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Author Topic: The Mammoth  (Read 199 times)
Description: Starting with ideas on its extinction
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Baja Bush Pilot
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« on: May 25, 2007, 05:34:21 PM »

Lawrence Berkeley Lab scientist involved in new theory that explosion 12,900 years ago altered North American climate...

ACAPULCO, Mexico -- There's a new extraterrestrial suspect in the mysterious, highly debated disappearance of the woolly mammoth some 12,900 years ago. A team of two dozen scientists say the culprit was likely a comet that exploded in the atmosphere above North America.

The explosions sent a heat and shock wave across the continent, pelted the ground with a layer of telltale debris, ignited massive wildfires and triggered a major cooling of the climate, said nuclear analytic chemist Richard Firestone of Lawrence Berkeley Laboratory, one of the scientists who presented the controversial new theory Thursday at a conference of the American Geophysical Union in Acapulco.

At least 15 species, mostly large mammals including mammoths, mastadons, giant ground sloths, camels and horses, were wiped out about the same time. Firestone and his colleagues think some may have been killed by the explosions, and the rest died off after fires burned the vegetation they depended on.

"It seems awfully coincidental that the mammoths died at exactly the same moment where we find this impact layer," said Allen West, a member of the team from GeoScience consulting in Dewey, Ariz.

The scientists are bracing themselves for fiery reaction to their theory.

The extinctions were already a hotly debated event with scientists split between two theories. The leading theory is that man hunted the animals into extinction soon after arriving in North America, but some scientists think climate upheaval as the earth warmed up from the last ice age was the killer. Others think it was more of a one-two punch with climate change weakening the animal populations and hunters delivering the final blow.

But the impact theory has the advantage that it would explain why the Clovis hunting culture disappeared along with the animals, said archeologist Douglas Kennett of the University of Oregon.

For 300 years, Clovis people hunted mammoths and other animals with distinctive spear heads with fluted ends known as Clovis points.

The team visited archaeological sites containing Clovis points across North America and collected samples of the sediment that covered the last signs of Clovis people and the last mammoth bones.

They found many distinctive signs of an extraterrestrial impact, including rounded magnetic grains that formed when pieces of the comet were thrown back into space after the explosion and then melted into round grains as they re-entered the atmosphere.

They also found high levels of iridium and titanium, a special form of carbon molecules known as fullerenes that had helium atoms trapped inside, and microscopic diamonds called nanodiamonds. They also found strange rounded carbon grains and glass-like carbon that looks like hardened black taffy. Lots of soot and charcoal are evidence of the ensuing wildfires.

"We really have found the mother lode of impact material," Firestone said.

Above this layer of strange sediment there are no signs of mammoths or many of the other large mammal species of the day, or of the distinctive Clovis points. At many of the sites there is a gap in evidence of humans for several hundred years before new types of spear heads show up.

Just like the mammoths, many of the Clovis people could have been killed by the comet. Those who lived would have struggled to survive once many of the animals they hunted died. The remaining people may have delivered the final blow to the last of the large mammals. These people made it through, and slowly the human population rebounded.

Post-Clovis people were more culturally diverse, as reflected by an array of different spear heads, Kennett said. "This may suggest population fragmentation."

The survivors could have been separated into smaller groups across the continent that developed differing cultural traditions and spear head designs.

The explosion may also be the key to an enigmatic episode of cooler climate, known as the Younger Dryas, that began about the same time and lasted about 1,000 years. The earth had been steadily warming up after the last ice age due to cyclical changes in the planet's orbit that brought it slightly closer to the sun. Then suddenly, the climate started cooling for no obvious reason at a time when it should have still been warming up.

Previously, the leading theory for the cause of the cooling was that as the ice sheet that covered most of North America retracted to the north, the meltwater that had been flowing to the south switched to the east as eastern river drainages were uncovered. This surge of fresh water into the Atlantic caused a change in the ocean circulation that shut down a northward flow of warm water that had acted as a heater for the northern hemisphere.

"Earth was warming and then suddenly went back into cooling for 1,000 years," Firestone said.

The evidence for a change in ocean circulation fits with the comet theory as well, said paleoceanographer James Kennett of UC Santa Barbara. He argues that the massive explosion above the North American ice sheet would have caused a huge amount of melting and destabilization around the edges of the ice that would have sent a torrent of fresh water into the Atlantic Ocean that could have affected circulation.

The new theory will undoubtedly come under fire from several directions, including the scientists that study the North American extinctions as well as from those who study extraterrestrial impacts.

Princeton University paleontologist Gerta Keller studies impacts and is skeptical that the explosion 12,900 years ago was big enough to have had such a big effect on climate and animals.

Keller has found evidence that much larger impacts did not cause any major extinctions. According to her, even the asteroid that left a massive crater on the Yucatan Peninsula known as Chicxulub and is thought to have killed off the dinosaurs did not actually cause their extinction.

"If Chicxulub didn't cause extinctions, then how could something this piddling cause these extinctions, and how could it have changed climate for 1,400 years?" she asked.




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« Reply #1 on: June 28, 2007, 03:54:26 AM »

WASHINGTON: Freddie Flintstone and his friends in Bedrock won't be the only persons to see a woolly mammoth alive, if researchers have their way.

Palaeontologists are piecing together the complete genome species of long-dead species such as the woolly mammoth and the Neanderthals in an effort to bring them back to life, much like billionaire John Hammond resurrected the extinct dinosaurs in Steven Spielberg's Jurassic Park.

A team led by Stephan Schuster and Webb Miller at Pennsylvania State University, US, and Tom Gilbert at the University of Copenhagen, Denmark, is working on the genome of woolly mammoths preserved in the Siberian permafrost.

Scientists have already deciphered the complete gene sequences � or genomes � for many living species, including humans, dogs, and mice. However, they are divided over how they should do it in the case of long extinct species, and whether it's even feasible.

Max Planck researcher Svante Paabo, who together with colleagues, is aiming to assemble a Neanderthal genome from bones preserved in arid caves, in a paper appearing in this week's Proceedings of the National Academy of Sciences (PNAS) said only certain types of errors appeared in ancient DNA.

As such, its not that difficult to piece together much of the original genetic instructions.

However, he is unsure whether the animals can be resurrected completely.

"Resurrecting these animals is for the most part science fiction," said Paabo.

"Retrieval of DNA from ancient specimens is relatively easy now," said Alan Cooper, of the University of Adelaide in Australia.

"I think it's definitely feasible to assemble these genomes. But it's going to be extremely hard work," National Geographic quoted Eske Willerslev of the University of Copenhagen in Denmark, as saying.

According to Cooper, the basic problem is that living animals package their DNA with proteins that help it wind up into chromosomes. This packaging is crucial to making the DNA work properly, and this is something absent in these fossils.

Willerslev however, believes it is possible to bring back an extinct species like a mammoth only if an extremely well-preserved cell is found.

"That's extremely unlikely to happen, because all parts of a cell break down over time, even in mammoths that have been encased in ice since they died. But, researchers working on cloning have contacted me wanting to get a hold of mammoth tissue so they could try to clone a mammoth," he said.

According to Hendrick Poinar of McMaster University in Canada, "it's theoretically possible" to recreate a woolly mammoth.

"I think it's going to be done at some point. Once you have the genome of a mammoth, you could compare it with the genome of its closest relative, the Asian elephant. Then you could genetically engineer the elephant DNA, point by point, so that it matches the mammoth DNA," he said.

"Then, by inserting this modified DNA into an elephant's egg cell, and implanting it in an elephant's womb, you could create a modified elephant that's nearly identical to the original mammoth. Or it could become possible to make entire chromosomes from scratch. I wouldn't be surprised if, in ten years, you'd be able to synthesize chromosome-length DNA," he said.

"Five years ago everybody was saying you'd never be able to sequence the genomes of extinct animals ... but here we are. We're not that far away now," he added.



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« Reply #2 on: June 28, 2007, 10:22:07 AM »

Fresh from the Siberian tundra, an 18,000-year- old frozen woolly mammoth went on display today at the opening of the 2005 World Exposition in Aichi, Japan. Still partially tufted with hair, the Ice Age plant-eater's head and other parts are stored in a giant refrigerator-turned-laboratory.

Woolly Mammoth DNA Reveals Elephant Family Tree
Brian Handwerk
for National Geographic News

Geneticists have sketched out the woolly mammoth's family tree using ancient DNA found preserved in Siberia.

The extinct beasts are more closely related to Asian elephants than to African elephants, the researchers found, and the three species diverged within a surprisingly short period of time.

Michael Hofreiter of the Max Planck Institute in Leipzig, Germany, and his colleagues used bone fragments to reconstruct the mitochondrial genome of the mammoth.

Mitochondrial DNA is passed from mother to offspring, which makes it useful for tracing the lineage of a species.

The DNA revealed that woolly mammoths had more genetic similarities to modern Asian elephants than to the African species, though not by much, Hofreiter's team reports.

The DNA also showed that elephant species split from each other more quickly than had been thought.

Modern elephants and woolly mammoths share a common ancestor that split into separate species about 6 million years ago, the study reports.

At that time African elephants branched off first. Then just 440,000 years later, a blink of an eye in evolutionary time, Asian elephants and mammoths diverged into their own separate species.

Hofreiter says that this close timing may have an interesting parallel among primates, which include humans.

"It's interesting that gorillas, chimpanzees, and humans also split by two speciation events within a very short time," he explained.

His team's research appears this week in the journal Nature.

New DNA research reveals that woolly mammoths were more closely related to modern Asian elephants than to African elephants. The study also shows that elephant species split from each other more quickly than had been thought. Illustration by Kavel Havlicek

Toward A Complete Genome?
The team, led by biologist Ross D. E. MacPhee of the American Museum of Natural History, compiled some 13 million DNA base pairs�a small but significant part of the animal's complete genome.

"This new genomic sequence of the woolly mammoth is orders of magnitude better than any previous result," MacPhee said, "and it raises the possibility that scientists could sequence the whole mammoth genome in the near future, possibly within the next year."

The human genome was decoded only six years ago, and no complete genomes have yet been sequenced for extinct animals.

The results raise the specter of cloning or recreating the extinct animals from frozen bits of their ancient DNA, perhaps to populate some type of real-life "Jurassic Park."

MacPhee explained that such an event, if possible, remains far down the road.

"While we can now retrieve the entire genome of the woolly mammoth, that does not mean we can put together the genome � with all the functional apparatus needed for life. We can't even do that with modern DNA," he said.

Though the mammoth genome might not bring the extinct animals back to life, it could help scientists learn why they vanished.

Comparing ancient DNA with the genomes of living animals might help scientists learn what factors cause new species to arise while others perish.

Permafrost Museum?
Retrieving mammoth bone, even well-preserved bone that can yield DNA, is not as difficult as might be supposed, scientists say.

The beasts roamed Siberia until about 10,000 years ago, when scientists believe they became extinct due to warming weather, human hunters, disease, or some combination of these factors.

There are believed to be millions of mammoths buried in Siberia's permafrost. Only about a hundred specimens have been uncovered in the sparsely populated countryside�but some of them have been remarkably well preserved.

"There are hundreds or perhaps even thousands of samples that contain DNA," Hofreiter said.

Geneticists may now be able to put those samples to better use.

"Using the knowledge we've gained, this technology can be used quite widely on ancient DNA to resolve the [evolutionary histories] of both extinct and extant species," Hofreiter said.

"We may even be able to conduct population studies using ancient mitochondrial DNA. There will be some things to resolve and maybe some interesting surprises as well."

Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae
Johannes Krause1, Paul H. Dear2, Joshua L. Pollack3, Montgomery Slatkin3, Helen Spriggs2, Ian Barnes4, Adrian M. Lister4, Ingo Ebersberger5, Svante P��bo1 and Michael Hofreiter1
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In studying the genomes of extinct species, two principal limitations are typically the small quantities of endogenous ancient DNA and its degraded condition1, even though products of up to 1,600 base pairs (bp) have been amplified in rare cases2. Using small overlapping polymerase chain reaction products, longer stretches of sequences or even whole mitochondrial genomes3, 4 can be reconstructed, but this approach is limited by the number of amplifications that can be performed from rare samples. Thus, even from well-studied Pleistocene species such as mammoths, ground sloths and cave bears, no DNA sequences of more than about 1,000 bp have been reconstructed5, 6, 7. Here we report the complete mitochondrial genome sequence of the Pleistocene woolly mammoth Mammuthus primigenius. We used about 200 mg of bone and a new approach that allows the simultaneous retrieval of multiple sequences from small amounts of degraded DNA. Our phylogenetic analyses show that the mammoth was more closely related to the Asian than to the African elephant. However, the divergence of mammoth, African and Asian elephants occurred over a short time, corresponding to only about 7% of the total length of the phylogenetic tree for the three evolutionary lineages.
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   1. Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
   2. MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
   3. Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
   4. Department of Biology, University College London, London WC1E 6BT, UK
   5. WE Informatik, Heinrich Heine Universit�t, Universit�tsstr. 1, D-40225 D�sseldorf, Germany

Correspondence to: Michael Hofreiter1 Correspondence and requests for materials should be addressed to M.H. (Email: ). The complete mammoth mitochondrial DNA sequence has been deposited in GenBank under accession number DQ188829.

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« Reply #3 on: July 26, 2007, 10:59:59 PM »

Elephants, Human Ancestors Evolved in Synch, DNA Reveals

Hope Hamashige, for National Geographic News

July 23, 2007

The tooth of a mastodon buried beneath Alaska's permafrost for many thousands of years is yielding surprising clues about the history of elephants�and humans.

A team of researchers recently extracted DNA from the tooth to put together the first complete mastodon mitochondrial genome.

The study, published in the journal PLoS Biology, significantly alters the evolutionary timeline for elephants and their relatives.

The research may put to rest a contentious debate by showing that woolly mammoths are more closely related to Asian elephants than African elephants.

Comparing the new genome with that of other animals in the elephant family also provides evidence that the elephant family diverged on roughly the same timeline that primates separated, suggesting there may have been a common cause for the splits.

"I think the divergence is the most interesting thing from this study," said lead author Michael Hofreiter, an evolutionary biologist at the Max Plank Institute for Evolutionary Anthropology in Leipzig, Germany.

Reason to Evolve

According to Hofreiter's research, African elephants diverged from mastodons about 7.6 million years ago, about the same time gorillas split from the line that gave rise to humans and chimpanzees.

Mammoths and Asian elephants speciated around 6.7 million years ago, roughly the same time humans and chimps split.

Alfred Roca is a geneticist at the Laboratory of Genomic Diversity in Frederick, Maryland, part of the U.S. National Cancer Institute. He was not involved in the new research.

He called Hofreiter's work "outstanding," noting that the research pushes the previously believed dates for the divergence of elephants by several million years.

He added that several groups of modern animals�not just elephants and humans�went through significant change during that time, the late Miocene period. (Related: "Mastodons Driven to Extinction by Tuberculosis, Fossils Suggest" [October 3, 2006].)

The most widely held theory about what happened then is that climate change led to the expansion of grasslands in Africa, which fragmented habitats and spurred many species to evolve.

The new study lends further credibility to the notion that climate change can lead to evolutionary change.

"Ours is one more piece of evidence that definitely supports the idea that climate change is a key event in speciation," lead study author Hofreiter said.

Pieced Together

The new research marks a significant departure from previous studies.

Until now, scientists had reconstructed the history of the elephant family primarily using fossil evidence.

Mitochondrial DNA, which is passed on only from mother to child, provides an easy way to trace lineages and is a more accurate source of information. But its use has always been limited, because DNA in ancient fossils begins to breaks down.

Hofreiter and his colleagues, however, developed a way to piece together the genome from small samples of fragmented DNA.

They applied the technique to a mastodon tooth collected in 1999 from Alaska's Ikpikpuk River.

Radiocarbon dating of the collagen in the tooth places its age at at least 50,000 years. But researchers have concluded, based on the dating of other material from the area, that the fossil may be as old as 130,000 years old.

Never before have researchers successfully sequenced a genome from such an ancient piece of bone. Previously, Hofreiter said, the oldest fossil from which scientists were able to extract a complete genome was about 30,000 years old.

In this case, the team cut about 7 ounces (200 grams) from the root of the molar of a mastodon and extracted small fragments of the DNA from bone. By piecing together the overlapping fragments, the team was able to sequence the entire genome.

"It is amazing they were able to extract a complete genome from a bone that old," noted Anna-Sapfo Malaspinas, a researcher at the University of California, Berkeley and one of the authors who helped to analyze the sequencing after the genome was extracted.

Because the animal was encased in permafrost before being exposed to river erosion, the DNA in the mastodon was fairly well preserved, researchers say.

"It is hard, using fossils to come up with accurate dates," Roca, the geneticist, said. "But using DNA makes it easier."

Elephant in the Room

This new research may also put to rest a heated debate about the history of elephants.

"There has been controversy over whether woolly mammoths are more closely related to Asian or African elephants," said Stephen O'Brien, lab chief at the Laboratory of Genomic Diversity.

Both fossil evidence and incomplete mitochondrial genomes had previously indicated that woolly mammoths' closest relatives were African elephants.

Two years ago, however, Hofreiter was also the first to sequence a complete mitochondrial genome from a woolly mammoth. His research contradicted earlier studies because it indicated a tighter kinship to the Asian elephant.

The information extracted from the mastodon, a close relative to both mammoths and elephants, supports Hofreiter's earlier work.

According to O'Brien, studies using incomplete genome sequences from woolly mammoths are likely not as reliable.

"This is the most robust data we have seen to date."



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