Scientists recover an ancient woman’s DNA from a 20,000-year-old pendant

 

 

IMAGE: PIERCED DEER TOOTH DISCOVERED FROM DENISOVA CAVE IN SOUTHERN SIBERIA THAT YIELDED ANCIENT HUMAN DNA. view more 

CREDIT: © MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY

Artefacts made of stone, bones or teeth provide important insights into the subsistence strategies of early humans, their behavior and culture. However, until now it has been difficult to attribute these artefacts to specific individuals, since burials and grave goods were very rare in the Palaeolithic. This has limited the possibilities of drawing conclusions about, for example, division of labor or the social roles of individuals during this period.

In order to directly link cultural objects to specific individuals and thus gain deeper insights into Paleolithic societies, an international, interdisciplinary research team, led by the Max Planck Institute for Evolutionary Anthropology in Leipzig, has developed a novel, non-destructive method for DNA isolation from bones and teeth. Although they are generally rarer than stone tools, the scientists focused specifically on artefacts made from skeletal elements, because these are more porous and are therefore more likely to retain DNA present in skin cells, sweat and other body fluids.

A new DNA extraction method

Before the team could work with real artefacts, they first had to ensure that the precious objects would not be damaged. “The surface structure of Paleolithic bone and tooth artefacts provides important information about their production and use. Therefore, preserving the integrity of the artefacts, including microstructures on their surface, was a top priority” says Marie Soressi, an archaeologist from the University of Leiden who supervised the work together with Matthias Meyer, a Max Planck geneticist.

The team tested the influence of various chemicals on the surface structure of archaeological bone and tooth pieces and developed a non-destructive phosphate-based method for DNA extraction. “One could say we have created a washing machine for ancient artifacts within our clean laboratory," explains Elena Essel, the lead author of the study who developed the method. "By washing the artifacts at temperatures of up to 90°C, we are able to extract DNA from the wash waters, while keeping the artifacts intact.”

Early setbacks

The team first applied the method to a set of artefacts from the French cave Quinçay excavated back in the 1970s to 1990s. Although in some cases it was possible to identify DNA from the animals from which the artefacts were made, the vast majority of the DNA obtained came from the people who had handled the artefacts during or after excavation. This made it difficult to identify ancient human DNA.

To overcome the problem of modern human contamination, the researchers then focused on material that had been freshly excavated using gloves and face masks and put into clean plastic bags with sediment still attached. Three tooth pendants from Bacho Kiro Cave in Bulgaria, home to the oldest securely dated modern humans in Europe, showed significantly lower levels of modern DNA contamination; however, no ancient human DNA could be identified in these samples.

A pendant from Denisova Cave

The breakthrough was finally enabled by Maxim Kozlikin and Michael Shunkov, archaeologists excavating the famous Denisova Cave in Russia. In 2019, unaware of the new method being developed in Leipzig, they cleanly excavated and set aside an Upper Paleolithic deer tooth pendant. From this, the geneticists in Leipzig isolated not only the DNA from the animal itself, a wapiti deer, but also large quantities of ancient human DNA. “The amount of human DNA we recovered from the pendant was extraordinary” says Elena Essel, “almost as if we had sampled a human tooth.”

Based on the analysis of mitochondrial DNA, the small part of the genome that is exclusively inherited from the mother to their children, the researchers concluded that most of the DNA likely originated from a single human individual. Using the wapiti and human mitochondrial genomes they were able to estimate the age of the pendant at 19,000 to 25,000 years, without sampling the precious object for C14 dating.

In addition to mitochondrial DNA, the researchers also recovered a substantial fraction of the nuclear genome of its human owner. Based on the number of X chromosomes they determined that the pendant was made, used or worn by a woman. They also found that this woman was genetically closely related to contemporaneous ancient individuals from further east in Siberia, the so called ‘Ancient North Eurasians’ for whom skeletal remains have previously been analyzed. “Forensic scientists will not be surprised that human DNA can be isolated from an object that has been handled a lot” says Matthias Meyer, “but it is amazing that this is still possible after 20,000 years.”

The scientists now hope to apply their method to many other objects made from bone and teeth in the Stone Age to learn more about the genetic ancestry and sex of the individuals who made, used, or wore them.

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JOURNAL

Nature

DOI

10.1038/s41586-023-06035-2 

Stone tools reflect three waves of migration of the earliest Sapiens into Europe Lebanese and French artifacts from up to 54,000 years ago show shared

 

IMAGE: THE PAPER PROVIDES EVIDENCE FOR 3 DISTINCT WAVES OF EARLY MIGRATION OF SAPIENS IN EUROPE FROM THE EAST MEDITERRANEAN COAST. THE IMAGE SHOWS 3 TECHNICAL TRADITIONS OF EACH OF THESE SAPIENS MIGRATIONS. PHASE 1, AROUND THE 54TH MILLENNIUM, IS REPRESENTED BY THE NERONIAN/INITIAL UPPER PALEOLITHIC; PHASE 2 BY THE CHÂTELPERRONIAN/EARLY UPPER PALEOLITHIC AROUND THE 45TH MILLENNIUM, AND PHASE 3 BY THE PROTOAURIGNACIAN/SOUTHERN EARLY AHMARIAN AROUND THE 42ND MILLENNIUM. view more 

CREDIT: LUDOVIC SLIMAK, CC-BY 4.0 (HTTPS://CREATIVECOMMONS.ORG/LICENSES/BY/4.0/)

The first modern humans spread across Europe in three waves during the Paleolithic, according to a study published May 3, 2023 in the open-access journal PLOS ONE by Ludovic Slimak of the CNRS and University of Toulouse III, France.

The archaeological record of Paleolithic Europe leaves many open questions regarding the nature of the arrival of modern humans into the region and the nature of how these newcomers interacted with the resident Neanderthal populations. In this study, Slimak compared records of stone tool technology across western Eurasia to document the sequence of early human activity in the region.

This study primarily focused on comparative analysis of tens of thousands of stone tools from two sites: Ksar Akil in Lebanon and Grotte Mandrin in France, that recently revealed the earliest Sapiens migration in Europe dating to 54,000 years old. The study analyzed their precise technical connections with the earliest modern technologies in the continent. The author identifies a similar sequence of three technological phases in both regions, suggesting three distinct waves of migration of Homo sapiens across Europe.

These trans-Mediterranean technological connections allow for a reinterpretation of the pattern of human arrival in Europe and its precise relations with the Levantine region. Further examination of these apparent phases of human migration will establish a clearer picture of the sequence of events as Homo sapiens spread across the region and, in doing so, gradually replaced Neanderthals.

Slimak adds: “Until 2022, it was believed that Homo sapiens had reached Europe between the 42nd and 45th millennium. The study shows that this first Sapiens migration would actually be the last of three major migratory waves to the continent, profoundly rewriting what was thought to be known about the origin of Sapiens in Europe. Chatelperronian culture, one of the first modern traditions in western Europe and since then attributed to Neanderthals, should in fact signal the second wave of Homo sapiens migration in Europe, impacting deeply our understanding of the cultural organization of the last Neanderthals.”

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The freely available article in PLOS ONE: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0277444

Researchers solve ancient mystery of Maya calendar

 

The 819-day calendar used by ancient Mayans has long stumped researchers, but anthropologists from Tulane University may have finally deciphered its secrets.

Researchers long suspected the calendar followed astronomical events, specifically how long it takes a planet to appear in the same place in the night sky as seen from Earth, known as the synodic periods of planets. But, according to the study published in Ancient Mesoamerica, the cycles in the Maya calendar cover a much larger timeframe than scholars previously thought.

“Although prior research has sought to show planetary connections for the 819-day count, its four-part, color-directional scheme is too short to fit well with the synodic periods of the visible planets,” wrote anthropologists John Linden, a Tulane alumnus, and Victoria Bricker, PhD, professor emerita at Tulane University School of Liberal Arts. “By increasing the calendar length to 20 periods of 819-days, a pattern emerges in which the synodic periods of all the visible planets commensurate with station points in the larger 819-day calendar.”

Previously, researchers thought the calendar referred to four cycles of 819, but that time span didn’t sync neatly with the synodic periods of all the planets that can be seen with the naked eye: Mercury, Venus, Mars, Jupiter, and Saturn. The researchers discovered it takes 20 cycles of 819 days, which is about 45 years, to align with the synodic periods of all visible planets.

Within 20 cycles, each planet goes through some number of synodic periods a whole number of times: Mercury every cycle, Venus every 5 cycles, Saturn every 6 cycles, Jupiter every 19 cycles, and Mars every 20 cycles.

 

Each synodic period is less than 819 days, but only Mercury has one that happens a whole number of times within a single cycle. Combining the cycles allows for prediction of the placement of the planets, which Linden and Bricker say is also connected to important dates and celebrations.
 

“Rather than limit their focus to any one planet, the Maya astronomers who created the 819-day count envisioned it as a larger calendar system that could be used for predictions of all the visible planet's synodic periods,” the authors wrote.

This research is a key part of understanding how the ancient Maya studied astronomy and is part of a decades-long quest to understand the complexity of ancient Maya calendars.

 

 

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JOURNAL

Ancient Mesoamerica

DOI

10.1017/S0956536122000323 

Modern-day Scottish, Welsh and Northern Irish people have Pictish ancestry

The Picts of Scotland who have long intrigued and have been ascribed exotic origins in fact descended from indigenous Iron Age society and were genetically most similar to people living today in Scotland, Wales, North Ireland and Northumbria. Adeline Morez of Liverpool John Moores University and Linus Girdland-Flink of the University of Aberdeen report these findings in a new study published April 27 in the journal PLOS Genetics.

Complete article:

 PLOS Genetics:

http://journals.plos.org/plosgenetics/article?id=10.1371/journal. pgen.1010360

The Picts, who inhabited early medieval Scotland from about 300-900 AD, formed the first documented kingdoms of eastern Scotland, but have often been a subject of mystery due to the lack of historical and archaeological evidence and due to their enigmatic symbol tradition inscribed on stone. In their new study, Morez and Girdland-Flink sampled Pictish burials to extract genomes to explore how the Picts are related to other cultural groups in Britain. They sequenced DNA from two individuals from central and northern Scotland that dated from the fifth to the seventh century AD. They compared the resulting high-quality genomes to more than 8,300 previously published ancient and modern genomes.

The analysis revealed that Picts descended from local Iron Age populations, who lived across Britain before the arrival of mainland Europeans. Additionally, the researchers found genetic similarities between the Picts and present-day people living in western Scotland, Wales, Northern Ireland and Northumbria. Medieval traditions, including from the time of the Picts themselves, had ascribed exotic origins to the Picts including them coming from Thrace (north of the Aegean Sea), Scythia (eastern Europe), or isles north of Britain, but the new research suggests much less sensational origins.

A further analysis of DNA sequenced from seven individuals interred in a Pictish cemetary showed that the individuals did not share a common ancestor on their mother’s side. This finding suggests that females may have married outside their own social group and runs counter to older speculation, such as that mentioned by the great English scholar Bede, that the Picts were matrilineal; that they had had a society based on kinship through the mother’s lineage.

The new findings support current archaeological theories that Picts descended from Iron Age people in Britain. The study also provides novel insights into the genetic relationships that existed amongst Pictish individuals buried in cemeteries together and between ancient Picts and present-day groups in the United Kingdom.

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Author Interview:

PLOS: What first drew you to study paleogenetics?

Dr. Morez: I always have been fascinated by human evolution overall: where are we from? How did we manage to settle worldwide and adapt to the wide diversity of environments? I chose to focus on paleogenetics, the study of ancient DNA, as it is a formidable opportunity to gain direct knowledge of an individual ancestry or a population's genetic diversity, free from inference based on modern genomes. And now, we actually see that the migrations and population mixtures are more numerous and complex than previously hypothesised.

PLOS:  What did you choose to investigate in this study, and why?

Dr. Morez: In this study, I chose to investigate the genetic ancestry of the Picts - people living in Scotland during the early medieval period (here from individuals buried in eastern and northern Scotland). It has never been done and many historical-based hypotheses stated that they were biologically diverse from their neighbours, with possible ties from the Eurasian steppes. Once we realised they were actually genetically very similar to their contemporaries living in the UK, we decided to push the limit in terms of analytical resolution using imputation of genotypes and analyses based on the autosomal haplotype information (chunks of DNA shared from parents to offspring, modify by mutation and recombination). It allows us to study the fine-scale genetic structure between the Picts and ancient and modern individuals from the UK and Europe.

PLOS: What are the key findings from your research on ancient Pictish genetics?

Dr. Morez: The two Picts studied here showed a greater affinity (by haplotype sharing) with present-day populations from western Scotland, Wales, Northern Ireland and Northumbria compared to the populations from southern England, which is important for understanding how present-day diversity formed in the UK.

Thanks to comparison with previously published genomes from Pictish people living in the Orkney islands, we could also show that individuals living in the Orkney and in mainland Scotland, likely gathered under the same cultural unit, were slightly divergent likely because of limited gene flow between the two regions and small population size in Orkney, which is known to speed up genetic divergence.

PLOS: What most surprised or interested you about your findings?

Dr. Morez: I was surprised to find that the two Pictish genomes from eastern and northern Scotland show a slightly higher but noticeable haplotype sharing with present-day people living in western Scotland, rather than with those from the East where Pictish culture is believed to thrive. This was unexpected and may be caused by several reasons; either we are detecting a population movement from the west of Scotland toward the east but which did not leave a long-lasting genetic signature, or later population movements in the East replaced some of the Pictish ancestry. We still don’t know which one is correct.

PLOS: What do you hope your findings might lead to, and what are the next steps for your research?

Dr. Morez: I hope the fascination for the Iron Age and medieval period in the UK will increase and lead to more genomes being discovered and analysed, to get a better understanding of the genetic structure across Scotland. Thanks to these genomes, those already published and the many more yet to come, the UK will soon become the first country where we understand in detail how genetic diversity has formed.

Future research will provide new information on the Pictish lifestyle, thanks to archaeologists from the University of Aberdeen and co-authors of the study. Gordon Noble who is reassessing and excavating new Pictish sites, and Kate Britton who investigates dietary habits and mobility using stable isotopes. Linus Girdland Flink (senior author, University of Aberdeen) is coordinating further research on Pictish DNA. This ongoing project will provide an excellent tool to facilitate interdisciplinary research to connect archaeology, archaeological science, history, and human population genetics.

New insight into the mystery of ancient Gaza wine

 

Research into grape pips found from an excavated Byzantine monastery in Israel hints at the origins of the ‘mysterious’ Gaza wine and the history of grapevine cultivation in desert conditions.

The pips from settlements in Israel’s Negev desert - one of which was dated to the 8th century - were likely from a white grape, and is potentially the earliest of its kind documented anywhere in the world. 

It is thought it could be linked to the sweet white wine - the Gaza wine - that archaeologists have seen references to in historical records, but a lack of evidence of white varieties from the period has until now left a question mark over its true origins.

The wine was produced in the Negev and shipped across the Byzantine Empire, as well as to Germany, France and Britain, where it is thought to have been enjoyed by royal households. 

Researchers from the University of York, Tel Aviv University, and the University of Copenhagen, used genetic analyses to identify several different grape cultivars that were grown in Negev vineyards including both white and black grapes. 

Dr Nathan Wales, from the University of York's Department of Archaeology, said: “This is the first time that genetics has been used to identify the colour of an ancient grape, and gives us a glimpse into the internationally famous Gaza wine during the period.  

“It also gave us the opportunity to link ancient seeds with modern varieties that are still grown around the Mediterranean today. 

“Identifying the grape varieties that grew in the Negev during the Byzantine period and the genetic characteristics that were nurtured in these dry, desert conditions, could provide valuable insights into how plant varieties could be developed to resist the extremes of climate conditions today.”

The grapevines made some of the largest profits of any crop in Byzantine times and trade from Negev, with Lebanon and Crete for example, have sprung modern varieties of red wine that are still produced in these areas today.

The research, also in collaboration with the University of Haifa and the Israel Antiquities Authority, is published in the journal Proceedings of the National Academy of Science of the United States of America (PNAS).

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JOURNAL

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.221356312 

Oldest human remains from Puerto Rico reveal a complex cultural landscape since 1800BC

 

IMAGE: VIEW ACROSS BOQUERÓN BAY, CABO ROJO, PUERTO RICO, WITH THE ORTIZ SITE IN THE DISTANCE. view more 

CREDIT: WILLIAM J. PESTLE, CC-BY 4.0 (HTTPS://CREATIVECOMMONS.ORG/LICENSES/BY/4.0/)

The earliest inhabitants of Puerto Rico might have used common burial sites and mortuary practices across many centuries, according to a study published April 26, 2023, in the open-access journal PLOS ONE by William J. Pestle of the University of Miami, Florida and colleagues.

Puerto Rico was inhabited by people for several thousand years prior to the Ceramic Age, but little is known about these earliest inhabitants due to a paucity of evidence and research, with only 20 ancient individuals reported from this time period. In this study, Pestle and colleagues describe five adult individuals from burials at the Ortiz site in Cabo Rojo, southwestern Puerto Rico, representing a substantial addition to archaeological information about this time period.

Radiocarbon dating of the remains yielded ages as old as 1800BC and as young as 800BC, thus including the oldest directly dated human remains from Puerto Rico and representing as much as 1,000 years of burials at the Ortiz site. The mortuary practices, including the positioning of the bodies and the associated grave goods, are similar to other early sites, indicating standard burial practices over many centuries. In addition, Strontium isotope analysis also indicates that these buried individuals were born in different nearby geographical locales. Thus, the Ortiz site might have held cultural significance as a common mortuary space for various local communities.

The authors caution that it is difficult to draw broad conclusions from limited evidence, but these results hint at a long history of persistent and formalized use of a common site over centuries. The earliest inhabitants of Puerto Rico have been traditionally interpreted in a simplistic fashion, but the results from this study and hopefully future studies shed light on what was likely a more vibrant and varied cultural landscape than previously appreciated.

The authors add: “This study assiduously documents the oldest dated burials from the island of Puerto Rico and provides detailed scientific and cultural insights into the lives of some of the earliest people to inhabit that island. We hope that this work contributes to the ongoing re-framing of our understanding of the deep past of Puerto Rico and the Caribbean.”

Searching for ancient bears in an Alaskan cave led to an important human discovery

The first people to live in the Americas migrated from Siberia across the Bering land bridge more than 20,000 years ago. Some made their way as far south as Tierra del Fuego, at the tip of South America. Others settled in areas much closer to their place of origin where their descendants still thrive today.

In “A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska,” published Friday in the journal iScience, University at Buffalo evolutionary biologist Charlotte Lindqvist and collaborators show, using ancient genetic data analyses, that some modern Alaska Natives still live almost exactly where their ancestors did some 3,000 years ago.

Lindqvist, PhD, associate professor of biological sciences in the UB College of Arts and Sciences, is senior author of the paper. In the course of her extensive studies in Alaska, she explored mammal remains that had been found in a cave in the state’s southeast coast. One bone was initially identified as coming from a bear. However, genetic analysis showed it to be the remains of a human female.

“We realized that modern Indigenous peoples in Alaska, should they have remained in the region since the earliest migrations, could be related to this prehistoric individual,” says Alber Aqil, a UB PhD student in biological sciences and the first author of the paper. This discovery led to efforts to solve this mystery, which DNA analyses are well suited to address when archeological remains are as sparse as these were.

Learning from an ancestor

The earliest peoples had already started moving south along the Pacific Northwest Coast before an inland route between ice sheets became viable. Some, including the female individual from the cave, made their home in the area that surrounds the Gulf of Alaska. That area is now home to the Tlingit Nation and three other groups: Haida, Tsimshian, and Nisga’a.

As Aqil and colleagues analyzed the genome from this 3,000-year-old individual — “research that was not possible just 20 years ago,” Lindqvist noted — they determined that she is most closely related to Alaska Natives living in the area today. This fact showed it was necessary to carefully document as clearly as possible any genetic connections of the ancient female to present-day Native Americans.

In such endeavors, it is important to collaborate closely with people living in lands where archeological remains are found. Therefore, cooperation between Alaska Native peoples and the scientific community has been a significant component of the cave explorations that have taken place in the region. The Wrangell Cooperative Association named the ancient individual analyzed in this study as “Tatóok yík yées sháawat” (Young lady in cave).

Genetic continuity in Southeast Alaska persists for thousands of years

Indeed, Aqil and Lindqvist’s research demonstrated that Tatóok yík yées sháawat is in fact closest related to present-day Tlingit peoples and those of nearby tribes along the coast. Their research therefore strengthens the idea that genetic continuity in Southeast Alaska has continued for thousands of years.

Human migration into North America, although it began some 24,000 years ago, came in waves — one of which, about 6,000 years ago — included the Paleo-Inuit, formerly known as Paleo-Eskimos. Importantly for understanding Indigenous peoples’ migrations from Asia, Tatóok yík yées sháawat’s DNA did not reveal ancestry from the second wave of settlers, the Paleo-Inuit. Indeed, the analyses performed by Aqil and Lindqvist helped shed light on the continuing discussion of migration routes, mixtures among people from these different waves, as well as modern territorial patterns of inland and coastal people of the Pacific Northwest in the pre-colonial era.

Oral history links an ancient woman to people living in Southeast Alaska today

The oral origin narratives of the Tlingit people include the story of the most recent eruption of Mount Edgecumbe, which would place them exactly in the region by 4,500 years ago. Tatóok yík yées sháawat, their relative, therefore informs not just modern-day anthropological researchers but also the Tlingit people themselves.

Out of respect for the right of the Tlingit people to control and protect their cultural heritage and their genetic resources, data from the study of Tatóok yík yées sháawat will be available only after review of its use by the Wrangell Cooperative Association Tribal Council.

“It’s very exciting to contribute to our knowledge of the prehistory of Southeast Alaska,” said Aqil.