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A new chapter in the history of evolution

Discovery of world’s oldest DNA breaks record by one million years

Two-million-year-old DNA has been identified for the first time opening a new chapter in the history of evolution.

oldest DNA breaks record by one million years
Reconstruction of Kap København formation two-million years ago in a time where the temperature was significantly warmer than northernmost Greenland today. Credits: Beth Zaiken/bethzaiken.com

Microscopic fragments of environmental DNA were found in Ice Age sediment in northern Greenland. The fragments are one million years older than the previous record for DNA sampled from a Siberian mammoth bone.

The ancient DNA has been used to map a two-million-year-old ecosystem which weathered extreme climate change. The results could help predict the long-term environmental toll of today’s global warming.

The discovery was made by a team of scientists led by Professor Eske Willerslev and Professor Kurt Kjær. Professor Willerslev is a Fellow of St John’s College, University of Cambridge and Director of the Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen where Professor Kjær, a geology expert, is also based.

The results of the 41 usable samples found hidden in clay and quartz are published today in Nature.

“A new chapter spanning one million extra years of history has finally been opened and for the first time we can look directly at the DNA of a past ecosystem that far back in time,” says Willerslev.

“DNA can degrade quickly but we’ve shown that under the right circumstances, we can now go back further in time than anyone could have dared imagine.”

“The ancient DNA samples were found buried deep in sediment that had built-up over 20,000 years,” says Kjær. “The sediment was eventually preserved in ice or permafrost and, crucially, not disturbed by humans for two million years.”

Close-up of organic material in the coastal deposits. The organic layers show traces of the rich plant flora and insect fauna that lived two million years ago in Kap København in North Greenland. Credits: Professor Kurt H. Kjær

The incomplete samples, a few millionths of a millimetre long, were taken from the København Formation, a sediment deposit almost 100 metres thick tucked in the mouth of a fjord in the Arctic Ocean in Greenland’s northernmost point. The climate in Greenland at the time varied between Arctic and temperate and was between 10-17C warmer than Greenland is today. The sediment built up metre by metre in a shallow bay.

Evidence of animals, plants and microorganisms including reindeer, hares, lemmings, birch and poplar trees were discovered. Researchers even found that Mastodon, an Ice Age mammal, roamed as far as Greenland before later becoming extinct. Previously it was thought the range of the elephant-like animals did not extend as far as Greenland from its known origins of North and Central America.

Detective work by 40 researchers from Denmark, the UK, France, Sweden, Norway, the USA and Germany, unlocked the secrets of the fragments of DNA. The process was painstaking – first they needed to establish whether there was DNA hidden in the clay and quartz, and if there was, could they successfully detach the DNA from the sediment to examine it? The answer, eventually, was yes. The researchers compared every single DNA fragment with extensive libraries of DNA collected from present-day animals, plants and microorganisms. A picture began to emerge of the DNA from trees, bushes, birds, animals and microorganisms.

A two million- year-old trunk from a larch tree still stuck in the permafrost within the coastal deposits. The tree was carried to the sea by the rivers that eroded the former forested landscape. Credits: Professor Svend Funder

Some of the DNA fragments were easy to classify as predecessors to present-day species, others could only be linked at genus level, and some originated from species impossible to place in the DNA libraries of animals, plants and microorganisms still living in the 21st century.

The two-million-year-old samples also help academics build a picture of a previously unknown stage in the evolution of the DNA of a range of species still in existence today.

“Expeditions are expensive and many of the samples were taken back in 2006 when the team were in Greenland for another project, they have been stored ever since,” says Kjær.

“It wasn’t until a new generation of DNA extraction and sequencing equipment was developed that we’ve been able to locate and identify extremely small and damaged fragments of DNA in the sediment samples. It meant we were finally able to map a two-million-year-old ecosystem.”

“The Kap København ecosystem, which has no present-day equivalent, existed at considerably higher temperatures than we have today – and because, on the face of it, the climate seems to have been similar to the climate we expect on our planet in the future due to global warming,” says co-first author Assistant Professor Mikkel Pedersen of the Lundbeck Foundation GeoGenetics Centre.

“One of the key factors here is to what degree species will be able to adapt to the change in conditions arising from a significant increase in temperature. The data suggests that more species can evolve and adapt to wildly varying temperatures than previously thought. But, crucially, these results show they need time to do this. The speed of today’s global warming means organisms and species do not have that time so the climate emergency remains a huge threat to biodiversity and the world – extinction is on the horizon for some species including plants and trees.”

 

While reviewing the ancient DNA from the Kap København Formation, the researchers also found DNA from a wide range of microorganisms, including bacteria and fungi, which they are continuing to map. A detailed description of how the interaction – between animals, plants and single-cell organisms – within the former ecosystem at Greenland’s northernmost point worked biologically will be presented in a future research paper.

It is now hoped that some of the ‘tricks’ of the two-million-year-old plant DNA discovered may be used to help make some endangered species more resistant to a warming climate.

“It is possible that genetic engineering could mimic the strategy developed by plants and trees two million years ago to survive in a climate characterised by rising temperatures and prevent the extinction of some species, plants and trees,” says Kjær. “This is one of the reasons this scientific advance is so significant because it could reveal how to attempt to counteract the devastating impact of global warming.”

oldest DNA breaks record by one million years
Discovery of world’s oldest DNA breaks record by one million years: Artist’s impression of Kap København Formation today. Credits: Artist Beth Zaiken

The findings from the Kap København Formation in Greenland have opened up a whole new period in DNA detection.

“DNA generally survives best in cold, dry conditions such as those that prevailed during most of the period since the material was deposited at Kap København,” says Willerslev. “Now that we have successfully extracted ancient DNA from clay and quartz, it may be possible that clay may have preserved ancient DNA in warm, humid environments in sites found in Africa.

“If we can begin to explore ancient DNA in clay grains from Africa, we may be able to gather ground-breaking information about the origin of many different species – perhaps even new knowledge about the first humans and their ancestors – the possibilities are endless.”

oldest DNA breaks record by one million years
Newly thawed moss from the permafrost coastal deposits. The moss originates from erosion of the river that cut through the landscape at Kap København some two million years ago. Credits: Professor Nicolaj K. Larsen

Bibliographic information:

A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA, Nature (7-Dec-2022), DOI: 10.1038/s41586-022-05453-y

 

Press release from the University of Cambridge on the discovery of world’s oldest DNA.

Hubble sees new atmosphere forming on a rocky exoplanet, GJ 1132 b

The planet GJ 1132 b appears to have begun life as a gaseous world with a thick blanket of atmosphere. Starting out at several times the radius of Earth, this so-called “sub-Neptune” quickly lost its primordial hydrogen and helium atmosphere, which was stripped away by the intense radiation from its hot, young star. In a short period of time, it was reduced to a bare core about the size of Earth.

GJ 1132 b
This image is an artist’s impression of the exoplanet GJ 1132 b. For the first time, scientists using the NASA/ESA Hubble Space Telescope have found evidence of volcanic activity reforming the atmosphere on this rocky planet, which has a similar density, size, and age to that of Earth. To the surprise of astronomers, new observations from Hubble have uncovered a second atmosphere that has replaced the planet’s first atmosphere. It is rich in hydrogen, hydrogen cyanide, methane and ammonia, and also has a hydrocarbon haze. Astronomers theorise that hydrogen from the original atmosphere was absorbed into the planet’s molten magma mantle and is now being slowly released by volcanism to form a new atmosphere. This second atmosphere, which continues to leak away into space, is continually being replenished from the reservoir of hydrogen in the mantle’s magma. Credit: NASA, ESA, and R. Hurt (IPAC/Caltech), CC BY 4.0

To the surprise of astronomers, new observations from Hubble [1] have uncovered a secondary atmosphere that has replaced the planet’s first atmosphere. It is rich in hydrogen, hydrogen cyanide, methane and ammonia, and also has a hydrocarbon haze. Astronomers theorise that hydrogen from the original atmosphere was absorbed into the planet’s molten magma mantle and is now being slowly released by volcanism to form a new atmosphere. This second atmosphere, which continues to leak away into space, is continually being replenished from the reservoir of hydrogen in the mantle’s magma.

“This second atmosphere comes from the surface and interior of the planet, and so it is a window onto the geology of another world,” explained team member Paul Rimmer of the University of Cambridge, UK. “A lot more work needs to be done to properly look through it, but the discovery of this window is of great importance.”

Pictured here is the region around the host star of the exoplanet GJ 1132 b. Credit:
ESA/Hubble, Digitized Sky Survey 2, CC BY 4.0.
Acknowledgement: Davide De Martin

“We first thought that these highly radiated planets would be pretty boring because we believed that they lost their atmospheres,” said team member Raissa Estrela of the Jet Propulsion Laboratory at the California Institute of Technology in Pasadena, California, USA. But we looked at existing observations of this planet with Hubble and realised that there is an atmosphere there.”

“How many terrestrial planets don’t begin as terrestrials? Some may start as sub-Neptunes, and they become terrestrials through a mechanism whereby light evaporates the primordial atmosphere. This process works early in a planet’s life, when the star is hotter,” said team leader Mark Swain of the Jet Propulsion Laboratory. “Then the star cools down and the planet’s just sitting there. So you’ve got this mechanism that can cook off the atmosphere in the first 100 million years, and then things settle down. And if you can regenerate the atmosphere, maybe you can keep it.”

In some ways, GJ 1132 b has various parallels to Earth, but in some ways it is also very different. Both have similar densities, similar sizes, and similar ages, being about 4.5 billion years old. Both started with a hydrogen-dominated atmosphere, and both were hot before they cooled down. The team’s work even suggests that GJ 1132 b and Earth have similar atmospheric pressure at the surface.

This plot shows the spectrum of the atmosphere of an Earth sized rocky exoplanet, GJ 1132 b, which is overlaid on an artist’s impression of the planet. The orange line represents the model spectrum. In comparison, the observed spectrum is shown as blue dots representing averaged data points, along with their error bars.  This analysis is consistent with GJ 1132 b being predominantly a hydrogen atmosphere with a mix of methane and hydrogen cyanide. The planet also has aerosols which cause scattering of light.  This is the first time a so-called “secondary atmosphere,” which was replenished after the planet lost its primordial atmosphere, has been detected on a world outside of our solar system. Credit:
NASA, ESA, and P. Jeffries (STScI)

However, the planets’ formation histories are profoundly different. Earth is not believed to be the surviving core of a sub-Neptune. And Earth orbits at a comfortable distance from our yellow dwarf Sun. GJ 1132 b is so close to its host red dwarf star that it completes an orbit the star once every day and a half. This extremely close proximity keeps GJ 1132 b tidally locked, showing the same face to its star at all times — just as our moon keeps one hemisphere permanently facing Earth.

“The question is, what is keeping the mantle hot enough to remain liquid and power volcanism?” asked Swain. “This system is special because it has the opportunity for quite a lot of tidal heating.”

The phenomenon of tidal heating occurs through friction, when energy from a planet’s orbit and rotation is dispersed as heat inside the planet. GJ 1132 b is in an elliptical orbit, and the tidal forces acting on it are strongest when it is closest to or farthest from its host star. At least one other planet in the host star’s system also exerts a gravitational pull on the planet. The consequences are that the planet is squeezed or stretched by this gravitational “pumping.” That tidal heating keeps the mantle liquid for a long time. A nearby example in our own Solar System is the Jovian moon, Io, which has continuous volcanism as a result of a tidal tug-of-war between Jupiter and the neighbouring Jovian moons.

The team believes the crust of GJ 1132 b is extremely thin, perhaps only hundreds of feet thick. That’s much too feeble to support anything resembling volcanic mountains. Its flat terrain may also be cracked like an eggshell by tidal flexing. Hydrogen and other gases could be released through such cracks.

“This atmosphere, if it’s thin — meaning if it has a surface pressure similar to Earth — probably means you can see right down to the ground at infrared wavelengths. That means that if astronomers use the James Webb Space Telescope to observe this planet, there’s a possibility that they will see not the spectrum of the atmosphere, but rather the spectrum of the surface,” explained Swain. “And if there are magma pools or volcanism going on, those areas will be hotter. That will generate more emission, and so they’ll potentially be looking at the actual geological activity — which is exciting!”

This result is significant because it gives exoplanet scientists a way to figure out something about a planet’s geology from its atmosphere,” added Rimmer. “It is also important for understanding where the rocky planets in our own Solar System — Mercury, Venus, Earth and Mars, fit into the bigger picture of comparative planetology, in terms of the availability of hydrogen versus oxygen in the atmosphere.”

###

Notes:

[1] The observations were conducted as part of the Hubble observing program #14758 (PI: Zach Berta-Thomson).

Why are plants green?

UC Riverside-led research team’s model to explain photosynthesis lays out the next challenging phase of research on how green plants transform light energy into chemical energy

UC Riverside-led research team’s model to explain photosynthesis lays out the next challenging phase of research on how green plants transform light energy into chemical energy. Credits: Gabor lab, UC Riverside

When sunlight shining on a leaf changes rapidly, plants must protect themselves from the ensuing sudden surges of solar energy. To cope with these changes, photosynthetic organisms — from plants to bacteria — have developed numerous tactics. Scientists have been unable, however, to identify the underlying design principle.

An international team of scientists, led by physicist Nathaniel M. Gabor at the University of California, Riverside, has now constructed a model that reproduces a general feature of photosynthetic light harvesting, observed across many photosynthetic organisms.

Nathaniel Gabor is an associate professor of physics at UC Riverside. Credits: CIFAR

Light harvesting is the collection of solar energy by protein-bound chlorophyll molecules. In photosynthesis — the process by which green plants and some other organisms use sunlight to synthesize foods from carbon dioxide and water — light energy harvesting begins with sunlight absorption.

The researchers’ model borrows ideas from the science of complex networks, a field of study that explores efficient operation in cellphone networks, brains, and the power grid. The model describes a simple network that is able to input light of two different colors, yet output a steady rate of solar power. This unusual choice of only two inputs has remarkable consequences.

“Our model shows that by absorbing only very specific colors of light, photosynthetic organisms may automatically protect themselves against sudden changes — or ‘noise’ — in solar energy, resulting in remarkably efficient power conversion,” said Gabor, an associate professor of physics and astronomy, who led the study appearing today in the journal Science. “Green plants appear green and purple bacteria appear purple because only specific regions of the spectrum from which they absorb are suited for protection against rapidly changing solar energy.”

Gabor first began thinking about photosynthesis research more than a decade ago, when he was a doctoral student at Cornell University. He wondered why plants rejected green light, the most intense solar light.  Over the years, he worked with physicists and biologists worldwide to learn more about statistical methods and the quantum biology of photosynthesis.

Richard Cogdell, a renowned botanist at the University of Glasgow in the United Kingdom and a coauthor on the research paper, encouraged Gabor to extend the model to include a wider range of photosynthetic organisms that grow in environments where the incident solar spectrum is very different.

“Excitingly, we were then able to show that the model worked in other photosynthetic organisms besides green plants, and that the model identified a general and fundamental property of photosynthetic light harvesting,” he said. “Our study shows how, by choosing where you absorb solar energy in relation to the incident solar spectrum, you can minimize the noise on the output — information that can be used to enhance the performance of solar cells.”

Coauthor Rienk van Grondelle, an influential experimental physicist at Vrije Universiteit Amsterdam in the Netherlands who works on the primary physical processes of photosynthesis, said the team found the absorption spectra of certain photosynthetic systems select certain spectral excitation regions that cancel the noise and maximize the energy stored.

“This very simple design principle could also be applied in the design of human-made solar cells,” said van Grondelle, who has vast experience with photosynthetic light harvesting.

Gabor explained that plants and other photosynthetic organisms have a wide variety of tactics to prevent damage due to overexposure to the sun, ranging from molecular mechanisms of energy release to physical movement of the leaf to track the sun. Plants have even developed effective protection against UV light, just as in sunscreen.

“In the complex process of photosynthesis, it is clear that protecting the organism from overexposure is the driving factor in successful energy production, and this is the inspiration we used to develop our model,” he said. “Our model incorporates relatively simple physics, yet it is consistent with a vast set of observations in biology. This is remarkably rare. If our model holds up to continued experiments, we may find even more agreement between theory and observations, giving rich insight into the inner workings of nature.”

To construct the model, Gabor and his colleagues applied straightforward physics of networks to the complex details of biology, and were able to make clear, quantitative, and generic statements about highly diverse photosynthetic organisms.

“Our model is the first hypothesis-driven explanation for why plants are green, and we give a roadmap to test the model through more detailed experiments,” Gabor said.

Photosynthesis may be thought of as a kitchen sink, Gabor added, where a faucet flows water in and a drain allows the water to flow out. If the flow into the sink is much bigger than the outward flow, the sink overflows and the water spills all over the floor.

“In photosynthesis, if the flow of solar power into the light harvesting network is significantly larger than the flow out, the photosynthetic network must adapt to reduce the sudden over-flow of energy,” he said. “When the network fails to manage these fluctuations, the organism attempts to expel the extra energy. In doing so, the organism undergoes oxidative stress, which damages cells.”

The researchers were surprised by how general and simple their model is.

“Nature will always surprise you,” Gabor said. “Something that seems so complicated and complex might operate based on a few basic rules. We applied the model to organisms in different photosynthetic niches and continue to reproduce accurate absorption spectra. In biology, there are exceptions to every rule, so much so that finding a rule is usually very difficult. Surprisingly, we seem to have found one of the rules of photosynthetic life.”

Gabor noted that over the last several decades, photosynthesis research has focused mainly on the structure and function of the microscopic components of the photosynthetic process.

“Biologists know well that biological systems are not generally finely tuned given the fact that organisms have little control over their external conditions,” he said. “This contradiction has so far been unaddressed because no model exists that connects microscopic processes with macroscopic properties. Our work represents the first quantitative physical model that tackles this contradiction.”

Next, supported by several recent grants, the researchers will design a novel microscopy technique to test their ideas and advance the technology of photo-biology experiments using quantum optics tools.

“There’s a lot out there to understand about nature, and it only looks more beautiful as we unravel its mysteries,” Gabor said.

Gabor, Cogdell, and van Grondelle were joined in the research by Trevor B. Arp, Jed Kistner-Morris, and Vivek Aji at UCR.

The research was supported by the Air Force Office of Scientific Research Young Investigator Program, the National Science Foundation, and through a U.S. Department of the Navy’s Historically Black Colleges and Universities/Minority Institutions award. Gabor was also supported through a Cottrell Scholar Award and a Canadian Institute for Advanced Research Azrieli Global Scholar Award. Other sources of funding were the NASA MUREP Institutional Research Opportunity program, the U.S. Department of Energy, the Biotechnological and Biological Sciences Research Council, the Royal Netherlands Academy of Arts and Sciences, and the Canadian Institute for Advanced Research.

The research paper is titled, “Quieting a noisy antenna reproduces photosynthetic light harvesting spectra.”

 

 

 

Press release from the University of California, Riverside