Denisovan DNA found in sediments of Baishiya Karst Cave on Tibetan Plateau

One year after the publication of research on the Xiahe mandible, the first Denisovan fossil found outside of Denisova Cave, the same research team has now reported their findings of Denisovan DNA from sediments of the Baishiya Karst Cave (BKC) on the Tibetan Plateau where the Xiahe mandible was found. 

Baishiya Karst Cave [Credit: HAN Yuanyuan]

The research team was led by Prof. CHEN Fahu from the Institute of Tibetan Plateau Research (ITP) of the Chinese Academy of Sciences (CAS), Prof. ZHANG Dongju from Lanzhou University, Prof. FU Qiaomei from the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of CAS, Prof. Svante Paabo from the Max Planck Institute for Evolutionary Anthropology, and Prof. LI Bo from University of Wollongong.

Using cutting-edge paleogenetic technology, the researchers successfully extracted Denisovan mtDNA from Late Pleistocene sediment samples collected during the excavation of BKC. Their results show that this Denisovan group is closely related to the late Denisovans from Denisova Cave, indicating Denisovans occupied the Tibetan Plateau for a rather long time and had probably adapted to the high-altitude environment.

Denisovans were first discovered and identified in 2010 by a research team led by Prof. Svante Paabo. Almost a decade later, the Xiahe mandible was found on the Tibetan Plateau. As the first Denisovan fossil found outside of Denisova Cave, it confirmed that Denisovans had occupied the roof of the world in the late Middle Pleistocene and were widespread. Although the Xiahe mandible shed great new light on Denisovan studies, without DNA and secure stratigraphic and archaeological context, the information it revealed about Denisovans was still considerably restricted.

Collecting sediment DNA samples [Credit: HAN Yuanyuan]

In 2010, a research team from Lanzhou University led by Prof. CHEN Fahu, current director of ITP, began to work in BKC and the Ganjia basin where it is located. Since then, thousands of pieces of stone artifacts and animal bones have been found. Subsequent analysis indicated that the stone artifacts were mainly produced using simple core-flake technology. Among animal species represented, gazelles and foxes dominated in the upper layers, but rhinoceros, wild bos and hyena dominated in the lower layers. Some of the bones had been burnt or have cut-marks, indicating that humans occupied the cave for a rather long time.

To determine when people occupied the cave, researchers used radiocarbon dating of bone fragments recovered from the upper layers and optical dating of sediments collected from all layers in the excavated profile. They measured 14 bone fragments and about 30,000 individual grains of feldspar and quartz minerals from 12 sediment samples to construct a robust chronological framework for the site. Dating results suggest that the deepest excavated deposits contain stone artifacts buried over ~190 ka (thousand years). Sediments and stone artifacts accumulated over time until at least ~45 ka or even later.

To determine who occupied the cave, researchers used sedimentary DNA technology to analyze 35 sediment samples specially collected during the excavation for DNA analysis. They captured 242 mammalian and human mtDNA samples, thus enriching the record of DNA related to ancient hominins. Interestingly, they detected ancient human fragments that matched mtDNA associated with Denisovans in four different sediment layers deposited ~100 ka and ~60 ka.

Preparing sediment samples in IVPP cleanroom [Credit: WANG Xiao]

More interestingly, they found that the hominin mtDNA from 60 ka share the closest genetic relationship to Denisova 3 and 4 - i.e., specimens sampled from Denisova Cave in Altai, Russia. In contrast, mtDNA dating to ~100 ka shows a separation from the lineage leading to Denisova 3 and 4.

Using sedimentary DNA from BKC, researchers found the first genetic evidence that Denisovans lived outside of Denisova Cave. This new study supports the idea that Denisovans had a wide geographic distribution not limited to Siberia, and they may have adapted to life at high altitudes and contributed such adaptation to modern humans on the Tibetan Plateau.

However, there are still many questions left. For example, what's the latest age of Denisovans in BKC? Due to the reworked nature of the top three layers, it is difficult to directly associate the mtDNA with their depositional ages, which are as late as 20-30 ka BP. Therefore, it is uncertain whether these late Denisovans had encountered modern humans or not. In addition, just based on mtDNA, we still don't know the exact relationship between the BKC Denisovans, those from Denisova Cave in Siberia and modern Tibetans. Future nuclear DNA from this site may provide a tool to further explore these questions.

The study was published in Science.

Source: Chinese Academy of Sciences [October 30, 2020]

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The traits of Florisbad skull reinforce the mosaic hypothesis of human evolution

Emiliano Bruner, a paleoneurologist at the Centro Nacional de Investigacion sobre la Evolucion Humana (CENIEH), in collaboration with Marlize Lombard, of the University of Johannesburg, has just published a study in the Journal of Anthropological Sciences which describes the braincase traits of Florisbad, a fossil found in South Africa in 1932, and its similarities with other species like Homo sapiens, H. neanderthalensis and H. heidelbergensis.

Florisbad skull [Credit: E. Bruner et al. 2020]

The frontal bone of this individual, dated to around 260,000 years ago, has a completely modern shape, which suggests a spatial relationship between face and cranial vault very similar to that of Homo sapiens, although the frontal lobes are particularly broad, like in H. neanderthalensis. Nonetheless, the parietal bone displays an anatomy very similar to more archaic species such as H. heidelbergensis.

"The Florisbad cranium might be key to investigating the origin of our species. It could be from a very early population of Homo sapiens or an extinct group belonging to another independent, parallel human lineage," says Bruner.

Fossils with a mixture of more highly evolved characters in the face and more primitive ones in the posterior regions of the cranium have also been found in Europe and Asia, which corroborates the idea that human evolution did not proceed linearly but mosaically.

Source: CENIEH [October 30, 2020]

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Plankton turn hunters to survive dinosaur-killing asteroid impact

New research by an international team of scientists shows how marine organisms were forced to 'reboot' to survive following the asteroid impact 66 million years ago which killed three quarters of life on earth.

High-resolution scanning electron microscope (SEM) images of fossil cell coverings of nannoplankton
 (coccolithophores) highlighting holes that would have allowed flagella and haptonema to emerge
from the cell and draw in food particles (red dots). We have shown a reconstruction
of one of these ancient cells based on living coccolithophores and related algae
[Credit: Paul Bown]

Researchers from the University of Southampton and UCL, along with colleagues in Paris, California, Bristol and Edinburgh used an exceptional record of plankton fossils and eco-evolutionary modelling techniques to examine how organisms behaved before and after this extinction event - and why some survived and some didn't.

The team found that prior to the asteroid impact, species of nannoplankton - microscopic algae - were exclusively reliant on harnessing energy from sunlight (photoautotrophs), but those living afterwards were capable of capturing food and eating it in addition to using photosynthesis to feed (mixotrophs). This suggests the blocking of light from the sun played an important role in killing off some species and over time, encouraging others to evolve and adapt.

The research team's breakthrough came when they found that many of the nannoplankton skeletons (coccospheres) post mass-extinction included a large hole, indicating the position of flagella - tiny tail like structures used by the algae for movement and feeding. This indicates these microscopic organisms, which survived the asteroid strike, were capable of hunting and ingesting food.

"Those species that were lost at the mass extinction show no evidence of a mixotrophic lifestyle and were likely to be completely reliant on sunlight and photosynthesis," explains Dr Samantha Gibbs of the University of Southampton. "Fossils following the Cretaceous-Paleogene (K-Pg) extinction show that mixotrophy dominated and our model indicates this is because of the exceptional abundance of small prey cells - most likely surviving bacteria - and reduced numbers of larger 'grazers' in the post-extinction oceans."

A SEM view of a seafloor after the extinction showing the abundance of these cells with flagellar
 openings. These cells are around 7 microns in diameter (7/1000ths of a millimetre) with
the scale bars next to each image showing the size of a micron (1/1000th mm)
[Credit: Paul Bown]

Opposing evolutionary forces led to the emergence of more diverse feeding strategies and eventually a return to greater reliance on photosynthesis in open ocean nannoplankton. Most nannoplankton today only photosynthesise. So, what caused this devastating mass extinction of photoautotrophs and other species?

The simple answer is a lack of light. The K/Pg event was triggered by an asteroid impact that formed the Chicxulub crater in Mexico, and is well known for the extinction of dinosaurs, plesiosaurs, ammonites and many other groups.

"This huge impact flung vast amounts of debris, aerosols and soot into the atmosphere, causing darkness, cooling and acidification over days and years," says Paul Bown, Professor of Micropalaeontology at UCL. "The significant bias found in the nannoplankton extinctions - removal of open-ocean photoautotrophs but survival of mixotrophs that could hunt and feed - can only be fully explained by the darkness caused by the asteroid impact acting as a kill mechanism."

Graphic explaining the research method and findings
[Credit: Gibbs et al., 2020]

Samantha Gibbs adds: "This 'blackout' or shutdown of primary productivity would have been felt across all of Earth's ecosystems and reveals that the K/Pg event is distinct from all other mass extinctions that have shaped the history of life, both in its rapidity, related to an instantaneous impact event, and its darkness kill mechanism, which shook the foundations of the food chains. The K/Pg boundary event likely represents the only truly geologically instantaneous mass extinction event."

Findings are published in the journal Science Advances.

Source: University of South Hampton [October 30, 2020]

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Evidence suggests more mega-droughts are coming

Mega-droughts—droughts that last two decades or longer—are tipped to increase thanks to climate change, according to University of Queensland-led research.

Credit: University of Queensland

UQ's Professor Hamish McGowan said the findings suggested climate change would lead to increased water scarcity, reduced winter snow cover, more frequent bushfires and wind erosion. The revelation came after an analysis of geological records from the Eemian Period—129,000 to 116,000 years ago—which offered a proxy of what we could expect in a hotter, drier world.

"We found that, in the past, a similar amount of warming has been associated with mega-drought conditions all over south eastern Australia," Professor McGowan said. "These drier conditions prevailed for centuries, sometimes for more than 1000 years, with El Nino events most likely increasing their severity."

The team engaged in paleoclimatology—the study of past climates—to see what the world will look like as a result of global warming over the next 20 to 50 years.

"The Eemian Period is the most recent in Earth's history when global temperatures were similar, or possibly slightly warmer than present," Professor McGowan said. "The 'warmth' of that period was in response to orbital forcing, the effect on climate of slow changes in the tilt of the Earth's axis and shape of the Earth's orbit around the sun. In modern times, heating is being caused by high concentrations of greenhouse gasses, though this period is still a good analog for our current-to-near-future climate predictions."

Researchers worked with the New South Wales Parks and Wildlife service to identify stalagmites in the Yarrangobilly Caves in the northern section of Kosciuszko National Park. 

Small samples of the calcium carbonate powder contained within the stalagmites were collected, then analyzed and dated at UQ. That analysis allowed the team to identify periods of significantly reduced precipitation during the Eemian Period.

"They're alarming findings, in a long list of alarming findings that climate scientists have released over the last few decades," Professor McGowan said. "We hope that this new research allows for new insights to our future climate and the risks it may bring, such as drought and associated bushfires. But, importantly, if humans continue to warm the planet, this is the future we may all be looking at."

The study was published in Scientific Reports.

Source: University of Queensland [October 30, 2020]

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How many habitable planets are out there?

Thanks to new research using data from the Kepler space telescope, it's estimated that there could be as many as 300 million potentially habitable planets in our galaxy. Some could even be pretty close, with several likely within 30 light-years of our Sun. The findings will be published in The Astronomical Journal, and research was a collaboration of scientists from NASA, the SETI Institute, and other organizations worldwide.

This illustration depicts one possible appearance of the planet Kepler-452b, the first
near-Earth-size world to be found in the habitable zone of a star similar to our Sun
[Credit: NASA Ames/JPL-Caltech]

"This is the first time that all of the pieces have been put together to provide a reliable measurement of the number of potentially habitable planets in the galaxy," said co-author Jeff Coughlin, an exoplanet researcher at the SETI Institute and Director of Kepler's Science Office. "This is a key term of the Drake Equation, used to estimate the number of communicable civilizations—we're one step closer on the long road to finding out if we're alone in the cosmos."

The Drake Equation is a probabilistic argument that details the factors to consider when estimating the potential number of technologically advanced civilizations in the galaxy that could be detected. The Drake Equation is also often considered to be a roadmap for astrobiology and guides much of the research at the SETI Institute.

To develop a reasonable estimate, the researchers looked at exoplanets similar in size to Earth and thus most likely to be rocky planets. They also looked at so-called Sun-like stars, around the same age as our Sun and approximately the same temperature. Another consideration for habitability is whether the planet could have the conditions necessary to support liquid water.

Previous estimates about determining the number of potentially habitable exoplanets there are in our galaxy were heavily based on the planet's distance from its star. This new research also considers how much light hits the planet from its star, which would impact the likelihood that the planet could support liquid water. To do this, the team looked not only at Kepler data, but also at data from the European Space Agency's Gaia mission about how much energy the planet's star emits.

An illustration representing the legacy of NASA's Kepler space telescope. After nine years in deep
space collecting data that revealed our night sky to be filled with billions of hidden planets –
more planets even than stars – NASA’s Kepler space telescope ran out of fuel needed for
further science operations in 2018 [Credit: NASA/Ames Research Center/W. Stenzel]

By taking both Kepler and Gaia data into account, the results better reflect the diversity of stars, solar systems, and exoplanets in our galaxy.

"Knowing how common different kinds of planets are is extremely valuable for the design of upcoming exoplanet-finding missions," said co-author Michelle Kunimoto, who worked on this paper after finishing her doctorate on exoplanet occurrence rates at the University of British Columbia, and recently joined the Transiting Exoplanet Survey Satellite, or TESS, team at the Massachusetts Institute of Technology in Cambridge, Massachusetts. "Surveys aimed at small, potentially habitable planets around Sun-like stars will depend on results like these to maximize their chance of success."

More research will be needed to understand the role a planet's atmosphere has on its capacity to support liquid water. In this analysis, researchers used a conservative estimate of the atmosphere's effect to estimate the occurrence of Sun-like stars with rocky planets that could have liquid water.

The Kepler mission, which officially ceased collecting data in 2018, has identified over 2,800 confirmed exoplanets, with several thousand more candidates waiting to be confirmed. So far, researchers have identified several hundred planets in the habitable zone of their star in Kepler data. It may take a while to find all 300 million!

Source: SETI Institute [October 30, 2020]

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Assessing the habitability of planets around old red dwarfs

A new study using data from NASA's Chandra X-ray Observatory and Hubble Space Telescope gives new insight into an important question: how habitable are planets that orbit the most common type of stars in the Galaxy? The target of the new study, as reported in our press release, is Barnard's Star, which is one of the closest stars to Earth at a distance of just 6 light years. Barnard's Star is a red dwarf, a small star that slowly burns through its fuel supply and can last much longer than medium-sized stars like our Sun. It is about 10 billion years old, making it twice the age of the Sun.

Credit: Chandra X-ray Center

The authors used Barnard's Star as a case study to learn how flares from an old red dwarf might affect any planets orbiting it. This artist's illustration depicts an old red dwarf like Barnard's Star (right) and an orbiting, rocky planet (left).

The research team's Chandra observations of Barnard's Star taken in June 2019 uncovered one X-ray flare (shown in the inset box) and their Hubble observations taken in March 2019 revealed two ultraviolet high-energy flares (shown in an additional graphic). Both observations were about seven hours long and both plots show X-ray or ultraviolet brightness extending down to zero. Based on the length of the flares and of the observations, the authors concluded that Barnard's Star unleashes potentially destructive flares about 25% of the time.

The team then studied what these results mean for rocky planets orbiting in the habitable zone—where liquid water could exist on their surface—around an old red dwarf like Barnard's Star. Any atmosphere formed early in the life of a habitable-zone planet was likely to have been eroded away by high-energy radiation from the star during its volatile youth. Later on, however, planet atmospheres might regenerate as the star becomes less active with age. This regeneration process may occur by gases released by impacts of solid material or gases being released by volcanic processes.

However, the onslaught of powerful flares like those reported here, repeatedly occurring over hundreds of millions of years, may erode any regenerated atmospheres on rocky planets in the habitable zone. The illustration shows the atmosphere of the rocky planet being swept away to the left by energetic radiation from flares produced by the red dwarf. This would reduce the chance of these worlds supporting life. The team is currently studying high-energy radiation from many more red dwarfs to determine whether Barnard's Star is typical.

A paper describing these results was published in The Astronomical Journal.

Source: NASA [October 30, 2020]

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2,000-year old seal bearing portrait of Apollo found in Jerusalem

A gem was found in the The Archaeological Sifting Project in the Tzurim Valley National Park, carried out under the auspices of the City of David and the Nature and Parks Authority. The gem features an engraved portrait of the god Apollo. According to researchers, this rare find is the third secured gem sealing (also called an intaglio which is a gem with a design carved into the upper side of the stone) from the Second Temple period to have ever been discovered in Jerusalem. 

This 2,000-year-old gem seal bearing the image of Apollo was found in earth excavated
from the foundations of the Western Wall in the Old City of Jerusalem
[Credit: Eliyahu Yanai, City of David]

The gem is cut from dark brown jasper, and has remnants of yellow-light, brown, and white layers. In antiquity, jasper was considered a precious stone. The gem seal was embedded in a ring, dated to the 1st century CE (Second Temple period).

The gem is tiny, oval-shaped, 13 mm long, 11 mm wide, and 3 mm thick. Because the gem is an intaglio, its main function was as a stamp to be used on soft material, usually beeswax, for personal signatures on contracts, letters, wills, goods or bundles of money. The gem features an engraving of Apollo’s head in profile to the left, with long hair flowing over a wide, pillar-like neck, a large nose, thick lips, and a small prominent chin. The hair is styled in a series of parallel lines directed to the apex, and surrounded by a braid above the forehead. One line of hair marks a strand that covers the ear; long curls flow over part of the neck, reaching the left shoulder. Thin diagonal lines at the base of the head mark the upper end of the garment and the body.

Credit: Eliyahu Yanai, City of David

According to researchers - archaeologist Eli Shukron, Prof. Shua Amorai-Stark, and senior archaeologist Malka Hershkovitz - although Apollo is an Olympian deity of the Greek and Roman cultures, it is highly probable that the person wearing the ring was a Jew.

In the opinion of archaeologist Eli Shukron, who conducted the excavation in which the gem was found: “It is rare to find seal remains bearing the image of the god Apollo at sites identified with the Jewish population. To this day, two such gems (seals) have been found in Masada, another in Jerusalem inside an ossuary (burial box) in a Jewish tomb on Mount Scopus, and the current gem that was discovered in close proximity to the Temple Mount.” Mr. Shukron added: “When we found the gem, we asked ourselves ‘what is Apollo doing in Jerusalem? And why would a Jew wear a ring with the portrait of a foreign god?’ The answer to this, in our opinion, lies in the fact that the owner of the ring wore it not as a ritual act that expresses religious belief, but as a means of making use of the impact that Apollo’s figure represents: light, purity, health, and success.”

Prof. Shua Amorai-Stark, a researcher of engraved gems, stated that: “At the end of the Second Temple period, the sun god Apollo was one of the most popular and revered deities in Eastern Mediterranean regions. Apollo was a god of manifold functions, meanings, and epithets. Among Apollo’s spheres of responsibility, it is likely that association with sun and light (as well as with logic, reason, prophecy, and healing) fascinated some Jews, given that the element of light versus darkness was prominently present in Jewish worldview in those days. The fact that the craftsman of this gem left the yellow-golden and light brown layers on the god’s hair probably indicates a desire to emphasize the aspect of light in the god’s persona, as well as in the aura that surrounded his head. The choice of a dark stone with yellow coloring of hair suggests that the creator or owner of this intaglio sought to emphasize the dichotomous aspect of light and darkness and/or their connectedness.”

Source: City of David [October 29, 2020]

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