Ancient 'chewing gum' reveals stone age diet

What did people eat on the west coast of Scandinavia 10,000 years ago? A new study of the DNA in a chewing gum shows that deer, trout and hazelnuts were on the diet. It also shows that one of the individuals had severe problems with her teeth.

Some 9,700 years ago, a group of people were camping on the west coast of Scandinavia, north of what is today Göteborg.

They had been fishing, hunting and collecting resources for food.

And some teenagers, both boys and girls, were chewing resin to produce glue, just after munching on trout and deer, as well as on hazelnuts.

Due to a bad case of periodontitis (severe gum infection that can lead to tooth loss and bone loss), one of the teenagers had problems eating the chewy deer-meat, as well as preparing the resin by chewing it.

We know this because an international research team has been working with the chewed resin from Huseby Klev for some time.

"There is a richness of DNA sequences in the chewed mastic from Huseby-Klev, and in it we find both the bacteria that we know are related to periodontitis, and DNA from plants and animals that they had chewed before," says Dr. Emrah Kırdök, from Mersin University Department of Biotechnology, who coordinated the metagenomic work on the Mesolithic chewing gum.

Emrah Kırdök started to analyse the material when he was a postdoc at the Department of Archaeology and Classical Studies at Stockholm University, but the study has grown much since then.

The site Huseby Klev on the island Orust was excavated 30 years ago.

Chewed resin was found together with remains of stone tools in a context dated to c. 9700 years ago.

The stone material also indicated a Mesolithic chronology. The chewed material from Huseby Klev has already generated a study on the human genetic data from three individuals, and the DNA in the material that was not of human origin has also been analysed and published.

Identifying the different species present in the kind of mix of DNA that was present in the Mesolithic chewing gum was challenging.

Dr Andrés Aravena, from the Department of Molecular Biology and Genetics at Istanbul University spent much time on the computer analysing the data together with Dr. Emrah Kırdök. "We had to apply several computational heavy analytical tools to single out the different species and organisms. All the tools we needed were not ready to be applied to ancient DNA; but much of our time was spent on adjusting them so that we could apply them," concludes Andrés Aravena.

Metagenomics on ancient DNA is an expanding area, but there have yet only been a few studies on this type of chewed material.

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Bizarre new fossils shed light on ancient plankton

A scientist from the University of Leicester has discovered a new type of fossil that reveals life in the oceans half a billion years ago.

The tiny organisms, detailed in a new study in the journal Proceedings of the Royal Society B, resemble modern-day algae and might also give scientists an insight into the climate changes that affected our oceans.

The fossils are microscopic and look like spiny balls connected together. The study's author Dr Tom Harvey, from the University of Leicester School of Geography, Geology and the Environment, said: "When I first saw them, I had no idea what they were. I wondered if they could be animal eggs, or some new type of organism. There's nothing quite like them, living or extinct."

But as further specimens came to light, Dr Harvey identified similarities with modern green algae that live floating in the plankton of ponds and lakes. He explains: "The fossils have the same sort of colonial structure as the modern algae, with cells linking together, explaining their neat, geometric arrangements. Surprisingly, though, the fossil examples lived in the sea, giving a rare glimpse of the early marine plankton."

The importance of the fossils lies in their immense age. They lived around the time when animals were first evolving, during the Cambrian 'explosion' of life -- and this is probably no coincidence. In today's world, phytoplankton provides the fundamental food source for almost all life in the oceans. However, the modern groups of phytoplankton evolved relatively recently, and we do not know which groups inhabited the Cambrian oceans.

Dr Harvey explains: "When we look at modern plankton, we see that algae develop colonies when animals are trying to eat them. It's a defence mechanism. So, the existence of colonial algae in the Cambrian Period suggests that early animals were evolving to feed in the plankton, starting a predator-prey relationship that has continued ever since.

"Considering that the plankton underpins life in the oceans, and fossil plankton helps us build ancient climate models, these small fossils have a big role in telling the history of life on Earth."

The new discovery will prompt a re-think on other early microfossils. For years, scientists have thought that the spiny balls found individually were the dormant cysts of single-celled life.

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Ancient sea monster remains reveal oldest mega-predatory pliosaur

The fossils of a 170-million-year-old ancient marine reptile from the Age of Dinosaurs have been identified as the oldest-known mega-predatory pliosaur -- a group of ocean-dwelling reptiles closely related to the famous long-necked plesiosaurs. The findings are rare and add new knowledge to the evolution of plesiosaurs. The study has been published in the journal Scientific Reports.

The fossils were found 40 years ago in north-eastern France. An international team of palaeontologists from the Naturkunde-Museum Bielefeld in Germany, the Institute of Paleobiology of the Polish Academy of Sciences in Warsaw, Poland, the Natural History Museum in Luxembourg and The Museum of Evolution at Uppsala University in Sweden have now analysed them and identified them as a new pliosaur genus: Lorrainosaurus.

Pliosaurs were a type of plesiosaur with short necks and massive skulls. They appeared over 200 million years ago, but remained minor components of marine ecosystems until suddenly developing into enormous apex predators. The new study shows that this adaptive shift followed feeding niche differentiation and the global decline of other predatory marine reptiles over 170 million years ago.

Lorrainosaurus is the oldest large-bodied pliosaur represented by an associated skeleton. It had jaws over 1.3 m long with large conical teeth and a bulky 'torpedo-shaped' body propelled by four flipper-like limbs.

"Lorrainosaurus was one of the first truly huge pliosaurs. It gave rise to a dynasty of marine reptile mega-predators that ruled the oceans for around 80 million years," explains Sven Sachs, a researcher at the Naturkunde-Museum Bielefeld, who led the study.

This giant reptile probably reached over 6 m from snout to tail, and lived during the early Middle Jurassic period. Intriguingly, very little is known about plesiosaurs from that time.

"Our identification of Lorrainosaurus as one of the earliest mega-predatory pliosaurs demonstrates that these creatures emerged immediately after a landmark restructuring of marine predator ecosystems across the Early-to-Middle Jurassic boundary, some 175 to 171 million years ago. This event profoundly affected many marine reptile groups and brought mega-predatory pliosaurids to dominance over 'fish-like' ichthyosaurs, ancient marine crocodile relatives, and other large-bodied predatory plesiosaurs," adds Daniel Madzia from the Institute of Paleobiology of the Polish Academy of Sciences, who co-led the study.

Pliosaurs were some of the most successful marine predators of their time.

"Famous examples, such as Pliosaurus and Kronosaurus -- some of the world's largest pliosaurs -- were absolutely enormous with body-lengths exceeding 10 m. They were ecological equivalents of today's Killer whales and would have eaten a range of prey including squid-like cephalopods, large fish and other marine reptiles. These have all been found as preserved gut contents," said senior co-author Benjamin Kear, Curator of Vertebrate Palaeontology and Researcher in Palaeontology at The Museum of Evolution, Uppsala University.

The recovered bones and teeth of Lorrainosaurus represent remnants of what was once a complete skeleton that decomposed and was dispersed across the ancient sea floor by currents and scavengers.

"The remains were unearthed in 1983 from a road cutting near Metz in Lorraine, north-eastern France. Palaeontology enthusiasts from the Association minéralogique et paléontologique d'Hayange et des environs recognised the significance of their discovery and donated the fossils to the Natural History Museum in Luxembourg," said co-author Ben Thuy, Curator at the Natural History Museum in Luxembourg.

Other than a brief report published in 1994, the fossils of Lorrainosaurus remained obscure until this new study re-evaluated the finds. Lorrainosaurus indicates that the reign of gigantic mega-predatory pliosaurs must have commenced earlier than previously thought, and was locally responsive to major ecological changes affecting marine environments covering what is now western Europe during the early Middle Jurassic.

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Large sub-surface granite formation signals ancient volcanic activity on Moon's dark side

A large formation of granite discovered below the lunar surface likely was formed from the cooling of molten lava that fed a volcano or volcanoes that erupted early in the Moon's history -- as long as 3.5 billion years ago.

A team of scientists led by Matthew Siegler, an SMU research professor and research scientist with the Planetary Science Institute, has published a study in Nature that used microwave frequency data to measure heat below the surface of a suspected volcanic feature on the Moon known as Compton-Belkovich. The team used the data to determine that the heat being generated below the surface is coming from a concentration of radioactive elements that can only exist on the Moon as granite.

Granites are the igneous rock remnants of the plumbing systems below extinct volcanos. The granite formation left when lava cools without erupting is known as a batholith.

"Any big body of granite that we find on Earth used to feed a big bunch of volcanoes, much like a large system is feeding the Cascade volcanoes in the Pacific Northwest today," Siegler said. "Batholiths are much bigger than the volcanoes they feed on the surface. For example, the Sierra Nevada mountains are a batholith, left from a volcanic chain in the western United States that existed long ago."

The lunar batholith is located in a region of the Moon previously identified as a volcanic complex, but researchers are surprised at its size, with an estimated diameter of 50 kilometers.

Granite is somewhat common on Earth, and its formation is generally driven by water and plate tectonics, which aid in creating large melt bodies below the Earth's surface. However, granites are extremely rare on the Moon, which lacks these processes.

Finding this granite body helps explain how the early lunar crust formed.

"If you don't have water it takes extreme situations to make granite," Siegler said. "So, here's this system with no water, and no plate tectonics -- but you have granite.

Was there water on the moon -- at least in this one spot? Or was it just especially hot?"

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Lasers and chemistry reveal how ancient pottery was made -- and how an empire functioned

Peru’s first great empire, the Wari, stretched for more than a thousand miles over the Andes Mountains and along the coast from 600-1000 CE. The pottery they left behind gives archaeologists clues as to how the empire functioned. In a new study in the Journal of Archaeological Science: Reports, researchers showed that rather than using “official” Wari pottery imported from the capital, potters across the empire were creating their own ceramics, decorated to emulate the traditional Wari style. To figure it out, the scientists analyzed the pottery’s chemical make-up, with help from laser beams.

“In this study, we looked at the idea of cosmopolitanism, of incorporating different cultures and practices into a society,” says M. Elizabeth Grávalos, a postdoctoral researcher at the Field Museum in Chicago and the study’s lead author. “We’re trying to show that potters were influenced by the Wari, but this influence was blended with their own local cultural practices.”

Grávalos says this model of cosmopolitanism is a little like trying to replicate a recipe from another culture, but with a local spin. “If you live in the US and you’re making pad thai at home, you might not have access to all the ingredients that someone living in Thailand would have, so you substitute some things,” she says. “Wari ceramics are a little like that — people throughout the empire were interested in Wari material culture, but they weren’t necessarily getting it directly from the Wari heartland. More often than not, we see local people trying to make their own version of Wari pottery.”

Grávalos and her colleagues led archaeological digs throughout Peru, working with local communities to excavate the thousand-year-old remains of households, tombs, and administrative centers, in search of Wari lifeways. The researchers were then granted permission from Peru’s Ministry of Culture to bring samples of ceramics from their excavations to Chicago for analysis.

Clay from different regions has a different chemical makeup, so studying the ceramics’ chemical makeup could tell the researchers if the pots were produced in different places or if they were all imported from the Wari capital.

“We’d take a tiny piece of a pot and used a laser to cut an even tinier piece, basically extracting a piece of the ceramic’s clay paste,” says Grávalos. “Then helium gas carried it to the mass spectrometer, which measures the elements present in the  clay paste.” (The lab set-up didn’t have open laser beams and floating shards of pottery cutting across the room, though — the whole process takes place on a microscopic scale inside a big boxy machine.)

The analysis showed that the pots excavated from distinct regions of Peru have different chemical signatures, and were therefore made with distinct clays. That helps show how the Wari culture spread.

Some empires, like the ancient Romans, took a “top-down” approach to spreading their aesthetic, shipping pottery across the Mediterranean so that people throughout the empire were using the official Roman style. Local potters emulating the traditional Wari style in their own work seems to hint at a more “bottom-up” approach.

“Of course, local people in all empires have some degree of agency and creative control — the only empire that’s truly top-down is the Borg from Star Trek,” says Patrick Ryan Williams, Curator of Archaeological Science and Director of the Elemental Analysis Facility  at the Field Museum and the study’s senior author. “Even the Romans had local people doing things their own way. But what we’re finding in this study is the agency of local peoples and the importance of local economies. In some regions, we find that Wari colonists had their own production centers and were recreating Wari lifeways locally. In other areas, we see that local communities made Wari pottery in their own way. I think that’s what’s really important about this study.”

The researchers say that the patterns revealed by this pottery could help explain why the Wari empire was able to thrive for so long. “Local production, even in a cosmopolitan society with lots of far-flung connections, makes a society more resilient,” says Williams. “If you’re entirely dependent on someone far away sending you things you need, you’re extremely vulnerable.”

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Ancient proteins offer new clues about origin of life on Earth

By simulating early Earth conditions in the lab, researchers have found that without specific amino acids, ancient proteins would not have known how to evolve into everything alive on the planet today -- including plants, animals, and humans.

The findings, which detail how amino acids shaped the genetic code of ancient microorganisms, shed light on the mystery of how life began on Earth.

"You see the same amino acids in every organism, from humans to bacteria to archaea, and that's because all things on Earth are connected through this tree of life that has an origin, an organism that was the ancestor to all living things," said Stephen Fried, a Johns Hopkins chemist who co-led the research with scientists at Charles University in the Czech Republic. "We're describing the events that shaped why that ancestor got the amino acids that it did."

The findings are newly published in the Journal of the American Chemical Society.

In the lab, the researchers mimicked primordial protein synthesis of 4 billion years ago by using an alternative set of amino acids that were highly abundant before life arose on Earth.

They found ancient organic compounds integrated the amino acids best suited for protein folding into their biochemistry. In other words, life thrived on Earth not just because some amino acids were available and easy to make in ancient habitats but because some of them were especially good at helping proteins adopt specific shapes to perform crucial functions.

"Protein folding was basically allowing us to do evolution before there was even life on our planet," Fried said. "You could have evolution before you had biology, you could have natural selection for the chemicals that are useful for life even before there was DNA."

Even though the primordial Earth had hundreds of amino acids, all living things use the same 20 of these compounds. Fried calls those compounds "canonical." But science has struggled to pinpoint what's so special -- if anything -- about those 20 amino acids.

In its first billion years, Earth's atmosphere consisted of an assortment of gases like ammonia and carbon dioxide that reacted with high levels of ultraviolet radiation to concoct some of the simpler canonical amino acids. Others arrived via special delivery by meteorites, which introduced a mixed bag of ingredients that helped life on Earth complete a set of 10 "early" amino acids.

How the rest came to be is an open question that Fried's team is trying to answer with the new research, especially because those space rocks brought much more than the "modern" amino acids.

"We're trying to find out what was so special about our canonical amino acids," Fried said. "Were they selected for any particular reason?"

Scientists estimate Earth is 4.6 billion years old, and that DNA, proteins, and other molecules didn't begin to form simple organisms until 3.8 billion years ago. The new research offers new clues into the mystery of what happened during the time in between.

"To have evolution in the Darwinian sense, you need to have this whole sophisticated way of turning genetic molecules like DNA and RNA into proteins. But replicating DNA also requires proteins, so we have a chicken-and-egg problem," Fried said. "Our research shows that nature could have selected for building blocks with useful properties before Darwinian evolution."

Scientists have spotted amino acids in asteroids far from Earth, suggesting those compounds are ubiquitous in other corners of the universe. That's why Fried thinks the new research could also have implications for the possibility of finding life beyond Earth.

"The universe seems to love amino acids," Fried said. "Maybe if we found life on a different planet, it wouldn't be that different."

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Ancient disease has potential to regenerate livers

Leprosy is one of the world's oldest and most persistent diseases but the bacteria that cause it may also have the surprising ability to grow and regenerate a vital organ.

Scientists have discovered that parasites associated with leprosy can reprogramme cells to increase the size of a liver in adult animals without causing damage, scarring or tumors.

The findings suggest the possibility of adapting this natural process to renew ageing livers and increase healthspan -- the length of time living disease-free -- in humans.

Experts say it could also help regrow damaged livers, thereby reducing the need for transplantation, which is currently the only curative option for people with end-stage scarred livers.

Previous studies promoted the regrowth of mouse livers by generating stem cells and progenitor cells -- the step after a stem cell that can become any type of cell for a specific organ -- via an invasive technique that often resulted in scarring and tumour growth.

To overcome these harmful side-effects, Edinburgh researchers built on their previous discovery of the partial cellular reprogramming ability of the leprosy-causing bacteria, Mycobacterium leprae.

Working with the US Department of Health and Human Services in Baton Rouge, Louisiana, the team infected 57 armadillos -- a natural host of leprosy bacteria -- with the parasite and compared their livers with those of uninfected armadillos and those that were found to be resistant to infection.

They found that the infected animals developed enlarged -- yet healthy and unharmed -- livers with the same vital components, such as blood vessels, bile ducts and functional units known as lobules, as the uninfected and resistant armadillos.

The team believe the bacteria 'hijacked' the inherent regenerative ability of the liver to increase the organ's size and, therefore, to provide it with more cells within which to increase.

They also discovered several indicators that the main kinds of liver cells -- known as hepatocytes -- had reached a "rejuvenated" state in the infected armadilllos.

Livers of the infected armadillos also contained gene expression patterns -- the blueprint for building a cell -- similar to those in younger animals and human fetal livers.

Genes related to metabolism, growth and cell proliferation were activated and those linked with aging were downregulated, or suppressed.

Scientists think this is because the bacteria reprogramed the liver cells, returning them to the earlier stage of progenitor cells, which in turn became new hepatocytes and grow new liver tissues.

The team are hopeful that the discovery has the potential to help develop interventions for aging and damaged livers in humans. Liver diseases currently result in two million deaths a year worldwide.

The findings have been published in the journal Cell Reports Medicine. This work has been funded by the UK's Medical Research Council and the US National Institutes of Health and National Institute of Allergy and Infectious Diseases.

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Ancient ice age valleys offer clues to future ice sheet change

Deep valleys buried under the seafloor of the North Sea record how the ancient ice sheets that used to cover the UK and Europe expelled water to stop themselves from collapsing.

A new study published this week has surprised the research team, who discovered that the valleys took just hundreds of years to form as they transported vast amounts of meltwater away from under the ice and out into the sea.

This new understanding of when the vast ice sheets melted 20,000 years ago has implications for how glaciers may respond to climate warming today. The study is published in the journal Quaternary Science Reviews.

Tunnel valleys are enormous channels, sometimes up to 150km long, 6km wide and 500m deep (each several times larger than Loch Ness), that drain water from beneath melting ice sheets. There are thousands buried beneath the seafloor of the North Sea that record the melting of ice sheets that have covered the UK and Western Europe over the last two million years.

Lead author James Kirkham, from British Antarctic Survey (BAS) and the University of Cambridge, says:

"This is an exciting discovery. We know that these spectacular valleys are carved out during the death throes of ice sheets. By using a combination of state-of-the-art subsurface imaging techniques and a computer model, we have learnt that tunnel valleys can be eroded rapidly beneath ice sheets experiencing extreme warmth."

The team analysed 'jaw-droppingly detailed' seismic images that provide a 3D scan of the Earth's buried layers. Informed by delicate clues discovered within the valleys, the authors performed a series of computer modelling experiments to simulate valley development, and test how quickly they formed as the last ice sheet to cover the UK melted away at the end of the most recent ice age about 20,000 years ago.

The research suggests that this process is quick by geological timescales, with the melting ice forming giant tunnel valleys within hundreds of years, expelling water that could otherwise accelerate rates of ice loss.

Traditionally, the drainage of water from beneath ice sheets is thought to stabilise ice flow, a process that could potentially buffer modern ice sheets from collapse in a warming climate. But while inspecting the detailed seismic scans, the authors began to find tell-tale signatures of both stagnant and rapid ice movement within the valleys, complicating the picture of how these rapidly forming channels might affect future ice sheet behaviour.

What is certain, is that the surprisingly fast rate at which these tunnels form means that scientists need to start considering their effects in models of how today's ice sheets will evolve in the coming decades to centuries.

There are no modern analogues for this rapid process, but these ancient valleys, now buried hundreds of metres beneath the muds of the North Sea seafloor, record a mechanism for how ice sheets respond to extreme warmth that is missing from present-day ice sheet models. Such models do not currently resolve fine-scale water drainage processes, despite them appearing to be an important control on future ice loss rates and ultimately sea level rise.

James Kirkham continues: "The pace at which these giant channels can form means that they are an important, yet currently ignored, mechanism that may potentially help to stabilise ice sheets in a warming world. As climate change continues to drive the retreat of the modern-day Greenland and Antarctic ice sheets at ever increasing rates, our results call for renewed investigation of how tunnel valleys may help to stabilise contemporary ice losses, and therefore sea level rise, if they switch on beneath the Earth's ice sheets in the future."

Dr Kelly Hogan, co-author and a geophysicist at BAS, says:

"We have been observing these huge meltwater channels from areas covered by ice sheets in the past for more than a century but we did not really understand how they formed. Our results show, for the first time, that the most important mechanism is probably summer melting at the ice surface that makes its way to the bed through cracks or chimneys-like conduits and then flows under the pressure of the ice sheet to cut the channels. Surface melting is already hugely important for the Greenland Ice Sheet today, and this process of water transport through the system will only increase as our climate warms. The crucial question now is will this "extra" meltwater flow in channels cause our ice sheets to flow more quickly, or more slowly, into the sea."

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Study of ancient skulls sheds light on human interbreeding with Neanderthals

Research has established that there are traces of Neandertal DNA in the genome of modern humans. Now an exploratory study that assessed the facial structure of prehistoric skulls is offering new insights, and supports the hypothesis that much of this interbreeding took place in the Near East -- the region ranging from North Africa to Iraq.

"Ancient DNA caused a revolution in how we think about human evolution," says Steven Churchill, co-author of the study and a professor of evolutionary anthropology at Duke University. "We often think of evolution as branches on a tree, and researchers have spent a lot of time trying to trace back the path that led to us, Homo sapiens. But we're now beginning to understand that it isn't a tree -- it's more like a series of streams that converge and diverge at multiple points."

"Our work here gives us a deeper understanding of where those streams came together," says Ann Ross, corresponding author of the study and a professor of biological sciences at North Carolina State University.

"The picture is really complicated," Churchill says. "We know there was interbreeding. Modern Asian populations seem to have more Neandertal DNA than modern European populations, which is weird -- because Neandertals lived in what is now Europe. That has suggested that Neandertals interbred with what are now modern humans as our prehistoric ancestors left Africa, but before spreading to Asia. Our goal with this study was to see what additional light we could shed on this by assessing the facial structure of prehistoric humans and Neandertals."

"By evaluating facial morphology, we can trace how populations moved and interacted over time," Ross explains. "And the evidence shows us that the Near East was an important crossroads, both geographically and in the context of human evolution."

For this study, the researchers collected data on craniofacial morphology from the published literature. This ultimately resulted in a data set including 13 Neandertals, 233 prehistoric Homo sapiens, and 83 modern humans.

The researchers focused on standard craniofacial measurements, which are reproducible, and used those measurements to assess the size and shape of key facial structures. This then allowed the researchers to do an in-depth analysis to determine whether a given human population was likely to have interbred with Neandertal populations, as well as the extent of that likely interbreeding.

"Neandertals had big faces," Churchill says. "But size alone doesn't establish any genetic link between a human population and Neandertal populations. Our work here involved a more robust analysis of the facial structures."

The researchers also accounted for environmental variables that are associated with changes in human facial characteristics, to determine the likelihood that connections they established between Neandertal and human populations were the result of interbreeding rather than other factors.

"We found that the facial characteristics we focused on were not strongly influenced by climate, which made it easier to identify likely genetic influences," Ross says. "We also found that facial shape was a more useful variable for tracking the influence of Neandertal interbreeding in human populations over time. Neandertals were just bigger than humans. Over time, the size of human faces became smaller, generations after they had bred with Neandertals. But the actual shape of some facial features retained evidence of interbreeding with Neandertals."

"This was an exploratory study," Churchill says. "And, honestly, I wasn't sure this approach would actually work -- we have a relatively small sample size, and we didn't have as much data on facial structures as we would have liked. But, ultimately, the results we got are really compelling.

Read more at Science Daily

Ancient microbes may help us find extraterrestrial life forms

Using light-capturing proteins in living microbes, scientists have reconstructed what life was like for some of Earth's earliest organisms. These efforts could help us recognize signs of life on other planets, whose atmospheres may more closely resemble our pre-oxygen planet.

The earliest living things, including bacteria and single-celled organisms called archaea, inhabited a primarily oceanic planet without an ozone layer to protect them from the sun's radiation. These microbes evolved rhodopsins -- proteins with the ability to turn sunlight into energy, using them to power cellular processes.

"On early Earth, energy may have been very scarce. Bacteria and archaea figured out how to use the plentiful energy from the sun without the complex biomolecules required for photosynthesis," said UC Riverside astrobiologist Edward Schwieterman, who is co-author of a study describing the research.

Rhodopsins are related to rods and cones in human eyes that enable us to distinguish between light and dark and see colors. They are also widely distributed among modern organisms and environments like saltern ponds, which present a rainbow of vibrant colors.

Using machine learning, the research team analyzed rhodopsin protein sequences from all over the world and tracked how they evolved over time. Then, they created a type of family tree that allowed them to reconstruct rhodopsins from 2.5 to 4 billion years ago, and the conditions that they likely faced.

Their findings are detailed in a paper published in the journal Molecular Biology and Evolution.

"Life as we know it is as much an expression of the conditions on our planet as it is of life itself. We resurrected ancient DNA sequences of one molecule, and it allowed us to link to the biology and environment of the past," said University of Wisconsin-Madison astrobiologist and study lead Betul Kacar.

"It's like taking the DNA of many grandchildren to reproduce the DNA of their grandparents. Only, it's not grandparents, but tiny things that lived billions of years ago, all over the world," Schwieterman said.

Modern rhodopsins absorb blue, green, yellow and orange light, and can appear pink, purple or red by virtue of the light they are not absorbing or complementary pigments. However, according to the team's reconstructions, ancient rhodopsins were tuned to absorb mainly blue and green light.

Since ancient Earth did not yet have the benefit of an ozone layer, the research team theorizes that billions-of-years-old microbes lived many meters down in the water column to shield themselves from intense UVB radiation at the surface.

Blue and green light best penetrates water, so it is likely that the earliest rhodopsins primarily absorbed these colors. "This could be the best combination of being shielded and still being able to absorb light for energy," Schwieterman said.

After the Great Oxidation Event, more than 2 billion years ago, Earth's atmosphere began to experience a rise in the amount of oxygen. With additional oxygen and ozone in the atmosphere, rhodopsins evolved to absorb additional colors of light.

Rhodopsins today are able to absorb colors of light that chlorophyll pigments in plants cannot. Though they represent completely unrelated and independent light capture mechanisms, they absorb complementary areas of the spectrum.

"This suggests co-evolution, in that one group of organisms is exploiting light not absorbed by the other," Schwieterman said. "This could have been because rhodopsins developed first and screened out the green light, so chlorophylls later developed to absorb the rest. Or it could have happened the other way around."

Moving forward, the team is hoping to resurrect model rhodopsins in a laboratory using synthetic biology techniques.

"We engineer the ancient DNA inside modern genomes and reprogram the bugs to behave how we believe they did millions of years ago. Rhodopsin is a great candidate for laboratory time-travel studies," Kacar said.

Ultimately, the team is pleased about the possibilities for research opened up by techniques they used for this study. Since other signs of life from the deep geologic past need to be physically preserved and only some molecules are amenable to long-term preservation, there are many aspects of life's history that have not been accessible to researchers until now.

"Our study demonstrates for the first time that the behavioral histories of enzymes are amenable to evolutionary reconstruction in ways that conventional molecular biosignatures are not," Kacar said.

Read more at Science Daily

Pioneering study shows climate played crucial role in changing location of ancient coral reefs

The study, published in Nature Communications, demonstrates how changes in temperature and plate tectonics, where the positions of Earth's continents were in very different positions than today, have determined the distribution of corals through the ages.

Although climate has often been regarded as the main driver of the location of coral reefs, this had yet to be proven due to limited fossil records. Now, for the first time, a team of international scientists used habitat modelling and reconstructions of past climates to predict the distribution of suitable environments for coral reefs over the last 250 million years.

The researchers, from the University of Vigo, in Spain, the University of Bristol and University College London in the UK, then checked their predictions using fossil evidence of warm-water coral reefs. They showed that corals in the past, from 250 to about 35 million years ago, existed much further from the equator than today, due to warmer climatic conditions, and a more even distribution of shallow ocean floor.

"Our work demonstrates that warm-water coral reefs track tropical-to-subtropical climatic conditions over geological timescales. In warmer intervals, coral reefs expanded poleward. However, in colder intervals, they became constrained to tropical and subtropical latitudes," said first author Dr Lewis Jones, a computational palaeobiologist research fellow at the University of Vigo.

Suitable coral habitats became restricted to the tropical regions from about 35 million years ago, driven by global cooling and increases in shallow oceans resulting from tectonic changes of the Indo-Australian Archipelago which is recognised as a marine biodiversity hotspot.

Although this suggests warm temperatures permitted long-term poleward expansions of corals in the past, the researchers say coral reef ecosystems are unlikely to match the rapid rate of human-induced climate change.

"Current anthropogenic climate change will result in the poleward expansion of suitable habitat for coral reefs. In fact, we are already witnessing the expansion of some tropical reef corals. However, whether coral reef ecosystems -- and all the biodiversity they support -- can keep pace with the current rapid rate of anthropogenic climate change is another question," Jones said.

"Limiting global warming is fundamental to saving coral reefs, as well as the biodiversity they house. Yet, perhaps even more important is reducing the rate of global warming."

Warm-water coral reefs, also known as 'rainforests of the sea', support the greatest biodiversity of marine organisms on Earth. In today's oceans, these biologically rich ecosystems, including reef fishes, are limited to the tropics and subtropics, where temperatures of the ocean surface typically do not fall below 18ºC. A substantial proportion of this modern biodiversity is found in the Indo-Australian Archipelago. However, in the geological past, coral reef ecosystems also existed outside of the tropics and subtropics, with their fossil remains found much further from the equator.

Co-author Dr Alex Farnsworth, Senior Research Associate in meteorology and climate modelling from the University of Bristol Cabot Institute for the Environment, said: "Climate has changed significantly throughout geological time, however understanding how it has impacted coral reef ecosystems has been difficult due to a lack of quantifiable data which has significant gaps.

"Using this new combined data-model approach we can start to better understand reef ecosystems evolution and behaviour."

Previous work has failed to find a strong relationship between temperature and the distribution of coral reefs because the fossil record is incomplete and biased. For example, not all the remains of organisms or ecosystems that existed in the past are recorded in the fossil record, and it has been shown the single most important factor explaining the sampled distribution of ancient reefs is Gross Domestic Product, with the majority of known fossil reef data stemming from wealthy countries, purely because these are the regions where we have looked hardest.

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Palms at the poles: Fossil plants reveal lush southern hemisphere forests in ancient hothouse climate

For decades, paleobotanist David Greenwood has collected fossil plants from Australia -- some so well preserved it's hard to believe they're millions of years old. These fossils hold details about the ancient world in which they thrived, and Greenwood and a team of researchers including climate modeler and research David Hutchinson, from the University of New South Wales, and UConn Department of Geosciences paleobotanist Tammo Reichgelt, have begun the process of piecing together the evidence to see what more they could learn from the collection. Their findings are published in Paleoceanography & Paleoclimatology.

The fossils date back 55 to 40 million years ago, during the Eocene epoch. At that time, the world was much warmer and wetter, and these hothouse conditions meant there were palms at the North and South Pole and predominantly arid landmasses like Australia were lush and green. Reichgelt and co-authors looked for evidence of differences in precipitation and plant productivity between then and now.

Since different plants thrive under specific conditions, plant fossils can indicate what kinds of environments those plants lived in.

By focusing on the morphology and taxonomic features of 12 different floras, the researchers developed a more detailed view of what the climate and productivity was like in the ancient hothouse world of the Eocene epoch.

Reichgelt explains the morphological method relies on the fact that the leaves of angiosperms -- flowering plants -- in general have a strategy for responding to climate.

"For example, if a plant has large leaves and it is left out in the sun and doesn't get enough water, it starts to shrivel up and die because of excess evaporation," Reichgelt says. "Plants with large leaves also lose heat to its surroundings. Finding a large fossil leaf therefore means that most likely this plant was not growing in an environment that was too dry or too cold for excess evaporation or sensible heat loss to happen. These and other morphological features can be linked to the environment that we can quantify. We can compare fossils to modern floras around the world and find the closest analogy."

The second approach was taxonomic. "If you travel up a mountain, the taxonomic composition of the flora changes. Low on the mountain, there may be a deciduous forest that is dominated by maples and beeches and as you go further up the mountain, you see more spruce and fir forest," says Reichgelt. "Finding fossils of beech and maple therefore likely means a warmer climate then if we find fossils of spruce and fir." Such climatic preferences of plant groups can be used to quantitatively reconstruct the ancient climate in which a group of plants in a fossil assemblage was growing.

The results show that the Eocene climate would have been very different to Australia's modern climate. To sustain a lush green landscape, the continent required a steady supply of precipitation. Warmth means more evaporation, and more rainfall was available to move into Australia's continental interior. Higher levels of carbon dioxide in the atmosphere at the time, 1500 to 2000 parts per million, also contributed to the lushness via a process called carbon fertilization. Reichgelt explains that with the sheer abundance of CO2, plants were basically stuffing their faces.

"Southern Australia seems to have been largely forested, with primary productivity similar to seasonal forests, not unlike those here in New England today," Reichgelt says. "In the Northern Hemisphere summer today, there is a big change in the carbon cycle, because lots of carbon dioxide gets drawn down due to primary productivity in the enormous expanse of forests that exists in a large belt around 40 to 60 degrees north. In the Southern Hemisphere, no such landmass exists at those same latitudes today. But Australia during the Eocene occupied 40 degrees to 60 degrees south. And as a result, there would be a highly productive large landmass during the Southern Hemisphere summer, drawing down carbon, more so than what Australia is doing today since it is largely arid."

Hutchinson says the geological evidence suggests the climate is highly sensitive to CO2 and that this effect may be larger than what our climate models predict, "The data also suggests that polar amplification of warming was very strong, and our climate models also tend to under-represent this effect. So, if we can improve our models of the high-CO2 Eocene world, we might improve our predictions of the future."

Future projects will expand the data set beyond Australia to ask what global productivity does during a hothouse climate on a global scale.

"We have large datasets of plant fossils that have been collected around the world, so we can apply the same methods that we use here to ask what happens to global biosphere productivity," says Reichgelt.

With increasing carbon emissions, there is more research going into studying what happens in the biosphere with increased photosynthetic activity and water use efficiency in plants. Reichgelt explains that modern plants have not had the time to evolve to changing CO2 conditions. However, by looking to the past, we can glean some of that information.

Read more at Science Daily

Scientists shine new light on role of Earth's orbit in the fate of ancient ice sheets

Scientists have finally put to bed a long-standing question over the role of Earth's orbit in driving global ice age cycles.

In a new study published today in the journal Science, the team from Cardiff University has been able to pinpoint exactly how the tilting and wobbling of the Earth as it orbits around the Sun has influenced the melting of ice sheets in the Northern Hemisphere over the past 2 million years or so.

Scientists have long been aware that the waxing and waning of massive Northern Hemisphere ice sheets results from changes in the geometry of Earth's orbit around the Sun.

There are two aspects of the Earth's geometry that can influence the melting of ice sheets: obliquity and precession.

Obliquity is the angle of the Earth's tilt as it travels around the Sun and is the reason why we have different seasons.

Precession is how the Earth wobbles as it rotates, much like a slightly off-centre spinning top. The angle of this wobble means that sometimes the Northern Hemisphere is closest to the Sun and other times the Southern Hemisphere is closest, meaning that roughly every 10,000 years one hemisphere will have warmer summers compared to the other, before it switches.

Scientists have determined that over the past million years or so, the combined effects of obliquity and precession on the waxing and waning of Northern Hemisphere ice sheets has resulted, through complicated interactions within the climate system, in ice age cycles lasting approximately 100 thousand years.

However, before 1 million years ago, in a period known as the early Pleistocene, the duration of ice age cycles was controlled only by obliquity and these ice age cycles were almost exactly 41,000 years long.

For decades, scientists have been puzzled as to why precession did not play a more important part in driving ice age cycles during this period.

In their new study, the Cardiff University team reveal new evidence suggesting that precession did actually play a role during the early Pleistocene.

Their results show that more intense summers, driven by precession, have always caused Northern Hemisphere ice sheets to melt, but before 1 million years ago, these events were less devastating and did not lead to the complete collapse of ice sheets.

Lead author of the study Professor Stephen Barker, from Cardiff University's School of Earth and Environmental Sciences, said: "Early Pleistocene ice sheets in the northern hemisphere were smaller than their more recent counterparts, and limited to higher latitudes where the effects of obliquity dominate over precession. This probably explains why it has taken so long for us to find evidence of precession forcing during early Pleistocene.

"These findings are the culmination of a major effort, involving more than 12 years of painstaking work in the laboratory to process nearly 10,000 samples and the development of a range of new analytical approaches. Thanks to this we can finally put to rest a long-standing problem in paleoclimatology and ultimately contribute to a better understanding of Earth's climate system.

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Ancient ice reveals scores of gigantic volcanic eruptions

Ice cores drilled in Antarctica and Greenland have revealed gigantic volcanic eruptions during the last ice age. Sixty-nine of these were larger than any eruption in modern history. According to the University of Copenhagen physicists behind the research, these eruptions can teach us about our planet's sensitivity to climate change.

For many people, the mention of a volcanic eruption conjures up doomsday scenarios that include deafening explosions, dark ash billowing into the stratosphere and gloopy lava burying everything in its path as panicked humans run for their lives. While such an eruption could theoretically happen tomorrow, we have had to make do with disaster films and books when it comes to truly massive volcanic eruptions in the modern era.

"We haven't experienced any of history's largest volcanic eruptions. We can see that now. Eyjafjellajökull, which paralysed European air traffic in 2010, pales in comparison to the eruptions we identified further back in time. Many of these were larger than any eruption over the last 2,500 years," says Associate Professor Anders Svensson of the University of Copenhagen's Niels Bohr Institute.

By comparing ice cores drilled in Antarctica and Greenland, he and his fellow researchers managed to estimate the quantity and intensity of volcanic eruptions over the last 60,000 years. Estimates of volcanic eruptions more than 2,500 years ago have been associated with great uncertainty and a lack of precision, until now.

Sixty-nine eruptions larger than Mount Tambora

Eighty-five of the volcanic eruptions identified by the researchers were large global eruptions. Sixty-nine of these are estimated to be larger than the 1815 eruption of Mount Tambora in Indonesia -- the largest volcanic eruption in recorded human history. So much sulfuric acid was ejected into the stratosphere by the Tambora eruption that it blocked sunlight and caused global cooling in the years that followed. The eruption also caused tsunamis, drought, famine and at least 80,000 deaths.

"To reconstruct ancient volcanic eruptions, ice cores offer a few advantages over other methods. Whenever a really large eruption occurs, sulfuric acid is ejected into the upper atmosphere, which is then distributed globally -- including onto Greenland and Antarctica. We can estimate the size of an eruption by looking at the amount of sulfuric acid that has fallen," explains Anders Svensson.

In a previous study, the researchers managed to synchronize ice cores from Antarctica and Greenland -- i.e., to date the respective core layers on the same time scale. By doing so, they were able to compare sulphur residues in ice and deduce when sulfuric acid spread to both poles after globally significant eruptions.

When will it happen again?

"The new 60,000-year timeline of volcanic eruptions supplies us with better statistics than ever before. Now we can see that many more of these great eruptions occurred during the prehistoric Ice Age than in modern times. Because large eruptions are relatively rare, a long timeline is needed to know when they occur. That is what we now have," says Anders Svensson.

One may be left wondering when the next of these massive eruptions will occur. But Svensson isn't ready to make any concrete predictions:

"Three eruptions of the largest known category occurred during the entire period we studied, so-called VEI-8 eruptions (see fact box). So, we can expect more at some point, but we just don't know if that will be in a hundred or a few thousand years. Tambora sized eruptions appears to erupt once or twice every thousand years, so the wait for that may be shorter."

How was climate affected?

When powerful enough, volcanic eruptions can affect global climate, where there is typically a 5-10- year period of cooling. As such, there is great interest in mapping the major eruptions of the past -- as they can help us look into the future.

"Ice cores contain information about temperatures before and after the eruptions, which allows us to calculate the effect on climate. As large eruptions tell us a lot about how sensitive our planet is to changes in the climate system, they can be useful for climate predictions," explains Anders Svensson.

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Tilting of Earth’s crust governed the flow of ancient megafloods

As ice sheets began melting at the end of the last ice age, a series of cataclysmic floods called the Missoula megafloods scoured the landscape of eastern Washington, carving long, deep channels and towering cliffs through an area now known as the Channeled Scablands. They were among the largest known floods in Earth’s history, and geologists struggling to reconstruct them have now identified a crucial factor governing their flows.

In a study published February 14 in Proceedings of the National Academy of Sciences, researchers showed how the changing weight of the ice sheets would have caused the entire landscape to tilt, changing the course of the megafloods.

“People have been looking at high water marks and trying to reconstruct the size of these floods, but all of the estimates are based on looking at the present-day topography,” said lead author Tamara Pico, assistant professor of Earth and planetary sciences at UC Santa Cruz. “This paper shows that the ice age topography would have been different over broad scales due to the deformation of Earth’s crust by the weight of the ice sheets.”

During the height of the last ice age, vast ice sheets covered much of North America. They began to melt after about 20,000 years ago, and the Missoula megafloods occurred between 18,000 and 15,500 years ago. Pico’s team studied how the changing weight of the ice sheets during this period would have tilted the topography of eastern Washington, changing how much water would flow into different channels during the floods.

Glacial Lake Missoula formed in western Montana when a lobe of the Cordilleran ice sheet dammed the Clark Fork valley in the Idaho panhandle and melt water built up behind the dam. Eventually the water got so deep that the ice dam began to float, resulting in a glacial outburst flood. After enough water had been released, the ice dam resettled and the lake refilled. This process is thought to have been repeated dozens of times over a period of several thousand years.

Downstream from glacial Lake Missoula, the Columbia River was dammed by another ice lobe, forming glacial Lake Columbia. When Lake Missoula’s outburst floods poured into Lake Columbia, the water spilled over to the south onto the eastern Washington plateau, eroding the landscape and creating the Channeled Scablands.

During this period, the deformation of the Earth’s crust in response to the growing and shrinking of ice sheets would have changed the elevation of the topography by hundreds of meters, Pico said. Her team incorporated these changes into flood models to investigate how the tilting of the landscape would have changed the routing of the megafloods and their erosional power in different channels.

“We used flood models to predict the velocity of the water and the erosional power in each channel, and compared that to what would be needed to erode basalt, the type of rock on that landscape,” Pico said.

They focused on two major channel systems, the Cheney-Palouse and Telford-Crab Creek tracts. Their results showed that earlier floods would have eroded both tracts, but that in later floods the flow would have been concentrated in the Telford-Crab Creek system.

“As the landscape tilted, it affected both where the water overflowed out of Lake Columbia and how water flowed in the channels, but the most important effect was on the spillover into those two tracts,” Pico said. “What’s intriguing is that the topography isn’t static, so we can’t just look at the topography of today to reconstruct the past.”

The findings provide a new perspective on this fascinating landscape, she said. Steep canyons hundreds of feet deep, dry falls, and giant potholes and ripple marks are among the many remarkable features etched into the landscape by the massive floods.

“When you are there in person, it’s crazy to think about the scale of the floods needed to carve those canyons, which are now dry,” Pico said. “There are also huge dry waterfalls—it’s a very striking landscape.”

She also noted that the oral histories of Native American tribes in this region include references to massive floods. “Scientists were not the first people to look at this,” Pico said. “People may even have been there to witness these floods.”

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Nits on ancient mummies shed light on South American ancestry

Human DNA can be extracted from the 'cement' head lice used to glue their eggs to hairs thousands of years ago, scientists have found, which could provide an important new window into the past.

In a new study, scientists for the first time recovered DNA from cement on hairs taken from mummified remains that date back 1,500-2,000 years. This is possible because skin cells from the scalp become encased in the cement produced by female lice as they attach eggs, known as nits, to the hair.

Analysis of this newly-recovered ancient DNA -- which was of better quality than that recovered through other methods -- has revealed clues about pre-Columbian human migration patterns within South America. This method could allow many more unique samples to be studied from human remains where bone and tooth samples are unavailable.

The research was led by the University of Reading, working in collaboration with the National University of San Juan, Argentina; Bangor University, Wales; the Oxford University Museum of Natural History; and the University of Copenhagen, Denmark. It is published in the journal Molecular Biology and Evolution.

Dr Alejandra Perotti, Associate Professor in Invertebrate Biology at the University of Reading, who led the research, said: "Like the fictional story of mosquitos encased in amber in the film Jurassic Park, carrying the DNA of the dinosaur host, we have shown that our genetic information can be preserved by the sticky substance produced by headlice on our hair. In addition to genetics, lice biology can provide valuable clues about how people lived and died thousands of years ago.

"Demand for DNA samples from ancient human remains has grown in recent years as we seek to understand migration and diversity in ancient human populations. Headlice have accompanied humans throughout their entire existence, so this new method could open the door to a goldmine of information about our ancestors, while preserving unique specimens."

Until now, ancient DNA has preferably been extracted from dense bone from the skull or from inside teeth, as these provide the best quality samples. However, skull and teeth remains are not always available, as it can be unethical or against cultural beliefs to take samples from indigenous early remains, and due to the severe damage destructive sampling causes to the specimens which compromise future scientific analysis.

Recovering DNA from the cement delivered by lice is therefore a solution to the problem, especially as nits are commonly found on the hair and clothes of well preserved and mummified humans.

The research team extracted DNA from nit cement of specimens collected from a number of mummified remains from Argentina. The mummies were of people who 1,500-2,000 years ago reached the Andes mountains of the San Juan province, Central West Argentina. The team also studied ancient nits on human hair used in a textile from Chile and nits from a shrunken head originating from the ancient Jivaroan people of Amazonian Ecuador.

The samples used for DNA studies of nit cement were found to contain the same concentration of DNA as a tooth, double that of bone remains, and four times that recovered from blood inside far more recent lice specimens.

Dr Mikkel Winther Pedersen from the GLOBE institute at the University of Copenhagen, and first author, said: "The high amount of DNA yield from these nit cements really came as a surprise to us and it was striking to me that such small amounts could still give us all this information about who these people were, and how the lice related to other lice species but also giving us hints to possible viral diseases.

"There is a hunt out for alternative sources of ancient human DNA and nit cement might be one of those alternatives. I believe that future studies are needed before we really unravel this potential."

Read more at Science Daily

Geneticists’ new research on ancient Britain contains insights on language, ancestry, kinship, milk

New research revealing a major migration to the island of Great Britain offers fresh insights into the languages spoken at the time, the ancestry of present-day England and Wales, and even ancient habits of dairy consumption.

The findings are described in Nature by a team of more than 200 international researchers led by Harvard geneticists David Reich and Nick Patterson. Michael Isakov, a Harvard undergraduate who discovered the existence of the 3,000-year-old migration, is one of the co-first authors.

The analysis is one of two Reich-led studies of DNA data from ancient Britain that Nature published on Tuesday. Both highlight technological advances in large-scale genomics and open new windows into the lives of ancient people.

"This shows the power of large-scale genetic data in concert with archaeological and other data to get rich information about our past from a time before writing," said Reich, a professor in the Department of Human Evolutionary Biology and a professor of genetics at Harvard Medical School. "The studies are not only important for Great Britain, where we now have far more ancient DNA data than in any other region, but also because of what they show about the promise of similar studies elsewhere in the world."

The researchers analyzed the DNA of 793 newly reported individuals in the largest genome-wide study involving ancient humans. Their findings reveal a large-scale migration likely from somewhere in France to the southern part of Great Britain, or modern-day England and Wales, that eventually replaced about 50 percent of the ancestry of the island during the Late Bronze Age (1200 to 800 B.C.).

The study supports a recent theory that early Celtic languages came to Great Britain from France during the Late Bronze Age. It challenges two prominent theories: that the languages arrived hundreds of years later, in the Iron Age, or 1,500 years earlier at the dawn of the Bronze Age.

Previous research has shown that large-scale movement often accompanied language changes in pre-state societies. The Reich team argues that this untold migration event makes more sense for the spread of early Celtic languages into Britain.

"By using genetic data to document times when there were large-scale movements of people into a region, we can identify plausible times for a language shift," Reich said. "Known Celtic languages are too similar in their vocabularies to plausibly descend from a common ancestor 4,500 years ago, which is the time of the earlier pulse of large-scale migration, and very little migration occurred in the Iron Age. If you're a serious scholar, the genetic data should make you adjust your beliefs: downweighting the scenario of early Celtic language coming in the Iron Age [and early Bronze Age] and upweighting the Late Bronze Age."

As part of the genetic analysis, the researchers found that the ability to digest cow's milk dramatically increased in Britain from 1200 to 200 B.C., which is about a millennium earlier than it did in central Europe. These findings illuminate a different role for dairy consumption in Britain during this period compared with the rest of mainland Europe. More study is needed to define that role, the researchers said. Increased milk tolerance would have provided a big advantage in the former of higher survival rates among the children of people carrying this genetic adaptation.

The newly discovered ancestry change happened around 3,000 years ago, more than a millennium and a half before the Saxon period. The team was aware of a migration into England at some point during this gap because of an observation they made in research published in 2016. That study showed that contemporary English people have more DNA from early European farmers than people who lived in England about 4,000 years ago. The team set out to collect DNA from later periods to detect the shift.

The discontinuity -- a specific point in time when the percentage of farmer ancestry in English genomes changed -- was first noticed in the summer of 2019 by Isakov, an applied mathematics concentrator. He had started working as a researcher in Reich's lab the summer after his first year and was able to increase the statistical power of the group's ancestry tests. When he noticed some outliers in the data from people living 3,000 years ago, he led a closer analysis and discovered the migration.

"It's an extraordinary outcome and I'm very happy that I was able to get through it," said Isakov, who will graduate in May.

The second paper looks at kinship practices of 35 individuals who lived about 5,700 years ago and were buried in a tomb at Hazleton North in Gloucestershire, England. The researchers found a 27-person family -- three times larger than the second-largest documented ancient family -- whose kin relationships could be precisely determined by analyzing their DNA. The team created a family tree that covered five generations and found examples of polygyny, polyandry, adoption, and a key role for both patrilineal and matrilineal descent.

The lab's research illustrates the interdisciplinary collaborations that are required to tell the richest stories of the ancient past, Isakov said.

"It's sort of incredible that we have geneticists, we have statisticians, we have archaeologists, linguists, and even chemical analysis coming together. I think that the fact that we're able to like merge all these fields and have an actual insight that's culturally important is a great example of interdisciplinary science."

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DNA analysis confirms 2,000-year-old sustainable fishing practices of Tsleil-Waututh Nation

Ancient Indigenous fishing practices can be used to inform sustainable management and conservation today, according to a new study from Simon Fraser University.

Working with the Tsleil-Waututh Nation and using new palaeogenetic analytical techniques developed in SFU Archaeology's ancient DNA lab, directed by professor Dongya Yang, the results of a new collaborative study featured in Scientific Reports provides strong evidence that prior to European colonization, Coast Salish people were managing chum salmon by selectively harvesting males.

Selectively harvesting male salmon increases the overall size of the harvest, as male salmon are bigger than female salmon. It also helps ensure successful spawning as one male can mate with several females. This allows fisheries to maximize the size of their harvest without negatively impacting future returns.

"This management practice is also described in Coast Salish knowledge and, through archaeology, we were able to extend the time depth of this practice by 2,000 years," says Thomas Royle, a postdoctoral fellow working in the lab.

The research team applied the new palaeogenetic methods to archaeological salmon vertebrae to identify the sex of each sample, finding evidence to corroborate Coast Salish traditional knowledge that has been shared for centuries.

The Tsleil-Waututh ancestors worked to keep salmon populations plentiful for millennia, passing their knowledge on from one generation to the next. With current declines and collapses in many commercial fisheries, these traditional Tsleil-Waututh practices can potentially inform current management and conservation.

This research collaboration included the Tsleil-Waututh Nation (Michael George, Michelle George), SFU (Thomas C.A. Royle, Hua Zhang, Miguel Alcaide, Ryan Morin, Dongya Yang), University of British Columbia (Jesse Morin, Camilla Speller, Morgan Ritchie), and McMaster University (Aubrey Cannon) as part of a Tsleil-Waututh Nation project to establish the state of pre-contact ecosystems in Burrard Inlet.

The leadership of the Tsleil-Waututh Nation was an integral piece of the success of the collaboration and allowed cutting-edge science methods to be used to understand the traditional ecological knowledge of Tsleil-Waututh ancestors.

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A new Earth bombardment model

A team led by Southwest Research Institute has updated its asteroid bombardment model of the Earth with the latest geologic evidence of ancient, large collisions. These models have been used to understand how impacts may have affected oxygen levels in the Earth's atmosphere in the Archean eon, 2.5 to 4 billion years ago.

When large asteroids or comets struck early Earth, the energy released melted and vaporized rocky materials in the Earth's crust. The small droplets of molten rock in the impact plume would condense, solidify and fall back to Earth, creating round, globally distributed sand-size particles. Known as impact spherules, these glassy particles populated multiple thin, discrete layers in the Earth's crust, ranging in age from about 2.4 to 3.5 billion years old. These Archean spherule layers are markers of ancient collisions. "In recent years, a number of new spherule layers have been identified in drill cores and outcrops, increasing the total number of known impact events during the early Earth," said Dr. Nadja Drabon, a professor at Harvard University and a co-author of the paper.

"Current bombardment models underestimate the number of late Archean spherule layers, suggesting that the impactor flux at that time was up to 10 times higher than previously thought," said SwRI's Dr. Simone Marchi, lead author of a paper about this research in Nature Geoscience. "What's more, we find that the cumulative impactor mass delivered to the early Earth was an important 'sink' of oxygen, suggesting that early bombardment could have delayed oxidation of Earth's atmosphere."

The abundance of oxygen in Earth's atmosphere is due to a balance of production and removal processes. These new findings correspond to the geological record, which shows that oxygen levels in the atmosphere varied but stayed relatively low in the early Archean eon. Impacts by bodies larger than six miles (10 km) in diameter may have contributed to its scarcity, as limited oxygen present in the atmosphere of early Earth would have been chemically consumed by impact vapors, further reducing its abundance in the atmosphere.

"Late Archean bombardment by objects over six miles in diameter would have produced enough reactive gases to completely consume low levels of atmospheric oxygen," said Dr. Laura Schaefer, a professor at Stanford University and a co-author of the paper. "This pattern was consistent with evidence for so-called 'whiffs' of oxygen, relatively steep but transient increases in atmospheric oxygen that occurred around 2.5 billion years ago. We think that the whiffs were broken up by impacts that removed the oxygen from the atmosphere. This is consistent with large impacts recorded by spherule layers in Australia's Bee Gorge and Dales Gorge."

SwRI's results indicate that the Earth was subject to substantial numbers of large impacts throughout the late Archean era. Around 2.4 billion years ago, during the tail end of this bombardment, the Earth went through a major shift in surface chemistry triggered by the rise of atmospheric oxygen, dubbed the Great Oxidation Event (GOE), which is attributed to changes in the oxygen production-sink balance. Among the proposed scenarios are a presumed increase in oxygen production and decrease in gases capable of removing oxygen, either from volcanic sources or through their gradual loss to space.

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Ancient feces shows people in present-day Austria drank beer and ate blue cheese up to 2,700 years ago

Human feces don't usually stick around for long -- and certainly not for thousands of years. But exceptions to this general rule are found in a few places in the world, including prehistoric salt mines of the Austrian UNESCO World Heritage area Hallstatt-Dachstein/Salzkammergut. Now, researchers who've studied ancient fecal samples (or paleofeces) from these mines have uncovered some surprising evidence: the presence of two fungal species used in the production of blue cheese and beer. The findings appear in the journal Current Biology on October 13.

"Genome-wide analysis indicates that both fungi were involved in food fermentation and provide the first molecular evidence for blue cheese and beer consumption during Iron Age Europe," says Frank Maixner (@FrankMaixner) of the Eurac Research Institute for Mummy Studies in Bolzano, Italy.

"These results shed substantial new light on the life of the prehistoric salt miners in Hallstatt and allow an understanding of ancient culinary practices in general on a whole new level," adds Kerstin Kowarik (@KowarikKerstin) of the Museum of Natural History Vienna. "It is becoming increasingly clear that not only were prehistoric culinary practices sophisticated, but also that complex processed foodstuffs as well as the technique of fermentation have held a prominent role in our early food history."

Earlier studies already had shown the potential for studies of prehistoric paleofeces from salt mines to offer important insights into early human diet and health. In the new study, Maixner, Kowarik, and their colleagues added in-depth microscopic, metagenomic, and proteomic analyses -- to explore the microbes, DNA, and proteins that were present in those poop samples.

These comprehensive studies allowed them to reconstruct the diet of the people who once lived there. They also could get information about the ancient microbes that inhabited their guts. Gut microbes are collectively known as the gut microbiome and are now recognized to have an important role in human health.

Their dietary survey identified bran and glumes of different cereals as one of the most prevalent plant fragments. They report that this highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products.

In keeping with their plant-heavy diet, the ancient miners up to the Baroque period also had gut microbiome structures more like those of modern non-Westernized individuals, whose diets are also mainly composed of unprocessed food, fresh fruits and vegetables. The findings suggest a more recent shift in the Western gut microbiome as eating habits and lifestyles changed.

When the researchers extended their microbial survey to include fungi, that's when they got their biggest surprise: an abundance in one of their Iron Age samples of Penicillium roqueforti and Saccharomyces cerevisiae DNA.

"The Hallstatt miners seem to have intentionally applied food fermentation technologies with microorganisms which are still nowadays used in the food industry," Maixner says.

Read more at Science Daily