Denisovan DNA influences immune system of modern day Oceanian populations

WELLCOME TRUST SANGER INSTITUTE

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More than 120,000 novel human genetic variations that affect large regions of DNA have been discovered, some of which are linked to immune response, disease susceptibility or digestion. Scientists at the Wellcome Sanger Institute identified these changes affecting multiple bases of DNA, known as structural variations, in a study of the most diverse worldwide populations examined to date. This included variations in medically-important genes in populations from Papua New Guinea that were inherited from Denisovan ancestors.

The resource, published today in Cell (11 June), adds new regions of sequence to the human reference genome, the world standard for all of human genetics, which is nevertheless incomplete. These previously-unknown variations in medically-important genes, which could affect the efficacy of medical treatments in certain populations, will be a valuable resource for the field of precision medicine around the globe.

Structural variations are genetic changes that can encompass anything from a few to millions of base pairs of DNA and are therefore particularly likely to affect how genes function. Some genes, such as those that influence immune response, are considered to be 'medically important'. DNA changes affecting how these genes function can lead to health problems or increased resistance or susceptibility to particular diseases.

Up until now, most large-scale genetic studies have generally focused on changes affecting single base pairs of DNA.

Scientists at the Wellcome Sanger Institute had previously led the sequencing of 911 genomes from 54 geographically, linguistically and culturally diverse populations from across the globe, and have now searched for structural variations* in these sequences.

The sequences were compared to the human reference genome to create a catalogue of structural variations, over three quarters of which were previously unknown. The team then investigated how common these structural variations are in each of the 54 populations, and which of them were inherited from Neanderthal or Denisovan ancestors.

Among the 126,018 structural variations discovered were medically-important variations inherited from Denisovan ancestors in Oceanian populations from Papua New Guinea and nearby, including a high-frequency deletion in the AQR gene that plays a role in detection of viruses and regulation of antiviral immune response.

Mohamed Almarri, first author of the study and PhD student at the Wellcome Sanger Institute, said: "By analysing the genomes of understudied populations we've been able to find high-frequency structural variations not uncovered by previous large-scale sequencing projects. Several of these are in medically-important genes that tell us how a population has evolved to resist a certain disease or why they might be susceptible to others. This is vital knowledge and will help to ensure that treatments can be tailored to each specific population."

Other notable structural variations were uncovered by the study that, together with existing knowledge of human evolution and the role of specific genes, shine a light on how individual populations have evolved.

The Karitiana people, who reside in modern-day Brazil, were found to carry a variation in the MGAM gene that affects starch digestion. The Karitiana diet is derived from fishing, hunting and farming, so a decrease in starch digestion is probably disadvantageous and therefore surprising. It is thought that bad luck may have concentrated this variation in the small population that survived a population crash within the last 5,000 years.

The team also discovered novel 'runaway duplications', where populations have evolved to carry multiple copies of genes. For example, all of the African populations included in the study carried multiple copies of the HPR gene, which is associated with resistance to sleeping sickness**. The highest numbers of copies (up to nine) were carried by Central and West African populations, where the disease is most prevalent.

Dr Ed Hollox, an expert in the field from the University of Leicester, said: "This is a very valuable study showing the importance of structural variation of the human genome in the genetic diversity of humans around the world. The work supports the concept that some human adaptations to different environments are due to the loss or gain of whole genes, or parts of genes. Structural variation can be challenging to find, and this study also provides a well-founded structural variation reference set which will serve as an important springboard for future studies."

The study adds almost two million newly-identified base pairs to the human reference genome sequence. Because the human reference genome was assembled from a small number of people, regions of DNA that were not present in these individuals are missing from the reference sequence.

The team recreated 25 diverse human genomes from scratch using a recent technological innovation called de novo genome assembly. By directly comparing these assembled genomes to the reference, the researchers were able to identify missing sequences present in multiple populations. This illustrates the limitation of a single human reference and the need for high-quality reference genomes from diverse populations.

Dr Yali Xue, recently retired from the Wellcome Sanger Institute, said: "Structural variants are complicated yet very important functionally, evolutionarily and medically. The discovery of these new structural variations provides one of the richest resources of this kind of variation so far, which not only offers unique insights into population histories and improves the currently used human reference genome, but will also substantially benefit future medical studies."

Tropical disease in medieval Europe revises the history of a pathogen related to syphilis

Genomic analysis of plague victims from a mass burial in Lithuania identifies a medieval woman who was also infected with yaws -- a disease today found only in the tropics

MAX PLANCK INSTITUTE FOR THE SCIENCE OF HUMAN HISTORY

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IMAGE: MULTIPLE BURIAL IN VILNIUS, LITHUANIA CONTAINING AN INDIVIDUAL INFECTED WITH BOTH PLAGUE AND YAWS. view more 

CREDIT: PHOTO COURTESY OF ROBERTAS �UKOVSKIS AND SCIENTIFIC REPORTS.

Mass burials are common remnants of the many plague outbreaks that ravaged Medieval Europe. A number of these graveyards are well documented in historical sources, but the locations of most, and the victims they contain, have been lost to the pages of time. In Vilnius, Lithuania, one such cemetery was found in a typical way: accidental discovery during a routine city construction project.

A new study published in the journal Scientific Reports details the findings of genomic analyses on these medieval skeletons, with important implications for the history of syphilis in Europe.

Just another plague pit?

"Historical information on this Vilnius graveyard is unavailable, but the burial context, along with its location outside of the medieval city limits, pointed to plague, or some other major infectious disease outbreak," comments Rimantas Jankauskas, Professor of the Faculty of Medicine, Vilnius University. "To be certain, we needed confirmation through DNA analysis."

Kirsten Bos, a group leader for Molecular Palaeopathology at the Max Planck Institute for the Science of Human History (MPI-SHH) in Jena, Germany, is frequently contacted by archaeologists requesting such analyses.

"Plague was a common disease at the time, and the information we get from all the ancient DNA work can tell us a lot about how it was spreading," says Bos, a specialist in ancient pathogen DNA recovery who led the current study.

Working in Bos's team, doctoral candidate Karen Giffin took on DNA analysis of the putative plague victims and quickly identified the pathogen's DNA in the teeth of several individuals.

"I was happy to have identified them as victims of medieval plague," says Giffin, "but we wanted to see if the new techniques we were developing in molecular detection of pathogens could allow us to learn anything more about the health of this population."

More than just plague

"The typical method for pathogen detection in archaeological bone requires that you have some idea of what you're looking for," explains Alexander Herbig, group leader of Computational Pathogenomics at the MPI-SHH. "In this case we applied a relatively new hypothesis-free DNA screening approach to search for any other pathogens we might be able to identify at the molecular level."

This process unlocked a second secret of the 15th century graveyard. One of the four plague victims, a young woman, also showed a weak signal of something that seemed related to modern syphilis.

"It was impressive to find traces of such a disease in an historical skeleton because their molecular preservation in ancient bone is known to be problematic," comments Bos.

Diseases in the syphilis family, known as the treponemal diseases, are assumed to have had a long history with humans, though their inferred history in Europe is laden with controversy. The prevailing opinion holds that the first outbreak of syphilis in Europe coincided with Charles VIII's 1495 siege of Naples, where a debilitating disease erupted amongst his infantry and quickly spread around Europe. Since this outbreak happened just after the return of Columbus and his crew from their first trans-Atlantic voyage, most discussants believe syphilis was a newcomer to Europe that originated in the New World. But support is growing for a different theory. An increasing number of specialists in bone pathology believe they have properly identified examples of pre-1493 syphilis in Europe, which has ignited on-going debates about models of its evolution.

"We were able to reconstruct an impressively well-preserved genome that, to our surprise, fell within the diversity of modern yaws," comments Giffin. Yaws is a lesser-known treponemal disease primarily of the skin that affects both humans and other primates in warm, tropical environments. "Finding it in northern Europe in the mid-15th century was unexpected," she adds.

Yaws seems much younger than we thought

Since yaws infects both humans and non-human primates, some believe it to be a very old disease, having been with humans before the massive Pleistocene migrations that spread us around the globe.

"To our surprise, the yaws genome we reconstructed was just a few genetic steps away from the ancestor of all yaws varieties known in humans and non-human primates," says Bos. "Given the age of our medieval skeletons, it seems that all strains of yaws that we know today appeared on the scene only about 1000 years ago."

"This has important implications for the history of treponemal disease in Europe," Bos adds. "We can now confirm that yaws was circulating in medieval Europe, and given its similarity to syphilis and its recent emergence, it's possible that yaws contributed in some way to the famous late 15th to 16th century outbreak that we normally ascribe only to syphilis."

One possibility is that yaws emerged in either humans or other primates in West Africa within the last millennium and made its way to Europe in the mid-15th century. European presence in West Africa increased in the 15th century, as did the forced relocations of Africans to Europe through establishment of the transatlantic slave trade. These activities would have rapidly disseminated a new and highly contagious disease such as yaws.

"The enigma about the origin of syphilis is still open," says Bos, "but disease ecology in medieval Europe is clearly more complex than we think."

###

Link to the paper: https://www.nature.com/articles/s41598-020-66012-x

Discovery of the oldest Chinese work of art

A small bird carving--the oldest instance of East Asian three-dimensional art ever discovered--is described in a study published June 10, 2020 in the open-access journal PLOS ONE by Zhanyang Li from Shandong University, China, and colleagues.

European animal and human mammoth ivory carvings dated to 40-38 ka are our earliest examples of prehistoric humans three-dimensionally representing the world around them--though due to a lack of evidence, it's unclear when this type of three-dimensional representation became part of the cultural repertoire of prehistoric groups around the rest of the world. In this study, Li and colleagues describe the remarkable discovery of a small standing bird carving from the Paleolithic site of Lingjing, in Henan, China, that sheds further light on humanity's earliest three-dimensional art.

During Li's initial excavation at Lingjing in 2005, he uncovered eleven distinct stratified layers ranging in age from 120,000 years ago to the Bronze Age --and found that most of the fifth layer had been removed during a well-digging operation in 1958. However, the refuse heap from the well's creation was still intact and remained nearby. After sifting through the sediment in the refuse heap, the authors discovered black flint identical to (and only found in) what remained of Layer 5 at the dig site. They also uncovered several artifacts, including pottery sherds, burned animal remains, and the bird figurine, which is carved from bone and shaped like a songbird on a pedestal.

Using radiocarbon dating on the uncovered burned animal remains (including one bone with anthropogenic gouging marks also observed on the bird carving), the authors were able to estimate the age of the bird figurine and associated bone material to be approximately 13.4-13.2 ka cal BP. Based on evidence from other Northern Chinese sites of similar age, this suggests that hunter-gatherers with stone tool technologies occupied Lingjing and created the bird carving during this time.

Bird representations are a theme in Chinese Neolithic art, with the oldest example a jade songbird dated to approximately 5 ka BP. This Paleolithic bone bird figurine from Lingjing predates previously known instances from this region by almost 8,500 years, and has several technological and stylistic elements distinguishing it from contemporaneous representations of birdlike creatures from Western Europe and Siberia (such as the pedestal on which the Lingjing bird is perched). Though more examples of Paleolithic carving art are needed to confirm this possibility, the Lingjing bird figurine suggests the presence of a longstanding artistic tradition specific to East Asia, with origins much earlier in the Paleolithic.

The authors add: "This discovery identifies an original artistic tradition and pushes back by more than 8,500 years the representation of birds in Chinese art. The figurine differs technologically and stylistically from other specimens found in Western Europe and Siberia, and it could be the missing link tracing the origin of Chinese statuary back to the Palaeolithic period."

CNRS

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IMAGE: PHOTO (TOP) AND 3D RECONSTRUCTION USING MICROTOMOGRAPHY (BOTTOM) OF THE MINIATURE BIRD SCULPTURE. ITS PRODUCTION COMBINED FOUR DIFFERENT TECHNIQUES (ABRASION, GOUGING, SCRAPING AND INCISION), WHICH LEFT 68 MICROFACETS ON THE... view more 

CREDIT: © FRANCESCO D'ERRICO AND LUC DOYON

Carved from burnt bone, this miniature bird statuette is the oldest known Chinese work of art, according to an international team involving the CNRS, the universities of Bordeaux (France), Shandong (China), Bergen (Norway), and the Weizmann Institute of Science (Israel). It was unearthed at Lingjing, a site in Henan Province, in an archaeological context dated to between 13,800 and 13,000 years ago. This discovery pushes back the origins of animal sculpture and representations in East Asia by more than 8,500 years (1). The stylistic and technical particularities of the figurine - it is the only known Palaeolithic sculpture representing an animal standing on a pedestal - point to an original artistic tradition, different from those known in Western Europe and Siberia. The object's exceptional state of preservation and the researchers' use of state-of-the-art analytical techniques, such as confocal microscopy and microtomography, have enabled the team to meticulously reconstruct the Palaeolithic artist's approach. This discovery is published on June 10th 2020 in the journal PLOS ONE.

Entire Roman city revealed without any digging

For the first time, archaeologists have succeeded in mapping a complete Roman city, Falerii Novi in Italy, using advanced ground penetrating radar (GPR), allowing them to reveal astonishing details while it remains deep underground. The technology could revolutionise our understanding of ancient settlements.

The team, from the University of Cambridge and Ghent University, has discovered a bath complex, market, temple, a public monument unlike anything seen before, and even the city's sprawling network of water pipes. By looking at different depths, the archaeologists can now study how the town evolved over hundreds of years.

The research, published today in Antiquity, harnessed recent advances in GPR technology which make it possible to explore larger areas in higher resolution than ever before. This is likely to have major implications for the study of ancient cities because many cannot be excavated either because they are too large, or because they are trapped under modern structures.

GPR works like regular radar, bouncing radio waves off objects and using the 'echo' to build up a picture at different depths.* By towing their GPR instruments behind a quad bike, the archaeologists surveyed all 30.5 hectares within the city's walls -- Falerii Novi was just under half the size of Pompeii -- taking a reading every 12.5cm.

Located 50 km north of Rome and first occupied in 241 BC, Falerii Novi survived into the medieval period (until around AD 700). The team's GPR data can now start to reveal some of the physical changes experienced by the city in this time. They have already found evidence of stone robbing.

The study also challenges certain assumptions about Roman urban design, showing that Falerii Novi's layout was less standardised than many other well-studied towns, like Pompeii. The temple, market building and bath complex discovered by the team are also more architecturally elaborate than would usually be expected in a small city.

In a southern district, just within the city's walls, GPR revealed a large rectangular building connected to a series of water pipes which lead to the aqueduct. Remarkably, these pipes can be traced across much of Falerii Novi, running beneath its insulae (city blocks), and not just along its streets, as might normally be expected. The team believes that this structure was an open-air natatio or pool, forming part of a substantial public bathing complex.

Even more unexpectedly, near the city's north gate, the team identified a pair of large structures facing each other within a porticus duplex (a covered passageway with central row of columns). They know of no direct parallel but believe these were part of an impressive public monument, and contributed to an intriguing sacred landscape on the city's edge.

Corresponding author, Professor Martin Millett from the University of Cambridge's Faculty of Classics, said:

"The astonishing level of detail which we have achieved at Falerii Novi, and the surprising features that GPR has revealed, suggest that this type of survey could transform the way archaeologists investigate urban sites, as total entities."

Millett and his colleagues have already used GPR to survey Interamna Lirenas in Italy, and on a lesser scale, Alborough in North Yorkshire, but they now hope to see it deployed on far bigger sites.

"It is exciting and now realistic to imagine GPR being used to survey a major city such as Miletus in Turkey, Nicopolis in Greece or Cyrene in Libya," Millett said. "We still have so much to learn about Roman urban life and this technology should open up unprecedented opportunities for decades to come."

The sheer wealth of data produced by such high-resolution mapping does, however, pose significant challenges. Traditional methods of manual data analysis are too time consuming, requiring around 20 hours to fully document a single hectare. It will be some time before the researchers finish examining Falerii Novi but to speed the process up they are developing new automated techniques.

Falerii Novi is well documented in the historical record, is not covered by modern buildings and has been the subject of decades of analysis using other non-invasive techniques, such as magnetometry, but GPR has now revealed a far more complete picture.

Further information

*GPR is so effective because it relies on the reflection of radio waves off items in the ground. Different materials reflect waves differently, which can be used to create maps of underground features. Although this principle has been employed since the 1910s, over the past few years technological advances have made the equipment faster and higher resolution.

Radiocarbon dating pins date for construction of Uyghur complex to the year 777

IMAGE: THIS IS AN AERIAL VIEW OF POR-BAJIN FROM THE WEST. THE COMPLEX IS SITUATED ON AN ISLAND IN A LAKE. SCIENTISTS HAVE PINNED ITS CONSTRUCTION ON THE YEAR 777... view more 

CREDIT: ANDREI PANIN

Dating archaeological objects precisely is difficult, even when using techniques such as radiocarbon dating. Using a recently developed method, based on the presence of sudden spikes in carbon-14 concentration, scientists at the University of Groningen, together with Russian colleagues, have pinned the date for the construction of an eighth-century complex in southern Siberia to a specific year. This allows archaeologists to finally understand the purpose for building the complex - and why it was never used. The results were published in Proceedings of the National Academy of Sciences on 8 June.

The Por-Bajin complex, on the border of the Russian Federation and Mongolia, measures 215 x 162 metres and has outer walls of twelve metres high. All of the walls are made of clay (Por-Bajin translates as 'clay house') on a foundation of wooden beams. The complex was created by nomadic Uyghurs, sometime in the eighth century. But archaeologists did not know the purpose of the complex and why it appears to never have been used.

Khans

'In order to understand this, the exact construction date was required to find out which local leader, or khan, gave the orders for the construction,' explains Margot Kuitems, a postdoctoral researcher at the Centre for Isotope Research at the University of Groningen. She currently works on the Exact Chronology of Early Societies (ECHOES) project, funded by the European Research Council and led by Assistant Professor of Isotope Chronology Michael Dee, who is also an author on the PNAS paper.

For the early mediaeval period, radiocarbon dating is generally precise to a few decades. This is good enough for most applications. However, as khans came and went during the eighth century, the exact construction date was required to link it to a specific leader. Within the ECHOES project, Kuitems applied a recently developed method to date her samples exactly.

Spike

Carbon-14 (a radioactive isotope of carbon) is created in the upper atmosphere. Plants absorb carbon dioxide, which includes a tiny amount of carbon-14. When the plant - or the animal that ate the plant - dies, the carbon uptake stops and the carbon-14 slowly decays. Every 5,730 years, half of the carbon-14 decays. Therefore, the carbon-14 concentration tells you how old the object (animal, plant or any other organic material) is.

Production rates of carbon-14 in the atmosphere are not constant. However, changes in atmospheric carbon-14 were believed to show little variation from one year to the next. Then, in 2013, the Japanese Professor Fusa Miyake analysed individual tree rings and found a spectacular spike in carbon-14 content in the year 775. 'When you find wood at an archaeological site from that period, you can look for the spike by measuring the carbon-14 content of subsequent tree rings,' explains Kuitems. The spike tells you which tree ring grew in the year 775. And when the sample includes the bark, it is even possible to determine when the tree was felled.

Chinese princess

This approach was used to analyse a beam taken from the very foundation of the Por-Bajin complex. The sample that they used had 45 rings, followed by the bark. Measurements showed that the spike that dated to the year 775 was present in the 43rd ring. 'So, we knew the tree was felled in 777. Tree ring specialist and co-author Petra Doeve determined that the final, partial ring was created in the spring.' In southern Siberia, there is a clear distinction between summer and winter wood.

Russian archaeologists previously reported that the entire complex was completed in a very short time, about two years. Por-Bajin is situated on an island in a lake and it was determined that the trees came from the surrounding area. 'We are fairly certain that they were felled for the construction of the complex, and it is therefore highly likely that construction took place around 777.' Previously, the site had been dated to 750, based on a runic inscription on a monument called the 'Selenga Stone', which described the construction of a large complex. In 750, Bayan-Chur Khan ruled the Uyghurs. He was married to a Chinese princess and this may explain why some Chinese influences were found in the Por-Bajin complex. 'However, previous radiocarbon dating attempts already suggested that the buildings might be slightly younger.'

Manichaeism

In the year 777, Tengri Bögü Khan was in charge. He had converted to Manichaeism, a gnostic religion that was strongly opposed. Indeed, Bögü Khan was killed during an anti-Manichaean rebellion in 779. 'All this ties in neatly with the archaeological evidence,' explains Kuitems. It is likely that the complex was built to serve as a Manichaean monastery. 'This explains why it was never used after the anti-Manichaeans defeated Bögü Khan. If it had been a palace or a fortress, it is more likely that the victors would have moved in.'

The study shows how carbon-14 spikes can help to solve archaeological conundrums, says Kuitems: 'This technology can be really useful in cases where an exact date is required.' And as ever more spikes are identified, their uses will become more widespread.

Simple Science Summary

At the border between the Russian Federation and Mongolia stands a large clay complex of buildings called Por-Bajin. Archaeologists are not sure who built it and what its purpose was. They do know that it was never used. Scientists have used a promising method to pinpoint the construction date. Normal carbon dating of wood leads to a range of a few decades at best. However, sometimes a spike in carbon-14 levels can be found in one particular tree ring, all across the world. These spikes have been dated to the year by counting the rings in continuous records from known-age wood from tree-ring archives. In the complex, the scientists found a beam with a spike from the year 775. As they were able to ascertain that the tree was felled two years later, the complex must have been constructed in 777. Shortly before this, the local leader (khan) had converted to the Manichaean religion but he was killed by anti-Manichaeans in 779. It was concluded that the complex was built as a Manichaean monastery but was never used since anti-Manichaeans took control of the area.

Oldest connection with Native Americans identified near Lake Baikal in Siberia

Using human population genetics, ancient pathogen genomics and isotope analysis, a team of researchers assessed the population history of the Lake Baikal region, finding the deepest connection to date between the peoples of Siberia and the Americas. The current study, published in the journal Cell, also demonstrates human mobility, and hence connectivity, across Eurasia during the Early Bronze Age.

Modern humans have lived near Lake Baikal since the Upper Paleolithic, and have left behind a rich archaeological record. Ancient genomes from the region have revealed multiple genetic turnovers and admixture events, indicating that the transition from the Neolithic to the Bronze Age was facilitated by human mobility and complex cultural interactions. The nature and timing of these interactions, however, remains largely unknown.

A new study published in the journal Cell reports the findings of 19 newly sequenced ancient human genomes from the region of Lake Baikal, including one of the oldest reported from that region. Led by the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History, the study illuminates the population history of the region, revealing deep connections with the First Peoples of the Americas, dating as far back as the Upper Paleolithic period, as well as connectivity across Eurasia during the Early Bronze Age.

The deepest link between peoples

"This study reveals the deepest link between Upper Paleolithic Siberians and First Americans," says He Yu, first author of the study. "We believe this could shed light on future studies about Native American population history."

Past studies have indicated a connection between Siberian and American populations, but a 14,000-year-old individual analysed in this study is the oldest to carry the mixed ancestry present in Native Americans. Using an extremely fragmented tooth excavated in 1962 at the Ust-Kyahta-3 site, researchers generated a shotgun-sequenced genome enabled by cutting edge techniques in molecular biology.

This individual from southern Siberia, along with a younger Mesolithic one from northeastern Siberia, shares the same genetic mixture of Ancient North Eurasian (ANE) and Northeast Asian (NEA) ancestry found in Native Americans, and suggests that the ancestry which later gave rise to Native Americans in North- and South America was much more widely distributed than previously assumed. Evidence suggests that this population experienced frequent genetic contacts with NEA populations, resulting in varying admixture proportions across time and space.

"The Upper Paleolithic genome will provide a legacy to study human genetic history in the future," says Cosimo Posth, a senior author of the paper. Further genetic evidence from Upper Paleolithic Siberian groups is necessary to determine when and where the ancestral gene pool of Native Americans came together.

A web of prehistoric connections

In addition to this transcontinental connection, the study presents connectivity within Eurasia as evidenced in both human and pathogen genomes as well as stable isotope analysis. Combining these lines of evidence, the researchers were able to produce a detailed description of the population history in the Lake Baikal region.

The presence of Eastern European steppe-related ancestry is evidence of contact between southern Siberian and western Eurasian steppe populations in the preamble to the Early Bronze Age, an era characterized by increasing social and technological complexity. The surprising presence of Yersinia pestis, the plague-causing pathogen, points to further wide-ranging contacts.

Although spreading of Y. pestis was postulated to be facilitated by migrations from the steppe, the two individuals here identified with the pathogen were genetically northeastern Asian-like. Isotope analysis of one of the infected individuals revealed a non-local signal, suggesting origins outside the region of discovery. In addition, the strains of Y. pestis the pair carried is most closely related to a contemporaneous strain identified in an individual from the Baltic region of northeastern Europe, further supporting the high mobility of those Bronze age pathogens and likely also people.

"This easternmost appearance of ancient Y. pestis strains is likely suggestive of long-range mobility during the Bronze Age," says Maria Spyrou, one of the study's coauthors. "In the future, with the generation of additional data we hope to delineate the spreading patterns of plague in more detail." concludes Johannes Krause, senior author of the study.

New Papua New Guinea research solves archaeological mysteries

UNIVERSITY OF OTAGO

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IMAGE: PROFESSOR GLENN SUMMERHAYES AT THE "JOES' GARDEN " SITE IN THE IVANE VALLEY IN THE NEW GUINEA HIGHLANDS. view more 

CREDIT: UNIVERSITY OF OTAGO

New research which "fills in the blanks" on what ancient Papuan New Guineans ate, and how they processed food, has ended decades-long speculation on tool use and food stables in the highlands of New Guinea several thousand years ago.

Findings from the "Joe's Garden" site in the Ivane Valley in the New Guinea highlands end several decades of academic speculation about what a formally manufactured mortar and other tools were used for, and shows a variety of once widely eaten starchy plants were processed in the area.

Report co-author and University of Otago Archaeology Professor Glenn Summerhayes says the research means several archaeological "mysteries have finally been solved".

"Although ground stone bowls, known as mortars, have been found throughout most of New Guinea, little was known of their function or age. Most have been found from surface collections or dug by in and re-used by locals while gardening. Only a couple had been excavated in archaeological contexts and their use was unknown. This paper presents the discovery of a mortar fragment excavated from the Ivane Valley of Papua New Guinea in contexts dated to four and a half thousand years ago."

Clinging to the stone tools recovered from the site are microscopic starch grains from tree nuts (Castanopsis acumeninatissma) and Pueraria labota (tuber), which were first proposed as common stables by researchers in the mid-1960s.

"Usewear and residue analysis on the fragment has shown it was used for processing starch rich plants such as nut and tuber, and insights into past subsistence patterns are rare, especially for 4,400 year ago!"Professor Summerhayes says.

The research adds to the findings from other studies by demonstrating the long-term survival of starchy residues in an open site in a montane setting at 2000m above sea level, and confirms the resilience of these microfossils in equatorial/tropical contexts.

Summerhayes says over the last 300 or so years, the predominance of sweet potato in subsistence gardening practices has led to a range of starchy plants falling into disuse. While previous studies in the region have mainly focused on the use of taro, banana and some yams, the researchers found several species, including Castanopsis sp. - commonly referred to as chinquapin or chinkapin - may have played an important, if up until now an invisible, role in highland diets over the millennia.

Similarly, the widely available, C. acuminatissima - commonly known as white oak or New Guinea oak - has been recorded as eaten on hunting trips but has never been clearly identified as a common starchy staple. As with pestles from the Waim site, the Ivane mortars confirm consumption of these tree nuts was widespread.

Some areas recognise these dietary links with the past; in the highland Kaironk Valley in Madang Province at least one stand of C. acuminatissima has conservation status.

"This regional example is an exciting addition to our wider project on understanding of the trajectories of diverse plant food exploitation and ground stone technology development witnessed globally in the Holocene," Professor Summerhayes says.