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Woolly Mammoth - Mammuthus primigenius
Researchers Solve Mammoth Evolutionary Puzzle: The Woollies Weren't Picky, Happy to Interbreed

ScienceDaily (May 30, 2011) — A DNA-based study sheds new light on the complex evolutionary history of the woolly mammoth, suggesting it mated with a completely different and much larger species.

The research, which appears in the BioMed Central's open access journal Genome Biology, found the woolly mammoth, which lived in the cold climate of the Arctic tundra, interbred with the Columbian mammoth, which preferred the more temperate regions of North America and was some 25 per cent larger.

"There is a real fascination with the history of mammoths, and this analysis helps to contextualize its evolution, migration and ecology" says Hendrik Poinar, associate professor and Canada Research Chair in the departments of Anthropology and Biology at McMaster University.

Poinar and his team at the McMaster Ancient DNA Centre, along with colleagues from the United States and France, meticulously sequenced the complete mitochondrial genome of two Columbian mammoths, one found in the Huntington Reservoir in Utah, the other found near Rawlins, Wyoming. They compared these to the first complete mitochrondrial genome of an endemic North American woolly mammoth.

"We are talking about two very physically different 'species' here. When glacial times got nasty, it was likely that woollies moved to more pleasant conditions of the south, where they came into contact with the Columbians at some point in their evolutionary history," he says. "You have roughly 1-million years of separation between the two, with the Columbian mammoth likely derived from an early migration into North American approximately 1.5-million years ago, and their woolly counterparts emigrating to North America some 400,000 years ago."

"We think we may be looking at a genetic hybrid," says Jacob Enk, a graduate student in the McMaster Ancient DNA Centre. "Living African elephant species hybridize where their ranges overlap, with the bigger species out-competing the smaller for mates. This results in mitochondrial genomes from the smaller species showing up in populations of the larger. Since woollies and Columbians overlapped in time and space, it's not unlikely that they engaged in similar behaviour and left a similar signal."

The samples used for the analyses date back approximately 12,000 years. All mammoths became extinct approximately 10,000 years ago except for small isolated populations on islands off the coast of Siberia and Alaska.

Funding for this study was provided by the Natural Science and Engineering Research Council and the Canadian Research Chairs program.

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Illustration comparing Columbian mammoth and the woolly mammoth.


Journal Reference:

Jacob Enk, Alison Devault, Regis Debruyne, Christine E King, Todd Treangen, Dennis O'Rourke, Steven L Salzberg, Daniel Fisher, Ross MacPhee and Hendrik Poinar. Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. Genome Biology, 2011; 12: R51 DOI: 10.1186/gb-2011-12-5-r51
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Mammoths' extinction not due to inbreeding, study finds

By Dhruti Shah BBC News
23 March 2012 Last updated at 16:44 GMT

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Scientists say research into mammoths could influence modern conservation programmes.

The last known population of woolly mammoths did not "inevitably" die out because of inbreeding and lack of genetic diversity, a study suggests.

Scientists used techniques normally used to tackle crime scenes to carry out DNA analysis of samples taken from Wrangel Island in the Arctic Ocean.

They said that it was more likely that human activity or environmental factors killed off the healthy creatures.

Their work is published in the journal Molecular Ecology.

Although mammoths generally died out and disappeared from mainland Eurasia and North America around 10,000 years ago, about 500-1,000 mammoths continued to survive on Wrangel Island for a further 6,000 years.

The 7,000 sq km Wrangel is about 140km from the Russian mainland.

Diversity problems

Scientists working together in the UK and Sweden also say their research could have immense implications for modern-day conservation programmes.

They examined bones, teeth and tusks from the island and compared these with samples found in Chukotka in north-east Siberia.

Report co-author Dr Love Dalen from the department of molecular systematics at the Swedish Museum of Natural History told the BBC the team had been working on the study since 2008.

He said: "We wanted to find out why these mammoths became extinct.

"Wrangel Island is not that big and it was initially thought that such a small population could have suffered problems of inbreeding and a lack of genetic diversity."

He said many previous studies of mammoth DNA had focused on using mitochondrial DNA - genetic information which is passed down on the maternal line.

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The laboratory work took place in Sweden and the UK

As cells contain multiple copies of the mitochondrial genome, this DNA is easier to extract from ancient remains than the DNA found in the nucleus of cells.

"But the problem is mammoths don't display that much genetic variation - especially towards the end of their line," Dr Dalen explained.

"We decided to focus on microsatellites (repeated sequences in the DNA) to compare genetic fingerprints of each individual mammoth. This gave us access to nuclear DNA and gave us far stronger results."

He said that during the ice age, the total mammoth population in Eurasia dipped from tens of thousands to very few.

Dr Dalen added: "The DNA investigations found there was a 30% loss in genetic diversity as the population levels dropped - but that was to be expected.

"But when we examined the samples from the island, there reached a point when this reached a plateau and there was no more loss. This stage continued until the creatures became extinct.

"This therefore rejects the inbreeding theory. The mammoths on the island were isolated for nearly 6,000 years but yet managed to maintain a stable population."

The report concluded that the island was large enough for the creatures and so the final extinction was "not a delayed outcome of an inevitable process" such as inbreeding.

"This suggests that the final extinction was caused by a rapid change in the mammoths' environment, such as the arrival of humans or a change in climate, rather than a gradual decline in population size," the study concludes.

Dr Dalen said further investigation focusing on finding the last few woolly mammoths was needed but added: "If humans hunted them to extinction, I would expect us to find evidence of that. I'm personally leaning towards environmental change."

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The scientists analysed DNA from tusks, bones and teeth of mammoths

The researchers - who studied 76 samples altogether - also used a computational approach to investigate the population size on the island and how the genetic make-up of the creatures had changed over the years.

The team found that there was a sharp decease in the numbers of mammoths in north-east Siberia during the Pleistocene/Holocene transition (about 12,000 years ago). But the group concluded this was likely to be because the Wrangel Island mammoths became increasingly isolated as the sea levels rose around them.

Dr Dalen said: "We took a statistical approach to the genetics and data. We found that there were at least 500-1,000 mammoths at any one time living on the island before they died out.

Significant moment

He said this had immense implications for current research.

"What's really interesting is that maintaining 500 effective individuals is a very common target in conservation programmes.

"Our results therefore support the idea that such an effective population size is enough to maintain genetic diversity for thousands of years.

"These mammoths did fine with what was originally considered to be a small number," he said.

The scientists' work has been reviewed by evolutionary geneticist and University College London Professor Mark Thomas.

He said they had produced a significant moment in mammoth research.

"They have carried out the detailed research in the way it needs to be done but hadn't yet been done before.

"They examined the DNA of multiple samples and they showed that by having a constant size population, the Wrangel Island mammoths were not just doomed to die.

"Something happened to kill all of them - but what that is we do not know yet. That is the next step," he said.
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Woolly mammoth may have been killed by humans

By Ben Aviss Reporter, BBC Nature
4 April 2012 Last updated at 02:14

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The mammoth which was found in a frozen ice cliff in Siberia is "exquisitely preserved"

The discovery of a well-preserved juvenile woolly mammoth suggests that ancient humans "stole" mammoths from hunting lions, scientists say.

Bernard Buigues of the Mammuthus organisation acquired the frozen mammoth from tusk hunters in Siberia.

Scientists completed an initial assessment of the animal, known as Yuka, in March this year.

Wounds indicate that both lions and humans may have been involved in the ancient animal's death.

"Already there is dramatic evidence of a life-and-death struggle between Yuka and some top predator, probably a lion," says leading mammoth expert, Daniel Fisher, professor of earth and environmental sciences at the University of Michigan.

"Even more interesting, there are hints that humans may have taken over the kill at an early stage."

If further investigation by Mr Buigues, Professor Fisher and fellow scientists at the Sakha Academy of Sciences in Yakutsk confirms this analysis, it will be the first carcass to show signs of interaction with ancient humans found in this part of the world.

The Yuka mammoth was filmed as part of the BBC/Discovery Co-Production programme Woolly Mammoth: Secrets from the Ice.

By analysing the teeth and tusks, the team estimate Yuka was about two and a half years old when it died.

Teeth, tusks and bone are the most common ways extinct animals such as mammoths are studied, as these parts of the body take a relatively long time to decompose.

Soft tissues such as muscle, skin and internal organs decompose far quicker, and are very rarely found on old carcasses. This means that vital information is usually lost.

But much of Yuka's soft tissue as well as its woolly coat has remained intact, well-preserved in its icy tomb for possibly more than 10,000 years.

Kevin Campbell, associate professor of environmental and evolutionary physiology at the University of Manitoba said: "These are remarkably rare finds and have huge significance."

One of the most striking things about Yuka is its strawberry-blonde hair, he said.

The possibility of mammoths having lighter coat colours was proposed in 2006 after scientists studied the genes extracted solely from a mammoth bone.

Yuka provides direct evidence that mammoths did have lighter-coloured coats.

Associate Professor Campbell said the find "will be a boon to researchers as it will help them link observed phenotypes (morphological features that we can see) with genotype (DNA sequences)".

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The Yuka mammoth Yuka was found with many bones missing and cuts that may have been made by ancient hunters

These links will allow scientists to determine how widespread physical traits such as eye and hair colour were "within and among mammoth populations" simply from studying genes from bone or hair samples in the future.

Professor Fisher agreed the find was extraordinary: "It's like a diary or journal someone has just handed you - you just haven't had a chance to read it."

Lion attacks

Healed scratches found on the skin indicate a lion attack that Yuka survived earlier in its relatively short life.

However, similar deep cuts that had not healed suggest a subsequent lion attack that either caused or happened very near the time of Yuka's death.

Also, when moving one of Yuka's legs, Professor Fisher recognised evidence of a freshly broken leg when it died and suggested this may have occurred as Yuka tried to flee from attackers.

The lions in question (Panthera leo spelea) are an extinct subspecies of the African lion, known commonly as Eurasian cave lions but were present at the same time as the mammoths.

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Yuka mammoth foot Yuka's foot pads and hair remain intact after more than 10,000 years

"Did we know lions hunted mammoths? Well, we guessed they did. But could we ever have expected to see such graphic evidence? No - but here it is," explained Professor Fisher.

In modern-day Africa, young elephants are attacked by lions, providing a means of comparing their injuries with Yuka's.

Lions will usually enter the carcass through the belly, clamp their teeth over the mouth in order to suffocate their prey, and chew at an elephant's muscular trunk.

However, Yuka's trunk is not damaged and there is only slight damage to the hide around the face.

Instead of entering Yuka's body via the belly, there is what Professor Fisher describes as "a bizarre set of damage on the hide".

This includes a "long, straight cut that stretches from the head to the centre of the back" as well as "very unusual patterned openings" into the skin and "scalloped margins" on the upper right-hand flank.

The skull, spine, ribs and pelvis were all removed from Yuka's body, but the skull and pelvis were found nearby. However, most of the spine and three-quarters of the ribs are missing.

Human interference

Each scalloped mark on the skin is made up by 15-30 small, serrations that "could be the saw-like motion of a human tool" and there are "some quite striking cut marks" on the leg bones, according to Professor Fisher.

Prof Fisher said they had questioned whether the cuts could have been made more recently.

"We asked the people who found this mammoth multiple times if they had done this. They replied 'No! We did not get our knives out' which suggests we're looking at some sort of interaction of humans, mammoths and lions.

"Were humans using the lions to catch mammoths and then moving the lions off their kill... was that what happened? I don't know but I wouldn't have thought about it without seeing it [the evidence]."

Supporting this argument, the Dorobo tribe still practise the art of stealing kills from lions in Kenya.

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Prof Alice Roberts with Lyuba, one of the best-preserved mammoths that had been previously found

"Each new specimen has something to teach us, but Yuka provides some of the most dramatic evidence yet available for events surrounding the death of a woolly mammoth on the arctic steppes of Siberia."

Professor Alice Roberts was part of the film crew that followed Yuka being recovered from the tusk hunters.

She said: "There are some odd things. What we need to do is find out if this was human interference near the time of death or was it something that happened much later?

"If it happened near the time of death then it means Yuka is a very important specimen as there are not many [mammoths] that show human interactions."

She said seeing Yuka in the flesh was almost "poignant".

"You feel it has only just died as it is so beautifully preserved."
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SpaceCoyote Wrote:[Image: mammoth-cloning.jpg]

Scalesofanubis Wrote:

Scientists Just Found a Wooly Mammoth That Still Had Liquid Blood

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[small]Photo: Kristin Marie Enns-Kavanagh[/small]

Russian researchers headed by well-known mammoth-hunter Semyon Grigoriev have just found something amazing in the ice on one of Siberia’s Lyakhovsky Islands—a frozen wooly mammoth that still had liquid blood.According to Agence France-Press, the mammoth is thought to have been around 60 years old when she died and was buried by ice between 10,000 and 15,000 years ago. Digging down through the ice, says Wired UK, the researchers found the preserved mammoth in temperatures around 14 Fahrenheit—far below freezing. Poking at ice cavities found alongside the mammoth’s frozen remains with an ice pick caused liquid blood to flow.

It can be assumed that the blood of mammoths had some cryo-protective properties,” Grigoriev said. “The blood is very dark, it was found in ice cavities below the belly and when we broke these cavities with a pick, the blood came running out.

Aside from flowing blood, the team also found mammoth muscle with the “natural red color of fresh meat,” says a release from the North-Eastern Federal University of Yakutsk.
Grigoriev told the AFP that the find is “the most astonishing case in my entire life.” Grigoriev is well-known among mammoth hunters for his long-standing quest to clone one of the long-extinct creatures. Back in September Grigoriev made headlines when his discovery of a mammoth that was thought to still have bone marrow raised the debate over mammoth cloning. The excitement over that find, says Wired UK, “soon dissipated when it became clear that a translation error had made the discovery seem more impressive than it was.”
According to the AFP, Grigoriev is hoping to find still-living mammoth cells, and a chance to reinvigorate his dream of cloning a furry friend. For Scientific American, Kate Wong has a slightly more skeptical outlook:

    From the sound of things, these remains may well revolutionize scientists’ understanding of mammoth physiology, which would be thrilling indeed. As for resurrecting this long-vanished creature, well, let’s hope it doesn’t come to that. As my colleagues and I argue in the June issue of Scientific American, de-extinction is a bad idea.
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DNA study suggests hunting did not kill off mammoth

11 September 2013 Last updated at 01:30 GMT S
Pallab Ghosh
By Pallab Ghosh
Science correspondent, BBC News

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The traditional view of the woolly mammoth as a hardy, abundant species will have to change

Researchers have found evidence to suggest that climate change, rather than humans, was the main factor that drove the woolly mammoth to extinction.

A DNA analysis shows that the number of creatures began to decrease much earlier than previously thought as the world's climate changed.

It also shows that there was a distinct population of mammoth in Europe that died out around 30,000 years ago.

The results have published in the Proceedings of the Royal Society B.

The view many researchers had about woolly mammoths is that they were a hardy, abundant species that thrived during their time on the planet.

But according to the scientist who led the research, Dr Love Dalen of the Swedish Museum of Natural History, the study shifts that view.

"The picture that seems to be emerging is that they were a fairly dynamic species that went through local extinctions, expansions and migrations. It is quite exciting that so much was going on," he told BBC News.

Dr Dalen worked with researchers in London to analyse DNA samples from 300 specimens from woolly mammoths collected by themselves and other groups in earlier studies

The scientists were able to work out how many mammoths existed at any given time from the samples as well as tracing their migration patterns. They looked at the genetic diversity in their samples - the less diverse the lower the population

They found that the species nearly went extinct 120,000 years ago when the world warmed up for a while. Numbers are thought to have dropped from several million to tens of thousands but numbers recovered as the planet entered another ice age.

The researchers also found that the decline that led to their eventual extinction began 20,000 years ago when the Ice Age was at its height, rather than 14,000 years ago when the world began to warm again as previously thought.

They speculate that it was so cold that the grass on which they fed became scarce. The decline was spurred on as the Ice Age ended, possibly because the grassland on which the creatures thrived was replaced by forests in the south and tundra in the north.

The reason they died out has been a matter of considerable scientific debate. Some have argued that humans hunted them to extinction while others have said that changes in the climate was the main factor.

A criticism of the climate extinction argument is that the world warmed well before the creatures became extinct and so that could not have been the cause.

The new results show that mammoths did indeed nearly go extinct between Ice Ages and so backs the view that climate change was the principal cause for their demise.

These results back a computer simulation of conditions at the time carried out by researchers at Durham University in 2010.

And of course other animals, including humans, became more active after the Ice Age and so competition with other species and hunting may also have been a factor in their extinction, though not the principle cause, argues Prof Adrian Lister of the NHM.

"During the last ice age, between about 50,000 and 20,000 years ago, there were substantial movements of mammoth populations - European populations being replaced by waves of migration from the east, for example," he said.

"But from about 20,000 years ago onwards, the population started the dramatic decline that led to its extinction, first on the mainland about 10,000 years ago, and finally on some outlying Arctic islands. The pattern seems to fit forcing by natural climate change: any role of humans in the process has yet to be demonstrated".'

Eleftheria Palkopoulou, Love Dalén, Adrian M. Lister, Sergey Vartanyan, Mikhail Sablin, Andrei Sher, Veronica Nyström Edmark, Mikael D. Brandström, Mietje Germonpré, Ian Barnes, and Jessica A. Thomas
Holarctic genetic structure and range dynamics in the woolly mammoth
Proc. R. Soc. B. 2013 280 20131910; doi:10.1098/rspb.2013.1910 (published 11 September 2013)

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred.
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Woolly Mammoths Wiped Out by Grass Invasion?
Tundra and steppe turning to less-nutritious grasses may have contributed to extinction of ancient Arctic beasts.

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Woolly mammoths roamed the northern steppes for at least 300,000 years before they died off.

Dan Vergano
National Geographic

Grasslands suddenly spreading across the Arctic about 10,000 years ago helped killed off the woolly mammoth and other prehistoric mammals, suggests a study of ancient Arctic vegetation.

Climate warming after the Ice Age, prehistoric hunters, and even a comet impact have been proposed as reasons for the extinction of the mammoth, woolly rhinoceros, and other oversized "megafauna" that once inhabited Siberia and North America's far northern plains. 

The new DNA analysis of Arctic vegetation over the past 50,000 years, published in Nature by a team led by Eske Willerslev of the University of Copenhagen, offers a new wrinkle on the climate-warming theory: The great beasts vanished because they weren't getting enough of the right food.

Some 10,000 years ago, the researchers found, the flowering, woody plants known as forbs—including sagebrush, yarrow, mums, and tansies—disappeared from Arctic steppes, which became more dominated by grasses. That vegetation change was "a likely key reason for the decline and extinction of many megafuana species," Willerslev says, by email.

DNA Detectives

The new theory is surprising because mammoths were thought to thrive on grass. The Nature study challenges a long-held picture of a grass-covered "mammoth steppe" covering the polar regions of Europe, Asia, and North America during the last Ice Age.

In the study, the team sampled permafrost cores dating back to 50,000 years ago from 17 locations in northern Russia, Canada, and Alaska. They found that DNA signatures in the cores indicate that the flowering species, and the tiny roundworms associated with them in the soil, once predominated over grasses on the ancient steppes.

What's more, the mammoths and other beasts seem to have favored those forbs. Willerslev and colleagues analyzed 18 preserved samples of stomach contents and scat from mammoths, woolly rhinos, horses, reindeer, and elk. They found that flowering species were a large part of the animals' diet.

The forbs could have been a key source of protein, Willerslev says, and they may have been easier to digest than grass. Previous research had missed that component of the mammoths' diet, he and his colleagues argue, because those studies relied on pollen counts to estimate past Arctic vegetation. Grasses produce abundant pollen, so such studies gave a misleading picture of the makeup of the steppes.

Farewell to Flowers

When the last Ice Age reached its peak around 20,000 years ago, the diversity of all plants in the Arctic declined, but flowering plants continued to dominate over grasses. The warming that ended the Ice Age, however, also brought a wetter climate that was more friendly to grasses. "This is the likely reason for the vegetation change in the Arctic into a system dominated by shrubs and grasses we see today," Willerslev says. Indeed, much of the ancient steppe has given way to mossy tundra.

The herds of mammoths and other megabeasts had probably also helped maintain the steppe they lived in, whether it was dominated by grasses or, as the new research suggests, by forbs. Grazing and trampling of vegetation allowed new seedlings to take root, and manure fertilized the plants. Human hunters, by reducing the population of mammoths, may thus have helped complete the vegetation transition that climate change began.

Woolly mammoths had roamed the northern steppes for at least 300,000 years before they died off. In parts of Alaska, at least six times more animals—such as mammoths, horses, and bison—lived in the region during that era than live there today. A last, isolated population of mammoths is thought to have finally gone extinct on Siberia's Wrangel Island about 3,700 years ago.

Journal Reference:
Eske Willerslev, John Davison, Mari Moora, Martin Zobel, Eric Coissac, Mary E. Edwards, Eline D. Lorenzen, Mette Vestergård, Galina Gussarova, James Haile, Joseph Craine, Ludovic Gielly, Sanne Boessenkool, Laura S. Epp, Peter B. Pearman, Rachid Cheddadi, David Murray, Kari Anne Bråthen, Nigel Yoccoz, Heather Binney, Corinne Cruaud, Patrick Wincker, Tomasz Goslar, Inger Greve Alsos, Eva Bellemain, Anne Krag Brysting, Reidar Elven, Jørn Henrik Sønstebø, Julian Murton, Andrei Sher, Morten Rasmussen, Regin Rønn, Tobias Mourier, Alan Cooper, Jeremy Austin, Per Möller, Duane Froese, Grant Zazula, François Pompanon, Delphine Rioux, Vincent Niderkorn, Alexei Tikhonov, Grigoriy Savvinov, Richard G. Roberts, Ross D. E. MacPhee, M. Thomas P. Gilbert, Kurt H. Kjær, Ludovic Orlando, Christian Brochmann, Pierre Taberlet. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature, 2014; 506 (7486): 47 DOI: 10.1038/nature12921

Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr BP (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25–15 kyr BP), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr BP, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.
Edited by Taipan, Nov 3 2017, 09:18 AM. View Edit History
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Inbreeding in woolly mammoths: Neck rib provide clues about decline and eventual extinction

Date: March 25, 2014
Source: PeerJ
Researchers recently noticed that the remains of woolly mammoths from the North Sea often possess a 'cervical' (neck) rib -- in fact, 10 times more frequently than in modern elephants (33.3 percent versus 3.3 percent). In modern animals, these cervical ribs are often associated with inbreeding and adverse environmental conditions during pregnancy. If the same factors were behind the anomalies in mammoths, this reproductive stress could have further pushed declining mammoth populations towards ultimate extinction.

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The arrow indicates a large articulation facet of a cervical rib on a fossil cervical vertebra of a woolly mammoth of the Natural History Museum Rotterdam.

Researchers recently noticed that the remains of woolly mammoths from the North Sea often possess a 'cervical' (neck) rib -- in fact, 10 times more frequently than in modern elephants (33.3% versus 3.3%). In modern animals, these cervical ribs are often associated with inbreeding and adverse environmental conditions during pregnancy. If the same factors were behind the anomalies in mammoths, this reproductive stress could have further pushed declining mammoth populations towards ultimate extinction.
Mammals, even the long-necked giraffes and the short-necked dolphins, almost always have seven neck vertebrae (exceptions being sloths, manatees and dugongs), and these vertebrae do not normally possess a rib. Therefore, the presence of a 'cervical rib' (a rib attached to a cervical vertebra) is an unusual event, and is cause for further investigation. A cervical rib itself is relatively harmless, but its development often follows genetic or environmental disturbances during early embryonic development. As a result, cervical ribs in most mammals are strongly associated with stillbirths and multiple congenital abnormalities that negatively impact the lifespan of an individual.
Researchers from the Rotterdam Museum of Natural History and the Naturalis Biodiversity Center in Leiden examined mammoth and modern elephant neck vertebrae from several European museum collections. "It had aroused our curiosity to find two cervical vertebrae, with large articulation facets for ribs, in the mammoth samples recently dredged from the North Sea. We knew these were just about the last mammoths living there, so we suspected something was happening. Our work now shows that there was indeed a problem in this population," said Jelle Reumer, one of the authors on the study published today in the open access journal PeerJ.
The incidence of abnormal cervical vertebrae in mammoths is much higher than in the modern sample, strongly suggesting a vulnerable condition in the species. Potential factors could include inbreeding (in what is assumed to have been an already small population) as well as harsh conditions such as disease, famine, or cold, all of which can lead to disturbances of embryonic and fetal development. Given the considerable birth defects that are associated with this condition, it is very possible that developmental abnormalities contributed towards the eventual extinction of these late Pleistocene mammoths.
The peer-reviewed study, entitled "Extraordinary incidence of cervical ribs indicates vulnerable condition in Late Pleistocene mammoths" was authored by Jelle Reumer of the Rotterdam Museum of Natural History and Clara ten Broek and Frietson Galis of Naturalis Biodiversity Center (Leiden).

Journal Reference:
Jelle W.F. Reumer, Clara M.A. ten Broek, Frietson Galis. Extraordinary incidence of cervical ribs indicates vulnerable condition in Late Pleistocene mammoths.PeerJ, 2014; 2: e318 DOI: 10.7717/peerj.318

The number of cervical vertebrae in mammals is highly conserved at seven. We have shown that changes of this number are selected against due to a coupling with major congenital abnormalities (pleiotropic effects). Here we show that the incidence of abnormal cervical vertebral numbers in Late Pleistocene mammoths from the North Sea is high (33.3%) and approximately 10 times higher than that of extant elephants (3.6%). Abnormal numbers were due to the presence of large cervical ribs on the seventh vertebra, which we deduced from the presence of rib articulation facets on sixth (posterior side) and seventh (anterior side) cervical vertebrae. The incidence of abnormal cervical vertebral numbers in mammoths appears to be much higher than in other mammalian species, apart from exceptional sloths, manatees and dugongs and indicates a vulnerable condition. We argue that the increased incidence of cervical ribs in mammoths is probably caused by inbreeding and adverse conditions that impact early pregnancies in declining populations close to extinction in the Late Pleistocene.
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Baby mammoth goes on display in UK

By Sarah White
BBC News, at the Natural History Museum
19 May 2014

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A perfectly preserved baby mammoth which died 42,000 years ago has been unveiled at the Natural History Museum in London.

Named Lyuba by the Siberian deer herder who discovered her in 2007, the specimen is 130cm tall and weighs 50kg.

Palaeontologist Prof Adrian Lister described seeing her for the first time as an "incredible experience".

Transported in a box that was opened on Monday, the juvenile female mammoth looked almost intact.

Prof Lister pointed out the small milk tusks that are barely visible, the almost flattened shape of the trunk designed to drink water from snow and a small layer of fat on top of the head which would have kept her warm in the permafrost of north-west Siberia.

Lyuba was found to have clay in her trunk, leading scientists to believe she suffocated on it while getting water. She is believed to have been discovered after her snowy grave thawed out during the spring and her remains washed up on a river bank.

The animal looked more like her distant elephant family relatives with wrinkled, leathery skin, as the hair which would have covered her warmly in life had eroded away, leaving just a few tufts.

Her only defect was the tail which has been gnawed off by animals.

Her body looks slightly deflated, which Prof Lister explains is from her effectively being mummified under the weight of all that ice for so long. Traces of the blue, powdery mineral vivianite, which is commonly found on fossils, can be seen on her body.

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The 42,000-year old carcass was discovered by a reindeer herder

Professor Lister said: "To see a three-dimensional mammoth in the flesh is absolutely extraordinary.

"To be eyeball to eyeball with a creature from the Ice Age which is so perfectly preserved and lifelike, looking like she is lying down and might walk away at any minute, is really moving. I have to pinch myself to think she died 42,000 years ago.

"It's wonderful to be able to share this with the public at the museum when she's never been outside of Russia and Asia before. It's really exciting and I'm sure others will be moved by seeing her."

Lyuba was named after the deer herder Yuri Khudi's wife (the name also means love in Russian). She was discovered by the Yuribei River, in the Yamal-Nenets district. Even her internal organs are intact.

Scientists regard the specimen as the most fully preserved mammoth ever found.

Mammoths first appeared in the Pliocene Epoch, some 4.8 million years ago. Climate change, overkill by human hunters, or a combination of both are among the explanations for their eventual disappearance about 5,000 years ago.

Lyuba, normally on display at the Yamal-Nenets Regional Museum-Exhibition Complex, will be on show at the Natural History Museum from Friday 23 May until 7 September.
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Short lives, violent deaths: Two CT-scanned Siberian mammoth calves yield trove of insights

Date: July 13, 2014
Source: University of Michigan
CT scans of two newborn woolly mammoths recovered from the Siberian Arctic are revealing previously inaccessible details about the early development of prehistoric pachyderms. In addition, the X-ray images show that both creatures died from suffocation after inhaling mud.

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CT images showing a side-by-side comparison of skulls from Lyuba (left) and Khroma, with bones of the front of the skull shown below.

CT scans of two newborn woolly mammoths recovered from the Siberian Arctic are revealing previously inaccessible details about the early development of prehistoric pachyderms. In addition, the X-ray images show that both creatures died from suffocation after inhaling mud.
Lyuba and Khroma, who died at ages 1 and 2 months, respectively, are the most complete and best-preserved baby mammoth specimens ever found. Lyuba's full-body CT scan, which used an industrial scanner at a Ford testing facility in Michigan, was the first of its kind for any mammoth.
"This is the first time anyone's been able to do a comparative study of the skeletal development of two baby mammoths of known age," said University of Michigan paleontologist Daniel Fisher.
"This allowed us to document the changes that occur as the mammoth body develops," Fisher said. "And since they are both essentially complete skeletons, they can be thought of as Rosetta Stones that will help us interpret all the isolated baby mammoth bones that show up at other localities."
Fisher, director of the U-M Museum of Paleontology, is lead author of a paper published online July 8 in a special issue of the Journal of Paleontology. The paper provides a detailed discussion of the findings from the Lyuba and Khroma CT scans and includes about 30 previously unpublished CT images.
The paper's 10 authors are from the United States, Russia and France. They include three recent U-M graduates and a collections manager at the U-M paleontology museum.

Siberian permafrost yields mammoth surprises
Lyuba and Khroma lived more than 40,000 years ago and belonged to mammoth populations separated by roughly 3,000 miles. Lyuba was found by reindeer herders in May 2007 on the banks of the Yuribei River on the Yamal Peninsula, in northwest Siberia. She was found frozen and partially dehydrated but otherwise appeared to be intact, except for the loss of most of her hair and all of her nails.
Khroma was found in October 2008 near the Khroma River in northernmost Yakutia, in northeast Siberia. She was frozen in permafrost in an upright position. Ravens and possibly arctic foxes scavenged exposed portions of her carcass, including parts of the trunk and skull and the fat hump that likely covered the back of her neck. Otherwise, the body was recovered in good condition.
Because of the remarkable preservation of Lyuba and Khroma, stringent conditions were placed on their study. Some dissection and limited sampling were allowed, but both specimens were left mostly intact. CT scans offered a non-destructive means of visualizing and analyzing much of their anatomy without compromising exhibit potential or options for future analysis.
CT scans of Lyuba were done in Tokyo in 2009 and in Wisconsin in 2010, using medical scanners. But because of Lyuba's size (about 110 pounds and slightly smaller than a baby elephant), the researchers could not acquire 3-D data from her entire body. They finally succeeded in October 2010 at Ford Motor Co.'s Nondestructive Evaluation Laboratory in Livonia, Mich., using a scanner designed for finding flaws in vehicle transmissions.
Khroma's CT scans were done at two French hospitals. Micro-CT scans of teeth from both mammoth calves were conducted at the University of Michigan School of Dentistry. From the dental studies, Fisher and colleagues determined that Lyuba died 30 to 35 days after birth and estimated that Khroma's age at death was between 52 and 57 days.

Dating technique more than 30 years in the making
The researchers used a technique developed by Fisher over the past 30-plus years that involves counting daily growth layers inside the teeth, a bit like counting the annual growth rings on a tree to determine its age. The dental studies also indicate that both mammoths were born in the spring.
Scans of Khroma's skull showed she had a brain slightly smaller than that of a newborn elephant, which hints at the possibility of a shorter gestation period for mammoths.
Lyuba's skull is conspicuously narrower than Khroma's, and her upper jawbones are more slender, while Khroma's shoulder blades and foot bones are more developed. These differences may simply reflect the one-month age difference between the calves, or they could relate to the different populations from which the two calves derived.
The researchers refer to both calves as mummies due to the high level of soft-tissue preservation. In addition to fully articulated skeletons, the carcasses held preserved muscle, fat, connective tissue, organs and skin. Khroma even had clotted blood inside intact blood vessels and undigested milk in the stomach.
"These two exquisitely preserved baby mammoths are like two snapshots in time. We can use them to understand how factors like location and age influenced the way mammoths grew into the huge adults that captivate us today," said co-author Zachary T. Calamari of the American Museum of Natural History, who began investigating mammoths as a U-M undergraduate working with Fisher.

Short lives, violent deaths
In addition to providing unprecedented insights into mammoth development, the CT scans of Lyuba and Khroma show that both youngsters died after inhaling mud, then suffocating, according to the authors of the Journal of Paleontology paper. This death scenario was suggested for Lyuba shortly after she was first examined. The Khroma CT scans demonstrate that she suffered a similar fate.
In Lyuba, the scans revealed a solid mass of fine-grained sediment blocking the air passages in the middle of the trunk. Sediment was also seen in Lyuba's throat and bronchial passages. If Lyuba had died by drowning rather than suffocation -- as some have suggested -- then traces of sediment should also have been detected in parts of the lungs beyond the bronchial passages, but that was not the case.
Slightly coarser sediment was found in Khroma's trunk, mouth and throat. Her lungs weren't available for study because they were scavenged before the carcass was recovered. Since both animals appear to have been healthy at the time of death, a "traumatic demise" involving the inhalation of mud and suffocation appears to be the most likely cause of death in both cases, according to the authors.
The researchers suspect that Lyuba died in a lake because sediments found in her respiratory tract include fine-grained vivianite, a deep blue iron- and phosphate-bearing mineral that commonly forms in cold, oxygen-poor settings such as lake bottoms.
It's possible that Lyuba crashed through the ice while crossing a lake during the spring melt. If she was struggling to breathe while submerged in a frigid lake, the mammalian "diving reflex" may have kicked in during her final moments, Fisher said. The reflex is triggered by cold water contacting the face, and it initiates physiological changes that enable animals to stay underwater for extended periods of time.
Those changes include a shifting of blood from the extremities to the body's core, including the brain and heart. The blood shift would help explain small vivianite nodules found on Lyuba's facial tissues during a necropsy. The CT scans revealed vivianite nodules, up to several millimeters in length, on the surface of the skull and inside it.

Blood provided iron source for vivianite nodules?
Blood coursing into Lyuba's brain, due to the mammalian diving reflex, may have provided the iron source for the vivianite nodules, according to the authors. Lactic acid-producing bacteria ate away at her bones after death, possibly liberating the phosphate ions used to make vivianite, Fisher said.
A possible death scenario for Khroma places the calf and her mother on a riverbank in the spring. Khroma had been nursing less than an hour before her death, as evidenced by undigested milk found in her stomach during a necropsy by a team of scientists that included Fisher.
"It looked like you'd just popped the top on a container of yogurt," Fisher recalled. "It was that white. It was that smooth. Just fresh, creamy milk from mama mammoth."
Perhaps the riverbank collapsed and the two mammoths, mother and daughter, plunged into the river. A fall would account for the fractured spinal column revealed by Khroma's CT scan, as well as the mud she inhaled.
The CT scan paper is part of a special Journal of Paleontology issue on three-dimensional visualization and analysis of fossils. In addition to Fisher and Calamari, the paper's authors are Ethan A. Shirley, Christopher D. Whalen and Adam Rountrey of the U-M Museum of Paleontology; Alexei N. Tikhonov of the Russian Academy of Sciences; Bernard Buigues of the International Mammoth Committee in France; Frederic Lacombat of the Musee de Paleontologie de Chilhac in France; and Semyon Grigoriev and Piotr A. Lazarev of the North-Eastern Federal University in Russia.
Fisher is the Claude W. Hibbard Collegiate Professor of Paleontology, a professor in the Department of Earth and Environmental Sciences, and a professor in the Department of Ecology and Evolutionary Biology. Calamari, Shirley and Whalen are recent U-M graduates and spent a month in Siberia with Fisher in 2012, searching for mammoth remains. Rountrey is the collections manager for vertebrates at the U-M Museum of Paleontology.
The research was supported by the U.S. National Science Foundation and by the National Geographic Society.

Journal Reference:
Daniel C. Fisher, Ethan A. Shirley, Christopher D. Whalen, Zachary T. Calamari, Adam N. Rountrey, Alexei N. Tikhonov, Bernard Buigues, Frédéric Lacombat, Semyon Grigoriev, Piotr A. Lazarev. X-ray computed tomography of two mammoth calf mummies. Journal of Paleontology, 2014; 88 (4): 664 DOI: 10.1666/13-092

Two female woolly mammoth neonates from permafrost in the Siberian Arctic are the most complete mammoth specimens known. Lyuba, found on the Yamal Peninsula, and Khroma, from northernmost Yakutia, died at ages of approximately one and two months, respectively. Both specimens were CT-scanned, yielding detailed information on the stage of development of their dentition and skeleton and insight into conditions associated with death. Both mammoths died after aspirating mud. Khroma's body was frozen soon after death, leaving her tissues in excellent condition, whereas Lyuba's body underwent postmortem changes that resulted in authigenic formation of nodules of the mineral vivianite associated with her cranium and within diaphyses of long bones. CT data provide the only comprehensive approach to mapping vivianite distribution. Three-dimensional modeling and measurement of segmented long bones permits comparison between these individuals and with previously recovered specimens. CT scans of long bones and foot bones show developmental features such as density gradients that reveal ossification centers. The braincase of Khroma was segmented to show the approximate morphology of the brain; its volume is slightly less (∼2,300 cm3) than that of neonate elephants (∼2,500 cm3). Lyuba's premaxillae are more gracile than those of Khroma, possibly a result of temporal and/or geographic variation but probably also reflective of their age difference. Segmentation of CT data and 3-D modeling software were used to produce models of teeth that were too complex for traditional molding and casting techniques.
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Woolly Mammoth Mummy Yields Well-Preserved Brain

By Agata Blaszczak-Boxe, Live Science Contributor | November 07, 2014 07:40am ET

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The mummified carcass of the 39,000-year-old woolly mammoth nicknamed Yuka.

The mummified brain of a well-preserved woolly mammoth found in the Siberian permafrost is the only mostly intact mammoth brain known to science, which has been described in a new study.

The mummified carcass of the 39,000-year-old woolly mammoth, which included the brain with folds and blood vessels visible, was found in August 2010 on the Laptev Sea coast near Yukagir, Russia. The mammoth, named Yuka, was 6 to 9 years old when it died, the researchers found.

The mummy mammoth was then transported from the coast and put into ice storage about 93 miles (150 kilometers) from the site, but has changed locations several times since. Having arrived at its most recent destination, Moscow, the specimen is on display until Nov. 6 at the first festival of the Russian Geographic Society.

In the new study, researchers examined the animal's brain using computed tomography (CT) and magnetic resonance imaging (MRI) scans. Thanks to the scanning technology, the investigators were able to study the well-preserved cerebellum, located at the back of the brain, and even see the white and gray matter of the cerebrum. The forebrain was in poorer condition than the cerebellum, the researchers wrote in the study, published online Oct. 25 in the journal Quaternary International.

"Until now, there was no opportunity to examine the whole brain of a woolly mammoth, which might have had complicated behavior, similar to modern elephants," Anastasia Kharlamova, of the Research Institute of Human Morphology, Russian Academy of the Medical Sciences, in Moscow, and colleagues write in the journal article.

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The brain from the mummified woolly mammoth carcass in dorsal view.

Moreover, the investigators even found traces of nervous tissue — the main component of the nervous system, responsible for reacting to stimuli and communicating impulses to different parts of the body — while examining the brain.

"The Yuka woolly mammoth specimen is the first mammoth [and large mammal] finding with the preserved brain from permafrost in the history of paleoneurology," Kharlamova told Live Science in an email.

"And it is still [the] only mammoth specimen with the preserved brain," she said, describing the presence of the brain in this large extinct species as something absolutely new in this field of research.

When the researchers trepanned the animal's skull to get to the brain, which means that they made a cut in the skull, using tools that included an angle grinder, a dental drill and chisels, they saw that there were still remains of soft tissue on its surface, according to the study. 

The mammoth specimen also had a well-preserved dura mater — Latin for "tough mother" — a dense membrane that protects the brain and spinal cord, as well as visible vessels and sinuses, the researchers wrote. The brain was stained brown due to oxidation, and it had shrunk, as its volume was 45 percent smaller than the volume of the cranial cavity, or the space inside the skull that houses the brain.

The brain may have thawed and frozen again several times, as the carcass has been stored in different conditions, the researchers wrote in the study. They found that the brain's structure was similar to that in modern-day elephants, which are related to mammoths, as both species belong to the same family of Elephantidae.

Based on their experience with Yuka, the researchers even came up with a set of tips that suggest the best strategies on how to proceed with preserving mammoth brains in the future.

"If there is an indication that the specimen discovered in permafrost has a preserved brain, it should be transported in a frozen condition," while it is inside the cranium, to avoid mechanical damage and deformations, they wrote in the study, also recommending that repeated thawing and freezing should be avoided at all costs.

This may be the first intact mammoth brain, but not the first of these ice-age animals to be unearthed. Two female baby woolly mammoths, dubbed Lyuba and Khroma, were uncovered from the Siberian permafrost in 2007 and 2009, respectively. The CT scans of these mammoths, whose stomach contents were found preserved, revealed skeletal differences between the two that may be due to some evolutionary change that occurred in the mammoth lineage — Khroma's remains dated to an earlier time than the 42,000-year-old Lyuba. Even so, their brains were not well preserved.
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Can the Long-Extinct Woolly Mammoth Be Cloned?

by Tia Ghose, Staff Writer | November 16, 2014 09:20am ET

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a mammoth carcass

A woolly mammoth carcass recently unearthed in Siberia could be the best hope yet for scientists aiming to clone the massive, long-extinct beast.

The mammoth specimen, which was discovered in 2013 in a remote part of Siberia, oozed a deep red liquid when it was first discovered. Scientists have now analyzed the mammoth to understand how it lived and died — and whether it will yield enough undamaged DNA to make cloning the extinct creature a reality.

Details from the mammoth autopsy will air in the Smithsonian Channel special called "How to Clone a Woolly Mammoth," on Nov. 29 at 8 p.m. ET/PT.

Stunning find

In May 2013, scientists from the Siberian Northeastern Federal University crossed the icy expanse of Siberia to reach Maly Lyakhovsky Island in the far north, where rumor had it a mammoth was lurking in the permafrost. At the time, two giant tusks were poking out of the ground, but when the researchers dug further, they found an almost complete mammoth, with three legs, most of the body, part of the head and the trunk still intact.

During excavations, the carcass oozed a dark red liquid that may have been fresh mammoth blood. In fact, the mammoth meat was reportedly fresh enough that one of the scientists took a bite of it.

"This is definitely one of the best samples people have ever found," Insung Hwang, a cloning scientist at the SOOAM Biotech Research Center, said in the show.

In the past, mammoths have yielded only a few dried specks of blood, and none of them left enough intact DNA for a cloning experiment.

Life and death

The researchers then took the carcass to Yakutsk in Russia, where a group of experts had just three days to thoroughly examine the specimen before it was refrozen to prevent rotting. The team used carbon dating to determine that the female mammoth, nicknamed Buttercup, lived about 40,000 years ago. Tests conducted on the mammoth's teeth revealed it was likely in its mid-50s.

Based on growth rates from the tusks, the team deduced that the mammoth had also successfully weaned eight calves and lost one baby. Feces and bacteria in the intestines revealed the ancient matriarch ate grassland plants such as buttercups and dandelions.

Tooth marks on her bones helped the scientists glean information about Buttercup's grisly end. The mammoth had become trapped in a peat bog and was eaten alive from the back by predators such as wolves.

While scientists probed the elbow of the mammoth, the large beast oozed more blood. Chemical analyses revealed that the blood cells were broken, but still contained hemoglobin, or oxygen-ferrying molecules. Unlike humans and other mammals, mammoths evolved a cold-resistant form of hemoglobin that could survive at the near-freezing temperatures present during the Ice Age.

"The fact that blood has been found is promising for us, because it just tells us how good of a condition the mammoth was kept in for 43,000 years," Hwang said.

Cloning a mammoth?

But whether or not Buttercup can be resurrected is another matter.

DNA is fragile and must be stored at low temperatures and in uniform humidity to stay intact. Past mammoth carcasses have looked exceptionally well-preserved, with some even yielding a preserved mammoth brain. Others have oozed what looked like blood, but ultimately did not have enough DNA to recreate the mammoth genome and clone it.

So far, the team hasn't found a complete copy of the mammoth's genome. But Buttercup's tissue has revealed some very long fragments that could potentially be pieced together to recreate the genome. Still, researchers are continuing to hunt for a complete copy.

Yet, even if a complete sample of undamaged DNA can't be found, there may be other ways to clone a mammoth, said Harvard University researcher George Church. He is hoping to combine DNA from Buttercup with modern-day elephants, essentially grafting the DNA for hair, tusks and other distinctive mammoth features into the genome of the animal's modern-day relatives.
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Entire genomes of woolly mammoths mapped: Clues to extinction, possibility of bringing mammoths back

Date: April 23, 2015
Source: McMaster University
An international team of researchers has sequenced the nearly complete genome of two Siberian woolly mammoths -- revealing the most complete picture to date -- including new information about the species' evolutionary history and the conditions that led to its mass extinction at the end of the Ice Age.

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Tip of the trunk of a baby mammoth.

An international team of researchers has sequenced the nearly complete genome of two Siberian woolly mammoths -- revealing the most complete picture to date -- including new information about the species' evolutionary history and the conditions that led to its mass extinction at the end of the Ice Age.
"This discovery means that recreating extinct species is a much more real possibility, one we could in theory realize within decades," says evolutionary geneticist Hendrik Poinar, director of the Ancient DNA Centre at McMaster University and a researcher at the Institute for Infectious Disease Research, the senior Canadian scientist on the project.
"With a complete genome and this kind of data, we can now begin to understand what made a mammoth a mammoth -- when compared to an elephant -- and some of the underlying causes of their extinction which is an exceptionally difficult and complex puzzle to solve," he says.
While scientists have long argued that climate change and human hunting were major factors behind the mammoth's extinction, the new data suggests multiple factors were at play over their long evolutionary history.
Researchers from McMaster, Harvard Medical School, the Swedish Museum of Natural History, Stockholm University and others produced high-quality genomes from specimens taken from the remains of two male woolly mammoths, which lived about 40,000 years apart.
One had lived in northeastern Siberia and is estimated to be nearly 45,000 years old. The other -believed to be from one of the last surviving mammoth populations -- lived approximately 4,300 years ago on Russia's Wrangel Island, located in the Arctic Ocean.
"We found that the genome from one of the world's last mammoths displayed low genetic variation and a signature consistent with inbreeding, likely due to the small number of mammoths that managed to survive on Wrangel Island during the last 5,000 years of the species' existence," says Love Dalén, an associate professor of Bioinformatics and Genetics at the Swedish Museum of Natural History.
Scientists used sophisticated technology to tease bits and pieces of highly fragmented DNA from the ancient specimens, which they then used to sequence the genomes. Through careful analysis, they determined the animal populations had suffered and recovered from a significant setback roughly 250,000 to 300,000 years ago. However, say researchers, another severe decline occurred in the final days of the Ice Age, marking the end.
"The dates on these current samples suggest that when Egyptians were building pyramids, there were still mammoths living on these islands," says Poinar. "Having this quality of data can help with our understanding of the evolutionary dynamics of elephants in general and possible efforts at de-extinction."
The latest research is the continuation of the pioneering work Poinar and his team began in 2006, when they first mapped a partial mammoth genome, using DNA extracted from carcasses found in permafrost in the Yukon and Siberia.
The study is published online in the Cell Press journal Current Biology.

Journal Reference:
Palkopoulou et al. Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Current Biology, 2015 DOI: 10.1016/j.cub.2015.04.007

•Complete high-quality genomes from two woolly mammoths were sequenced and analyzed
•40,000-year time difference between samples enabled calibration of molecular clock
•Demographic inference identified two severe bottlenecks in the species’ history
•One of the last surviving mammoths had low heterozygosity and signs of inbreeding

The processes leading up to species extinctions are typically characterized by prolonged declines in population size and geographic distribution, followed by a phase in which populations are very small and may be subject to intrinsic threats, including loss of genetic diversity and inbreeding [ 1 ]. However, whether such genetic factors have had an impact on species prior to their extinction is unclear [ 2, 3 ]; examining this would require a detailed reconstruction of a species’ demographic history as well as changes in genome-wide diversity leading up to its extinction. Here, we present high-quality complete genome sequences from two woolly mammoths (Mammuthus primigenius). The first mammoth was sequenced at 17.1-fold coverage and dates to ∼4,300 years before present, representing one of the last surviving individuals on Wrangel Island. The second mammoth, sequenced at 11.2-fold coverage, was obtained from an ∼44,800-year-old specimen from the Late Pleistocene population in northeastern Siberia. The demographic trajectories inferred from the two genomes are qualitatively similar and reveal a population bottleneck during the Middle or Early Pleistocene, and a more recent severe decline in the ancestors of the Wrangel mammoth at the end of the last glaciation. A comparison of the two genomes shows that the Wrangel mammoth has a 20% reduction in heterozygosity as well as a 28-fold increase in the fraction of the genome that comprises runs of homozygosity. We conclude that the population on Wrangel Island, which was the last surviving woolly mammoth population, was subject to reduced genetic diversity shortly before it became extinct.
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First comprehensive analysis of the woolly mammoth genome completed

Date: July 2, 2015
Source: University of Chicago Medical Center
The first comprehensive analysis of the woolly mammoth genome reveals extensive genetic changes that allowed mammoths to adapt Arctic life, including skin and hair development, insulin signaling, fat biology, and even traits such as small ears and short tails. A mammoth gene for temperature sensation was resurrected in the lab as a functional test.

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Rendering of a wooly mammoth family.

The first comprehensive analysis of the woolly mammoth genome reveals extensive genetic changes that allowed mammoths to adapt to life in the arctic. Mammoth genes that differed from their counterparts in elephants played roles in skin and hair development, fat metabolism, insulin signaling and numerous other traits. Genes linked to physical traits such as skull shape, small ears and short tails were also identified. As a test of function, a mammoth gene involved in temperature sensation was resurrected in the laboratory and its protein product characterized.

The study, published in Cell Reports on July 2, sheds light on the evolutionary biology of these extinct giants.

"This is by far the most comprehensive study to look at the genetic changes that make a woolly mammoth a woolly mammoth," said study author Vincent Lynch, PhD, assistant professor of human genetics at the University of Chicago. "They are an excellent model to understand how morphological evolution works, because mammoths are so closely related to living elephants, which have none of the traits they had."

Woolly mammoths last roamed the frigid tundra steppes of northern Asia, Europe and North America roughly 10,000 years ago. Well-studied due to the abundance of skeletons, frozen carcasses and depictions in prehistoric art, woolly mammoths possessed long, coarse fur, a thick layer of subcutaneous fat, small ears and tails and a brown-fat deposit behind the neck which may have functioned similar to a camel hump. Previous efforts to sequence preserved mammoth DNA were error-prone or yielded insights into only a limited number of genes.

To thoroughly characterize mammoth-specific genes and their functions, Lynch and his colleagues deep sequenced the genomes of two woolly mammoths and three Asian elephants -- the closest living relative of the mammoth. They then compared these genomes against each other and against the genome of African elephants, a slightly more distant evolutionary cousin to both mammoths and Asian elephants.

The team identified roughly 1.4 million genetic variants unique to woolly mammoths. These caused changes to the proteins produced by around 1,600 genes, including 26 that lost function and one that was duplicated. To infer the functional effects of these differences, they ran multiple computational analyses, including comparisons to massive databases of known gene functions and of mice in which genes are artificially deactivated.

Genes with mammoth-specific changes were most strongly linked to fat metabolism (including brown fat regulation), insulin signaling, skin and hair development (including genes associated with lighter hair color), temperature sensation and circadian clock biology -- all of which would have been important for adapting to the extreme cold and dramatic seasonal variations in day length in the Arctic. The team also identified genes associated with the mammoth body plan, such as skull shape, small ears and short tails.

Of particular interest was the group of genes responsible for temperature sensation, which also play roles in hair growth and fat storage. The team used ancestral sequence reconstruction techniques to "resurrect" the mammoth version of one of these genes, TRPV3. When transplanted into human cells in the laboratory, the mammoth TRPV3 gene produced a protein that is less responsive to heat than an ancestral elephant version of the gene. This result is supported by observations in mice that have TRPV3 artificially silenced. These mice prefer colder environments than normal mice and have wavier hair.

Although the functions of these genes match well with the environment in which woolly mammoths were known to live, Lynch warns that it is not direct proof of their effects in live mammoths. The regulation of gene expression, for example, is extremely difficult to study through the genome alone.

"We can't know with absolute certainty the effects of these genes unless someone resurrects a complete woolly mammoth, but we can try to infer by doing experiments in the laboratory," he said. Lynch and his colleagues are now identifying candidates for other mammoth genes to functionally test as well as planning experiments to study mammoth proteins in elephant cells.

While his efforts are targeted toward understanding the molecular basis of evolution, Lynch acknowledges that the high-quality sequencing and analysis of woolly mammoth genomes can serve as a functional blueprint for efforts to "de-extinct" the mammoth.

"Eventually we'll be technically able to do it. But the question is: if you're technically able to do something, should you do it?" he said. "I personally think no. Mammoths are extinct and the environment in which they lived has changed. There are many animals on the edge of extinction that we should be helping instead."

Story Source: University of Chicago Medical Center. "First comprehensive analysis of the woolly mammoth genome completed." ScienceDaily. (accessed July 3, 2015).

Journal Reference: 
Vincent J. Lynch, Oscar C. Bedoya-Reina, Aakrosh Ratan, Michael Sulak, Daniela I. Drautz-Moses, George H. Perry, Webb Miller, Stephan C. Schuster. Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic. Cell Reports, 2015 DOI: 10.1016/j.celrep.2015.06.027

•Complete genomes of three Asian elephants and two woolly mammoths were sequenced
•Mammoth-specific amino acid changes were found in 1,642 protein-coding genes
•Genes with mammoth-specific changes are associated with adaptation to extreme cold
•An amino acid change in TRPV3 may have altered temperature sensation in mammoths

Woolly mammoths and living elephants are characterized by major phenotypic differences that have allowed them to live in very different environments. To identify the genetic changes that underlie the suite of woolly mammoth adaptations to extreme cold, we sequenced the nuclear genome from three Asian elephants and two woolly mammoths, and we identified and functionally annotated genetic changes unique to woolly mammoths. We found that genes with mammoth-specific amino acid changes are enriched in functions related to circadian biology, skin and hair development and physiology, lipid metabolism, adipose development and physiology, and temperature sensation. Finally, we resurrected and functionally tested the mammoth and ancestral elephant TRPV3 gene, which encodes a temperature-sensitive transient receptor potential (thermoTRP) channel involved in thermal sensation and hair growth, and we show that a single mammoth-specific amino acid substitution in an otherwise highly conserved region of the TRPV3 channel strongly affects its temperature sensitivity.

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Mammoth remains, as far as the eye can see: Widest distribution of mammoths during the last Ice Age

Date: August 25, 2015
Source: Senckenberg Research Institute and Natural History Museum
Ice Age paleontologist recorded the maximum geographic distribution of the woolly mammoth during the last Ice Age and published the most accurate global map in this regard. The ice-age pachyderms populated a total area of 33,301,000 square kilometers and may thus be called the most successful large mammals of this era. The study determined that the distribution was limited by a number of climate-driven as well as climate-independent factors.

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Complete left tusk of an ice-age Woolly Mammoth (Mammuthus primigenius) from the Siberian Arctic on the Taimyr Peninsula. Each individual discovery increases our knowledge about the past distribution of these Ice Age giants.

Ice Age paleontologist Prof. Dr. Ralf-Dietrich Kahlke of the Senckenberg Research Station for Quaternary Paleontology in Weimar recorded the maximum geographic distribution of the woolly mammoth during the last Ice Age and published the most accurate global map in this regard. The ice-age pachyderms populated a total area of 33,301,000 square kilometers and may thus be called the most successful large mammals of this era. The study, recently published online in the scientific journal Quaternary International, determined that the distribution was limited by a number of climate-driven as well as climate-independent factors.

The mammoth is the quintessential symbol of the Ice Age -- and the status of these shaggy pachyderms has now been confirmed scientifically. "The recent research findings show that during the last Ice Age, mammoths were the most widely distributed large mammals, thus rightfully serving as a flagship species of the glacial era," according to Prof. Dr. Ralf-Dietrich Kahlke, an Ice Age researcher at the Senckenberg Research Station for Quaternary Paleontology in Weimar.

Kahlke has summarized the mammoth's distribution during the most recent Ice Age, i.e., the period between approx. 110,000 and 12,000 years ago, on a worldwide map. All in all, the Weimar paleontologist determined a total distribution area of 33,301,000 square kilometers for these large mammals -- almost 100 times the area of Germany today. From Portugal in the southwest across Central and Eastern Europe, Mongolia, Northern China, South Korea and Japan up to Northeastern Siberia, and thence to the American Midwest and Eastern Canada, from the shelf regions of the Arctic Ocean and Northwestern Europe to the bottom of the Adriatic Sea and to the mountains of Crimea: the fossil remains of woolly mammoths have been found everywhere.

"We related the computed distribution area to the real land surface at that time, thus generating the most precise map to date regarding the global habitats of the woolly mammoth," explains Kahlke, and he adds, "Such detailed knowledge regarding the distribution area is not even available for many species of animals alive today."

The generated map is based on decades of surveys of thousands of excavation sites on three continents. "Even sites under water, off the North American Atlantic shore and the North Sea, were taken into account. Due to the lower sea levels during the Ice Age -- a large volume of water was bound in glaciers -- these areas had fallen dry and were also inhabited by Mammuthus primigenius," according to Kahlke.

Only the ice-age bison (Bison priscus) had a widespread distribution similar to that of the mammoths. Kahlke explains, "The bison were clearly more variable than the woolly mammoths. Obviously, the mammoths had a higher tolerance toward various environmental factors and they were able to successfully settle in a variety of rather different open landscapes."

But there were certain factors that limited the distribution of the hirsute pachyderms: glaciers, mountain chains, semi-deserts and deserts, as well as changes in sea level and shifts in vegetation placed restrictions on the mammoths' distribution area. "The analysis of these limiting factors is useful in understanding the distribution of fossil species and their extinction -- as with the mammoths toward the end of the last Ice Age. In addition, the data aid in comprehending current changes in the distribution areas of recent animal species," offers Kahlke in summary.

Story Source: Senckenberg Research Institute and Natural History Museum. "Mammoth remains, as far as the eye can see: Widest distribution of mammoths during the last Ice Age." ScienceDaily. (accessed August 26, 2015).

Journal Reference:
Ralf-Dietrich Kahlke. The maximum geographic extension of Late Pleistocene Mammuthus primigenius (Proboscidea, Mammalia) and its limiting factors.Quaternary International, 2015; DOI: 10.1016/j.quaint.2015.03.023

The maximum geographic extension of fully developed woolly mammoth, Mammuthus primigenius, occurred during the last glacial period (MIS 5d–2), i.e. during the 110–14 ka interval. The mapping of the species' widest distribution reveals principal barriers to its expansion that were acting independent of short term environmental fluctuations. The maximum spread of M. primigenius was primarily controlled by the following trans-regional factors: (A) The configuration of inland glaciers; (B) The configuration of high mountain chains; © The configuration of semi-deserts and deserts; (D) The configuration of marine shorelines at year-round open water surfaces; (E) The exposure of continental shelf regions; and (F) The replacement of tundra-steppe by extended grasslands. Some of the biogeographic barriers were climate-independent; others were determined by long- or medium-term climatic processes. The effect of Eurasian and North American intra-continental steppes as obstacles to migration has not yet been fully elucidated.

The verifiable area of the Late Pleistocene distribution range of M. primigenius, based on geomorphological data, comprises approximately 33,301,000 km2 (surface area). When taking the geographical distribution of a species as a measure of its success, the Late Pleistocene woolly mammoth was one of the most successful large herbivores of the Holarctic Mammoth Fauna. 
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Woolly Mammoth Unearthed in Michigan—What Killed These Giants?
Ice Age bones raise question of whether people or a changing climate killed off the beasts.

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Farmers recently uncovered the remains of a woolly mammoth in a Chelsea, Michigan, soy field. Here, the skull is lifted onto a trailer for transport, with straps and ties to secure to cracks in the tusks. 

By Brian Switek, for National Geographic 
Video Editor Jason Kurtis, National Geographic 

The discovery of a nearly complete mammoth skeleton last week in Michigan raises the question of not only this animal's fate, but also what happened to the rest of the woolly mammoths. Did humans drive the Ice Age’s great beasts to extinction?

In news reports, University of Michigan paleontologist Dan Fisher proposed that prehistoric people killed and butchered the newly found mammoth, refrigerating what they didn’t immediately eat by sinking the rest of the carcass in a frigid lake. Other scientists say we can't be certain what killed the creature until the bones are examined for cut marks and other clues.

As for the rest of the woolly mammoths, whether humans are to blame for their disappearance, as well that of 36 other North American mammal species that went extinct at the end of the Ice Age, remains hotly disputed. The other leading contender: a changing climate.

Rare Find

Farmers digging a soy field near Chelsea, Michigan, were surprised to uncover the bones of a woolly mammoth that trod the region about 12,000 years ago.

Fisher excavated the bones, including a skull complete with tusks. While woolly mammoths have been found from Europe through Asia and North America, only about ten woolly mammoth skeletons have been dug up in Michigan, compared with around 300 of their more primitive cousin, the American mastodon.

Mammoths were probably rare in Michigan, Illinois State Museum paleontologist Chris Widga says, because of the waxing and waning of the glaciers there. “Michigan was under ice when mammoths were the only elephants on the landscape,” Widga says, the elephants grazing the cold grasslands south of the great ice sheets. “By the time the ice melted, mastodons were out-competing mammoths.”

The occurrence of even one more mammoth is reason to celebrate. “Even though this is just one site on the landscape, we’ve gotten better about eking out as much information as we can about individual animals,” Widga says, citing Fisher’s work on figuring out the life histories of particular mammoths through details preserves in their tusks.

What Killed the Mammoth?

Other experts are urging caution before chalking the new mammoth up as an Ice Age kill site. “It is fairly common to find mastodons and less commonly, mammoths, in lake or bog sediments dating to this time period,” Widga says.

In the absence of other lines of evidence such as cut marks on bones, there are other explanations for scattered elephant skeletons in the remnants of ancient lakes and bogs throughout the Midwest, such as the way bodies “blot and float” before gradually falling apart. “We can’t truly evaluate it until it is adequately investigated and published,” he adds.

Definitive evidence that humans hunted or scavenged mammoths is fairly rare, says University of Washington zooarchaeologist Donald Grayson. In a paper released earlier this year with Southern Methodist University colleague David Meltzer, Grayson notes that of 76 proposed Ice Age mammal kill sites, only 12 in the whole of North America suggest human hunting. That, the authors write, suggests that humans were not the primary drivers of North America’s Ice Age extinctions.

Climate may have been key to the recent catastrophe. At the same time humans were moving onto the continent, the global climate was rapidly changing, moving from cold and dry to warm and wet.

This changing climate rapidly winnowed away the cool, arid grasslands that woolly mammoths preferred. Combined with other ecological changes, such as the arrival of bison from Eurasia and forests springing up where “mammoth steppe” once spread, mammoths were squeezed out of their former range. The very last of the woolly mammoths, isolated on Wrangel Island off northern Siberia, perished about 4,000 years ago.

Extinction is rarely the outcome of a single cause, however, and the reason the last member of a species went extinct may not be the same reason that it became vulnerable in the first place.

Perhaps, as the Chelsea mammoth slowly yields its secrets, it will add a little more to the continuing discussion over life and death at the edge of the Ice Age. 
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