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Science

Mammoth DNA Breaks Record for World’s Oldest Sequence

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Researchers have sequenced the oldest known DNA in the world. Using material from the Early and Middle Pleistocene sub-epochs, the ancient DNA analysis shatters the record for the world’s oldest sequenced DNA. It comes from mammoth remains that were discovered in the Siberian permafrost and proves that under the right conditions ancient DNA can survive more than one million years.

But the analysis of that very ancient DNA depends upon researchers having the right technology too. Thankfully, an international team led by researchers at the Centre for Palaeogenetics in Stockholm, Sweden had advanced sequencing technology and bioinformatics available to them. A Nature news report for the new paper says that the researchers pushed current technology almost to its limits to enable the extraction of ancient DNA strands from mammoth teeth that had been preserved in the Siberian permafrost . Senior author of the Nature study, Love Dalén, a professor of evolutionary genetics at the Centre for Palaeogenetics, notes that the scientific team has been lucky, saying:

“It’s not like everything found in the permafrost always works. The vast majority of samples have crap DNA.”

How the Ancient Mammoth DNA has Broken Records

The discovery is truly amazing because after an organism dies its chromosomes gradually become smaller and smaller, and in most cases extremely ancient DNA strands have become so tiny that they have lost all their informational content. But a new article published in the journal Nature shows that the team has managed to obtain 49 million base pairs of nuclear DNA from a 1.65-million-year-old tooth found near a village called Krestovka (the tooth has been dubbed Krestovka as well). They also extracted  884 million base pairs of ancient DNA from a 1.3-million-year-old tooth they refer to as Adycha and 3.7 billion base pairs of DNA from a 600,000-year-old woolly mammoth tooth they’ve called Chukochya. The three mammoth remains were discovered in the 1970s and are part of the collection of the Russian Academy of Sciences in Moscow.

Love Dalén and co-lead author Patrícia Pečnerová with a mammoth tusk on Wrangel Island. (Credit: Gleb Danilov)

The Nature news report explains that the ancient mammoth DNA study hasn’t uncovered the oldest biomolecular information from the fossil record – that’s protein sequenced in 2016 from 3.8-million-year-old ostrich eggshells from Tanzania. In second place is a protein sequence from a 1.77-million-year-old rhinoceros tooth from Georgia, which was analyzed in 2019. However, while protein is hardier and can survive in extremely old fossils from places without permafrost, it isn’t as useful as DNA for researchers who want to study an organism’s ancestry.

That’s just one of the reasons why the new mammoth DNA study is so important – it contains genetic information which hasn’t been available in the older protein samples.

A second reason why the study is making headlines is that it has beaten ancient DNA from a genome from a 560,000 to 780,000-year-old horse leg bone found in the Yukon Territory of Canada for the oldest ancient DNA sequence. Putting the age of the mammoth samples into context, Dalén said:

“This DNA is incredibly old. The samples are a thousand times older than Viking remains, and even pre-date the existence of humans and Neanderthals.”

The First Example of Hybrid Speciation in Ancient DNA

The new study has also amplified the ability for researchers to track the evolutionary process of speciation – the formation of new and distinct species. A Nature press release states that this process generally occurs “over time periods that are thought to be beyond the limits of DNA research.”

A tusk from a woolly mammoth discovered in a creek bed on Wrangel Island in 2017. (Credit: Love Dalén)

Nonetheless, the scientists’ study of the mammoth DNA suggests that there was not one, but two different lineages of mammoth alive during the Early Pleistocene in the region of what is now eastern Siberia. Adycha and Chukochya are believed to be members of a species that spawned the woolly mammoth, but Krestovka appears to come from an unknown, and possibly entirely new, mammoth lineage. Tom van der Valk, the study’s lead author and a bioinformatician at the University of Uppsala in Sweden, explains the researchers’ shock at this discovery:

“This came as a complete surprise to us. All previous studies have indicated that there was only one species of mammoth in Siberia at that point in time, called the steppe mammoth. But our DNA analyses now show that there were two different genetic lineages, which we here refer to as the Adycha mammoth and the Krestovka mammoth. We can’t say for sure yet, but we think these may represent two different species.”

In their study, the researchers suggest that the Krestovka genome may have diverged from the other mammoths between 2.66 to 1.78 million years ago. They also believe that this mammoth lineage “was ancestral to the first mammoths to colonize North America.” It appears that the North American Columbian mammoths ( Mammuthus columbi ) can trace half of their ancestry to wooly mammoths and half to the previously unrecognized Krestovka mammoth lineage.

The Nature news report states that this means the new study has also provided the first evidence for ‘hybrid speciation’ – a new species forming through mixing – found in ancient DNA. Study co-lead author Patrícia Pečnerová, an evolutionary biologist at the Swedish Museum of Natural History, says that the team believes “that the Columbian mammoth, one of the most iconic Ice Age species of North America, evolved through a hybridisation that took place approximately 420 thousand years ago.”

How Far Back Can Researchers Go?

Finally, the ancient mammoth DNA study has inspired Dalén to analyze more permafrost animal samples that date back more than a million years. Next on his list? Musk oxen, moose, and lemmings. But the professor of evolutionary genetics knows that there is an age limit he won’t be able to cross when analyzing the ancient DNA – 2.6 million years – “That’s the limit of the permafrost. Before that, it was too warm,” he says.

Woolly mammoth tusk emerging from permafrost on central Wrangel Island, located in northeastern Siberia. (Credit: Love Dalén)

Top Image: The illustration represents a reconstruction of the steppe mammoths that preceded the woolly mammoth, based on the genetic knowledge we now have from the Adycha mammoth. Source: Beth Zaiken/Centre for Palaeogenetics

By Alicia McDermott

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Entertainment

Madison LeCroy Breaks Her Silence on Alex Rodriguez Affair Rumors

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Southern Charm star Madison LeCroy is addressing romance rumors involving herself and former baseball superstar Alex Rodriguez. 

Madison spoke to Page Six about the situation on Wednesday, Feb. 3 and claimed that she and the athlete, who is currently engaged to Jennifer Lopez, have “spoken on the phone” but “never met up.” According to Madison, they have “never been physical … never had any kind of anything. Just an acquaintance.”

She shared, “He’s never physically cheated on his fiancée with me.” Madison claimed that she has “talked to him randomly, but not consistent.” She did not clarify the nature of the calls or exactly when they occurred, except to say it was “innocent.” 

Madison said she believes that she “told the wrong person” and that it then became “like a game of telephone” among those close to her.

“All this stuff was a year ago, [but] it’s being aired now,” she said.

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Entertainment

Armie Hammer’s estranged wife Elizabeth Chambers breaks silence on his cannibalism controversy

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Elizabeth Chambers has broken her silence about the scandal surrounding her soon-to-be ex-husband, Armie Hammer.

Hammer, 34, has been under intense scrutiny after multiple women, some unidentified, have come forward claiming he’s shared his desire of twisted sex fantasies, including one alleged admission from him on social media that he is “100% a cannibal.” He has denied the claims.

In a bizarre twist, a new report noted that Hammer’s former “Call Me By Your Name” director Luca Guadagnino and co-star Timothee Chalamet are working on a project titled “Bones & All” which is reportedly about a woman who has the “urge to kill and eat the people that love her.”

Chambers caught wind of the movie’s plot on Instagram, where she subtly reacted for the first time.

ARMIE HAMMER’S EX-GIRLFRIEND SAYS ACTOR ‘HAS A DESIRE TO HURT WOMEN’

Elizabeth Chambers (left) and Armie Hammer (right) announced their split last July after 10 years of marriage.
(Axelle/Bauer-Griffin/FilmMagic via Getty Images)

“No. Words.,” she commented from her verified Instagram account.

Chambers had previously remained mum on the drama for the past few weeks. Shortly after the House of Effie Instagram account leaked messages allegedly sent to a woman by Hammer that shared his desire of graphic BDSM acts, the father of two exited his upcoming movie role in “Shotgun Wedding,” also starring Jennifer Lopez.

Last week, one of Hammer’s ex-girlfriends, 23-year-old model Paige Lorenze, gave an interview to Fox News about her decision to end her months-long romance with the actor. She said she believes he “has a desire to hurt women.”

ARMIE HAMMER INVESTIGATED BY POLICE OVER MISS CAYMAN VIDEO SCANDAL

Lorenze and Hammer struck up a romance last September in Los Angeles. The current college student said Hammer described it as a “polyamorous open relationship.” She said she consented to his BDSM desires during the four months they were together, but looks at it in hindsight as the opposite of “fun and safe.”

The ‘Call Me By Your Name’ actor exited a movie role for the upcoming film ‘Shotgun Wedding’ starring Jennifer Lopez amid the controversy.
(Gregg DeGuire/FilmMagic)

“Right away he definitely did get into things and had me do things that weren’t my norm. He wanted me to only call him ‘Sir’ or ‘Daddy’ in the bedroom. He’s obviously a very kinky person and he made that very clear to me, but I thought it was going to be fun and safe,” she claimed to us.

Lorenze said she became disturbed after Hammer voiced his desire of eating her ribs.

“He was talking about finding a doctor to remove my ribs that I don’t need — the ribs that are on the bottom — and that he had a smoker at his house. He wanted to smoke them and eat them. He wondered how they would taste and he basically was like, ‘I bet you they would taste good.'”

She’s also shared photographs of a scar she has above her groin area in the shape of an “A.” She claimed the actor branded the letter on her skin with a knife.

ARMIE HAMMER’S EX COURTNEY VUCEKOVICH CLAIMS HE WANTED TO ‘BARBECUE AND EAT’ HER RIBS AMID MESSAGING SCANDAL

“These assertions about Mr. Hammer are patently untrue. Any interactions with this person, or any partner of his, were completely consensual in that they were fully discussed, agreed upon, and mutually participatory. The stories being perpetuated in the media are a misguided attempt to present a one-sided narrative with the goal of tarnishing Mr. Hammer’s reputation, and communications from the individuals involved prove that,” Hammer’s attorney, Andrew Brettler, told Fox News in a statement.

Paige Lorenze (left) told Fox News the actor wanted to ‘smoke’ and ‘eat’ her ribs during their relationship last fall.
(Paige Lorenze Instagram/Getty)

Lorenze went on to allege that Hammer was “really obsessed with biting and leaving marks on me and bruising me.” She claimed the “Rebececa” star would “always brag” about her bruises and asked her to “show them off.”

Lorenze told Fox News she met Hammer’s family in Texas over Thanksgiving. This gave her a sense that the relationship could be “long-term” as Hammer sugggested, but she put an end to the relationship in December after she began “to feel really sick to my stomach, anxious, and very strange,” she said.

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Another woman named Courtney Vucekovich also claimed Hammer wanted to “barbecue” and “eat” her ribs. Meanwhile, writer Jessica Ciencin Henriquez who also reportedly dated Hammer last fall said on Instagram she believes the messages are “real.” 

Last July, Hammer and Chambers, announced their split on social media. They share two children together: daughter Harper Grace, 5, and son Ford Douglas Armand, 3.

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Hammer is best known for his roles in “The Social Network” and “Call Me by Your Name,” which earned him a Golden Globe nomination in 2018. His recent appearances include an episode of HBO’s “We Are Who We Are” and Netflix’s “Rebecca” remake.



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Science

Carbon at pressures 5 times that of the Earth’s core breaks crystal formation record

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An artist’s rendering of 55 Cancri e, a carbon-rich exoplanet. For the first time in a laboratory setting, experiments conducted through NIF’s Discovery Science program reach the extreme pressures that are relevant to understanding the structure of carbon that occupies the interior of these exoplanets. Credit: ESA/Hubble/M. Kornmesser

Carbon, the fourth most abundant element in the universe, is a building block for all known life and a material that sits in the interior of carbon-rich exoplanets.

Decades of intense investigation by scientists have shown that carbon’s crystal structure has a significant impact on its properties. In addition to graphite and diamond, the most common carbon structures found at ambient pressures, scientists have predicted several new structures of carbon that could be found at pressures greater than 1,000 gigapascals (GPa). These pressures, about 2.5 times the pressure in Earth’s core, are relevant for modeling exoplanet interiors but have been impossible to achieve in the laboratory.

That is, until now. Under the Discovery Science program, which allows academic scientists access to LLNL’s flagship National Ignition Facility (NIF), an international team of researchers led by LLNL and the University of Oxford has successfully measured carbon at pressures reaching 2,000 GPa (5 times the pressure in Earth’s core), nearly doubling the maximum pressure at which a crystal structure has ever been directly probed. The results were reported today in Nature.

“We discovered that, surprisingly, under these conditions carbon does not transform to any of the predicted phases but retains the diamond structure up to the highest pressure,” said LLNL physicist Amy Jenei, lead author on the study. “The same ultra-strong interatomic bonds (requiring high energies to break) which are responsible for the metastable diamond structure of carbon persisting indefinitely at ambient pressure are likely also impeding its transformation above 1,000 GPa in our experiments.”

The academic component of the collaboration was led by Oxford Professor Justin Wark, who praised the Lab’s open-access policy.

“The NIF Discovery Science program is immensely beneficial to the academic community,” he said. “It not only allows established faculty the chance to put forward proposals for experiments that would be impossible to do elsewhere, but importantly also gives graduate students, who are the senior scientists of the future, the chance to work on a completely unique facility.”

The team—which also included scientists from the University of Rochester’s Laboratory for Laser Energetics (LLE) and the University of York—leveraged NIF’s uniquely high power and energy and accurate laser pulse-shaping to compress solid carbon to 2,000 GPa using ramp-shaped laser pulses. This allowed them to measure the crystal structure using an X-ray diffraction platform and capture a nanosecond-duration snapshot of the atomic lattice. These experiments nearly double the record high pressure at which X-ray diffraction has been recorded on any material.

The researchers found that even when subjected to these intense conditions, solid carbon retains its diamond structure far beyond its regime of predicted stability, confirming predictions that the strength of the molecular bonds in diamond persists under enormous pressure. This results in large energy barriers that hinder conversion to other carbon structures.

“Whether nature has found a way to surmount the high energy barrier to formation of the predicted phases in the interiors of exoplanets is still an open question,” Jenei said. “Further measurements using an alternate compression pathway or starting from an allotrope of carbon with an atomic structure that requires less energy to rearrange will provide further insight.”

Checking out iron under pressure

More information:
A. Lazicki et al. Metastability of diamond ramp-compressed to 2 terapascals, Nature (2021). DOI: 10.1038/s41586-020-03140-4
Provided by
Lawrence Livermore National Laboratory

Citation:
Carbon at pressures 5 times that of the Earth’s core breaks crystal formation record (2021, January 28)
retrieved 28 January 2021
from https://phys.org/news/2021-01-carbon-pressures-earth-core-crystal.html

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