Thursday, July 30, 2020

Most of Stonehenge's large boulders share origin in west woods, Wiltshire

Origins of the sarsen megaliths at Stonehenge
Most of the hulking sandstone boulders - called sarsens - that make up the United Kingdom's famous Stonehenge monument appear to share a common origin 25 kilometers away in West Woods, Wiltshire, according to an analysis of the stones' chemical composition. The findings support the theory that the stones were brought to Stonehenge at around the same time, contradicting a previous suggestion that one large sarsen, the Heel Stone, originated in the immediate vicinity of the monument and was erected earlier than the others. The results may also help scientists identify the route the monument's ancient builders would have taken to transport the enormous rocks to their celebrated resting site. "Until recently we did not know it was possible to provenance a stone like sarsen," says David Nash, the lead author of the study. "It has been really exciting to use 21st century science to understand the Neolithic past and answer a question that archaeologists have been debating for centuries." Since technology for determining the origins of the enormous sarsens, which tower at up to 30 feet tall, weigh as much as 25 tons, and make up most of Stonehenge, did not exist until recently, most research has revolved around the monument's smaller "bluestones" - various types of rock that clearly were not gathered locally. To learn where the behemoth boulders came from, Nash and colleagues used portable x-ray fluorescence spectrometry (PXRF) to initially characterize their chemical composition, then analyzed the data statistically to determine their degree of chemical variability. Next, the researchers performed inductively coupled plasma mass spectrometry (ICP-MS) and ICP-atomic emission spectrometry (ICP-AES) of samples from a core previously drilled through one sarsen stone and a range of sarsen boulders from across southern Britain. After comparing these signatures, Nash et al. were able to point to West Woods as the sarsens' earliest home. The reason the monument's builders selected this site remains a mystery, although the researchers suggest the size and quality of West Woods' stones, and the ease with which the builders could access them, may have factored into the decision.

Wednesday, July 29, 2020

Bald's Eyesalve: Medieval medicine could provide new treatment for modern day infections


Antibiotic resistance is an increasing battle for scientists to overcome, as more antimicrobials are urgently needed to treat biofilm-associated infections. However scientists from the School of Life Sciences at the University of Warwick say research into natural antimicrobials could provide candidates to fill the antibiotic discovery gap.
Bacteria can live in two ways, as individual planktonic cells or as a multicellular biofilm. Biofilm helps protect bacteria from antibiotics, making them much harder to treat, one such biofilm that is particularly hard to treat is those that infect diabetic foot ulcers.
Researchers at the University of Warwick, Dr Freya Harrison, Jessica Furner-Pardoe, and Dr Blessing Anonye, have looked at natural remedies for the gap in the antibiotic market, and in the paper, 'Anti-biofilm efficacy of a medieval treatment for bacterial infection requires the combination of multiple ingredients' published in the journal Scientific Reports today the 28 July, researchers say medieval methods using natural antimicrobials from every day ingredients could help find new answers.
The Ancientbiotics research team was established in 2015 and is an interdisciplinary group of researchers including microbiologists, chemists, pharmacists, data analysts and medievalists at Warwick, Nottingham and in the United States.
Building on previous research done by the University of Nottingham on using medieval remedies to treat MRSA, the researchers from the School of Life Sciences at University of Warwick reconstructed a 1,000-year-old medieval remedy containing onion, garlic, wine, and bile salts, which is known as 'Bald's eyesalve', and showed it to have promising antibacterial activity. The team also showed that the mixture caused low levels of damage to human cells.
They found the Bald's eyesalve remedy was effective against a range of Gram-negative and Gram-positive wound pathogens in planktonic culture. This activity is maintained against the following pathogens grown as biofilms:
    1. Acinetobacter baumanii- commonly associated with infected wounds in combat troops returning from conflict zones.
    2. Stenotrophomonas maltophilia- commonly associated with respiratory infections in humans
    3. Staphylococcus aureus- a common cause of skin infections including abscesses, respiratory infections such as sinusitis, and food poisoning.
    4. Staphylococcus epidermidis- a common cause of infections involving indwelling foreign devices such as a catheter, surgical wound infections, and bacteremia in immunocompromised patients.
    5. Streptococcus pyogenes -- causes numerous infections in humans including pharyngitis, tonsillitis, scarlet fever, cellulitis, rheumatic fever and post-streptococcal glomerulonephritis.
All of these bacteria can be found in the biofilms that infect diabetic foot ulcers and which can be resistant to antibiotic treatment. These debilitating infections can lead to amputation to avoid the risk of the bacteria spreading to the blood to cause lethal bacteremia.
The Bald's eyesalve mixtures use of garlic, which contains allicin, can explain activity against planktonic cultures, however garlic alone has no activity against biofilms, and therefore the anti-biofilm activity of Bald's eyesalve cannot be attributed to a single ingredient and requires the combination of all ingredients to achieve full activity.
Dr Freya Harrison, from the School of Life Sciences at the University of Warwick comments:
"We have shown that a medieval remedy made from onion, garlic, wine, and bile can kill a range of problematic bacteria grown both planktonically and as biofilms. Because the mixture did not cause much damage to human cells in the lab, or to mice, we could potentially develop a safe and effective antibacterial treatment from the remedy.
"Most antibiotics that we use today are derived from natural compounds, but our work highlights the need to explore not only single compounds but mixtures of natural products for treating biofilm infections. We think that future discovery of antibiotics from natural products could be enhanced by studying combinations of ingredients, rather than single plants or compounds. In this first instance, we think this combination could suggest new treatments for infected wounds, such as diabetic foot and leg ulcers. "
Jessica Furner-Pardoe, from the Medical School at the University of Warwick comments:
"Our work demonstrates just how important it is to use realistic models in the lab when looking for new antibiotics from plants. Although a single component is enough to kill planktonic cultures, it fails against more realistic infection models, where the full remedy succeeds."
In previous research Christina Lee, from the School of English at the University of Nottingham, had examined the Bald's Leechbook, an Old English leatherbound volume in the British Library, to see if it really works as an antibacterial remedy. The Leechbook is widely thought of as one of the earliest known medical textbooks and contains Anglo-Saxon medical advice and recipes for medicines, salves and treatments. Christina adds: "Bald's eyesalve underlines the significance of medical treatment throughout the ages. It shows that people in Early Medieval England had at least some effective remedies. The collaboration which has informed this project shows the importance of the arts in interdisciplinary research."

Tuesday, July 28, 2020

Grape pips reveal collapse of ancient economy in the grip of plague and climate change

While we all try to understand the new reality imposed by the COVID-19 pandemic, many look to the past for historical precedents such as the Spanish flu of 1918 and the Black Plague of the 14th century. The first historically attested wave of what later became known as the Black Plague (caused by the bacterium Yersinia pestis) spread throughout the Byzantine Empire and beyond, in 541 CE. Known as Justinianic Plague, after the emperor Justinian who contracted the disease but survived, it caused high mortality and had a range of socio-economic effects. Around the same time, an enormous volcanic eruption in late 535 or early 536 CE marked the beginning of the coldest decade in the last two thousand years (another volcano of similar proportions erupted in 539 CE). However, scholars disagree as to just how far-reaching and devastating the mid-6th century epidemic and climate change were. This scholarly debate is unsurprising considering that even today, leaders and policymakers around the world differ on the severity and correct response to COVID-19, not to mention climate change. One reason that hindsight is not 20/20 when it comes to ancient plagues is that ancient reports tend to exaggerate, or underrepresent, the human tolls, while archaeological evidence for the social and economic effects of plague are very hard to find.
Recently, a team of Israeli archaeologists discovered new and compelling evidence for a significant economic downturn on the fringe of the Byzantine Empire in the aftermath of a major pandemic in the mid-6th century CE. The research, published today in the Proceedings of the National Academy of Sciences (PNAS), reconstructs the rise and fall of commercial viticulture in the middle of Israel's arid Negev desert.
Daniel Fuks, a PhD student in the Martin (Szusz) Department of Land of Israel Studies and Archaeology at Bar-Ilan University, led the study as a researcher in Prof. Ehud Weiss' Archaeobotany Lab, and as a team member of the Negev Byzantine Bio-Archaeology Research Program, "Crisis on the Margins of the Byzantine Empire", headed by Prof. Guy Bar-Oz of the University of Haifa. This project seeks to discover when and why the agricultural settlement of the Negev Highlands was abandoned.
Agriculture in this arid desert was made possible through rainwater runoff farming which reached its peak in the Byzantine period, as seen at sites like Elusa, Shivta and Nessana. At Negev Highland sites today, the ruins of well-built stone structures attest to their former glory, but Bar-Oz's team, guided by field archaeologists from the Israel Antiquities Authority (IAA), Dr. Yotam Tepper and Dr. Tali Erickson-Gini, discovered even more compelling evidence about life during that period in an unexpected place: the trash. "Your trash says a lot about you. In the ancient trash mounds of the Negev, there is a record of residents' daily lives - in the form of plant remains, animal remains, ceramic sherds, and more," explains Bar-Oz. "In the 'Crisis on the Margins' project, we excavated these mounds to uncover the human activity behind the trash, what it included, when it flourished, and when it declined."
The study of seeds found in archaeological excavations is part of the field known as archaeobotany (aka paleoethnobotany). The Bar-Ilan University Archaebotany Lab in which most of this research was conducted is the only lab in Israel dedicated to the identification of ancient seeds and fruits. Prof. Ehud Weiss, the lab's head, explains that the task of archaeobotany is to "get into the pantry - or, in this case, the trash - of ancient people and study their interactions with plants. Archaeobotany reconstructs ancient economy, environment and culture, but the way there is not easy. Grain by grain must be sorted through endless sediment samples, looking for seeds, identifying them and counting each one, as it is written '...if one can count the dust of the earth, then your seed too can be counted' (Genesis 13:16)." For the present study, nearly 10,000 seeds of grape, wheat and barley were retrieved and counted from 11 trash mounds at three sites. "Identifying seed and fruit remains is a unique capability of our lab," says Weiss, "and it relies on the Israel National Reference Collection of Plant Seeds and Fruit held in our lab, and on years of experience in retrieving, processing, and analyzing plant remains from sites of all periods in Israeli archaeology."
One of the researchers' first observations was the high numbers of grape seeds in the ancient trash mounds. This fit well with previous scholars' suggestions that the Negev was involved in export-bound viticulture. Byzantine texts laud the vinum Gazetum or "Gaza wine" as a sweet white wine exported from the port of Gaza throughout the Mediterranean and beyond. This wine was generally transported in a type of amphora known as "Gaza Jars" or "Gaza Wine Jars", which are also found in sites throughout the Mediterranean. In Byzantine Negev trash mounds, these Gaza Jars appear in high quantities.
Daniel Fuks, the Bar-Ilan University PhD student, sought to determine whether there were any interesting trends in the relative frequency of grape pips in the rubbish. In a Ted-style talk hosted by Bet Avichai last year, he said, "Imagine you're an ancient farmer with a plot of land to feed your family. On most of it, you plant cereals like wheat and barley because that's how you get your bread. On a smaller part, you plant a vineyard and other crops like legumes, vegetables and fruit trees, for your family's needs.
"But one day you realize that you could sell the excellent wine you produce, for export, and earn enough cash to buy bread and a bit more. Little by little you expand your vineyard and move from subsistence farming to commercial viticulture.
"If we look at your trash and count the seeds, we'll discover a rise in the proportion of grape pips relative to cereal grains. And that's exactly what we discovered: A significant rise in the ratio of grape pips to cereal grains between the 4th century CE and the mid-6th century. Then suddenly, it declines."
Meanwhile, Fuks and Dr. Tali Erickson-Gini, an expert in ancient Negev pottery, took this to the next level. They checked whether there were similar trends in the proportion of Gaza Wine Jars to Bag-Shaped Jars, the latter being much less suited to camelback transport from the Negev Highlands to the port at Gaza. Indeed, the rise and initial decline of Gaza Jars tracked the rise and fall of the grape pips.
The researchers concluded that the commercial scale of viticulture in the Negev, as seen in the grape pip ratios, was connected to Mediterranean trade, attested to by the Gaza Jar ratios. In other words, a novel archaeological testimony to an international commercial economy from some 1,500 years ago was discovered!
Like today, this situation brought unprecedented prosperity, but also greater vulnerability to shocks. In the mid-6th century, there were a few such shocks that could explain the decline. One of them was Justinianic plague, which had a high death toll in Byzantium and other parts of the empire. In the article, the authors explain that the resulting "contracting market for Gaza products would have detrimentally impacted the Negev economy, even while trade at nearby Gaza may have continued... If the plague reached the Negev, it could also have harmed the local production capacity and supply of agricultural products in general by inducing a shortage of agricultural laborers."
A different shock of that period was a volcanic eruption of global proportions in late 535/early 536 CE, which covered the Northern Hemisphere's atmosphere with dust and caused decade-long global cooling (another eruption of similar magnitude occurred in 539 CE). This led to drought in Europe, but may have increased precipitation, possibly including high-intensity flash flooding, in the southern Levant, causing detriment to local agriculture.
The Sisyphean task of sorting and counting seeds may not appear to be the most exciting, but the research on archaeological plant finds is innovative and influential, while also demonstrating the ingenuity and insightfulness involved in ancient peoples' interactions with plants. Guy Bar-Oz, of the University of Haifa, states,: "The discovery of the rise and fall of commercial viticulture in the Byzantine Negev supports other recent evidence unearthed by the 'Crisis on the Margins' project for major agricultural and settlement expansion in the 5th to mid-6th century followed by decline. It appears that agricultural settlement in the Negev Highlands received such a blow that it was not revived until modern times. Significantly, the decline came nearly a century before the Islamic conquest of the mid-seventh century."
Two of the most likely triggers for the mid-6th century collapse - climate change and plague - reveal inherent vulnerabilities in political-economic systems, then and now. "The difference is that the Byzantines didn't see it coming," explains Fuks. "We can actually prepare ourselves for the next outbreak or the imminent consequences of climate change. The question is, will we be wise enough to do so?"

Lead white pigments on Andean drinking vessels provide new historical context

Isotope analysis suggest clues to the manufacture and distribution of qeros
(Carlisle, Pa.) - Researchers studying lead white pigments on Andean ceremonial drinking vessels known as qeros have found new similarities among these artifacts that could help museums, conservators, historians and scholars better understand the timeline and production of these culturally significant items during the colonial period (1532-1821). In a study published in the journal Heritage Science, researchers used isotope measurements of lead white pigments in the decorative patterns on 20 colonial qeros to reveal linkages among vessels that were unknown previously.
The analysis identified only three isotope signatures among the lead white pigments decorating the qeros. Two of these isotopic signatures, present on a total of eight qeros, are the same as found in lead white paints used in European artwork from the same period. This match suggests these qeros are decorated with pigments imported to the Andes from Europe. The third signature, found on 12 of the qeros, suggests that the lead white was manufactured locally in the Andes.
The analysis was carried out by Allison Curley, a former Dickinson College undergraduate who is now a graduate student in earth & environmental sciences at the University of Michigan, and her mentor, geochemist Alyson Thibodeau, assistant professor of earth sciences at Dickinson, along with a team of researchers from the Smithsonian National Museum of the American Indian; the Metropolitan Museum of Art; the UCLA/Getty Program in Conservation of Archaeological and Ethnographic Materials; and the American Museum of Natural History.
"Little is known about the history of colonial qeros now in museum or private collections. The results could lead to a better understanding of the objects' chronology and production," explained Thibodeau. "For example, it is possible that qeros made earlier in the colonial period are decorated with European lead white, while qeros made later are decorated with lead white made from Andean ores. Further, the results strongly suggest some form of centralization in pigment acquisition, manufacture and distribution in the colonial period."
"The consistency of the data was both surprising and satisfying," said Curley, who has been collaborating with Thibodeau on this project since 2017. "It is exciting to see geochemistry provide insights into some longstanding historical and archaeological questions, and I was absolutely thrilled to present these findings to the Society for American Archaeology and to the conservators at the Smithsonian."
"It's important for those studying qeros all over the world to have a better understanding of the Andean people who made and used qeros during a time of colonial rule," said Emily Kaplan, conservator for the Smithsonian National Museum of the American Indian, which has the largest collection of qeros in the United States. Kaplan hopes the research will lead to more radiocarbon dating, which will reveal more about the chronology of qero production. "Style and iconography have been used to help establish production timelines, but there's a lot of guesswork involved," she said.
Ceremonial drinking vessels have been used for toasting rituals in the Andes for millennia. Wooden qeros made in the colonial period were typically fabricated in identical pairs to make ceremonial toasts for social, political and religious occasions. These items retain their cultural significance to this day and are recognized as a symbol of the Inka Empire. Because they provide a window into the Andean indigenous colonial experience, qeros have been studied by art historians, archaeologists and anthropologists.

Saturday, July 25, 2020

Stone tools move back the arrival of humans in America thousands of years

Stone tools move back the arrival of humans in America thousands of years
Findings of stone tools move back the first immigration of humans to America at least 15,000 years. This is revealed in a new international study from the University of Copenhagen, where researchers have analysed ancient material from a Mexican mountain cave.
The first humans arrived in America at least 30,000 years ago, approximately 15,000 before science was hitherto able to render it probable. This is the conclusion in new study published in the scientific journal, Nature.
The team behind the article consists of archaeologists and DNA experts from the University of Copenhagen and universities in Mexico, the UK, the US and Brazil, among others.
"The article in Nature is a scientific hand grenade. The fact that it moves back the time of early immigration to America significantly is guaranteed to ignite a heated debate," says Eske Willerslev, Professor and Head of Lundbeck Foundation Centre for GeoGenetics, Globe Institute at the University of Copenhagen.
Eske Willerslev and his two colleagues, Associate Professor Mikkel Winther Pedersen and Assistant Professor Martin Sikora, made up the Danish contribution to the international team of researchers.
The three scientists from UCPH have conducted the DNA analyses of ancient remains from animal and plant material found during the excavations of the Chiquihuite Cave in Northern Mexico.
1,900 stone tools
As far back as 30,000 years ago, humans had already developed techniques for producing tools. In the Mexican cave, researchers found 1,900 stone tools.
The unique feature of the Chiquihuite Cave is the "floor", which consists of six layers of detritus and dust - all in all, a ten-foot column of ancient remains - which is so compressed and stable that by using various advanced measuring methods, it has been possible to date the layers one by one, from top to bottom.
Each layer has contained deposits of stone tools such as knives, scrapers and arrowheads, which the researchers have also been able to date.
"The cave finds are extremely interesting. These archaeological finds are so far the oldest in America. And the excavated stone tools are of a type unique to America," Professor at Universidad Autónoma de Zacatecas, Mexico, Ciprian F. Ardelean, states.
Ice Cap Across North America
Until now, science has assumed that the earliest immigration to America took place approx. 15,000 years ago. At the time, a narrow opening in the ice along the northern Pacific coastline was created, which made it possible to walk from Siberia onto the American continent.
At the time, there were no other access routes to the continent, because North America was covered by a thick ice cap, which only later - approx. 13,000 years ago - melted enough to enable passage.
30,000 years ago, when the first stone tools were left in the Chiquihuite Cave, the massive ice cap had not yet covered all of North America, which means that it would have been possible to walk from Siberia and down through the American continent, Eske Willerslev explains.
"And that's how we must understand the presence of these humans in Mexico at this particular time - unfortunately though, we have no idea who they were. Because although we searched very thoroughly for human DNA in the samples we gathered during the ten days we spent at the Chiquihuite Cave, there were no human traces to be found. However, we may still be able to find some in the hundreds of earth samples we gathered, because we've not yet had time to analyse all of them."
According to Mikkel Winther Pedersen who was in charge of the DNA analyses, their finds contain DNA samples from numerous plants as well as animals. He elaborates:
"For example, we found DNA from an American black bear, a wide range of rodents, several types of bats as well as sparrow and falcon. These are all animals we would expect to find in Mexico at the time. Simultaneously, we were able to ascertain

Neandertals may have had a lower threshold for pain

People who inherited a special ion channel from Neandertals experience more pain
As several Neandertal genomes of high quality are now available researchers can identify genetic changes that were present in many or all Neandertals, investigate their physiological effects and look into their consequences when they occur in people today. Looking into one gene that carries such changes, Hugo Zeberg, Svante Pääbo and colleagues found that some people, especially from central and south America but also in Europe, have inherited a Neandertal variant of a gene that encodes an ion channel that initiates the sensation of pain.
By using data from a huge population study in the UK, the authors show that people in the UK who carry the Neandertal variant of the ion channel experience more pain. "The biggest factor for how much pain people report is their age. But carrying the Neandertal variant of the ion channel makes you experience more pain similar to if you were eight years older", says lead author Hugo Zeberg, a researcher at the Max Planck Institute for Evolutionary Anthropology and Karolinska Institutet. "The Neandertal variant of the ion channel carries three amino acid differences to the common, 'modern' variant", explains Zeberg. "While single amino acid substitutions do not affect the function of the ion channel, the full Neandertal variant carrying three amino acid substitutions leads to heightened pain sensitivity in present-day people."
On a molecular level, the Neandertal ion channel is more easily activated which may explain why people who inherited it have a lowered pain threshold. "Whether Neandertals experienced more pain is difficult to say because pain is also modulated both in the spinal cord and in the brain", says Pääbo. "But this work shows that their threshold for initiating pain impulses was lower than in most present-day humans."

Researchers find evidence of smallpox in the viking age

The fatal disease smallpox is older and more widespread than scientists so far have proved. A new study by an international team of researchers from the University of Copenhagen and the University of Cambridge shows that the Vikings also suffered from smallpox.
Through the ages, the highly infectious disease smallpox has killed hundreds of millions of people. But it is unclear exactly when the disease emerged. There has been found evidence of smallpox from individuals from the 17th century while written records suggest the disease is much older.
Now a new study shows that the disease dates 1,000 years further back in time than previously shown. Researchers from the University of Copenhagen (UCPH) and the University of Cambridge have found proof that smallpox also existed in the Viking Age. The new results have been published in the scientific journal Science.
"We have found the oldest evidence of smallpox. Moreover, it seems to have been surprisingly common as early as in the Viking Age," says Associate Professor Martin Sikora, Globe Institute, UCPH, and the University of Cambridge. He continues:
"Smallpox is the infection in the world that has killed most people. For that reason alone, it is very important and interesting to know how the disease developed. It gives us a unique opportunity to understand the viruses' evolution: How did it change and become the pathogen that we know of today."
Widespread in Northern Europe
The researchers have studied and analysed the DNA of 13 individuals from Northern Europe infected with smallpox. The samples are 1,000 years older than the previous oldest sample known to have been infected based on ancient DNA, and they thus push the timeline for smallpox further back in time.
The study also shows the disease has been more widespread than previously assumed. The general idea used to be that smallpox was not endemic to Northern Europe during that time period.
"We show that not only was it endemic in Europe, but it was actually quite widespread in Northern Europe already at the year 600. That means that the disease was almost certainly far more established at a much earlier age than previously thought," says Professor Eske Willerslev, Globe Institute, UCPH.
The researchers have also discovered that the viruses circulating during the Viking Age were distinct from their modern counterparts, and not directly ancestral to the viruses that caused the last big outbreak of smallpox in the 20th century.
"They share a common ancestor, but they also have unique features that differentiate them from the ones circulating later on in history. It turns out that the viruses we have found were some of these very, very early and different versions of the devastating pathogens known from the 20th century. It is the first time we can trace these early smallpox viruses and compare their genomes and mutations and see how the disease evolved over time," says Eske Willerslev.
Catalogue of Mutations
Even though the disease has been eradicated today, it is still very useful to know how it developed and mutated through the ages.
Smallpox is a so-called poxvirus, a large family of viruses with many different types infecting a diverse set of host species. One such example is monkeypox, which typically infects monkeys but has also been known to cause a disease similar to smallpox in humans. It is therefore useful to known how other types of poxviruses mutate and survive.
"When we know how the disease mutated through time, it gives us an opportunity to put together a catalogue of how these pathogens might mutate in the future: What mutations and combinations make such a pathogen viable and successful? If they had those mutations in the past, they can most likely get them again."
"It is one of a few examples where ancient genetic research has direct implications for present-day and future health," says Martin Sikora.
  • It is the variola virus that causes smallpox. It is a so-called poxvirus.
  • Written records of possible smallpox infections dating at least 3,000 years back.
  • The disease was declared eradicated in 1980 by WHO.
  • Smallpox virus still exists in two laboratories in the world: one in the US and one in Russia.

Thursday, July 23, 2020

Earliest humans stayed at the Americas 'oldest hotel' in Mexican cave

A cave in a remote part of Mexico was visited by humans around 30,000 years ago -- 15,000 years earlier than people were previously thought to have reached the Americas.
Painstaking excavations of Chiquihuite Cave, located in a mountainous area in northern Mexico controlled by drugs cartels, uncovered nearly 2000 stone tools from a small section of the high-altitude cave.
Archaeological analysis of the tools and DNA analysis of the sediment in the cave uncovered a new story of the colonisation of the Americas which now traces evidence of the first Americans back to 25,000-30,000 years ago.
The results, which have been published in Nature today (July 22 2020), challenge the commonly held theory that the Clovis people were the first human inhabitants of the Americas 15,000 years ago.
DNA scientist Professor Eske Willerslev, of St John's College, University of Cambridge, and director of The Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, led the study with archaeologist Dr Ciprian Ardelean, of the University of Zacatecas in Mexico.
Professor Willerslev said: "For decades people have passionately debated when the first humans entered the Americas. Chiquihuite Cave will create a lot more debate as it is the first site that dates the arrival of people to the continent to around 30,000 years ago -- 15,000 years earlier than previously thought. These early visitors didn't occupy the cave continuously, we think people spent part of the year there using it as a winter or summer shelter, or as a base to hunt during migration. This could be the Americas oldest ever hotel."
The 10-year long research project raises more questions about the early humans who lived in the Americas than it solves.
Dr Ardelean said: "We don't know who they were, where they came from or where they went. They are a complete enigma. We falsely assume that the indigenous populations in the Americas today are direct descendants from the earliest Americans, but now we do not think that is the case.
"By the time the famous Clovis population entered America, the very early Americans had disappeared thousands of years before. There could have been many failed colonisations that were lost in time and did not leave genetic traces in the population today."
Chiquihuite Cave is a high-altitude site, 2750 metres above sea level. Nearly 2000 stone tools and small tool fragments, known as flakes, were discovered. DNA analysis of the plant and animal remains from the sediment packed around the tools in the cave dates the tools and the human occupation of the site to 25,000-30,000 years ago. Human DNA was not found which adds weight to the theory that the early people didn't stay for long in the cave.
Dr Mikkel Winther Pedersen, a geneticist from the University of Copenhagen and one of the first authors of the paper, said: "We identified DNA from a wide range of animals including black bears, rodents, bats, voles and even kangaroo rats. We think these early people would probably have come back for a few months a year to exploit reoccurring natural resources available to them and then move on. Probably when herds of large mammals would have been in the area and who had little experience with humans so they would have been easy prey. The location of Chiquihuite Cave definitely rewrites what has conventionally been taught in history and archaeology and shows that we need to rethink where we look for sites of the earliest people in Americas."
The Chiquihuite Cave site is very difficult to reach and would have been a good vantage point for the early people to defend themselves from as they could look out for miles over the valley without being seen. It is in an area of Mexico that is now controlled by drugs cartels. The academics were escorted by armed police to the base of the mountain before they made their way up to the cave on foot.
Dr Pedersen said: "It was an unforgettable experience. It is a very unsafe place to travel so we were accompanied by Mexican police officers in armoured cars to the foot of the mountain. We left before sunrise to climb up to the cave so that we weren't spotted."
The visiting DNA scientists slept in the cave during their research visit and over the past 10 years Dr Ardelean has spent a number of months living in the cave to carry out the painstaking excavations.
Dr Ardelean added: "The peopling of the Americas is the last holy grail in modern archaeology. Unconventional sites need to be taken seriously and we need to go out and intentionally look for them. This site doesn't solve anything, it just shows that these early sites exist. We are dealing with a handful of humans from thousands of years ago so we cannot expect the signals to be very clear. We have literally dug deeper than anyone has done in the past."
The earliest human DNA from the Americas currently remains at 12,400 years ago, Dr Ardelean explained: "We have shown the previously long held date of human presence is not the oldest date for populating the Americas, it is the explosion date of populating the Americas."
Professor Willerslev concluded: "I will never forget being part of this research, it was an unbelievable experience. The implications of these findings are as important, if not more important, than the finding itself. This is only the start of the next chapter in the hotly debated early peopling of the Americas."

Monday, July 20, 2020

Archaeologists use tooth enamel protein to show sex of human remains

New method used in Bay Area excavation

A new method for estimating the biological sex of human remains based on reading protein sequences rather than DNA has been used to study an archaeological site in Northern California. The protein-based technique gave superior results to DNA analysis in studying 55 sets of human remains between 300 and 2,300 years old. The work is published July 17 in Scientific Reports.
The method targets amelogenin, a protein found in tooth enamel, said first author Tammy Buonasera, postdoctoral researcher working with Glendon Parker, adjunct associate professor in the Department of Environmental Toxicology at the University of California, Davis. The technique was developed in Parker's laboratory.
Buonasera, Parker, Jelmer Eerkens, professor of anthropology, and colleagues compared three methods for sex determination: the new proteomic method; DNA analysis; and osteology, or analysis of the size, shape and composition of the bones themselves. They applied these methods to remains from two ancestral Ohlone villages near Sunol, California. The site is being excavated by the Far West Anthropological Research Group of Davis in collaboration with the Muwekma Ohlone tribe.
Amelogenin is a protein found in tooth enamel, the hardest and most durable substance in the human body. The gene for amelogenin happens to be located on both the X and Y sex chromosomes, and the amelogenin-Y protein is slightly different from amelogenin-X.
The method works by retrieving a tiny amount of protein from a tooth. All proteins are made up of a chain of amino acids, so the protein is analyzed to give the amino acid sequence, which then defines the protein. Each of the 20 naturally occurring amino acids is specified by a three-letter code in DNA, so it is possible to work backward from the amino acid sequence and figure out the likely DNA code.
Superior to existing methods
The researchers were able to determine the sex of all of the remains using the new protein method and all but five using DNA methods. Results from osteology and proteomics agreed in almost all cases, although examining bones themselves was only effective for about half the skeletons.
The protein method allowed them to estimate sex for children, which is not possible from osteology. It was reliable even when the signal from DNA was weak.
"This is a more sensitive technique for older skeletons where we would expect more DNA degradation," Parker said.
Being able to determine the biological sex of human remains provides a greater window into the persona of each individual. Anthropologists are interested in determining biological sex because sex interacts with health and can have a large impact on how people form an identity and are treated within a society, Eerkens said.
"Almost every human society around the world incorporates sex and gender as a way to classify people, and these can affect your status and who you associate with in society," Eerkens said. While gender and biological sex are not the same thing, they are linked, so the ability to estimate sex gives archaeologists important insight when attempting to understand the cultural aspects of gender, which are not as readily preserved.
For example, in a society based on small villages, people often have to find mates outside their village. Depending on cultural rules, either men or women will leave the village to marry.

Neanderthals of Western Mediterranean did not become extinct because of changes in climate

Homo Neanderthaliensis did not become extinct because of changes in climate. At least, this did not happen to the several Neanderthals groups that lived in the western Mediterranean 42,000 years ago. A research group of the University of Bologna came to this conclusion after a detailed paleoclimatic reconstruction of the last ice age through the analysis of stalagmites sampled from some caves in Apulia, Italy.
The researchers focused on the Murge karst plateau in Apulia, where Neanderthals and Homo Sapiens coexisted for at least 3,000 years, from approximately 45,000 to 42,000 years ago. This study was published in Nature Ecology & Evolution. Data extracted from the stalagmites showed that climate changes that happened during that time span were not particularly significant. "Our study shows that this area of Apulia appears as a 'climate niche' during the transition from Neanderthals to Homo Sapiens" explains Andrea Columbu, researcher and first author of this study. "It doesn't seem possible that significant climate changes happened during that period, at least not impactful enough to cause the extinction of Neanderthals in Apulia and, by the same token, in similar areas of the Mediterranean".
The hypothesis that a changing climate was a factor in Neanderthals extinction (that happened, in Europe, nearly 42,000 years ago) found considerable support among the scientific community. According to this theory, during the last ice age, sharp and rapid changes in climate were a decisive factor in Neanderthals' extinction because of the increasingly cold and dry weather.
We can find confirmation of these sharp changes in the analysis of ice cores from Greenland and from other paleoclimatic archives of continental Europe. However, when it comes to some Mediterranean areas where Neanderthals had lived since 100,000 years ago, the data tell a different story. The Western Mediterranean is rich in prehistorical findings and, until now, no one ever carried out a paleoclimatic reconstruction of these Neanderthals-occupied areas.
Where to find answers about the climate past of the Western Mediterranean? The research group of the University of Bologna turned to the Murge plateau in Apulia. "Apulia is key to our understanding of anthropological movements: we know that both Neanderthals and Homo Sapiens lived there approximately 45,000 years ago", says Andrea Columbu. "Very few other areas in the world saw both species co-existing in a relatively small space. This makes the Murge plateau the perfect place to study the climate and the bio-cultural grounds of the transition from Neanderthal to Sapiens".
How is it possible to provide a climate reconstruction of such a remote period? Stalagmites have the answer. These rock formations rise from the floor of karst caves thanks to ceiling water drippings. "Stalagmites are excellent paleoclimatic and paleoenvironmental archives", explains Jo De Waele, research coordinator and professor at the University of Bologna. "Since stalagmites form through rainwater dripping, they provide unquestionable evidence of the presence or absence of rain. Moreover, they are made of calcite, which contains carbon and oxygen isotopes. The latter provide precise information about how the soil was and how much it rained during the formation period of stalagmites. We can then cross these pieces of information with radiometric dating, that provide an extremely precise reconstruction of the phases of stalagmites' formation".
The pace at which stalagmites formed is the first significant result of this study. Researchers found out that Apulian stalagmites showed a consistent pace of dripping in the last and previous ice ages. This means that no abrupt change in climate happened during the millennia under investigation. A draught would have been visible in the stalagmites.
Among all the stalagmites that were analysed, one was particularly relevant. Researchers sampled this 50-cm long stalagmite in the Pozzo Cucù cave, in the Castellana Grotte area (Bari) and they carried out 27 high-precision datings and 2,700 analyses of carbon and oxygen stable isotopes. According to dating, this stalagmite formed between 106,000 and 27,000 years ago. This stalagmite represents the longest timeline of the last ice age in the western Mediterranean and in Europe. Moreover, this stalagmite did not show any trace of abrupt changes in climate that might have caused Neanderthals' extinction.
"The analyses we carried out show little variation in rainfall between 50,000 and 27,000 years ago, the extent of this variation is not enough to cause alterations in the flora inhabiting the environment above the cave", says Jo De Waele. "Carbon isotopes show that the bio-productivity of the soil remained all in all consistent during this period that includes the 3,000 years-long coexistence between Sapiens and Neanderthals. This means that significant changes in flora and thus in climate did not happen".
The results seem to show that the dramatic changes in the climate of the last ice age had a different impact on the Mediterranean area than in continental Europe and Greenland. This may rule out the hypothesis that climate changes are responsible for Neanderthals dying out.
How do we explain their extinction after a few millennia of coexistence with Homo Sapiens? Stefano Benazzi, a palaeontologist at the University of Bologna and one of the authors of the paper, provides an answer to this question. "The results we obtained corroborate the hypothesis, put forward by many scholars, that the extinction of Neanderthals had to do with technology", says Benazzi. "According to this hypothesis, the Homo Sapiens hunted using a technology that was far more advanced than Neanderthals', and this represented a primary reason to Sapiens' supremacy over Neanderthals, that eventually became extinct after 3,000 years of co-existence".
The study was published in Nature Ecology & Evolution with the title "Speleothem record attests to stable environmental conditions during Neanderthal- modern human turnover in southern Italy". Representing the University of Bologna, we have Andrea Columbu, Veronica Chiarini and Jo De Waele from the Department of Biological, Geological and Environmental Sciences, and Stefano Benazzi from the Department of Cultural Heritage.