Earliest interbreeding event between ancient human populations discovered

Neanderthal and modern human skulls (stock image).

For three years, anthropologist Alan Rogers has attempted to solve an evolutionary puzzle. His research untangles millions of years of human evolution by analyzing DNA strands from ancient human species known as hominins. Like many evolutionary geneticists, Rogers compares hominin genomes looking for genetic patterns such as mutations and shared genes. He develops statistical methods that infer the history of ancient human populations.

In 2017, Rogers led a study which found that two lineages of ancient humans, Neanderthals and Denisovans, separated much earlier than previously thought and proposed a bottleneck population size. It caused some controversy -- anthropologists Mafessoni and Prüfer argued that their method for analyzing the DNA produced different results. Rogers agreed, but realized that neither method explained the genetic data very well.

"Both of our methods under discussion were missing something, but what?" asked Rogers, professor of anthropology at the University of Utah.

The new study has solved that puzzle and in doing so, it has documented the earliest known interbreeding event between ancient human populations -- a group known as the "super-archaics" in Eurasia interbred with a Neanderthal-Denisovan ancestor about 700,000 years ago. The event was between two populations that were more distantly related than any other recorded. The authors also proposed a revised timeline for human migration out of Africa and into Eurasia. The method for analyzing ancient DNA provides a new way to look farther back into the human lineage than ever before.

"We've never known about this episode of interbreeding and we've never been able to estimate the size of the super-archaic population," said Rogers, lead author of the study. "We're just shedding light on an interval on human evolutionary history that was previously completely dark."

The paper was published on Feb. 20, 2020, in the journal Science Advances.

Out of Africa and interbreeding

Rogers studied the ways in which mutations are shared among modern Africans and Europeans, and ancient Neanderthals and Denisovans. The pattern of sharing implied five episodes of interbreeding, including one that was previously unknown. The newly discovered episode involves interbreeding over 700,000 years ago between a distantly related "super-archaic" population which separated from all other humans around two million years ago, and the ancestors of Neanderthals and Denisovans.

The super-archaic and Neanderthal-Denisovan ancestor populations were more distantly related than any other pair of human populations previously known to interbreed. For example, modern humans and Neanderthals had been separated for about 750,000 years when they interbred. The super-archaics and Neanderthal-Denisovan ancestors were separated for well over a million years.

"These findings about the timing at which interbreeding happened in the human lineage is telling something about how long it takes for reproductive isolation to evolve," said Rogers.

The authors used other clues in the genomes to estimate when the ancient human populations separated and their effective population size. They estimated the super-archaic separated into its own species about two million years ago. This agrees with human fossil evidence in Eurasia that is 1.85 million years old.

The researchers also proposed there were three waves of human migration into Eurasia. The first was two million years ago when the super-archaics migrated into Eurasia and expanded into a large population. Then 700,000 years ago, Neanderthal-Denisovan ancestors migrated into Eurasia and quickly interbred with the descendants of the super-archaics. Finally, modern humans expanded to Eurasia 50,000 years ago where we know they interbred with other ancient humans, including with the Neanderthals.

"I've been working for the last couple of years on this different way of analyzing genetic data to find out about history," said Rogers. "It's just gratifying that you come up with a different way of looking at the data and you end up discovering things that people haven't been able to see with other methods."

Nathan S. Harris and Alan A. Achenbach from the Department of Anthropology at the University of Utah also contributed to the study.

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Materials provided by University of Utah. Note: Content may be edited for style and length.

Grey seals discovered clapping underwater to communicate

Seal swimming underwater (stock image).

Marine mammals like whales and seals usually communicate vocally using calls and whistles.

But now a Monash University-led international study has discovered that wild grey seals can also clap their flippers underwater during the breeding season, as a show of strength that warns off competitors and advertises to potential mates.

This is the first time a seal has been seen clapping completely underwater using its front flippers.

"The discovery of 'clapping seals' might not seem that surprising, after all, they're famous for clapping in zoos and aquaria," said lead study author Dr David Hocking from Monash University's School of Biological Sciences.

"But where zoo animals are often trained to clap for our entertainment -- these grey seals are doing it in the wild of their own accord."

The research, published today in the journal Marine Mammal Science, is based on video footage collected by naturalist Dr Ben Burville, a Visiting Researcher with Newcastle University, UK.

The footage -- which took Dr Burville 17 years of diving to catch on film -- shows a male grey seal clapping its paw-like flippers to produce a gunshot-like 'crack!' sound.

"The clap was incredibly loud and at first I found it hard to believe what I had seen," Dr Burville said.

"How could a seal make such a loud clap underwater with no air to compress between its flippers?"

"Other marine mammal species can produce similar types of percussive sound by slapping the water with their body or tail," said Associate Professor Alistair Evans from Monash University, who was also involved in the study.

The loud high-frequency noise produced by clapping cuts through background noise, sending out a clear signal to any other seals in the area.

"Depending on the context, the claps may help to ward off competitors and/or attract potential mates," Dr Hocking said.

"Think of a chest-beating male gorilla, for example. Like seal claps, those chest beats carry two messages: I am strong, stay away; and I am strong, my genes are good."

Dr Hocking said clapping seals demonstrates just how much there still is to learn about the animals living around us.

Clapping appears to be an important social behaviour for grey seals, so anything that disturbed it could impact breeding success and survival for this species.

"Human noise pollution is known to interfere with other forms of marine mammal communication, including whale song," Dr Hocking said.

"But if we do not know a behaviour exists, we cannot easily act to protect it."

Understanding the animals around us better may just help us to protect them, and their way of life.

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Materials provided by Monash University. Note: Content may be edited for style and length.

Genome stability: Intricate process of DNA repair discovered

DNA illustration (stock image).

An elaborate system of filaments, liquid droplet dynamics and protein connectors enables the repair of some damaged DNA in the nuclei of cells, researchers at the University of Toronto have found. The findings further challenge the belief that broken DNA floats aimlessly -- and highlight the value of cross-disciplinary research in biology and physics.

DNA repair helps ensure genome stability, which in turn allows cells to function and promotes health in all organisms. Double-strand DNA breaks are especially toxic to cells, and researchers had assumed for decades that these breaks floated inside cell nuclei without direction, until they trigger other cellular changes or happen on a fixer mechanism.

That thinking began to change in 2015, when Karim Mekhail and his lab showed that damaged DNA can be intentionally transported by motor protein 'ambulances' to DNA 'hospitals,' areas enriched with certain repair factors in the nuclei. The researchers later worked with U of T aerospace engineers to show that after a single double-strand break, DNA travels for repair via long 'autobahns' of thread-like microtubules, which are also moving.

In the current study, Mekhail and lead author Roxanne Oshidari looked at yeast cells with many DNA double-strand breaks, and showed that coordination between shorter types of microtubule filaments and liquid-like droplets composed of DNA repair proteins enables the creation and function of a DNA repair centre.

"The liquid droplets work with intranuclear microtubules to promote the clustering of damaged DNA sites," says Mekhail, an associate professor of laboratory medicine and pathobiology at U of T. "Repair proteins at these different sites assemble in droplets that fuse into a larger repair-centre droplet, through the action of the shorter nuclear microtubules."

This larger oil-like droplet then behaves like a spider, says Mekhail, shooting out a web of star-shaped filaments that tether to the longer autobahns along which damaged DNA can be transported to the DNA hospitals.

The journal Nature Communications published the findings today.

Mekhail turned to Nasser Ashgriz, a professor in U of T's department of mechanical and industrial engineering, to measure and understand the role of droplets in the repair process. "You couldn't ask for better expertise in fluid dynamics, and he was just across the road," Mekhail says of Ashgriz, who runs U of T's multi-phase flow and spray systems lab.

Mekhail brought a video of the droplets to Ashgriz, who projected it on a large screen in his office and confirmed that fluid dynamics appeared to be at play. But communication across the biology-physics divide was challenging. "Understanding what they do was very difficult in the beginning because our terminologies are totally different," says Ashgriz.

When he and Mekhail used plain language to describe how the droplets behaved, however, things started to make sense. "We focused on the physical aspects of the droplets," Ashgriz says. "The physics that cause their motion and dynamics became our common language."

After months of talks and experiments, computer simulations repeatedly predicted that the shorter filaments would move like pistons, lowering pressure in the nucleoplasm and creating a suction effect that leads to the fusion of droplets. Mekhail and his team confirmed that finding in their lab.

"Often when we dive deep in the specifics of a field, we get separated from one another," Ashgriz says. "Bringing together people with different views can really improve understanding, and this work was a good example -- with credit to Karim for his vision and initiative."

Mekhail and his team also uncovered further important properties of the repair droplets with U of T professors Hyun Kate Lee and Haley Wyatt in the department of biochemistry, in a process Mekhail likens to play with toys. They ran the droplets through many tests, bouncing them against each other and observing their behaviour, which turned out to be very similar in a petri dish and in cells.

The most surprising finding came after several cycles of droplet fusion, the researchers found. "It was very bizarre and totally unexpected, I still remember the day," Mekhail says. Oshidari observed that the larger droplets initiate an internal concentration of filament building blocks, forcing creation of a kind of self-interlocking brick road, which together with the spidery webs allow DNA to hook onto the longer autobahn filaments.

The complex process is easy to miss when looking at DNA damage sites, says Mekhail, largely because imaging in the field has become highly automated. Most software has been set up to see what has already been seen. "We can't rely on the old ways of observing," he says. "We need to update our software and also go back to looking with the human eye, guided by simulations when needed."

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Story Source:

Materials provided by University of Toronto. Original written by Jim Oldfield. Note: Content may be edited for style and length.

Genome stability: Intricate process of DNA repair discovered

DNA illustration (stock image).

An elaborate system of filaments, liquid droplet dynamics and protein connectors enables the repair of some damaged DNA in the nuclei of cells, researchers at the University of Toronto have found. The findings further challenge the belief that broken DNA floats aimlessly -- and highlight the value of cross-disciplinary research in biology and physics.

DNA repair helps ensure genome stability, which in turn allows cells to function and promotes health in all organisms. Double-strand DNA breaks are especially toxic to cells, and researchers had assumed for decades that these breaks floated inside cell nuclei without direction, until they trigger other cellular changes or happen on a fixer mechanism.

That thinking began to change in 2015, when Karim Mekhail and his lab showed that damaged DNA can be intentionally transported by motor protein 'ambulances' to DNA 'hospitals,' areas enriched with certain repair factors in the nuclei. The researchers later worked with U of T aerospace engineers to show that after a single double-strand break, DNA travels for repair via long 'autobahns' of thread-like microtubules, which are also moving.

In the current study, Mekhail and lead author Roxanne Oshidari looked at yeast cells with many DNA double-strand breaks, and showed that coordination between shorter types of microtubule filaments and liquid-like droplets composed of DNA repair proteins enables the creation and function of a DNA repair centre.

"The liquid droplets work with intranuclear microtubules to promote the clustering of damaged DNA sites," says Mekhail, an associate professor of laboratory medicine and pathobiology at U of T. "Repair proteins at these different sites assemble in droplets that fuse into a larger repair-centre droplet, through the action of the shorter nuclear microtubules."

This larger oil-like droplet then behaves like a spider, says Mekhail, shooting out a web of star-shaped filaments that tether to the longer autobahns along which damaged DNA can be transported to the DNA hospitals.

The journal Nature Communications published the findings today.

Mekhail turned to Nasser Ashgriz, a professor in U of T's department of mechanical and industrial engineering, to measure and understand the role of droplets in the repair process. "You couldn't ask for better expertise in fluid dynamics, and he was just across the road," Mekhail says of Ashgriz, who runs U of T's multi-phase flow and spray systems lab.

Mekhail brought a video of the droplets to Ashgriz, who projected it on a large screen in his office and confirmed that fluid dynamics appeared to be at play. But communication across the biology-physics divide was challenging. "Understanding what they do was very difficult in the beginning because our terminologies are totally different," says Ashgriz.

When he and Mekhail used plain language to describe how the droplets behaved, however, things started to make sense. "We focused on the physical aspects of the droplets," Ashgriz says. "The physics that cause their motion and dynamics became our common language."

After months of talks and experiments, computer simulations repeatedly predicted that the shorter filaments would move like pistons, lowering pressure in the nucleoplasm and creating a suction effect that leads to the fusion of droplets. Mekhail and his team confirmed that finding in their lab.

"Often when we dive deep in the specifics of a field, we get separated from one another," Ashgriz says. "Bringing together people with different views can really improve understanding, and this work was a good example -- with credit to Karim for his vision and initiative."

Mekhail and his team also uncovered further important properties of the repair droplets with U of T professors Hyun Kate Lee and Haley Wyatt in the department of biochemistry, in a process Mekhail likens to play with toys. They ran the droplets through many tests, bouncing them against each other and observing their behaviour, which turned out to be very similar in a petri dish and in cells.

The most surprising finding came after several cycles of droplet fusion, the researchers found. "It was very bizarre and totally unexpected, I still remember the day," Mekhail says. Oshidari observed that the larger droplets initiate an internal concentration of filament building blocks, forcing creation of a kind of self-interlocking brick road, which together with the spidery webs allow DNA to hook onto the longer autobahn filaments.

The complex process is easy to miss when looking at DNA damage sites, says Mekhail, largely because imaging in the field has become highly automated. Most software has been set up to see what has already been seen. "We can't rely on the old ways of observing," he says. "We need to update our software and also go back to looking with the human eye, guided by simulations when needed."

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Story Source:

Materials provided by University of Toronto. Original written by Jim Oldfield. Note: Content may be edited for style and length.

Missing molecule finally discovered

The evolution from the first molecule to the complex chemistry that exists in our universe today is now one step closer to being understood.

When we think of complex chemistry, we usually think of all the matter that exists on our planet which in our atmosphere is a massive 10 trillion trillion molecules per cubic meter. As we move away from our planet this drops exponentially. However, surprising as it may be, space space – like the interstellar and intergalactic regions – are host to a myriad of molecules. Albeit not at quite the same high densities.

How these molecules formed and became the complex chemistry that we see today remains to be fully understood. It is currently agreed that the early universe consisted of only a few kinds of atoms and it wasn’t until the age of 100,000 years that hydrogen and helium combined to form the first molecule – helium hydride. However, although theorized to exist it has never been detected. That was until a team of scientists from NASA’s SOFIA Science Center (Stratospheric Observatory for Infrared Astronomy) observed its signature – in our own galaxy.

Previously, scientists were able to successfully combine helium and ionic hydrogen to create helium hydride in the laboratory. They then speculated that astrophysical plasmas such as those found in planetary nebulae – an expanding shell of dust that has been ejected from its host star as it runs out of fuel – provided the prefect environment for helium hydride to form. The young, dense planetary nebula, NGC 7027, located around 3,000 light-years from Earth in the constellation Cygnus, seemed like the perfect candidate. However, the instruments of the time were not sufficient to distinguish its signal and the observations were thus inconclusive.

Finally, in 2016, utilizing the world’s largest airborne observatory SOFIA, scientists were able observe NGC 7027 above the interfering layers of Earth’s atmosphere and clearly distinguish the elusive signature of helium hydride.

RSF—in perspective

In the unified perspective everything is interconnected, and evolution is a natural consequence resulting from the information feedback dynamics of spacetime – or space memory. Read more here. This view sees a world where forms take familiar shapes and patterns are repeated across scales. Observations confirming the first molecule that led to molecular hydrogen and the complex chemistry we observe today will therefore add insight into the feedback dynamics that give rise to these fundamental patterns.

By: Dr. Amira Val Baker, RSF research scientist

Microbes harvest electrons: Novel process discovered

Bacteria illustration

Ever since scientists discovered that certain microbes can get their energy from electrical charges, researchers have wondered how they do it.

Bacteria don't have mouths, so they need another way to bring their fuel into their bodies. New research from Washington University in St. Louis reveals how one such bacteria pulls in electrons straight from an electrode source. The work from the laboratory of Arpita Bose, assistant professor of biology in Arts & Sciences, was published Nov. 5 in the scientific journal mBio.

"The molecular underpinning of this process has been difficult to unravel until our work," Bose said. "This is mostly due to the complex nature of the proteins involved in this process. But now, for the first time, we understand how phototrophic microbes can accept electrons from solid and soluble substances."

Dinesh Gupta, a PhD candidate in the Bose laboratory, is the first author on this new study. "I was excited when we found that these phototrophic bacteria use a novel processing step to regulate the production of key electron transfer protein involved in this process," Gupta said. "This study will aid in designing a bacterial platform where bacteria can feed on electricity and carbon dioxide to produce value-added compounds such as biofuels."

Getting the electricity across the outer layer of the bacteria is the key challenge. This barrier is both nonconductive and impermeable to insoluble iron minerals and/or electrodes.

Bose and her collaborators, including Robert Kranz, professor of biology, showed that the naturally occurring strain of Rhodopseudomonas palustris TIE-1 builds a conduit to accept electrons across its outer membrane. The bacteria relies on an iron-containing helper molecule called a deca-heme cytochrome c. By processing this protein, TIE-1 can form an essential bridge to its electron source.

Extracellular electron uptake, or EEU, can help microbes to survive under nutrient-scarce conditions.

Now that Bose has documented these mechanisms behind EEU, she hopes to use it as a biological marker to identify other electricity-eating bacteria in the wild. The findings will help researchers to understand the importance of this functionality in metabolic evolution and microbial ecology.

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Story Source:

Materials provided by Washington University in St. Louis. Original written by Talia Ogliore. Note: Content may be edited for style and length.

Microbes harvest electrons: Novel process discovered

Bacteria illustration

Ever since scientists discovered that certain microbes can get their energy from electrical charges, researchers have wondered how they do it.

Bacteria don't have mouths, so they need another way to bring their fuel into their bodies. New research from Washington University in St. Louis reveals how one such bacteria pulls in electrons straight from an electrode source. The work from the laboratory of Arpita Bose, assistant professor of biology in Arts & Sciences, was published Nov. 5 in the scientific journal mBio.

"The molecular underpinning of this process has been difficult to unravel until our work," Bose said. "This is mostly due to the complex nature of the proteins involved in this process. But now, for the first time, we understand how phototrophic microbes can accept electrons from solid and soluble substances."

Dinesh Gupta, a PhD candidate in the Bose laboratory, is the first author on this new study. "I was excited when we found that these phototrophic bacteria use a novel processing step to regulate the production of key electron transfer protein involved in this process," Gupta said. "This study will aid in designing a bacterial platform where bacteria can feed on electricity and carbon dioxide to produce value-added compounds such as biofuels."

Getting the electricity across the outer layer of the bacteria is the key challenge. This barrier is both nonconductive and impermeable to insoluble iron minerals and/or electrodes.

Bose and her collaborators, including Robert Kranz, professor of biology, showed that the naturally occurring strain of Rhodopseudomonas palustris TIE-1 builds a conduit to accept electrons across its outer membrane. The bacteria relies on an iron-containing helper molecule called a deca-heme cytochrome c. By processing this protein, TIE-1 can form an essential bridge to its electron source.

Extracellular electron uptake, or EEU, can help microbes to survive under nutrient-scarce conditions.

Now that Bose has documented these mechanisms behind EEU, she hopes to use it as a biological marker to identify other electricity-eating bacteria in the wild. The findings will help researchers to understand the importance of this functionality in metabolic evolution and microbial ecology.

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Story Source:

Materials provided by Washington University in St. Louis. Original written by Talia Ogliore. Note: Content may be edited for style and length.