Best of our wild blogs: 22 Dec 12

from The annotated budak

Pied Imperial-pigeon feeding on Rhopaloblaste ceramica fruits
from Bird Ecology Study Group

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Bat gene clue to beating bugs

Grace Chua Straits Times 22 Dec 12;

BATS harbour viruses that can infect and even kill humans and animals, like Sars, Hendra and Nipah. Yet infected bats rarely fall sick.

Now, a Singapore-led team of international scientists has worked out a possible reason and believes it could help stop viruses leaping to humans and other animals.

The findings could even help to treat viral illnesses.

The key lies in bat genes. In July, the researchers started sequencing the genomes - the whole set of genes - of two very different bats.

One was a large fruit bat, a member of a group called megachiroptera. The other was a small insect-eating one belonging to a group called microchiroptera.

As these species are so different, any genes they share come from the last common ancestor of both bats.

Professor Wang Linfa, director of the Duke-NUS graduate medical school's Emerging Infectious Diseases Programme, led the team, which studied which genes had been selected most successfully during evolution.

Bats are the only flying mammals, and flight takes a great deal of their energy. The higher metabolic rates that supply this energy also produce toxic by-products that damage DNA. But bats seem to have evolved ways to protect their cells against this damage, Prof Wang explained. These DNA-repair genes also play a role in immune pathways, so researchers think they may help to protect bats.

A group of genes involved in inflammation was completely absent in bats. Inflammation is the body's response to an invader, such as a virus, resulting in viral illness.

Said Prof Wang: "We don't want to jump to conclusions that this means bats have less inflammation during viral infection. It's only one discovery and we have to do more to functionally prove that it contributes to less pathology in viral infection in bats."

But simply responding less to viruses could be part of why bats do not fall ill, he said.

Prof Wang led an international team spanning Singapore, China, Denmark and the US. Its work, published yesterday in the journal Science, may one day help prevent transmission of these viruses. It may point to better ways to treat viral diseases by using gene therapy, for example, to control inflammation, Prof Wang said.

National University of Singapore evolutionary biologist Rudolf Meier, who was not involved in the study, said some changes in the bat genes were present in other species, including humans, but without the protective DNA-repair or immune-system effects. He said the results were not wrong, but not conclusive.

Bats' viral immunity linked to their ability to fly
Heng Wei Xiang Today Online 22 Dec 12;

SINGAPORE - The evolution of flight in bats may has contributed to the development of a highly effective immune system, allowing these mammals to harbour some of the world's deadliest viruses such as Ebola and SARS.

This is according to researchers at Duke-NUS Graduate Medical School, who published their findings in the international journal Science. Less than 10 per cent of research papers submitted to the journal are published.

Professor Wang Lin Fa, an infectious disease expert who led the study, hopes the findings could provide new research directions, especially in the treatment, prevention and control of emerging infectious diseases that affect both humans and livestock.

The researchers studied two bat species, the black flying fox and the mouse-eared bat. While a high metabolism is a prerequisite for bats to be able to fly, such metabolic rates also increase the amount of free radicals present within cells in the bat's body. Excessive amounts of free radicals lead to DNA damage, contributing to major bodily disorders. Researchers found gene variants in these bat species, enabling them to minimise and repair DNA damage.

However, the same gene variants also boost bats' immune systems, allowing them to resist many viruses such as Nipah, Ebola and SARS, which typically cause severe illness in other species, humans included.

"Our findings highlight the potential of using bats as a model system to study infection control, tumour biology, and the mechanisms of ageing," said Prof Wang, who was appointed Director of the Program in Emerging Infectious Diseases at Duke-NUS in July this year.

Long-lived bats offer clues on diseases, aging
Tan Ee Lyn Reuters Yahoo News 21 Dec 12;

HONG KONG (Reuters) - The bat, a reservoir for viruses like Ebola, SARS and Nipah, has for decades stumped scientists trying to figure out how it is immune to many deadly bugs but a recent study into its genes may finally shed some light, scientists said on Friday.

Studying the DNA of two distant bat species, the scientists discovered how genes dealing with the bats' immune system had undergone the most rapid change.

This may explain why they are relatively free of disease and live exceptionally long lives compared with other mammals of similar size, such as the rat, said Professor Lin-Fa Wang, an infectious disease expert at the Duke-NUS Graduate Medical School in Singapore who led the multi-centre study.

"We are not saying bats never get sick or never get infections. What we are saying is they handle infections a lot better," Wang said in a telephone interview.

What was missing from both species of bats was a gene segment known to trigger extreme, and potentially fatal, immune reactions to infections, called the cytokine storm.

Cytokine storms end up killing not only offending viruses in the body, but the host's own cells and tissues too.

"Viruses rarely kill the host. The killing comes from the host's immune response. So it looks like what bats are doing is depress the inflammation (cytokine storm). If we can learn that, we can design drugs to minimize the inflammation damage and control viral infection," Wang said.

The study, which saw the participation of researchers from China, Denmark, Australia and the United States, was published on Friday in the journal Science.

Compared with other mammals of similar size, bats live a long time, with lifespans of between 20 and 40 years. Rats live between 2 and 3 years, on average.


Interestingly, Wang and his colleagues found that the highly evolved genes that give bats their superior immune system also enable them to fly.

Out of more than 5,000 types of mammals on the planet, bats are the only one capable of sustained flight and some species can fly more than 1,000 km in a single night.

Such intense physical exertion is known to produce toxic "free radicals" that cause tissue damage and it is these same genes that give the bat the ability to repair itself, Wang said.

"What we found was the genes that evolved fastest were genes involved in repairing DNA damage. That makes sense ... because when you fly, metabolism goes up and it generates free radicals that are toxic to cells," Wang said.

"Because bats fly, they (would have had) to evolve and adapt ... to get genes that can repair DNA damage."

Wang said we have much to learn from the bat, which has evolved to avoid disease and live exceptionally long lives.

"Cancer, ageing and infectious disease, these are the three major areas of concern for people," he said.

"We have studied rats for 150 years to understand how to do better in these three areas. Now we have a system, the bat, that has done very well in evolution. We can learn from the bat. With modern techniques, we can design new drugs to slow down the ageing process, treat cancer, fight infections."

(Editing by Robert Birsel)

Bats' flight linked to immunity
Duke NUS Science Alert 7 Jan 13;

An international team led by an infectious disease expert, Professor Lin-Fa Wang, at the Duke-NUS Graduate Medical School (Duke-NUS) in Singapore has found that the evolution of flight in bats may have contributed to the development of a highly effective immune system, allowing bats to harbour some of the world’s deadliest viruses such as Ebola and SARS.

In their study, published in the prestigious international journal Science, Professor Wang and colleagues used a state-of-the-art whole-genome sequencing technique to analyse the genomes of two distantly-related bat species, the fruit bat Pteropus alecto (Black flying fox, a species native to Australia, Papua New Guinea, and Indonesia) and the insect-eating bat Myotis davidii (David's mouse-eared bat, a species endemic in China).

"This is the first in-depth study of bat genomes. Our study provided important genomics insights into the unique biological features of bats," said Professor Wang, an expert in bat-borne viruses who was appointed Director of the Program in Emerging Infectious Diseases at Duke-NUS in July this year.

The large collaborative team from China, Denmark, Australia, U.S., and Singapore compared the two bat genomes with the genomes of other mammals, and found genetic clues that may account for the unique characteristics of bats.

Although bats are the second largest group of mammals, with over 1,000 species of bats documented so far, they are distinctive because they are the only mammals capable of sustained flight; other mammals such as flying squirrels glide but do not fly.

Previous research has shown that this ability to fly may be linked to high metabolic rates in bats. However, increased metabolism also elevates the amount of free radicals in living cells, resulting in DNA damage that is harmful to the bats.

Through their analysis of bat genomes, the researchers have now solved the mystery of how bats tolerate high levels of free radicals. It appears that bats have evolved mechanisms to overcome this toxic side-effect of flying, as they possess gene variants that help them minimise and repair DNA damage.

And here is where bats' ability to fly and their immunity against viruses intersect: the same gene variants that minimise DNA damage in bats may also provide protection against viruses, boosting their innate immune system to ward off such attacks.

Having a highly active immune system may explain why bats are natural hosts of many viruses such as Hendra, Nipah, Ebola, and SARS, yet rarely show any signs of infection. In contrast, when these viruses are transmitted to humans or other animals, the resulting illness is often severe and even fatal.

Bats are also known for their exceptional longevity which is unusual because of their small size and high metabolic rate. The researchers raise the intriguing possibility that the same mechanisms underlying the evolution of flight and viral immunity in bats may also be responsible for their life expectancy, although further research is required to establish this link.

Professor Wang hopes that the findings from this study will provide new research directions into infectious diseases, especially in the treatment, prevention, and control of emerging infectious diseases that affect both humans and livestock animals.

"Our findings highlight the potential of using bats as a model system to study infection control, tumour biology, and the mechanisms of ageing," said Professor Wang, who intends to continue studying bat-borne viruses in Duke-NUS, tapping on Duke-NUS' strengths in human infectious disease research for viral diseases such as dengue and influenza, and to explore new collaborative research in tumour biology with scientists in the Cancer and Stem Cell Biology Program at Duke-NUS.

Professor Wang is also a Science Leader for the CSIRO Office of the Chief Executive and Senior Principal Research Scientist at the CSIRO Australian Animal Health Laboratory (AAHL) in Geelong, Australia.

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Malaysia: Dialog, Vopak Sign Customers for Oil Storage Terminal

Chong Pooi Koon & Ann Koh Bloomberg 21 Dec 12;

Dialog Group Bhd., (DLG) Malaysia’s second-biggest oil and gas services provider, said it signed some customers for the 1.9 billion-ringgit ($620 million) storage terminal it’s developing with Royal Vopak NV. (VPK)

Talks with other potential clients are continuing, Dialog Executive Chairman Ngau Boon Keat said in an interview Dec. 18 at Pengerang, Malaysia’s southern Johor state neighboring Singapore.

Dialog, Vopak and local government are developing the site at Pengerang, with initial capacity of 1.3 million cubic meters, to meet rising demand for oil storage in Asia and as space in Singapore dwindles. The companies are betting on the terminal’s location to capture trade flow between China, India and Asia, Ngau said at the site.

“Our location is blessed with 24-meter deep natural berth able to bring in very large crude carriers,” said Law Say Huat, chief executive officer of the venture developing the Pengerang terminal. “We are offering an alternative to the crude oil traders, refiners, or the suppliers to be able to bring here to blend up, to break bulk or to make bulk.”

The tanks will be for clean products and crude oil and will begin operating from 2014, Ngau said. Clean products include fuels such as gasoline, naphtha, diesel and kerosene. The company has no immediate plans to build fuel oil tanks.

“At the moment, there is quite a lot fuel oil storage,” Ngau said. “We’re more targeting crude oil storage.”

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Indonesia: Tribe Fight Palm Oil Plans

SP/Sahat Oloan Saragih Jakarta Globe 20 Dec 12;

Pontianak, West Kalimantan. Supporters of the Uud Dhanum Dayak tribe in West Kalimantan’s Sintang district have called on local authorities to declare their land a cultural conservation area, in a bid to protect it from a planned oil palm plantation.

Syamsuni Arman, an anthropologist at Tanjungpura University in Pontianak, the provincial capital, said at a seminar that the land in question was considered sacred to the Dayak and there must be guarantees in place to ensure that it would not be taken over or the tribe evicted.

“Economic development policies around the area where the Dayaks intend to establish their cultural conservation area must take into consideration the traditions and cultural sensitivities of the locals, as well as the need to conserve the existing biodiversity,” he said.

The call was made in response to revelations that the district administration had granted a 1,000-hectare concession in the area to a palm oil company.

Rafael Samsudin, the head of the Uud Dhanum Dayak tribal association, said that the Sintang authorities were perfectly aware that the area in the Sakai River basin was considered by the tribe as ancestral land and therefore sacred.

The concession was issued to Sinar Sawit Andalan, which is currently applying for a land use permit with the National Land Agency (BPN).

Rafael said his association had sent a letter to the BPN head office in Jakarta as well as to its provincial and district offices, calling on the agency not to issue the land use permit.

He said the tribe was worried that once the permit was awarded and the company started clearing the land for the plantation, the water table in the area would drop, affecting not just the tribe but also the local plant and animal life.

He pointed out that the forested area was home to many protected species, including several varieties of toucans, and if the forest was logged and replaced by oil palms the wildlife would disappear.

The tribe also fears that a drop in the water table would diminish the water level in the Sakai River, where they hoped to build a small hydroelectric plant to provide power for the community.

Rafael stressed that the tribe had safeguarded the forest for generations and would not allow it to be destroyed now for mere commercial gain.

Syamsuni said that in addition to conserving the area, the district and provincial authorities should also start recognizing and incorporating the Dayaks’ age-old forest stewardship practices into their own conservation policies.

He argued that their sustainable brand of forest management had allowed them to live and farm in the forest for generations with no adverse affect on the local wildlife or the integrity of the forest.

A national conference of indigenous peoples earlier this year highlighted another branch of the Dayak, the Iban Dayak in Kapuas Hulu district, West Kalimantan, as gaining official recognition for their forest stewardship practices.

The tribe has since 1819 practiced a quota system for logging trees and mapped their own forest zones.

“We sustain our forest by designating zones for housing and for preservation,” Samay, an Iban member, said at the conference in North Maluku in April.

“For instance, we don’t touch water catchment areas because that’s our source of clean water. We also allow each family to cut down just five trees a year, and the wood may only be used to build a house.”

The Iban’s forest stewardship methods were certified in 2008 by the Indonesian Ecolabel Foundation as sustainable forest management, making it the first community forest to get the certification.

But the community’s efforts at forest zoning have still not been acknowledged by authorities in their home district.

“We’ve tried to get acknowledgment for our mapping since 1998 from the local government, but still nothing,” Samay said.

“We need that acknowledgment because we’re worried that our lands could be changed for other uses. It’s not for us, it’s for our children and grandchildren.

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Coral Reefs Could Be Decimated by 2100

Eli Kintisch, ScienceNOW Wired 21 Dec 12;

Nearly every coral reef could be dying by 2100 if current carbon dioxide emission trends continue, according to a new review of major climate models from around the world. The only way to maintain the current chemical environment in which reefs now live, the study suggests, would be to deeply cut emissions as soon as possible. It may even become necessary to actively remove carbon dioxide from the atmosphere, say with massive tree-planting efforts or machines.

The world’s open-ocean reefs are already under attack by the combined stresses of acidifying and warming water, overfishing, and coastal pollution. Carbon emissions have already lowered the pH of the ocean a full 0.1 unit, which has harmed reefs and hindered bivalves’ ability to grow. The historical record of previous mass extinctions suggests that acidified seas were accompanied by widespread die-offs but not total extinction.

To study how the world’s slowly souring seas would affect reefs in the future, scientists with the Carnegie Institution for Science in Palo Alto, California, analyzed the results of computer simulations performed by 13 teams around the world. The models include simulations of how ocean chemistry would interact with an atmosphere with higher carbon dioxide levels in the future. This so-called “active biogeochemistry” is a new feature that is mostly absent in the previous generation of global climate models.

Using the models’ predictions for future physical traits such as pH and temperature in different sections of the ocean, the scientists were able to calculate a key chemical measurement that affects coral. Corals make their shells out of the dissolved carbonate mineral known as aragonite. But as carbon dioxide pollution steadily acidifies the ocean, chemical reactions change the extent to which the carbonate is available in the water for coral. That availability is known as its saturation, and is generally thought to be a number between 3 and 3.5.

No precise rule of thumb exists to link that figure and the health of reefs. But the Carnegie scientists say paleoclimate data suggests that the saturation level during preindustrial times—before carbon pollution began to accumulate in the sky and seas—was greater than 3.5.

The models that the Carnegie scientists analyzed were prepared for the major global climate report coming out next year: the Intergovernmental Panel on Climate Change report. The team compared the results of those simulations to the location of 6000 reefs for which there is data, two-thirds of the world total. That allowed them to do what amounted to a chemical analysis of future reef habitats.

In a talk reviewing the study at the fall meeting of the American Geophysical Union earlier this month, senior author and Carnegie geochemist Ken Caldeira showed how the amount of carbon emitted in the coming decades could have huge impacts on reefs’ fates. In a low-emissions trajectory in which carbon pollution rates were slashed and carbon actively removed from the air by trees or machines, between 77% and 87% of reefs that they analyzed stay in the safe zone with the aragonite saturation above 3.

“If we are on the [business as usual] emissions trajectory, then the reefs are toast,” Caldeira says. In that case, all the reefs in the study were surrounded by water with aragonite saturation below 3, dooming them. In that scenario, Caldeira says, “details about sensitivity of corals are just arguments about when they will die.”

“In the absence of deep reductions in CO2 emissions, we will go outside the bounds of the chemistry that surrounded all open ocean coral reefs before the industrial revolution,” says Carnegie climate modeler Katharine Ricke, the first author on the new study.

Greg Rau, a geochemist at Lawrence Livermore National Laboratory in California, says the work sheds new light onto the future of aragonite saturation levels in the ocean, also known as “omega.” “There is a very wide coral response to omega—some are able to internally control the [relevant] chemistry,” says Rau, who has collaborated with Caldeira in the past but did not participate in this research. Those tougher coral species could replace more vulnerable ones “rather than a wholesale loss” of coral. “[But] an important point made by [Caldeira] is that corals have had many millions of years of opportunity to extend their range into low omega waters. With rare exception they have failed. What are the chances that they will adapt to lowering omega in the next 100 years?”

This story provided by ScienceNOW, the daily online news service of the journal Science.

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Great Barrier Reef's collapsing sea floor could trigger tsunami

Sharnie Kim ABC News 21 Dec 12;

Researchers mapping the sea floor near the Great Barrier Reef say they have found a giant slab of collapsing sea floor that could trigger a tsunami in the future.
Audio: Sharnie Kim reports from Cairns (AM)

Marine geologists at James Cook University say it is only a matter of time before the slab, known as the Noggin Block, collapses.

Dr Robin Beaman says the slab is the remains of an underwater landslide deep in the Great Barrier Reef.

"It's actually up on the top of the continental slope in about 350 metres of water," he said.

"This block, which is about one cubic kilometre ... is in the very slow, early stages of starting to break away from the edge of the Great Barrier Reef."

He says the Noggin Block is stable at the moment, but warns a collapse could be catastrophic.

"The only thing that we could find that would trigger a block breaking away on that scale [would be] a very large earthquake in the near vicinity. That is very unlikely," he said.

"If it were to break away catastrophically, that is break away really quickly, what that would do is it would create a surface wave above it. It would actually cause a tsunami.

"That tsunami would travel across the Great Barrier Reef, it's about 70 kilometres offshore, and it would impact the local area, the North Queensland area."

It would take about an hour for the tsunami to hit nearby coastal areas like Mourilyan Harbour and Clump Point.

Dr Beaman and his colleagues hope use their sonar mapping technique to find more underwater areas at risk of collapsing.

"We should be aware that these things exist," he said.

"We don't really know when such a block might collapse. All I can say is sometime it eventually will."

The research is published in the journal Natural Hazards.

Slab of Barrier Reef sea floor breaking off: scientists
Channel NewsAsia 21 Dec 12;

SYDNEY: A huge slab of sea floor near the Great Barrier Reef is in the early stages of collapse and could generate a tsunami when it finally breaks off, researchers warned Friday.

Marine geologists from Australia's James Cook University have been using advanced 3D mapping techniques on the deepest parts of the reef -- below diving depth -- since 2007 and have discovered dozens of sub-marine canyons.

On a recent trip, they came across the one cubic kilometre slab of sea floor, the remains of an ancient underwater landslide, which is perched on the continental shelf.

"Undersea landslides are a well understood geological process but we didn't know there were any on the Barrier Reef," geologist Robin Beaman told AFP.

"We found this one large block that stood out. It is sitting on top of a sub-marine canyon, cutting into the slopes and it is in the preliminary stage of collapse."

He stressed that no one knew when a collapse may occur, "whether tomorrow or even in our lifetime", but that people should be aware that it was there.

"It is slowly giving way although it remains stable under current conditions," he said.

"But it is absolutely going to collapse and when it does fall it will fall one kilometre into the adjacent basin.

"This will generate a localised tsunami that will affect the Queensland coastline, which is around 70 kilometres (40 miles) away.

"We're not trying to alarm people, but we need to know it is there and what could happen when it falls," he added.

The geologists who made the discovery, which was published in the journal Natural Hazards, were travelling on the Southern Surveyor, an Australian maritime research vessel.

This is the same ship on which scientist Maria Seton last month discovered that a South Pacific landmass identified on Google Earth and world maps as Sandy Island does not exist.


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2012: A Year of Weather Extremes

Becky Oskin Yahoo News 21 Dec 12;

From unprecedented drought to killer cold, 2012 was a year of weather extremes.

In 2012, the United States suffered 11 weather-related events that cost $1 billion apiece, according to a preliminary list released Thursday (Dec. 20) by the National Oceanic and Atmospheric Administration (NOAA). Economic losses for Hurricane Sandy and the yearlong drought are still being calculated, but NOAA estimates 2012 will surpass 2011 in terms of aggregate costs for disasters (exceeding $60 billion).

Severe weather disasters hit beyond the United States, too, as super typhoons slammed into Asia and a cold snap froze Europe's rivers. Globally, countries battled heat waves and droughts.

The World Meteorological Organization projects 2012 to be the warmest year on record since 1850, even with the cooling effects of La Niña in the early months. And 2013 could be even hotter, the WMO estimates.

Cold lows and hot highs

Winter's extremes included January's record snowfall in Alaska, which hit as the rest of the country sauntered around in T-shirts. In February, Europe suffered through a cold snap that killed hundreds of people and froze the continent's rivers and canals, interrupting commerce.

An early, April start to tornado season raised fears of another devastating series of twisters, as happened in 2011. But this year, the funnels fizzled out. In the end, 2012 may go down as the year with the fewest tornadoes on record.

The combination of an ongoing drought and a crippling heat wave throughout the summer had lethal effects on people, animals and crops. Nebraska experienced its driest year since record keeping started more than a century ago, according to NOAA. Colorado suffered its worst fire season in more than a decade, with western wildfires charring 9.15 million acres (37,000 square kilometers) as of November, according to the National Interagency Fire Center. [2012: A Year of Weather Extremes]

Super storms

But 2012 may ultimately stand out in the history books mostly due to its continent-sized storms, which relentlessly pounded coastlines in the Atlantic and the Pacific.

In Asia, super typhoons swept across Korea, China and Japan like cars on a train, one after another, causing record flooding. Even into December, Super Typhoon Bopha destroyed homes in the Philippines, claiming more than 1,000 lives.

The Atlantic hurricane season produced 19 named storms, well above the yearly average of 12, according to a statement from NOAA. Two tropical storms, Alberto and Beryl, developed in Maybefore the season even officially began.

However, 2012 was the seventh consecutive year that no major hurricanes (Category 3, 4 or 5) hit the United States. But Hurricane Sandy showed it doesn't take a big hurricane to make a major impact. [Hurricane Sandy: Photos of a Frankenstorm]

Sandy, which was a post-tropical cyclone when it made landfall, will go down in the record books as the second-costliest storm in U.S. history. Its tremendous storm surge, coupled with a high tide, wreaked havoc along the New Jersey and New York coastlines. Sandy registered the lowest barometric pressure in the history of the Northeast.

A higher number of named storms and hurricanes than predicted hit the Atlantic basin, in large part because El Niño, which likely would have suppressed overall storm activity, never materialized as anticipated by many climate models, NOAA said in a statement.

Yet several storms this year went largely unnoticed because they stayed out over the Atlantic. A persistent jet stream pattern over the eastern portion of the country helped steer many of this season's storms away from the United States, according to NOAA.

Outlook for 2013

Instead of El Niño, NOAA predicts that the neutral phase of the El Niño/ La Niña Southern Oscillation (ENSO) index will prevail through spring. Jokingly called "La Nada," it is the middle ground between El Niño and La Niña (the pattern associated with cool water in the equatorial Pacific).

The lack of a reliable weather pattern to hang a prediction on makes forecasting harder. The temperature outlook through March indicates above-normal temperatures for the southern half of the continental United States, except for coastal southern California, Florida and part of the southeast coast, according to the National Weather Service's Climate Prediction Center.

The center also predicts colder-than-normal temperatures in the northern Rocky Mountains, northern Great Plains and southern Alaska.

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