-thirds of all tree species rely on native, fruit-eating mammals such as capuchin
monkeys who are able to travel fairly large distances and carry any ingested seeds far from their parent trees.
What happens to the forests when these seed dispersing animals are over hunted? [Credit: Varun Swamy]

In addition, the tree species dispersed by these animals also store the most carbon.

Unfortunately, the large-bodied animals and birds are the favorite quarry of hunters for bush meat.

The researchers examined tree communities in the tropical rain forests of Western Amazonia, in terms of forest spatial organization and carbon storage capacity. They did find that tree communities in hunted forests appear to be undergoing a reorganization, where saplings of species that rely on large hunted animals for dispersal are now growing closer to each other and forming denser clumps in hunted forests.

But the long-term implications for biodiversity and the biomass of forests are not yet clear. And the expectation that without their dispersers, seeds of these plant species will land in the "kill zone" of insects and diseases under their parents and be replaced by other species that store less carbon, culminating in huge decreases in the amount of carbon stored in tropical forests, has not materialized.

A number of factors could be contributing to the reason that previous theories are not proving true, Bagchi says.

Smaller seed dispersers that often increase when their larger competitors are hunted out may be compensating. Additionally, the trees analyzed in the study were already at least 10-15 years old, so follow-up studies will instead focus on the early lives of these trees, starting at the germination stage.

Questions the researchers hope to pursue include, What are the survival rates of undispersed seeds in hunted forests? Is limited dispersal by smaller animals enough to ensure a seed's survival? How do these stages fit together -- does high survival at a later stage compensate for low survival of undispersed seeds?

"We can't simplify the process to just a linear one," says Bagchi. "We need data following the whole process, from seed dispersal to trees growing into adults."

Bagchi also cautions that although these findings are somewhat hopeful in light of previous modeling studies, tropical forests in South America, Asia, and Africa are becoming ever more stripped of their diversity of flora and fauna, fundamentally changing the structure of these complex systems.

Source: University of Connecticut [February 15, 2018]

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Research identifies 'evolutionary rescue' areas for animals threatened by climate change

As winters arrive later and snow melts earlier, the worldwide decrease in snow cover already may have dramatic impacts on animals that change coat colors with the seasons. An international scientific team led by University of Montana Professor L. Scott Mills has set out to discover whether adaptive evolution can rescue these animals in the face of rapidly changing climate.

Brown and white snowshoe hares on snow at a University of Montana research facility
[Credit: L.S. Mills research photos by Jaco and Lindsey Barnard]

Twenty-one species of mammals and birds rely on the ability to change their coat color from brown in summer to white in winter to avoid fatal encounters with predators, but in some parts of their range individuals forgo the white molt and remain brown in winter.

"Weasels in the southern U.S. and mountain hares in Ireland, for example, have evolved to remain brown year-round," Mills said. "This is a genetic adaptation to retain camouflage in areas where snow is intermittent or sparse."

Mills' group previously found that winter white snowshoe hares confronting snowless ground have higher mortality rates that could drive massive population declines as snow duration continues to decrease. Other scientists have pointed to coat-color mismatch against snowless ground as a cause for recent range decreases of hares, ptarmigan and other species.

Brown and white snowshoe hares on bare ground at a University of Montana research facility
[Credit: L.S. Mills research photos by Jaco and Lindsey Barnard]

In a new article in Science, Mills' team identified areas that could foster rapid "evolutionary rescue" of these species particularly vulnerable to climate change. The study describes how the international team mapped "polymorphic zones" for eight color-changing species, including hares, weasels and the Arctic fox. In these zones, both brown and white individuals coexist in winter.

"These areas hold the special sauce for rapid evolutionary rescue," Mills said. "Because they contain winter-brown individuals better adapted to shorter winters, these polymorphic populations are primed to promote rapid evolution toward being winter brown instead of white as climate changes."

The authors emphasize that these hotspots for evolutionary rescue are not magic fortresses that will prevent climate change effects on wild animals.

"Ultimately, the world must reduce carbon dioxide emissions or else the climate effects will overwhelm the ability of many species to adapt," co-author Eugenia Bragina said. "But by mapping these adaptive hotspots, we identify places where people could help foster evolutionary rescue in the short term by working to maintain large and connected wildlife populations."

Source: The University of Montana [February 15, 2018]

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What fluffy bunnies can tell us about domestication: It didn't go the way you think

It turns out that nobody knows when rabbits were domesticated. Despite a well-cited story of the domestic bunny's origins, a review published in Trends in Ecology and Evolution finds that historical and archaeological records and genetic methods all suggest different timeframes for its domestication. But the researchers involved in the study don't think this puzzle is a dead end. Instead, they believe it's an indication that domestication happens on a continuum.

Credit: Bunny Blossom/Facebook

The story goes like this: rabbits were domesticated by monks in 600 A.D. after an edict from Pope Gregory declared that it was acceptable to eat fetal rabbits, known as laurices, during Lent. The problem is it isn't true--something that archaeologists Evan Irving-Pease and Greger Larson of the University of Oxford accidentally discovered while trying to test how well the molecular clock method works for genetically dating domestication.

This method compares the genomes of a domestic rabbit and a modern wild one to determine how long it took for them to diverge. Larson hoped to match the domestication date indicated by the rabbits' genomes to the date suggested by the historical record: 600 A.D. But the molecular clock method indicated a date during the last ice age, before the very first domesticated animals.

His team's analysis of these results suggested that the wild rabbits they used simply don't share a recent ancestor with the domestic ones we know and love. But archaeological records, which look for changes in the skeletal structure of the domesticated rabbit, point to the 17th or 18th century, when modern pet-keeping began. And upon closer examination of historical records, the 600 A.D. story of the laurices fell apart.

"I had cited it, colleagues of mine had cited it, it's all over Wikipedia, it's all over the web... but it turns out that the modern story is a complete house of cards," Larson says. "What was really interesting to me then was why nobody's really thought about it or been critical about it."

He thinks it has to do with the way we tell stories. "We really have trouble appreciating slow, continuous change over long periods of time," Larson says, even though that's how most change happens. "Our narrative structures work much better if you have a eureka moment." Domestication that happens at a specific moment in time, due to a concrete series of events, makes intuitive sense to us.

But in the case of rabbits, Irving-Pease, Larson, and colleagues suggest in the paper, domestication is more likely the cumulative effect of hunting rabbits during the Palaeolithic era, keeping them in Roman and medieval enclosures, moving them from place to place, and eventually breeding them as pets. "For the vast majority of human existence, no one said, 'I am going to grab this wild organism and bring it into captivity and, voila, I will create a domestic one,'" Larson says. "If you want to divide the continuum into a dichotomy of wild and domestic, you can do that, but you have to know that it's necessarily going to be arbitrary."

Rather than asking when domestication occurred, Larson believes we need to reconsider what domestication is and whether humans have ever really intended to cause it. His team's next step will be to reexamine the domestication of other plants and animals our civilization relies upon. "We have been slightly arrogant," says Irving-Pease. "We know a hell of a lot less about the origins of the things that matter most to us than we think we do."

Source: Cell Press [February 14, 2018]

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When it comes to extinction, body size matters

On a certain level, extinction is all about energy. Animals move over their surroundings like pacmen, chomping up resources to fuel their survival. If they gain a certain energy threshold, they reproduce, essentially earning an extra life. If they encounter too many empty patches, they starve, and by the end of the level it's game over.

In classic extinction models, animals move over their surroundings like pacmen, chomping up resources
to fuel their survival [Credit: Laura Chambliss/Studio Yopp]

Models for extinction risk are necessarily simple. Most reduce complex ecological systems to a linear relationship between resource density and population growth -- something that can be broadly applied to infer how much resource loss a species can survive.

This week in Nature Communications, an interdisciplinary team of scientists proposes a more nuanced model for extinction that also shows why animal species tend to evolve toward larger body sizes. The Nutritional State-structured Model (NSM) by ecologist Justin Yeakel (UC Merced), biologist Chris Kempes (Santa Fe Institute), and physicist Sidney Redner (Santa Fe Institute) incorporates body size and metabolic scaling into an extinction model where 'hungry' or 'full' animals, great and small, interact and procreate on a landscape with limited resources.

"Unlike many previous forager models, this one accounts for body size and metabolic scaling," Kempes explains. "It allows for predictions about extinction risk, and also gives us a systematic way of assessing how far populations are from their most stable states."

In the NSM, hungry animals are susceptible to mortality, and only full animals have the capacity to reproduce. Because animals' energetic needs change with body size, the researchers based their calculations for replenishment and reproduction on biological scaling laws that relate body size to metabolism.

They found that species of different sizes gravitate toward population states most stable against extinction. The states they derived in the model reproduce two oft-observed patterns in biology. The first, Damuth's law, is an inverse relationship between body size and population density: the bigger the species, the fewer of individuals cohabitate in a given area. Within the NSM, this fewer/larger more/smaller pattern emerges because large species are most stable against starvation in small numbers, while small species can afford to reach larger population densities.

The second relationship, Cope's rule, holds that terrestrial mammals tend to evolve toward larger body sizes. This NSM shows that, overall, larger animals with slower metabolisms are the most stable against extinction by starvation. It even predicts an energetically "ideal" mammal, robust in the face of starvation, which would be 2.5 times the size of an African elephant.

"As we incorporated more realism into how quickly organisms gain or lose body fat as they find or don't find resources, the results of our model began aligning with large-scale ecological and evolutionary relationships. Most surprising was the observation that the NSM accurately predicts the maximum mammalian body size observed in the fossil record," explains Yeakel. Though the model doesn't account for predation, it does offer a dynamic and systematic framework for understanding how foragers survive on limited resources.

"The dynamics of foraging and the interaction of body size in foraging and resource availability, these are all rich problems for which there is beautiful phenomenology," says Redner. "I hope some of this will have relevance in managing resources and ensuring species don't go extinct."

Source: Santa Fe Institute [February 13, 2018]

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