Thursday, November 29, 2018

Stone tools linked to ancient human ancestors in Arabia have surprisingly recent date

Stone handaxes, similar to those made by early humans as much as 1.5 million years ago, have been dated for the first time in the Arabian Peninsula, to less than 190,000 years old, where their production may have endured until the arrival of Homo sapiens.

Max Planck Institute for the Science of Human History
IMAGE: These are handaxes from the site of Saffaqah, Saudi Arabia. view more 
Credit: Palaeodeserts (Ian R. Cartwright)
Beginning more than 1.5 million years ago, early humans made stone handaxes in a style known as the Acheulean - the longest lasting tool-making tradition in prehistory. New research led by the Max Planck Institute for the Science of Human History and the Saudi Commission for Tourism and National Heritage has documented an Acheulean presence in the Arabian Peninsula dating to less than 190,000 years ago, revealing that the Arabian Acheulean ended just before or at the same time as the earliest Homo sapiens dispersals into the region.

Much attention has been given to understanding the spread of our own species, Homo sapiens, first within Africa and then beyond. However, less attention has been given to where diverse groups of close evolutionary cousins lived in Eurasia immediately prior to the arrival of Homo sapiens. Understanding this is critical because the spatial and temporal characteristics of such groups reveal the human and cultural landscape first encountered by our species on leaving Africa.

The youngest Acheulean site in Southwest Asia
In a paper published in Scientific Reports, an international team of researchers led by the Max Planck Institute for the Science of Human History and the Saudi Commission for Tourism and National Heritage reports the first ever dates obtained from an Acheulean site in Arabia, the site of Saffaqah, situated in Central Saudi Arabia. Saffaqah is the first stratified Acheulean site to be reported in the Arabian Peninsula and the dates reveal that early humans occupied the site until at least 190,000 years ago. These dates are surprisingly recent for a region known to feature among the oldest examples of such technology outside Africa. For example, dates from the Levant document an ancient Acheulean presence from 1.5 million years ago. Conversely the site of Saffaqah features the youngest Acheulean tools yet found in southwest Asia.

Over 500 stone tools, including handaxes and other artefacts known as cleavers, were recovered from the occupation levels. Some of the stone flakes used to make handaxes were in such fresh condition that they were recovered still resting on the stone nodules from which they had been detached. These and other artefacts show that the early humans responsible for making them were manufacturing stone tools at this site.

"It is not surprising that early humans came here to make stone tools," says Dr. Eleanor Scerri of the Max Planck Institute for the Science of Human History, the lead author of the study. "The site is located on a prominent andesite dyke that rises above the surrounding plain. The spot was both a source of raw material as well as a prime location to survey a landscape that, back then, sat between two major river systems."

This choice location also seems to have continued to be attractive to early humans at an even later date than those recorded by the researchers in this study. Layers containing identical stone handaxes are also found above the dense occupation layers that were dated, raising the possibility that Saffaqah is among the youngest Acheulean sites documented anywhere.

Hominins living at the edge
The new dating results both record the late persistence of the Acheulean in the Peninsula and also show that as yet unidentified hominin populations were using networks of now extinct rivers to disperse into the heart of Arabia during a time of increased rainfall in the region. This suggests that these hominins were able to live on the margins of habitable zones and take advantage of relatively brief "greening" episodes in a generally arid area. The dispersal of these hominins into the heart of Arabia may also help to explain the surprisingly late persistence of the Acheulean, as it suggests a degree of isolation.

"These hominins were resourceful and intelligent," adds Dr. Scerri, "They dispersed across a challenging landscape using technology commonly seen as reflecting a lack of inventiveness and creativity. Instead of perceiving the Acheulean this way, we should really be struck by how flexible, versatile and successful this technology was."

Cutting edge science
To date the sediments from the site of Saffaqah, the researchers used a combination of dating techniques known as luminescence methods, including a newly developed infrared-radiofluorescence (IR-RF) dating protocol for potassium rich feldspars. The method relies on the ability of such minerals to store energy induced by natural radioactivity and to release this energy in the form of light. "The application of IR-RF dating allowed us to obtain age estimates from sediments that were previously difficult to reliably date," explains Marine Frouin of the University of Oxford, one of the researchers involved in the dating program.

These discoveries and methods are already leading to new research. "One of the biggest questions we have is whether any of our evolutionary ancestors and close cousins met up with Homo sapiens, and if this could have happened somewhere in Saudi Arabia. Future field work will be dedicated to understanding possible cultural and biological exchanges at this critical time period," says Professor Michael Petraglia of the Max Planck Institute for the Science of Human History, the director of the project which led to the discoveries at Saffaqah.

Chipped stones and cut bones show early hominin presence in North Africa

Ancient stone tools and cut-marked animal bones discovered in Algeria suggest that modern humans' ancestors called northern Africa home much earlier than archaeologists once thought, a new study reports. The data indicates a rapid dispersal of stone tools out of East Africa and into other regions of the continent - or, alternatively, a multiple origin scenario of early hominin stone tool manufacture and use in both East and North Africa. East Africa is widely considered to be the birthplace of stone tool use by our ancient hominin ancestors - the earliest examples of which date as far back as about 2.6 million years ago.

Similar examples of stone tool manufacture and use have been identified in North Africa, dating to nearly 1.8 million years old and generally considered to be the oldest archaeological materials in all the region. In this report, however, Mohamed Sahnouni and colleagues present new archaeological evidence - Oldowan stone artifacts and fossilized butchered bones, nearly a half-million years older than those previously known.

Sahnouni et al. uncovered the artifacts at the site of Ain Boucherit, located in the High Plateaus of eastern Algeria, from two distinct strata estimated to be about 1.9 and 2.4 million years-old. The assemblages contained stone tool manufacturing lithic debris similar to that recovered from the earliest sites in East Africa.

Additionally, fossil bones, many showing the hallmark V-shaped gouges and microscopic chipping that suggest butchery and marrow extraction by stone, were also found. According to the authors, the new findings make Ain Boucherit the oldest site in northern Africa with in situ evidence of hominin meat use with associated stone tools and they suggest that other similarly early sites could be found outside of the Eastern Africa Rift.

New archaeological site revises human habitation timeline on Tibetan plateau

IMAGE: Stone artifacts on the surface view more 
Credit: IVPP
Human ancestors first set foot on the interior of the Qinghai-Tibetan Plateau around 30,000-40,000 years ago, according to new research by scientists from the Chinese Academy of Sciences (CAS). This new finding moves back the earliest data of habitation in the interior by 20,000 years or more.
The research team was led by Dr. ZHANG Xiaoling and Prof. GAO Xing from the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of CAS. Their study, published in Science, was based on investigations of Nwya Devu, the oldest and highest early Stone Age (Paleolithic) archaeological site known anywhere in the world.

This archaeological achievement is a major breakthrough in our understanding of the human occupation and evolution of the Qinghai-Tibetan Plateau as well as larger-scale prehistoric human migration and exchanges. It caps 60 years of effort trying to find evidence of the earliest human habitation on the plateau.

The high altitude, atmospheric hypoxia, cold year-round temperatures and low rainfall of the plateau creates an extremely challenging environment for human habitation. Archaeological evidence indicates it was one of the last habitats colonized by Homo sapiens. Today, the Qinghai-Tibetan Plateau is the third least-populous spot on the planet.

Before now, no concrete evidence existed of people inhabiting the interior of the plateau before the Holocene geological epoch (4,200-11,700 years ago). In addition, only a few reliably dated Pleistocene (11,700-2.58 million years ago) archaeological sites had been discovered around the plateau's margins.

The Nwya Devu Paleolithic site discovered by this team confirms that human ancestors set foot on the Qinghai-Tibet Plateau at elevations approaching 5,000 meters above sea level around 30,000-40,000 years ago. It is the first Paleolithic archaeological site discovered in Tibet that preserves intact stratigraphy allowing age-dating of the site's antiquity. Nwya Devu is located in the Changthang region of northern Tibet, about 300 km northwest of Lhasa, the capital of Tibet Autonomous Region, at about 4,600 meters above sea level.

The site comprises an extensive, dense surface distribution of stone artifacts and a buried continuous record of human occupation. It is the earliest Paleolithic site known on the Qinghai-Tibetan Plateau and the highest yet discovered anywhere in the world. Before this discovery, the earliest archaeological record of high-altitude human activity was from the Andean Altiplano, at about 4,480 meters above sea level, showing human habitation about 12,000 years ago.

This discovery deepens considerably the history of human occupation of the Qinghai-Tibetan Plateau and the antiquity of human high-altitude (>4,000 masl) adaptations.

The Late Pleistocene (about 12-000-125,000 years ago) was a crucial period for human evolution. During that time, the behavior and cognitive ability of ancient humans developed rapidly and the ability to adapt to a broader range of environments similarly increased. The prehistoric cultural artifacts from Nwya Devu provide important archaeological evidence of the survival strategies of early anatomically and behaviorally modern people to what is arguably the most rigorous terrestrial environment on earth. It also allows analysis of Paleolithic exchange and interactions between East and West suggesting possible migration routes.

The paper was vetted by three reviewers during the evaluation process, with one concluding it is " . . . quite original and very exciting, and will be of utmost interest to the readers of Science and researchers studying the origin and dispersal of modern humans and high altitude colonization. The results have profound implications for the understanding of the timing and dynamics of human settlement of the Tibetan Plateau."

Neanderthal populations from different Caucasus regions had strong social connections

IMAGE: A - obsidian in rocks formed during the eruption; B, C - obsidian boulders ( "bombs "), differing in color and shape. view more 
Credit: Ekaterina V. Doronicheva et al. / Journal of Archaeological Science: Reports 2018
Research group from Russia and the United States analyzed samples of obsidian volcanic glass in Kabardino-Balkaria. It turned out that more than 70 thousand years ago, Neanderthals transferred this mineral to distances up to 250 kilometers and used it to manufacture tools. These findings help to understand how populations from different regions communicated in antiquity. The study was supported by the Russian Science Foundation and is published in the Journal of Archaeological Science: Reports.

When volcanoes erupted, the ejected lava hardens formed a mixture of various minerals, including obsidian. In the Stone Age, the ancient people used this material extensively to create tools. In fact, we use it even now: in surgery, for the manufacture of dark glass and jewelry. The elemental composition of obsidian is unique not only for each volcano, but also for each eruption. This makes it possible to determine precisely the specific archaeological site, where particular obsidian sample originated from.

According to earlier studies, in the Paleolithic in Central Europe and the Caucasus, obsidians were actively transferred from one settlement to another, and over time the distance of its transportation increased from 100 to more than 700 kilometers.

Scientists from the non-profit organization "Laboratory of Prehistory" analyzed the elemental composition of obsidian samples from various Neanderthals ites of the Central and North-Western Caucasus, which were found during several expeditions. The obsidian composition turned out to be almost identical for many tools, which indicates their common origin. New data also indicates that obsidian was transported over more than 250 kilometers from sources in the Central Caucasus to the North-West Caucasus during the Middle Paleolithic. At the same time, new studies show that the Central Caucasus populations cultural tradition differed from the Neanderthals of the North-West Caucasus. So archaeologists have yet to figure out how the interaction between these different Neanderthals groups was build in this period.

Scientists also found that in the Upper Paleolithic, people transported obsidians from the Elbrus region and the South Caucasus to the Mezmay cave, which is located in the North-West Caucasus. The length of migration was 250 and 450 kilometers respectively. The researchers suggest that in the Upper Paleolithic there was already a developed social network between groups of people from different regions.

"The study of cultural areas, the impact of innovations and mechanisms for the dissemination of new technologies is one of the most important tasks of modern research. Our work reliably shows the existence of connections of the population of different regions in antiquity. These results can be widely used in university lectures, as well as in modern textbooks for middle and high school. Also, the results of recent studies can be used in the design of expositions of museums and thematic exhibitions," summarizes Ekaterina Doronicheva, one of the authors of the work, Ph.D., research associate of the "Laboratory of Prehistory".

Wednesday, November 28, 2018

First ancient DNA from mainland Finland reveals origins of Siberian ancestry in region

Researchers from the Max-Planck-Institute for the Science of Human History and the University of Helsinki have analyzed the first ancient DNA from mainland Finland. As described in Nature Communications, ancient DNA was extracted from bones and teeth from a 3,500 year-old burial on the Kola Peninsula, Russia, and a 1,500 year-old water burial in Finland. The results reveal the possible path along which ancient people from Siberia spread to Finland and Northwestern Russia.

Researchers found the earliest evidence of Siberian ancestry in Fennoscandia in a population inhabiting the Kola Peninsula, in Northwestern Russia, dating to around 4,000 years ago. This genetic ancestry then later spread to populations living in Finland. The study also found that people genetically similar to present-day Saami people inhabited areas in much more southern parts of Finland than the Saami today.

For the present study, genome-wide genetic data from 11 individuals were retrieved. Eight individuals came from the Kola Peninsula, six from a burial dated to 3,500 years ago, and two from an 18th to 19th century Saami cemetery. "We were surprised to find that the oldest samples studied here had the highest proportion of Siberian ancestry," says Stephan Schiffels, co-senior author of the study, of the Max Planck Institute for the Science of Human History.

The other three individuals analyzed for the study came from a water burial in Levänluhta, Finland. Levänluhta is one of the oldest known burials in Finland in which human bones have been preserved. The bodies were buried in what used to be a small lake or a pond, and this seems to have contributed to exceptionally good preservation of the remains.

Siberian ancestry persists today

The study compared the ancient individuals not only to each other, but also to modern populations, including Saami, Finnish and other Uralic language speakers. Among modern European populations, the Saami have the largest proportion of this ancient Siberian ancestry. Worldwide, the Nganasan people, from north Siberia, have the largest proportion of ancient Siberian ancestry.

"Our results show that there was a strong genetic connection between ancient Finnish and ancient Siberian populations," says Thiseas Lamnidis, co-first author of the study, "suggesting that ancient populations from Siberia may have also shared a subsistence strategy, languages and/or cultural behaviours with Bronze Age and Iron Age Finns, despite the large geographical distance." Ancient Finnish populations possibly lived a mobile, nomadic life, trading and moving over a large range, with far-reaching contacts to other populations.

People found in Levänluhta, Finland, most resemble modern-day Saami

The researchers found that the population in Levänluhta was more closely related to modern-day Saami people than to the non-Saami Finnish population today.

"People closely related to the Saami inhabited much more southern regions of Finland than the Saami do today," explains Kerttu Majander, co-first author, of the University of Helsinki and the Max Planck Institute for the Science of Human History. Interestingly, a recent linguistic study suggested that the place names around Levänluhta trace back to Saami languages.

"This is the first exploration of ancient DNA from Finland and the results are very interesting," states Schiffels. "However more ancient DNA studies from the area will be necessary to better understand whether the patterns we've seen are representative of Finland as a whole."

The study was conducted as a collaboration between the SUGRIGE-project (Universities of Helsinki and Turku), and the Max Planck Institute for the Science of Human History. The archaeological materials and expertise were provided by the Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) and the Levänluhta-project with the Finnish Heritage Agency.

As far back as 40,000 years ago, humans kept track of time using relatively sophisticated knowledge of the star,

Some of the world's oldest cave paintings have revealed how ancient people had relatively advanced knowledge of astronomy. Animal symbols represent star constellations in the night sky, and are used to mark dates and events such as comet strikes, analysis from the University of Edinburgh suggests.
Credit: Alistair Coombs
Some of the world's oldest cave paintings have revealed how ancient people had relatively advanced knowledge of astronomy.

The artworks, at sites across Europe, are not simply depictions of wild animals, as was previously thought. Instead, the animal symbols represent star constellations in the night sky, and are used to represent dates and mark events such as comet strikes, analysis suggests.

They reveal that, perhaps as far back as 40,000 years ago, humans kept track of time using knowledge of how the position of the stars slowly changes over thousands of years.

The findings suggest that ancient people understood an effect caused by the gradual shift of Earth's rotational axis. Discovery of this phenomenon, called precession of the equinoxes, was previously credited to the ancient Greeks.

Around the time that Neanderthals became extinct, and perhaps before humankind settled in Western Europe, people could define dates to within 250 years, the study shows.

The findings indicate that the astronomical insights of ancient people were far greater than previously believed. Their knowledge may have aided navigation of the open seas, with implications for our understanding of prehistoric human migration.

Researchers from the Universities of Edinburgh and Kent studied details of Palaeolithic and Neolithic art featuring animal symbols at sites in Turkey, Spain, France and Germany.

They found all the sites used the same method of date-keeping based on sophisticated astronomy, even though the art was separated in time by tens of thousands of years.

Researchers clarified earlier findings from a study of stone carvings at one of these sites -- Gobekli Tepe in modern-day Turkey -- which is interpreted as a memorial to a devastating comet strike around 11,000 BC. This strike was thought to have initiated a mini ice-age known as the Younger Dryas period.

They also decoded what is probably the best known ancient artwork -- the Lascaux Shaft Scene in France. The work, which features a dying man and several animals, may commemorate another comet strike around 15,200 BC, researchers suggest.

The team confirmed their findings by comparing the age of many examples of cave art -- known from chemically dating the paints used -- with the positions of stars in ancient times as predicted by sophisticated software.

The world's oldest sculpture, the Lion-Man of Hohlenstein-Stadel Cave, from 38,000 BC, was also found to conform to this ancient time-keeping system.

This study was published in Athens Journal of History.

Dr Martin Sweatman, of the University of Edinburgh's School of Engineering, who led the study, said: "Early cave art shows that people had advanced knowledge of the night sky within the last ice age. Intellectually, they were hardly any different to us today.

"These findings support a theory of multiple comet impacts over the course of human development, and will probably revolutionise how prehistoric populations are seen."

Monday, November 19, 2018

The 'Swiss Army knife of prehistoric tools' found in Asia

IMAGE: These artifacts found in China are among the nearly four dozen that reflect the Levallois technique of toolmaking. In a paper published Nov. 19 in Nature, researchers date these artifacts... view more 
Credit: Marwick et al.
New analysis of artifacts found at a South China archaeological site shows that sophisticated tool technology emerged in East Asia earlier than previously thought.

A study by an international team of researchers, including from the University of Washington, determines that carved stone tools, also known as Levallois cores, were used in Asia 80,000 to 170,000 years ago. Developed in Africa and Western Europe as far back as 300,000 years ago, the cores are a sign of more-advanced toolmaking -- the "multi-tool" of the prehistoric world -- but, until now, were not believed to have emerged in East Asia until 30,000 to 40,000 years ago.

With the find -- and absent human fossils linking the tools to migrating populations -- researchers believe people in Asia developed the technology independently, evidence of similar sets of skills evolving throughout different parts of the ancient world.

The study is published online Nov. 19 in Nature.

"It used to be thought that Levallois cores came to China relatively recently with modern humans," said Ben Marwick, UW associate professor of anthropology and one of the paper's corresponding authors. "Our work reveals the complexity and adaptability of people there that is equivalent to elsewhere in the world. It shows the diversity of the human experience."

Levallois-shaped cores -- the "Swiss Army knife of prehistoric tools," Marwick said -- were efficient and durable, indispensable to a hunter-gatherer society in which a broken spear point could mean certain death at the claws or jaws of a predator. The cores were named for the Levallois-Perret suburb of Paris, where stone flakes were found in the 1800s.

Featuring a distinctive faceted surface, created through a sequence of steps, Levallois flakes were versatile "blanks," used to spear, slice, scrape or dig. The knapping process represents a more sophisticated approach to tool manufacturing than the simpler, oval-shaped stones of earlier periods.

The Levallois artifacts examined in this study were excavated from Guanyindong Cave in Guizhou Province in the 1960s and 1970s. Previous research using uranium-series dating estimated a wide age range of the archaeological site -- between 50,000 and 240,000 years old -- but that earlier technique focused on fossils found away from the stone artifacts, Marwick said. Analyzing the sediments surrounding the artifacts provides more specific clues as to when the artifacts would have been in use.

Marwick and other members of the team, from universities in China and Australia, used optically stimulated luminescence (OSL) to date the artifacts. OSL can establish age by determining when a sediment sample, down to a grain of sand, was last exposed to sunlight -- and thus, how long an artifact may have been buried in layers of sediment.

"Dating for this site was challenging because it had been excavated 40 years ago, and the sediment profile was exposed to air and without protection. So trees, plants, animals, insects could disturb the stratigraphy, which may affect the dating results if conventional methods were used for dating," said Bo Li , an associate professor of archaeology at the University of Wollongong in Australia and one of the paper's corresponding authors. "To solve this problem we used a new single-grain dating technique recently developed in our OSL lab at the University of Wollongong to date individual mineral grains in the sediment. Luckily we found residual sediment left over by the previous excavations, so that allowed us to take samples for dating."

The researchers analyzed more than 2,200 artifacts found at Guanyindong Cave, narrowing down the number of Levallois-style stone cores and flakes to 45. Among those believed to be in the older age range, about 130,000 to 180,000 years old, the team also was able to identify the environment in which the tools were used: an open woodland on a rocky landscape, in "a reduced rainforest area compared to today," the authors note.

In Africa and Europe these kinds of stone tools are often found at archaeological sites starting from 300,000 and 200,000 years ago. They are known as Mode III technology, part of a broad evolutionary sequence that was preceded by hand-axe technology (Mode II) and followed by blade tool technology (Mode IV).

Archaeologists thought that Mode IV technologies arrived in China by migration from the West, but these new finds suggest they could have been locally invented. At the time people were making tools in Guanyindong Cave, the Denisovans -- ancestors to Homo sapiens and relative contemporaries to Neandertals elsewhere in the world -- roamed East Asia. But while hundreds of fossils of archaic humans and related artifacts, dating as far back as more than 3 million years ago, have been found in Africa and Europe, the archaeological record in East Asia is sparser.

That's partly why a stereotype exists, that ancient peoples in the region were behind in terms of technological development, Marwick said.

"Our work shows that ancient people there were just as capable of innovation as anywhere else. Technological innovations in East Asia can be homegrown, and don't always walk in from the West," he said.

The independent emergence of the Levallois technique at different times and places in the world is not unique in terms of prehistoric innovations. Pyramid construction, for one, appeared in at least three separate societies: the Egyptians, the Aztecs and the Mayans. Boatbuilding began specific to geography and reliant on a community's available materials. And writing, of course, developed in various forms with distinct alphabets and characters.

In the evolution of tools, Levallois cores represent something of a middle stage. Subsequent manufacturing processes yielded more-refined blades made of rocks and minerals that were more resistant to flaking, and composites that, for example, combined a spear point with blades along the edge. The appearance of blades later in time indicates a further increase in the complexity and the number of steps required to make the tools.

"The appearance of the Levallois strategy represents a big increase in the complexity of technology because there are so many steps that have to work in order to get the final product, compared to previous technologies," Marwick said.

Thursday, November 15, 2018

New virtual reconstruction of a Neanderthal thorax suggests another breathing mechanism

The results show significant morphological differences pointing to a respiratory mechanism that was different compared with that of modern humans
University of the Basque Country
IMAGE: This is an image of the reconstruction of the thorax of Kebara 2. Scale = 5 cm. view more 
Credit: A. Gómez-Olivencia, A. Barash and E. Been
Neanderthals were hunter-gatherers who inhabited western Eurasia for more than 200 thousand years during glacial as well as interglacial periods until they became extinct around 40 thousand years ago. While some of the anatomical regions of these extinct humans are well known, others, such as the vertebral column and the ribs, are less well known because these elements are more fragile and not well preserved in the fossil record. In 1983 a partial Neanderthal skeleton (known officially as Kebara 2, and nicknamed "Moshe") belonging to a young male Neanderthal individual who died some 60,000 years ago was found in the Kebara site (Mount Carmel, Israel). While this skeleton does not preserve the cranium because some time after burial the cranium was removed, probably as a consequence of a funerary ritual. However, all the vertebrae and ribs are preserved, and so are other fragile anatomical regions, such as the pelvis or the hyoid bone (a bone in the neck to which some of the tongue muscles are attached). So it is the skeleton that preserves the most complete thorax in the fossil record.
New statistical and virtual reconstruction methods have enabled the researchers to extract new information, which has just been published in the prestigious journal Nature Communications.
For over 150 years, Neanderthal remains have been found at many sites in Europe and Western Asia (including the Middle East), and the thorax morphology of this human species has been a subject of debate since 1856, when the first ribs belonging to this human group were found. Over the past decade, virtual reconstructions have become a new tool that is increasingly being used in fossil study. This methodology is particularly useful with fragile fossils, such as the vertebra and ribs that form the thorax. Nearly two years ago, the same research team created a reconstruction of the spine of this Neanderthal individual; it displays the preserved spine of Kebara 2 showing less pronounced curves in these humans when compared with Homo sapiens. The team's paper, published in the book "Human Paleontology and Prehistory," pointed to a straighter spine than that of modern humans.
For this virtual model of the thorax, researchers used both direct observations of the Kebara 2 skeleton, currently housed at Tel Aviv University, and medical CT (computerized axial tomography) scans of the vertebrae, ribs and pelvic bones. Once all the anatomical elements had been assembled, the virtual reconstruction was done by means of 3D software specifically designed for this purpose. "This was meticulous work," said Alon Barash of Bar Ilan University in Israel. "We had to scan each vertebra and all of the rib fragments individually and then reassemble them in virtual 3D."
"In the reconstruction process, it was necessary to virtually 'cut' and realign some of the parts that displayed deformation, and mirror-image the ribs that had been best preserved in order to substitute the poorly preserved ones on the other side," said Asier Gómez-Olivencia, an Ikerbasque research fellow at the University of the Basque Country.
"The differences between the thorax of a Neanderthal and of a modern human are striking," said Daniel García-Martínez and Markus Bastir, researchers at the National Museum of Natural Sciences (MNCN-CSIC) and co-authors of the work. "The Neanderthal spine is located more inside the thorax with respect to the ribs, which provides more stability. The thorax is also wider in its lower part," added Mikel Arlegi (UPV/EHU).
"The wider lower thorax of Neanderthals and the more horizontal orientation of the ribs, as shown in its reconstruction, suggest that Neanderthals relied more on the diaphragm for breathing," said Ella Been of the Ono Academic College. "Modern humans rely on both the diaphragm and on the expansion of the rib cage. Here we can see how new technologies and methodologies in the study of fossil remains are providing new information to understand extinct species."
This new information is consistent with the recent works on the larger lung capacity of Neanderthals published by two of the co-authors of this study, Markus Bastir and Daniel García-Martínez (Virtual Anthropology Laboratory of the MNCN), in which they support the presence of greater lung capacity in the Neanderthals.).
Patricia Kramer of the University of Washington sums it all up thus: "This is the culmination of 15 years of research into the Neanderthal thorax; we hope that future genetic analyses will provide additional clues about the respiratory physiology of the Neanderthals".

Ashkenazi Jewish founder mutation identified for Leigh Syndrome

IMAGE: Chuckie Barnett at age 3 (left) and Michael Barnett at age 5. view more 
Credit: Marsha Barnett
Over 30 years ago, Marsha and Allen Barnett lost their sons to a puzzling childhood disease that relentlessly attacked their nervous systems and sapped their energy. After five-year-old Chuckie died suddenly in 1981, doctors provided a name for the disease: Leigh syndrome. Leigh syndrome is a complex disorder typically caused by dysfunctional mitochondria, the tiny batteries inside all cells that generate our energy. Two years later, the same disease killed Michael, Chuckie's older brother, when he was 10 years old.
Earlier this year, Mrs. Barnett, who lives in southeastern Pennsylvania, received a phone call from a physician she knew, Marni J. Falk, MD, at Children's Hospital of Philadelphia (CHOP), where Barnett has long supported research in mitochondrial medicine. "She asked about Chuckie's and Michael's symptoms, then told me, 'I think we found the causal gene mutation,'" she said.
Falk, the Executive Director of CHOP's Mitochondrial Medicine Frontier Program, led a research team that identified the inherited mutation in the Barnett family, a change in one nuclear gene that arose spontaneously generations ago among both parents' Ashkenazi Jewish ancestors. Scores of different genes harbor mutations that may cause Leigh syndrome, by many different possible inheritance patterns. The mutation in this family was present on both copies of the same gene in both affected brothers, and was also seen in two other children in the study with Leigh syndrome who were not related to them.
The study team, a research collaboration involving multiple centers to prove that the gene mutation definitely impaired mitochondrial function, published its findings in the October 2018 issue of Human Molecular Genetics. Falk's co-study leader was Michio Hirano, MD, of Columbia University, and the study's co-first authors were Rebecca D. Ganetzky, MD, of CHOP, and Emanuele Barca, PhD, of Columbia University.
Leigh syndrome, named after a British neuropsychologist who first described it in 1951, involves metabolic strokes deep in the brain, with a loss of skills from stressors such as fever, illness and anesthesia. It has historically had a high mortality rate in childhood or adolescence. Over 90 different genes necessary for mitochondria to function properly are now known to cause it, with disease-causing gene variants rooted in DNA, either within a cell's nucleus or in the separate mitochondrial genome.
Impaired cellular energy production in Leigh syndrome causes patients to experience progressive weakening of their muscles, heart and central nervous system. Both Chuckie and Michael eventually lost control of their eye muscles, for instance.
Falk and colleagues analyzed data from four subjects affected with Leigh syndrome who did not have a specific genetic diagnosis: the Barnett boys and two unrelated patients from Ashkenazi families now living with Leigh syndrome who are followed by the CHOP Mitochondrial Medicine Frontier Program. The team identified a common causative mutation in the nuclear gene USMG5, a gene not previously associated with any human disease. USMG5 encodes a protein component of complex V, the molecular motor within the mitochondrial energy system that directly generates ATP, each cell's chemical energy currency.
The change in USMG5 is a founder mutation, one that originated by chance, most likely centuries ago in an unidentified individual from an Ashkenazi Jewish population, possibly in Eastern Europe. The mutation causes an autosomal recessive disease, so someone can carry the mutation in one of their pair of USMG5 genes without having disease symptoms. However, if both parents are mutation carriers--as is true of Marsha and Allen--each child has a 25 percent chance of inheriting the mutation on both copies of their gene, and being affected with Leigh syndrome. The youngest Barnett son, now 40 years old, does not have Leigh syndrome.
Nearly 30 years ago Marsha and Allen Barnett established a foundation to support research in mitochondrial disease, which subsequently supported the recruitment to CHOP of mitochondrial medicine pioneer Douglas C. Wallace, PhD, where he established the Center for Mitochondrial and Epigenomic Medicine in 2010. Wallace holds the Michael and Charles Barnett Endowed Chair in Pediatric Mitochondrial Medicine and Metabolic Disease.
Insights from the current research have implications for preventive medicine and genetic counseling, says Falk. The USMG5 mutation should be added to the list of mutations tested for at the time of prenatal genetic carrier screening in prospective Ashkenazi Jewish parents. The mutation is relatively common in the Ashkenazi population, where roughly one in 175 individuals are carriers. It should also be added to the list of genes to be evaluated in children with Leigh syndrome.
"What we've learned from these four children recognized to suffer from USMG5 deficiency will enable future children diagnosed with this condition to be very carefully monitored and managed when they face stressors such as fever or anesthesia, to avoid decompensation," said Falk. Decompensation is a rapid medical deterioration that may occur when a patient's system is stressed. In the longer run, Falk and other researchers are working to realize precision medicines for mitochondrial disease. In the future, children known to have this gene disorder may be able to receive treatments targeted to their specific disease.
"This work highlights the importance to families and medicine of continuing to work to solve cases that have never before been fully understood," says Falk. "The current revolution in genomic sequencing methods, combined with highly collaborative research investigations to validate genetic leads, continues to deepen our knowledge of mitochondrial disease, and with it, precision diagnosis, counseling, management, and therapies."

Historian tells new story about England's venerated 'Domesday book'

Nearly a thousand years ago, a famous king created a famous book, later given the title "Domesday" (pronounced "doomsday").

At least that's been the common story: William the Conqueror, 20 years after his 1066 invasion of England from Normandy, ordered a massive survey of his new realm. One year later, he got a book with the results - a record of the nation's wealth and resources, everything from property to sheep to servants.

The "Great Domesday Book," as it was later named, is perhaps the most famous document in English history after the Magna Carta.

The book's origin story, however, had not been thoroughly investigated until University of Illinois history professor Carol Symes took up the task. "What had never been resolved is how this massive text was really created," Symes said, "and in this incredibly narrow timeframe."

Now, after years of research, Symes makes the case in the journal Speculum that the final "Great Domesday Book" came years and perhaps decades later than the 1087 date to which it's attributed, also the year of William's death.

It also was not the orderly bureaucratic enterprise that's often assumed, but instead "enabled hundreds of thousands of individuals and communities to air grievances and to make their own ideas of law and justice a matter of public record," Symes wrote.

"This is documentation of the trauma of conquest. We're watching people pushing back, or at least letting their voices be heard because they're fed up," she said. In one example, the text records townspeople bitterly complaining about the leveling of houses to build a castle.

"We need to rethink what has seemed to be a rather straightforward, top-down royal project, but is revealed to be the tip of a big, monstrous iceberg that involves the agency of many historical actors and often preserves their voices. This helps to tell a very different story about one of the landmark events of England - the Norman conquest and its aftermath - that is not just a story about 'the great man.'"

The universe of the "Domesday Book" is complicated, to say the least. The name is attached to two different bodies of text, "Great Domesday" and "Little Domesday" - the first covering all of the country's shires except three in the southeast, the second covering those three, but in more detail, suggesting it was an earlier draft.

There's also "Exeter Domesday," a collection of 103 booklets that appears to be an even earlier draft of survey results, mostly covering three shires in the southwest.

Curiously, London does not appear in any of these records, which likely is a sign its citizens either ignored the inquest or overwhelmed it with grievances, Symes said. The Exeter collection is just one of many "satellite" documents that have some connection with the survey or book but have received little scholarly attention, Symes said. For many who focus their research on "Great Domesday," the book has been "the sun around which everything else spins."
 Among Symes' contributions is to suggest ways that the different texts relate to each other, since that hasn't been clear. "I think I have figured out the workings behind how this book ("Great Domesday") was made," she said.

Most of Symes' research focused on the Exeter collection and another satellite document, a small fragment of parchment roll, perhaps the oldest in England, from an abbey at Burton-on-Trent in the northwest of the country. In both cases, she examined the original documents.

The Exeter documents provide numerous clues on how "Great Domesday" was assembled, but also serve as a window on the people and the process. A bishop can be seen intervening with the king's advisers when his property is not recorded. Teenage scribes make drinking plans in the marginal notes of manuscripts.

The abbey's parchment fragment, however, is key to Symes' contention that the final book came years and even decades later. She ties its contents to the comings and goings of a man who served at one time as its abbot, who had access to the survey data that went into "Domesday" and may even have been involved in the survey.

"It plugs a huge hole that we had in our evidence. It suggests that the process of creating the thing we call 'Great Domesday' actually took a lot longer than people had thought." Symes said she was attracted to this particular book as part of her interest in medieval manuscripts, especially the complex ways in which they were "mediated" - i.e., written, handled, copied, recopied, added to, edited, interpreted and heard by audiences, all in an age before the printing press. Historians need to take a text's complex mediation into account, she said, even considering the parchment on which it was written, to fully understand and not misinterpret it.

Symes also likes messiness - finding out "how the sausage gets made." She was attracted to Domesday, in part, "because it's a messy document that people pretend is not messy. It's taken to be this pristine, transparent thing when it's not."

One value in the Domesday research, she said, is in "realizing that the people of almost a thousand years ago were real people with real human emotions and needs. We're putting on a different set of glasses to look at these sources, and what we see is all those people who were written out of the record. We're getting to see and hear them again."

The "wonderful irony," Symes said, is that we can do that through one of the most famous books created in the Middle Ages, by a king.

Wednesday, November 14, 2018

Climate change likely caused migration, demise of ancient Indus Valley civilization

More than 4,000 years ago, the Harappa culture thrived in the Indus River Valley of what is now modern Pakistan and northwestern India, where they built sophisticated cities, invented sewage systems that predated ancient Rome's, and engaged in long-distance trade with settlements in Mesopotamia. Yet by 1800 BCE, this advanced culture had abandoned their cities, moving instead to smaller villages in the Himalayan foothills.

A new study from the Woods Hole Oceanographic Institution (WHOI) found evidence that climate change likely drove the Harappans to resettle far away from the floodplains of the Indus.

Beginning in roughly 2500 BCE, a shift in temperatures and weather patterns over the Indus valley caused summer monsoon rains to gradually dry up, making agriculture difficult or impossible near Harappan cities, says Liviu Giosan, a geologist at WHOI and lead author on the paper that published Nov. 13, 2018, in the journal Climate of the Past.

"Although fickle summer monsoons made agriculture difficult along the Indus, up in the foothills, moisture and rain would come more regularly," Giosan says. "As winter storms from the Mediterranean hit the Himalayas, they created rain on the Pakistan side, and fed little streams there. Compared to the floods from monsoons that the Harappans were used to seeing in the Indus, it would have been relatively little water, but at least it would have been reliable."

Evidence for this shift in seasonal rainfall--and the Harapans' switch from relying on Indus floods to rains near the Himalaya in order to water crops--is difficult to find in soil samples. That's why Giosan and his team focused on sediments from the ocean floor off Pakistan's coast. After taking core samples at several sites in the Arabian Sea, he and his group examined the shells of single-celled plankton called foraminifera (or "forams") that they found in the sediments, helping them understand which ones thrived in the summer, and which in winter.

Once he and the team identified the season based on the forams' fossil remains, they were able to then focus on deeper clues to the region's climate: paleo-DNA, fragments of ancient genetic material preserved in the sediments.

"The seafloor near the mouth of the Indus is a very low-oxygen environment, so whatever grows and dies in the water is very well preserved in the sediment," says Giosan. "You can basically get fragments of DNA of nearly anything that's lived there."

During winter monsoons, he notes, strong winds bring nutrients from the deeper ocean to the surface, feeding a surge in plant and animal life. Likewise, weaker winds other times of year provide fewer nutrients, causing slightly less productivity in the waters offshore.

"The value of this approach is that it gives you a picture of the past biodiversity that you'd miss by relying on skeletal remains or a fossil record. And because we can sequence billions of DNA molecules in parallel, it gives a very high-resolution picture of how the ecosystem changed over time," adds William Orsi, paleontologist and geobiologist at Ludwig Maximilian University of Munich, who collaborated with Giosan on the work.

Sure enough, based on evidence from the DNA, the pair found that winter monsoons seemed to become stronger--and summer monsoons weaker--towards the later years of the Harappan civilization, corresponding with the move from cities to villages.

"We don't know whether Harappan caravans moved toward the foothills in a matter of months or this massive migration took place over centuries. What we do know is that when it concluded, their urban way of life ended," Giosan says.

The rains in the foothills seem to have been enough to hold the rural Harapans over for the next millennium, but even those would eventually dry up, likely contributing to their ultimate demise.
"We can't say that they disappeared entirely due to climate--at the same time, the Indo-Aryan culture was arriving in the region with Iron Age tools and horses and carts. But it's very likely that the winter monsoon played a role," Giosan says.

The big surprise of the research, Giosan notes, is how far-flung the roots of that climate change may have been. At the time, a "new ice age" was settling in, forcing colder air down from the Arctic into the Atlantic and northern Europe. That in turn pushed storms down into the Mediterranean, leading to an upswing in winter monsoons over the Indus valley.

"It's remarkable, and there's a powerful lesson for today," he notes. "If you look at Syria and Africa, the migration out of those areas has some roots in climate change. This is just the beginning--sea level rise due to climate change can lead to huge migrations from low lying regions like Bangladesh, or from hurricane-prone regions in the southern U.S. Back then, the Harappans could cope with change by moving, but today, you'll run into all sorts of borders. Political and social convulsions can then follow."

Friday, November 9, 2018

Ancient human population histories revealed in Central and South America

UNM researchers part of discovery of ancient ancestry linking two continents
University of New Mexico
The first high quality ancient DNA data from Central and South America--49 individuals some as old as 11,000 years--has revealed a major and previously unknown exchanges between populations.
Unprecedented details about the ancestry of the people of Central and South America have been uncovered in a new study in the journal Cell by archaeologists and geneticists at The University of New Mexico, Harvard Medical School, the Howard Hughes Medical Institute, the Max Planck Institute for the Science of Human History, the University of California Santa Cruz, the Pennsylvania State University, the University of São Paulo, and other institutions in Brazil, Belize, Chile, Argentina, Peru, the European Union and the U.S.
The researchers analyzed DNA data from precisely dated skeletons found in excavations in Central and South America. Some of these people were over 10,000 years old. Previously, the only genomes that had been reported from this region and that provided sufficient quality data to analyze were less than 1,000 years old.
After obtaining official permits to excavate, the researchers conducted analysis on ancient human remains, and consulted with local governmental agencies and indigenous organizations.
By comparing ancient and modern genomes from the Americas and other parts of the globe, they were able to obtain qualitatively new insights into the early history of Central and South America.
University of New Mexico Anthropology Professor Keith Prufer and his colleagues from Pennsylvania State and Exeter University (UK) contributed the Central American component of this unprecedented study as part of an NSF and Alphawood Foundation funded project studying the earliest humans to settle in the American tropics.
Prufer led excavations in Belize where the they recovered three of the oldest skeletons from the region, all with well-preserved DNA.
This UNM project focuses on early human adaptations in remote tropical rainforests in the Americas. The data from these excavations are reshaping how researchers view Early Holocene relationships between humans living in North, Central, and South America.
Link between a Clovis culture-associated individual and the oldest Central and South Americans
"A key discovery was that a Clovis culture-associated individual from North America dating to around 12,800 years ago shares distinctive ancestry with the oldest Chilean, Brazilian and Belizean individuals," explains co-lead author Cosimo Posth of the Max Planck Institute for the Science of Human History. "This supports the hypothesis that the expansion of people who spread the Clovis culture in North America also reached Central and South America."
These individuals from Chile, Brazil and Belize date to more than 9,000 years ago. However, younger individuals and present-day people in South America do not share the Clovis culture-associated ancestry that characterizes the oldest individuals. Says co-senior author David Reich from Harvard Medical School and the Howard Hughes Medical Institute, "This is our second key discovery: we have shown that there was a continent-wide population replacement that began at least 9,000 years ago."
According to Prufer, there are many remarkable aspects to this research finding.
"For the first time, we have archaeological and genetic evidence linking some of the oldest humans in Central America to the earliest known populations to arrive in the New World, and clear indications of an early relationship between this region and South America," says Prufer. "It is also a testament to the power of interdisciplinary research involving archaeologists and geneticists and how it is revolutionizing the study of ancient humans."
The promise of ancient DNA research in the Americas
The researchers emphasize that their study gives only a glimpse of the discoveries that may come through future work. To learn about the initial movements of people into Central and South America, it would be necessary to obtain ancient DNA from individuals dating to before 11,000 years ago.
Additionally, even for the period between 11,000 and 3,000 years ago that is best covered in this study the picture is far from complete.
"We lacked ancient data from Amazonia, northern South America and the Caribbean, and thus cannot determine how individuals in these regions relate to the ones we analyzed," explains Reich. "Filling in these gaps should be a priority for future work."
"We are excited about the potential of research in this area," states co-senior author Johannes Krause of the Max Planck Institute for the Science of Human History. "With future, regionally focused studies with large sample sizes, we could realize the potential of ancient DNA to reveal how the human diversity of this region came to be the way it is today."

Experts find that stone tools connected communities

Stone tools from the Middle Stone Age in South Africa shows that different communities were connected over long time periods over vast geographical areas.
University of the Witwatersrand
IMAGE: This is an overview of the Klipdrift Complex from sea. view more 
Credit: Magnus Haaland
The tools - mainly blades and backed knives from the Howiesons Poort - were found in various layers in the Klipdrift Shelter, in the southern Cape in South Africa. They were examined by a group of lithic experts, who found distinct similarities to tools from sites in South Africa's Western Cape, over 300km away, in particular with the Diepkloof Rock Shelter site.
"While regional specificities in the tools from the various sites exist, the similarities of Klipdrift Shelter with the site of Diepkloof Rock Shelter are astonishing," says Dr Katja Douze, the corresponding author of the study that was published in PLOS ONE on November 7. Douze is a researcher at the laboratory of Archaeology and Populations in Africa at the University of Geneva, Switzerland. Douze was a post-doctoral fellow at the Center of Excellence in Palaeosciences at the Evolutionary Studies Institute, at University of the Witwatersrand (Wits), at the time of the study. She led the analysis together with Dr Anne Delagnes, Research Director at the French National Center for Research (CNRS) and director of the laboratory PACEA, at the University of Bordeaux, and with Dr Sarah Wurz, Associate professor at the School of Geography, Archaeology and Environmental Sciences, University of the Witwatersrand and also associated with the DST/NRF SARChI Chair in The Origins of Modern Human Behaviour and the SapienCE - Centre for Early Sapiens Behaviour (SFF CoE).
The team, under the leadership of Professor Christopher Henshilwood from Wits University and the University of Bergen's SapienCE Centre for Early Sapiens Behaviour, examined thousands of stone tools that were excavated from seven layers that represent a time period of between 66 000 years ago and 59 000 years ago, to establish the differences in stone tool design over time. They then also compared the stone tools to various other sites in Howiesons Poort.
"The site of Klipdfrift Shelter is one of the few containing a long archaeological sequence that provides data on cultural changes over time during the Howiesons Poort," says Douze. "This makes it perfect to study the change in culture over time."
However, what was even more exciting for the researchers was the fact that for the first time they could show closely networked interaction between distant communities through the way they designed stone tools.
"There was an almost perfect match between the tools from the Klipdrift and Diepkloof shelters," says Douze. "This shows us that there was regular interaction between these two communities."
"This is the first time that we can draw such a parallel between different sites based on robust sets of data, and show that there was mobility between the two sites. This is unique for the Middle Stone Age," says Douze.
The Middle Stone Age in Africa stretches from 350 000 years ago to 25 000 years ago and is a key period for understanding the development of the first Homo sapiens, their behavioral changes through time and their movements in-and-out of Africa.
Named after Howieson's Poort Shelter archeological site near Grahamstown in South Africa, the Howiesons Poort is a specific techno-culture within the Middle Stone Age that evolves in southern Africa after 100 000 years ago at the Diepkloof Shelter, but between 66 000 - 59 000 years at most other Howiesons Poort sites. The characteristics of the Howiesons Poort are strongly distinctive from other Middle Stone Age industries as it is characterised by the production of small blades and backed tools, used as hunting armatures as much as for cutting flesh, while other MSA industries show flake, large blade and point productions.
The tools found in the deeper layers of the Klipdrift Shelter that represent the earlier phases of the Howiesons Poort were found to be made from heat-treated silcrete, while those from later phases were made from less homogeneous rocks such as quartz and quartzite. This change happens together with changes in tool production strategies. "The changes over time seems to reflect cultural changes, rather than immediate alterations forced on the designers by changes in climate", says Douze.
"Our preconceived idea of prehistoric groups is that they just struggled to survive, but in fact they were very adaptable to environmental circumstances. There seem to be no synchrony between modification in design choices and environmental changes. However, the aridification of the area over time might have led to a very gradual change that led to the end of the Howiesons Poort."
The team also attempted to establish why and how the Howiesons Poort ended, and to see whether it came to a sudden, or gradual end.
"The decline of the Howiesons Poort at Klipdrift Shelter shows a gradual and complex pattern of changes, from which the first "symptoms" can be observed much earlier than the final abandonment of typical Howiesons Poort technology and toolkits," says Douze.
"This does not support a catastrophic scenario involving alarming demographic drops or massive population replacements. The fact that a similar pattern of gradual change has been described for at least three other southern African Howiesons Poort sites (Rose Cottage Cave, Diepkloof Rock Shelter and Klasies River main site), further ascertains convergent evolutions in cultural trajectories rather than isolated groups promptly reacting to locally determined pressures."

The new face of South American people

Study by 72 researchers from eight countries concludes that the Lagoa Santa people are descendants of Clovis culture migrants from North America; distinctly African features attributed to Luzia were wrong
Fundação de Amparo à Pesquisa do Estado de São Paulo
IMAGE: Study by 72 researchers from eight countries concludes that the Lagoa Santa people are descendants of Clovis culture migrants from North America. Distinctly African features attributed to Luzia were wrong view more 
Credit: André Strauss e Caroline Wilkinson
The history of the peopling of the Americas has just been interpreted afresh. The largest and most comprehensive study ever conducted on the basis of fossil DNA extracted from ancient human remains found on the continent has confirmed the existence of a single ancestral population for all Amerindian ethnic groups, past and present.
Over 17,000 years ago this original contingent crossed the Bering Strait from Siberia to Alaska and began peopling the New World. Fossil DNA shows an affinity between this migratory current and the populations of Siberia and northern China. Contrary to the traditional theory it had no link to Africa or Australasia.
The new study also reveals that once they had settled in North America the descendants of this ancestral migratory flow diversified into two lineages some 16,000 years ago.
The members of one lineage crossed the Isthmus of Panama and peopled South America in three distinct consecutive waves.
The first wave occurred between 15,000 and 11,000 years ago. The second took place at most 9,000 years ago. There are fossil DNA records from both migrations throughout South America. The third wave is much more recent but its influence is limited as it occurred 4,200 years ago. Its members settled in the Central Andes.
An article on the study has just been published in the journal Cell a group of 72 researchers from eight countries, affiliated with the University of São Paulo (USP) in Brazil, Harvard University in the United States, and Max Planck Institute for the Science of Human History in Germany, among others.
According to the researchers' findings, the lineage that made the north-south journey between 16,000 and 15,000 years ago belonged to the Clovis culture, named for a group of archeological sites excavated in the western US and dating from 13,500-11,000 years ago.
The Clovis culture was so named when flint spearheads were found in the 1930s at a dig in Clovis, New Mexico. Clovis sites have been identified throughout the US and in Mexico and Central America. In North America, the Clovis people hunted Pleistocene megafaunas such as giant sloth and mammoth. With the decline of the megafauna and its extinction 11,000 years ago, the Clovis culture eventually disappeared. Long before that, however, bands of hunter-gatherers had traveled south to explore new hunting grounds. They ended up settling in Central America, as evidenced by 9,400-year-old human fossil DNA found in Belize and analyzed in the new study.
At a later date, perhaps while pursuing herds of mastodons, Clovis hunter-gatherers crossed the Isthmus of Panama and spread into South America, as evidenced by genetic records from burial sites in Brazil and Chile revealed now. This genetic evidence corroborates well-known archeological finds such as the Monte Verde site in southern Chile, where humans butchered mastodons 14,800 years ago.
Among the many known Clovis sites, the only burial site associated with Clovis tools is in Montana, where the remains of a baby boy (Anzick-1) were found and dated to 12,600 years ago. DNA extracted from these bones has links to DNA from skeletons of people who lived between 10,000 and 9,000 years ago in caves near Lagoa Santa, Minas Gerais State, Brazil. In other words, the Lagoa Santa people were partial descendants of Clovis migrants from North America.
"From the genetic standpoint, the Lagoa Santa people are descendants of the first Amerindians," said archeologist André Menezes Strauss, who coordinated the Brazilian part of the study. Strauss is affiliated with the University of São Paulo's Museum of Archeology and Ethnology (MAE-USP).
"Surprisingly, the members of this first lineage of South Americans left no identifiable descendants among today's Amerindians," he said. "Some 9,000 years ago their DNA disappears completely from the fossil samples and is replaced by DNA from the first migratory wave, prior to the Clovis culture. All living Amerindians are descendants of this first wave. We don't yet know why the genetic stock of the Lagoa Santa people disappeared."
One possible reason for the disappearance of DNA from the second migration is that it was diluted in the DNA of the Amerindians who are descendants of the first wave and cannot be identified by existing methods of genetic analysis.
According to Tábita Hünemeier, a geneticist at the University of São Paulo's Bioscience Institute (IB-USP) who took part in the research, "one of the main results of the study was the identification of Luzia's people as genetically related to the Clovis culture, which dismantles the idea of two biological components and the possibility that there were two migrations to the Americas, one with African traits and the other with Asian traits".
"Luzia's people must have resulted from a migratory wave originating in Beringia," she said, referring to the now-submerged Bering land bridge that joined Siberia to Alaska during the glaciations, when sea levels were lower.
"The molecular data suggests population substitution in South America since 9,000 years ago. Luzia's people disappeared and were replaced by the Amerindians alive today, although both had a common origin in Beringia," Hünemeier said.
Brazilian contribution
The Brazilian researchers' contribution to the study was fundamental. Among the 49 individuals from which fossil DNA was taken, seven skeletons dated to between 10,100 and 9,100 years ago came from Lapa do Santo, a rock shelter in Lagoa Santa.
The seven skeletons, alongside dozens of others, were found and exhumed in successive archeological campaigns at the site, led initially by Walter Alves Neves, a physical anthropologist at IB-USP, and since 2011 by Strauss. The archeological campaigns led by Neves between 2002 and 2008 were funded by São Paulo Research Foundation - FAPESP.
Altogether the new study investigated fossil DNA from 49 individuals found at 15 archeological sites in Argentina (two sites, 11 individuals dated to between 8,900 and 6,600 years ago), Belize (one site, three individuals dated to between 9,400 and 7,300 years ago), Brazil (four sites, 15 individuals dated to between 10,100 and 1,000 years ago), Chile (three sites, five individuals dated to between 11,100 and 540 years ago) and Peru (seven sites, 15 individuals dated to between 10,100 and 730 years ago).
The Brazilian skeletons come from the archeological sites Lapa do Santo (seven individuals dated to about 9,600 years ago), Jabuticabeira II in Santa Catarina State (a sambaqui or shell midden with five individuals dated to about 2,000 years ago), as well as from two river middens in the Ribeira Valley, São Paulo State: Laranjal (two individuals dated to about 6,700 years ago), and Moraes (one individual dated to about 5,800 years ago).
Paulo Antônio Dantas de Blasis, an archeologist affiliated with MAE-USP, led the dig at Jabuticabeira II, which was also supported by FAPESP through a Thematic Project.
The digs at the river midden sites in São Paulo State were led by Levy Figuti, also an archeologist at MAE-USP, and were also supported by FAPESP.
"The Moraes skeleton (5,800 years old) and the Laranjal skeleton (6,700 years old) are among the most ancient from the South and Southeast of Brazil," Figuti said. "These locations are strategically unique because they're between the highlands of the Atlantic plateau and the coastal plain, contributing significantly to our understanding of how the Southeast of Brazil was peopled."
These skeletons were found between 2000 and 2005. From the start, they presented a complex mixture of coastal and inland cultural traits, and the results of their analysis generally varied except in the case of one skeleton diagnosed as Paleoindian (analysis of its DNA is not yet complete).
"The study that's just been published represents a major step forward in archeological research, exponentially increasing what we knew until only a few years ago about the archaeogenetics of the peopling of the Americas," Figuti said.
Hünemeier has also recently made a significant contribution to the reconstruction of human history in South America using paleogenomics.
Amerindian genetics
Not all the human remains found at some of the most ancient archeological sites in Central and South America belonged to genetic descendants of the Clovis culture. The inhabitants of several sites did not have Clovis-associated DNA.
"This shows that besides its genetic contribution the second migration wave to South America, which was Clovis-associated, may also have brought with it technological principles that would be expressed in the famous fishtail points that are found in many parts of South America," Strauss said.
How many human migrations from Asia came to the Americas at the end of the Ice Age more than 16,000 years ago was hitherto unknown. The traditional theory, formulated in the 1980s by Neves and other researchers, was that the first wave had African traits or traits similar to those of the Australian Aboriginals.
The well-known forensic facial reconstruction of Luzia was performed in accordance with this theory. Luzia is the name given to the fossil skull of a woman who lived in the Lagoa Santa region 12,500 years ago and is sometimes referred to as the "first Brazilian".
The bust of Luzia with African features was built on the basis of the skull's morphology by British anatomical artist Richard Neave in the 1990s.
"However, skull shape isn't a reliable marker of ancestrality or geographic origin. Genetics is the best basis for this type of inference," Strauss explained.
"The genetic results of the new study show categorically that there was no significant connection between the Lagoa Santa people and groups from Africa or Australia. So the hypothesis that Luzia's people derived from a migratory wave prior to the ancestors of today's Amerindians has been disproved. On the contrary, the DNA shows that Luzia's people were entirely Amerindian."
A new bust has replaced Luzia in the Brazilian scientific pantheon. Caroline Wilkinson, a forensic anthropologist at Liverpool John Moores University in the UK and a disciple of Neave, has produced a facial reconstruction of one of the individuals exhumed at Lapa do Santo. The reconstruction was based on a retrodeformed digital model of the skull.
"Accustomed as we are to the traditional facial reconstruction of Luzia with strongly African features, this new facial reconstruction reflects the physiognomy of the first inhabitants of Brazil far more accurately, displaying the generalized and indistinct features from which the great Amerindian diversity was established over thousands of years," Strauss said.
The study published in Cell, he added, also presents the first genetic data on Brazilian coastal sambaquis.
"These monumental shell mounds were built some 2,000 years ago by populous societies that lived on the coast of Brazil. Analysis of fossil DNA from shell mound burials in Santa Catarina and São Paulo shows these groups were genetically akin to the Amerindians alive today in the South of Brazil, especially the Kaingang groups," he said.
According to Strauss, DNA extraction from fossils is technically very challenging, especially if the material was found at a site with a tropical climate. For almost two decades extreme fragmentation and significant contamination prevented different research groups from successfully extracting genetic material from the bones found at Lagoa Santa.
This has now been done thanks to methodological advances developed by the Max Planck Institute. As Strauss enthusiastically explained, much more remains to be discovered.
"Construction of Brazil's first archaeogenetic laboratory is scheduled to begin in 2019, thanks to a partnership between the University of São Paulo's Museum of Archeology and Ethnology (MAE) and its Bioscience Institute (IB) with funding from FAPESP. When it's ready, it will give a new thrust to research on the peopling of South America and Brazil," Strauss said.
"To some extent, this study not only changes what we know about how the region was peopled but also changes considerably how we study human skeletal remains," Figuti said.
Human remains were first found in Lagoa Santa in 1844, when Danish naturalist Peter Wilhelm Lund (1801-1880) discovered some 30 skeletons deep in a flooded cave. Almost all these fossils are now at the Natural History Museum of Denmark in Copenhagen. A single skull has stayed in Brazil. It was donated by Lund to the Brazilian History and Geography Institute in Rio de Janeiro.
Colonization by leaps and bounds
On the same day as the Cell article was published (November 8, 2018), a paper in the journal Science also reported new findings on fossil DNA from the first migrants to the Americas. André Strauss is one of the authors.
Among the 15 ancient skeletons from which genetic material was taken, five belong to the Lund Collection in Copenhagen. They date from between 10,400 and 9,800 years ago. They are the oldest in the sample, alongside an individual from Nevada estimated to be 10,700 years old.
The sample comprised fossilized human remains from Alaska, Canada, Brazil, Chile, and Argentina. The results of its molecular analysis suggested the peopling of the Americas by the first human groups out of Alaska did not come about merely through gradual occupation of territory concomitantly with population growth.
According to the researchers responsible for the study, the molecular data suggests that the first humans to invade Alaska or neighboring Yukon, split into two groups. This happened between 17,500 and 14,600 years ago. One group colonized North and Central America, the other South America.
The peopling of the Americas ensued by leaps and bounds, as small bands of hunter-gatherers traveled far and wide to settle in new areas until they reached Tierra del Fuego in a movement lasting one or at most two millennia.
Among the 15 individuals whose DNA was analyzed, three of the Lagoa Santa five were found to have some genetic material from Australasia, as suggested by the theory proposed by Neves for the occupation of South America. The researchers are unable to explain the origin of this Australasian DNA or how it ended up in only a few of the Lagoa Santa people.
"The fact that the genomic signature of Australasia has been present for 10,400 years in Brazil but is absent in all the genomes tested to date, which are as old or older, and found farther north, is a challenge considering its presence in Lagoa Santa," they said.
Other fossils collected during the twentieth century include the Luzia skull, found in the 1970s. Almost 100 skulls excavated by Neves and Strauss in the past 15 years are now held at USP. A similar number of fossils are held at the Pontifical Catholic University of Minas Gerais (PUC-MG).
But the vast majority of these osteological and archeological treasures, belonging to perhaps more than 100 individuals, were deposited at the National Museum in Rio de Janeiro and were presumably destroyed in the fire that raged through this historic building on September 2, 2018.
The Luzia skull was on display at the National Museum alongside Neave's facial reconstruction. Scientists feared it had been lost to the fire but fortunately it was one of the first objects to be recovered from the ruins. It had broken up but survived. The fire destroyed the original facial reconstruction (of which there are several copies).

Thursday, November 8, 2018

Ancient DNA evidence reveals two unknown migrations from North to South America

IMAGE: This visual abstract depicts the findings of Posth et al., who conducted a large-scale analysis of ancient genomes from Central and South America yields insights into the peopling of the... view more 
Credit: Posth et al./Cell
An international research team has used genome-wide ancient DNA data to revise Central and South American history. Their analysis of DNA from 49 individuals spanning about 10,000 years in Belize, Brazil, the Central Andes, and southern South America has concluded that the majority of Central and South American ancestry arrived from at least three different streams of people entering from North America, all arising from one ancestral lineage of migrants who crossed the Bering Strait some time before 15,000 years ago.
The evidence, presented November 8 in the journal Cell, shows that within this one ancestral lineage, there were two previously undocumented streams of gene flow from North to South America, one of which was later displaced in a major population replacement that began at least 9,000 years ago.
"Our work multiplied the number of ancient genomes available from these areas by about 20, giving us a much more comprehensive picture of indigenous history in the Americas," says co-senior author David Reich, a geneticist at Harvard Medical School and the Howard Hughes Medical Institute. "This broader dataset reveals a common origin of North, Central, and South Americans as well as two previously unknown genetic exchanges between North and South America."
"Nearly all Central and South Americans arose from a star-like radiation of the first lineage into at least three branches," says co-lead author Cosimo Posth, an archaeogeneticist from the Max Planck Institute for the Science of Human History. "That means that nearly all the ancestry of Central and South Americans came from the same source population, albeit one that had already diversified prior to its spread into South America. With DNA evidence largely based on present-day people, those multiple gene flow events are undetectable, highlighting the power of ancient DNA data."
The genome analysis also yielded new insights on the Clovis culture-related people, who were mainly distributed across North America from about 13,000 years ago. Archaeological evidence from Clovis sites shows that the spread of Clovis artefacts did not expand throughout South America. But when the researchers used genome-sequencing technology to generate and compare genomes from a previously published ~13,000-year-old Clovis-related genome in Montana to the earliest genomes analyzed from South and Central America dating to between ~9,000 and ~11,000 years ago, they noticed significant shared ancestry. That suggested that the people who spread the Clovis culture also left a major impact much father south through people producing non-Clovis-specific stone tools.
"We weren't expecting to find a relation to people associated with the Clovis culture in South America," says co-first author Nathan Nakatsuka, a PhD student in Reich's lab at Harvard. "But it seems the expansion of the Clovis-associated lineage extended to parts of Central and South America."
The paper concludes that this Clovis-related lineage contributed substantially to a group of 9,000-10,000-year-old individuals from Lagoa Santa in Brazil, inconsistent with the hypothesis that the people from this site derived from a separate migration from Asia. The authors also detected the Clovis-related genetic affinity in an even older, almost ~11,000-year-old individual from Chile and a slightly younger, more than ~9,000-year-old individual from Belize.
Beginning around ~9,000 years ago with ancient samples in Peru, however, the authors detected an almost complete disappearance of the Clovis culture-associated ancestry in Central and South America, documenting a remarkable population replacement. The large-scale population replacement is a process that was not widely expected by archaeologists," says Reich. "This is an exciting example of how ancient DNA studies can reveal events in the past that were not confirmed and thus can stimulate new work in archaeology."
The researchers also showed that after this major population turnover, there was striking continuity compared to other parts of the world like Eurasia and Africa. "There is remarkable continuity between earlier and later skeletons with South Americans today," says Posth. "For example, modern-day Quechua and Aymara from the Central Andes can trace their ancestry back to the ancient people of the Cuncaicha site from 9,000 years ago onwards. This is a longer-standing continuity than you see in other continents."
The researchers recognize that there is much more work to do to fully flesh out the history of the Americas.
"We're very enthusiastic about the prospects for a much richer understanding of American population history, but this is still a vast region full of geographic and chronological holes," says Reich. "We'd like to collect more genetic material from earlier and later sites and from more countries, such as Colombia, Venezuela, and other parts of Brazil. We also want to examine the evolution of genetic traits over time."

History of early settlement and survival in Andean highlands revealed by ancient genomes

Adaptations to the harsh environment spare Andean highlanders from complete devastation due to European contact
University of Chicago Medical Center
IMAGE: This is the location of ancient samples near Lake Titicaca, elevation 3812 meters, in what is now Peru and Bolivia. view more 
Credit: Authors of the study
A multi-center study of the genetic remains of people who settled thousands of years ago in the Andes Mountains of South America reveals a complex picture of human adaptation from early settlement, to a split about 9,000 years ago between high and lowland populations, to the devastating exposure to European disease in the 16th-century colonial period.
Led by Anna Di Rienzo, PhD, and John Lindo, PhD, JD, from the University of Chicago; Mark Aldenderfer, PhD, from the University of California, Merced; and Ricardo Verdugo from the University of Chile, the researchers used newly available samples of DNA from seven whole genomes to study how ancient Andean people--including groups that clustered around Lake Titicaca in Peru and Bolivia, 12,000 feet above sea level--adapted to their environment over the centuries.
In the journal Science Advances, they compared their seven historical genomes to 64 modern-day genomes from a current highland Andean population, the agropastoral Aymara of Bolivia, and the lowland hunter-gatherer Huilliche-Pehuenche in coastal Chile.
The goals were (1) to date the initial migration to the Andean highlands, (2) to identify the genetic adaptations to the high-altitude environment that allowed that settlement, (3) to estimate the impact of the European contact starting in the 1530s that caused the near annihilation of many lowland communities of South America.
"We have very ancient samples from the high Andes," said Di Rienzo. "Those early settlers have the closest affinity to the people who now live in that area. This is a harsh, cold, resource-poor environment, with low oxygen levels, but people there adapted to that habitat and the agrarian lifestyle."
The study, "The Genetic prehistory of the Andean highlands 7,000 years BP through European contact," uncovered several unexpected features.
The researchers found that highland Andeans experienced much smaller than expected population declines following contact with European explorers who first came to South America in the 1530s. In the lowlands, demographic modeling and historical records infer that up to 90 percent of residents may have been wiped-out after the arrival of Europeans. But the people living in the upper Andes had only a 27-percent population reduction.
Even though the highlanders lived in altitudes above 8,000 feet, which meant reduced oxygen, frequent frigid temperatures and intense ultra-violet radiation, they did not develop the responses to hypoxia seen in natives of other high-altitude settings, such as Tibet.
The Andeans may have adapted to high altitude hypoxia "in a different way, via cardiovascular modifications," the researchers suggest. They found evidence of alterations in a gene called DST, which is associated with the formation of cardiac muscle. Andean highlanders tend to have enlarged right ventricles. This may have improved oxygen intake, enhancing blood flow to the lungs.
But the strongest adaptation signal the researchers found was in a gene called MGAM (maltase-glucoamylase) an intestinal enzyme. It plays an important role in the digestion of starchy foods such as potatoes--a food native to the Andes. A recent study suggests that the potato may have been domesticated in the region at least 5,000 years ago. Positive selection on the MGAM gene, the authors note, "may represent an adaptive response to greater reliance upon starchy domesticates."
The early presence of this variant in Andean peoples suggests "a significant shift in diet from one that was likely more meat based to one more plant based," said UC Merced's Aldenderfer, an anthropologist. "The timing of the appearance of the variant is quite consistent with what we know of the paleo-ethno-botanical record in the highlands."
Although Andean settlers consumed a high-starch diet after they started to farm, their genomes did not develop additional copies of the starch related amylase gene, commonly seen in European farming populations.
A comparison of the ancient genomes with their living descendants also revealed selection for immune-related genes soon after the arrival of Europeans, suggesting that Andeans who survived may have had an advantage with regard to the newly introduced European pathogens.
"Contact with Europeans had a devastating impact on South American populations, such as the introduction of disease, war, and social disruption," explained Lindo. "By focusing on the period before that, we were able to distinguish environmental adaptations from adaptations that stemmed from historical events."
"In our paper," said Aldenderfer, "there was none of this prioritization of genes at the expense of archaeological data. We worked back and forth, genetics and archeology, to create a narrative consistent with all of the data at hand."