American Association for the Advancement of Science (AAAS)
A genomic study encompassing more than 300 genomes spanning the last 50,000 years has revealed how a single wave of Neandertal gene flow into early modern humans left an indelible mark on human evolution. Among other findings, the study reports that modern humans acquired several Neanderthal genes that ended up being advantageous to our lineage, including those involved in skin pigmentation, immune response, and metabolism. To date, sequencing of Neanderthal and Denisovan genomes has revealed substantial gene flow between these archaic hominins and modern human ancestors, even as scientists have also reported that Neanderthal ancestry is unevenly distributed across the genome. Moreover, certain regions of the genome – known as archaic deserts – completely lack Neandertal ancestry, while others exhibit high frequencies of Neanderthal variants, potentially due to beneficial adaptive mutations. However, much about the nature of this ancient admixture, including the role evolutionary forces like genetic drift or natural selection played in shaping these patterns, remains unclear. Using genomic data from 334 modern humans, including 59 ancient individuals ranging from 45,000 to 2,200 years old, and 275 present-day individuals from diverse global populations, Leonardo Iasi et al. performed a comprehensive evaluation of Neanderthal ancestry variation in modern humans over the last ~50,000 years. Iasi et al. discovered that the vast majority of Neanderthal gene flow is attributable to a single, shared extended period of gene flow that likely occurred 50,500 to 43,500 years ago, which is consistent with archeological evidence for the overlap of modern humans and Neandertals in Europe. Additionally, the findings demonstrate that Neanderthal ancestry underwent rapid natural selection – both positive and negative – within 100 generations after gene flow, especially on the X chromosome.
Nature is publishing a related paper, “Earliest modern human genomes constrain timing of Neanderthal admixture,
Max Planck Institute for Evolutionary Anthropology
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The researchers identified regions with Neandertal ancestry in over 300 individuals. They assessed sharing of segments, inferred gene flow, and looked at variation to identify candidates for positive and negative selection.
The study of ancient DNA has greatly advanced our knowledge of human evolution, including the discovery of gene flow from Neandertals into the common ancestors of modern humans. Neandertals and modern humans diverged about 500,000 years ago, with Neandertals living in Eurasia for the past 300,000 years. Then, sometime around 40,000 to 60,000 years ago, modern human groups left Africa and spread across Eurasia, encountering Neandertals along the way. As a result, most non-Africans harbor one to two percent Neandertal ancestry today. However, the precise timing and functional legacy of Neandertals remains elusive.
In a new study, researchers from the Max Planck Institute for Evolutionary Anthropology, Leipzig, and the University of California, Berkeley, examined the genomes of 300 present-day and ancient modern humans, including 59 individuals who lived between 2,000 and 45,000 years ago. "We set out to determine the timing and duration of Neandertal gene flow and the resulting impact on modern humans. To do this, we created a catalog of Neandertal ancestry segments. By comparing the segments among individuals from different time periods and geographic locations, we were able to show that the vast majority of Neandertal ancestry can be traced to a single, shared, extended period of gene flow into the common ancestors of all non-African individuals today," says Priya Moorjani from the University of California, Berkeley.
Neandertal ancestry revisited
By observing the length of the Neandertal DNA segments, which is related to the number of generations since the gene flow, the researchers inferred that the gene flow began about 50,000 years ago and continued for about 7,000 years. "This timeline closely matches the archaeological evidence for the overlap of Neandertals and modern humans in Europe. Some early modern humans - Oase, Ust'-Ishim, Zlatý kůň, and Bacho Kiro - possess substantial unique Neandertal ancestry that is not shared with modern humans after 40,000 years," says first author Leonardo Iasi from the Max Planck Institute for Evolutionary Anthropology.
These dates have several implications for human dispersal after the Out-of-Africa event, as they provide a lower bound on the timing of migration and the settlement of regions outside of Africa. For example, this suggests that the major migration out of Africa occurred no later than 43,500 years ago. Moreover, the population receiving Neandertal ancestry may have been highly structured during the gene flow event. "Diversification of humans outside of Africa may have begun during or soon after the Neandertal gene flow, which could partially explain the different levels of Neandertal ancestry among non-African populations and also reconcile our dates with archaeological evidence for the presence of modern humans in Southeast Asia and Oceania by about 47,000 years,“ says Benjamin Peter from the Max Planck Institute for Evolutionary Anthropology and the University of Rochester. "Studying more ancient genomes from Eurasia and Oceania could further our understanding of when humans spread to these regions.“
Functional impact of Neandertal ancestry
To understand the functional legacy of Neandertal ancestry, the researchers examined changes in Neandertal ancestry across the genome and over time. They identified some Neandertal regions that are present at high frequency, possibly because they were beneficial as early modern humans began to explore new environments outside of Africa. "These include genes related to immune function, skin pigmentation and metabolism," says Manjusha Chintalapati from the University of California, Berkeley. "On the other hand, there are also large regions of the genome that are completely devoid of Neandertal ancestry. These regions formed rapidly after the gene flow and were also absent from the earliest modern human genomes, 30,000 to 45,000-year-old individuals. Many Neandertal sequences may have been deleterious to humans and were therefore actively and rapidly selected against by evolution.“
This study sheds light on the complex history of gene flow from Neandertals into modern humans. It also highlights the power of genomic data to elucidate the legacy of human migrations and gene flow.
After modern humans left Africa, they met and interbred with Neandertals, resulting in around two to three percent Neandertal DNA that can be found in the genomes of all people outside Africa today. However, little is known about the genetics of these first pioneers in Europe and the timing of the Neandertal admixture with non-Africans.
A key site in Europe is Zlatý kůň in Czechia, where a complete skull from a single individual who lived around 45,000 years ago was discovered and previously genetically analyzed. However, due to the lack of archaeological context, it was not possible to link this individual to any archaeologically defined group. A nearby site, the Ilsenhöhle in Ranis in Germany, about 230 km from Zlatý kůň, is known for a specific type of archaeology, the Lincombian-Ranisian-Jerzmanowician (LRJ), which dates to around 45,000 years ago. It has long been debated whether the LRJ culture was produced by Neandertals or early modern humans. Although mostly small fragments of bones are preserved in Ranis, a previous study was able to analyze mitochondrial DNA from thirteen of these remains and found that they belonged to modern humans and not Neandertals. However, since the mitochondrial sequence only constitutes a miniscule part of the genetic information, the relationships to other modern humans remained a mystery.
Linking Zlatý kůň and Ranis
A new study published today in Nature analyzed the nuclear genomes of the thirteen specimens from Ranis and found that they represented at least six individuals. The size of the bones indicated that two of these individuals were infants and, genetically, three were males and three were females. Interestingly, among these individuals were a mother and daughter, as well as other, more distant, biological relatives. The team also sequenced more DNA from the female skull found at Zlatý kůň, producing a high-quality genome for this individual. ”To our surprise, we discovered a fifth- or sixth-degree genetic relationship between Zlatý kůň and two individuals from Ranis.” says Arev Sümer, lead author of the study, ”This means that Zlatý kůň was genetically part of the extended family of Ranis and likely also made LRJ-type tools”.
Among the six individuals from Ranis, one bone was particularly well preserved, in fact it is the best preserved modern human bone from the Pleistocene for DNA retrieval. This allowed the team to obtain a high-quality genome from this male individual, referred to as Ranis13. Together, the Ranis13 and Zlatý kůň genomes represent the oldest high-quality modern human genomes sequenced to date. When analyzing genetic variants related to phenotypic traits, they found that Ranis and Zlatý kůň individuals carried variants associated with dark skin and hair color as well as brown eyes, reflecting the recent African origin of this early European population.
By analyzing the segments inherited from the same ancestor in the Ranis and Zlatý kůň genomes, the researchers estimate that their population consisted of at most a few hundred individuals who may have been spread out over a larger territory. The authors found no evidence that this small early modern human population contributed to later Europeans or any other world-wide population.
A narrower timeframe for the shared Neandertal admixture
Members of the Zlatý kůň/Ranis population coexisted with Neandertals in Europe, raising the possibility that they may have had Neandertals among their recent ancestors after they migrated to Europe. Previous studies on modern humans from over 40,000 years ago, had found evidence of such recent admixture events between modern humans and Neandertals. However, no such evidence for recent Neandertal admixture was detected in the genomes of the Zlatý kůň/Ranis individuals. “The fact that modern human groups, which may have arrived in Europe later, carry such Neandertal ancestry while Ranis and Zlatý kůň do not could mean that the older Zlatý kůň/Ranis lineage may have entered Europe by a different route or did not overlap as extensively with the regions where Neandertals lived” speculates Kay Prüfer, who co-supervised the study.
The Zlatý kůň/Ranis population represents the earliest known divergence from the group of modern humans that migrated out of Africa and dispersed later across Eurasia. Despite this early separation, the Neandertal ancestry in Zlatý kůň and Ranis originated from the same ancient admixture event that can be detected in all people outside Africa today. By analyzing the length of the segments contributed from Neandertals in the high-coverage Ranis13 genome and using direct radiocarbon dates on this individual, the researchers dated this shared Neandertal admixture to between 45,000 and 49,000 years ago. Since all present-day non-African populations share this Neandertal ancestry with Zlatý kůň and Ranis, this means that around 45,000 to 49,000 years ago, a coherent ancestral non-African population must still have existed.
“These results provide us with a deeper understanding of the earliest pioneers that settled in Europe,” says Johannes Krause, senior author of the study. “They also indicate that any modern human remains found outside Africa that are older than 50,000 years could not have been part of the common non-African population that interbred with Neanderthals and is now found across much of the world.”
Archaeological context of Kosenivka. A: Map showing the location of the settlement of Kosenivka and the Chalcolithic sites referred to in the text. B: Photo showing the location of house 6 within the landscape. C: Photo showing house 6 being excavated, in 2004 (Map: R. Hofmann. Photos: republished from Kruts et al. [22] under a CC BY license with permission from V. Chabanyuk, original copyright 2005).
Credit: Fuchs et al., 2024, PLOS ONE, CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)
A research group led by Johannes Müller at the Institute of Prehistoric and Protohistoric Archaeology, at Kiel University, Germany, have shed light on the lives of people who lived over 5,600 years ago near Kosenivka, Ukraine. Published on December 11, 2024, in the open-access journal PLOS ONE, the researchers present the first detailed bioarchaeological analyses of human diets from this area and provide estimations on the causes of death of the individuals found at this site.
The people associated with the Neolithic Cucuteni-Trypilla culture lived across Eastern Europe from approximately 5500 to 2750 BCE. With up to 15,000 inhabitants, some of their mega-sites are among the earliest and largest city-like settlements in prehistoric Europe. Despite the vast number of artefacts the Trypillia left behind, archeologists have found very few human remains. Due to this absence, many facets of the lives of this ancient people are still undiscovered.
The researchers studied a settlement site near Kosenivka, Ukraine. Comprised of several houses, this site is unique for the presence of human remains. The 50 human bone fragments recovered among the remains of a house stem from at least seven individuals—children, adults, males and a female, perhaps once inhabitants of the house. The remains of four of the individuals were also heavily burnt. The researchers were keen to explore potential causes for these burns, such as an accidental fire, or a rare form of burial rite.
The burnt bone fragments were largely found in the center of the house, and previous studies surmised the inhabitants of this site died in a house fire. Scrutinizing the pieces of bone under a microscope, the researchers concluded that the burning probably occurred quickly after death. In the case of an accidental fire, the researchers propose that some individuals could have died of carbon monoxide poisoning, even if they fled the house.
According to radiocarbon dating, one of the individuals died ca. 100 years later. The death of this person cannot be connected to the fire, but is otherwise unknown. Two other individuals with unhealed cranial injuries raise the question of whether violence could have played a role as well. A review of Trypillian human bone finds showed the researchers that less than 1% of the dead were cremated, and even more rarely buried within a house.
While bones can help archeologists speculate how ancient people died, these remains can also help us understand how they lived. By analyzing the carbon and nitrogen present in the bones—as well as in grains and the remains of animals found at the site—the researchers determined meat made up less than 10% of the inhabitants’ diets. This is in line with teeth found at the site, which have wear marks that indicate chewing on grains and other plant fibers. That Trypillia diets consisted mostly of plants supports theories that cattle in these cultures were primarily used for manuring the fields and milk rather than meat production.
Katharina Fuchs, first author of the study, adds: “Skeletal remains are real biological archives. Although researching the Trypillia societies and their living conditions in the oldest city-like communities in Eastern Europe will remain challenging, our ‘Kosenvika case’ clearly shows that even small fragments of bone are of great help. By combining new osteological, isotopic, archaeobotanical and archaeological information, we provide an exceptional insight into the lives—and perhaps also the deaths—of these people.”
Africa is the site of the longest history of the habitation of human beings and their ancestors on our planet. It was on the African continent that human history began, with new cultural techniques and strategies of subsistence then being disseminated throughout the entire world. Africa as a continent boasts a fascinating diversity in terms of its natural environment. Human beings in Africa have had to constantly adapt to (environmental) changes and develop new strategies for survival. Such experiences of adaptation are more important today than ever. Archaeological finds and historical visual and written sources offer insights into the arts, crafts, technologies and environmental conditions of bygone eras and provide evidence of dialogues that were maintained across large geographical distances. Excavations at different settlement sites have uncovered urban structures that were contemporaneous with nomadic forms of life.
Planet Africa: Archaeological Time Travel is a unique, intercontinental exhibition project focussing on African archaeology.
Exhibition Sites in Germany and Africa
The exhibition tour will commence at the end of 2024 with the opening at the James-Simon-Galerie in Berlin. The show will then be exhibited in Munich, Chemnitz and other locations throughout Germany. The exhibition will also be presented in parallel at a number of locations across the African continent, where it will be organised by teams of local curators.
The exhibition has already opened in Rabat (Morocco) and Nairobi (Kenya) in November 2024. Planet Africa will be presented in Maputo (Mozambique), Accra (Ghana) and Lobamba (Eswatini) next year. Joint activities between German and African locations are planned.
The exhibition is centred around the results of research conducted by the DFG Priority Programme Entangled Africa. It will incorporate work by African street artists, who will produce illustrations and film works on the featured topics.
An Exhibition in Six Modules
The exhibition sheds light on more than two million years of human history, coupled with more than 200 years of research tradition. The wealth of research is presented in six thematic modules, which collate the key findings:
Variety – Natural Abundance Through Diversity
Becoming Human – The First Crucial Steps
Know-How – Agile Knowledge and Flexible Technology
Signs and Images – Visualising Knowledge
Raw Materials – Exchange, Commerce, Power
New Perspectives – African Archaeology Today
The individual modules repeatedly reference the contemporary research projects that are responsible for contributing many of the images, diagrams and films featured in the exhibition. The modules cover a range of topics, from the origins of the human race to the emergence of new cultural techniques and food strategies that were spread from Africa to the wider world. The result is a comprehensive overview of a continent whose natural diversity continues to fascinate and enthrall, and that has always required the development of new survival strategies due to constant environmental changes, adjustment processes and migratory movements.
Archaeology and Research
Archaeological finds and historical visual and written sources offer a comprehensive insight into the arts, crafts, technologies and environmental conditions of bygone eras and provide evidence of dialogues and connections that were maintained between people across large geographical distances. Excavations at different settlement sites and urban centres have uncovered social and political structures of coexistence that were contemporaneous with nomadic forms of life in many regions of the continent.
The exhibition also showcases the contemporary application of ancient knowledge and the archaeological exploration of their own past by the African researchers and artists involved in the research projects and exhibition. As such, the exhibition also looks at the viability of archaeology as a unifying link for pan-African and intercontinental solidarity.
Curatorial Team
The exhibition project Planet Africa: Archaeological Time Travel is the work of a team of curators led by Jörg Linstädter and Miriam Rotgänger, Commission for Archaeology of Non-European Cultures of the German Archaeological Institute, with support from Wazi Apoh, University of Ghana, Legon, Accra, Gerd-Christian Weniger, museum consultant, Matthias Wemhoff and Ewa Dutkiewicz, Museum für Vor- und Frühgeschichte, and a host of African and German archaeologists.
Credit: Assaf Peretz, Israel Antiquities Authority
CLEVELAND (Dec. 9)—A cave in Galilee, Israel, has yielded evidence for ritualistic gathering 35,000 years ago, the earliest on the Asian continent. Three Israeli researchers led the team that published its results today in the journal Proceedings of the National Academy of Sciences.
And researchers from the Case Western Reserve University (CWRU) School of Dental Medicine helped unearth the cave’s secrets over more than a decade of excavation.
Manot Cave was used for thousands of years as a living space for both Neanderthals and humans at different times. In 2015, researchers from Case Western Reserve helped identify a 55,000-year-old skull that provided physical evidence of interbreeding between Neanderthal and homo sapiens, with characteristics of each clearly visible in the skull fragment.
The cave’s living space was near the entrance, but in the deepest, darkest part of the cave, eight stories below, the new paper describes a large cavern with evidence it was used as a gathering space, possibly for rituals that enhanced social cohesion.
The cavern’s touchstone is an engraved rock, deliberately placed in a niche in the cavern, with a turtle-shell design carved into its surface. The three-dimensional turtle is contemporaneous with some of the oldest cave paintings in France.
“It may have represented a totem or spiritual figure,” said Omry Barzilai, Head of Material Culture PaleoLab at the University of Haifa and the Israel Antiquities Authority, who led the team. “Its special location, far from the daily activities near the cave entrance, suggests that it was an object of worship.”
The cavern has natural acoustics favorable for large gatherings, and evidence of wood ash on nearby stalagmites suggests prehistoric humans carried torches to light the chamber.
Manot Cave was discovered in 2008 by workers building condominiums in a mountain resort close to Israel’s border with Lebanon. Case Western Reserve’s School of Dental Medicine got involved in the excavation in 2012. The dean at the time, Jerold Goldberg, committed $20,000 annually for 10 years to CWRU’s Institute for the Science of Origins; the money was used to fund dental students’ summer research in Israel.
“I’m an oral and maxillofacial surgeon by training,” Goldberg said. “I provided the commitment and the money because I wanted people to understand the breadth and intellectual interest that dental schools have.”
And although not trained in archaeology, dental students can quickly identify bone fragments from rock, which makes them invaluable at excavations like Manot Cave.
“Most people would not suspect that a dental school would be involved in an archaeological excavation,” said Mark Hans, professor and chair of orthodontics at the dental school. “But one of the things that are preserved very well in ancient skeletons are teeth, because they are harder than bone. There is a whole field of dental anthropology. As an orthodontist, I am interested in human facial growth and development, which, it turns out, is exactly what is needed to identify anthropological specimens.”
For 10 years, Case Western Reserve sent 10 to 20 dental students every summer to help with the Manot Cave excavation. The summer research became so popular that students from other dental and medical schools began applying to visit Israel with the CWRU team, according to Yvonne McDermott, the project coordinator.
Case Western Reserve also collaborated closely with Linda Spurlock, a physical anthropologist at Kent State University, whose expertise is putting a face on a skull using clay to build out the tissues that would have covered the bone when the person was alive.
“One of the things I liked most about working on this excavation was how much we learned from the other researchers,” Hans said. “Everyone has a narrow focus, like mammals, uranium-dating, hearths; and we all came together and shared our knowledge. We learned a lot over 10 years.”
The Manot Cave project is supported by the Dan David Foundation, the Israel Science Foundation, the United States-Israel Binational Science Foundation, the Irene Levi Sala CARE Archaeological Foundation and the Leakey Foundation. The research also involved experts from the Israel Antiquities Authority, Cleveland State University, the Geological Survey of Israel, the Hebrew University of Jerusalem, the University of Haifa, Tel Aviv University, Ben-Gurion University, the University of Vienna, the University of Barcelona, the University of Siena and Simon Fraser University.
Reconstruction of the production-consumption process involving pottery and food in early Shangshan culture. (A) Plant procurement: collecting wild plants and harvesting rice; (B) plant processing: for food and pottery making; (C) food processing: cooking food and making qu starter with molds, yeast, and rice; (D) food consumption: eating and drinking.
A collaborative study has uncovered evidence of rice beer dating back approximately 10,000 years at the Shangshan site in Zhejiang Province, China, providing new insights into the origins of alcoholic beverage brewing in East Asia.
This discovery highlights the connection between rice fermentation at Shangshan and the region’s cultural and environmental context as well as the broader development of early rice agriculture and social structures.
The study was jointly conducted by researchers from Stanford University, the Institute of Geology and Geophysics (IGG) of the Chinese Academy of Sciences, and the Zhejiang Provincial Institute of Cultural Relics and Archaeology (ICRA) in China. It was published in the latest issue of Proceedings of the National Academy of Sciences (PNAS) on Dec. 9.
Uncovering Early Alcoholic Beverage Brewing
The research team analyzed twelve pottery sherds from the early phase of the Shangshan site in Pujiang County, Zhejiang Province (10,000–9000 BP). “These sherds were associated with various vessel types, including those for fermentation, serving, storage, cooking, and processing,” said Prof. JIANG Leping from ICRA.
The researchers conducted microfossil extraction and analysis on residues from the inner surfaces of the pottery as well as the pottery clay and surrounding cultural layer sediments.
“We focused on identifying phytoliths, starch granules, and fungi, providing insights into the pottery’s uses and the food processing methods employed at the site,” said Prof. LIU Li from Stanford University, the first author of the paper as well as a co-corresponding author.
Phytolith analysis revealed a significant presence of domesticated rice phytoliths in the residues and pottery clay. “This evidence indicates that rice was a staple plant resource for the Shangshan people,” said Prof. ZHANG Jianping from IGG, also a co-corresponding author of the study.
Evidence also showed that rice husks and leaves were used in pottery production, further demonstrating the integral role of rice in Shangshan culture.
The team also found a variety of starch granules in the pottery residues, including rice, Job's tears, barnyard grass, Triticeae, acorns, and lilies. Many of the starch granules exhibited signs of enzymatic degradation and gelatinization, which are characteristic of fermentation processes.
In addition, the study uncovered abundant fungal elements, including Monascus molds and yeast cells, some of which displayed developmental stages typical of fermentation. These fungi are closely associated with qu starters used in traditional brewing methods, such as those used in producing hongqujiu (red yeast rice wine) in China.
The research team analyzed the distribution of Monascus and yeast remains across different pottery vessel types, observing higher concentrations in globular jars compared to a cooking pot and a processing basin. This distribution suggests that vessel types were closely linked to specific functions, with globular jars purposely produced for alcohol fermentation.
The findings suggest that the Shangshan people employed broad-spectrum subsistence strategies during the early phases of rice domestication and used pottery vessels, particularly globular jars, to brew qu-based rice alcoholic beverages.
Linking Technology, Agriculture, and Climate
The emergence of this brewing technology in the early Shangshan culture was closely linked to rice domestication and the warm, humid climate of the early Holocene.
“Domesticated rice provided a stable resource for fermentation, while favorable climatic conditions supported the development of qu-based fermentation technology, which relied on the growth of filamentous fungi,” said Prof. LIU.
To rule out potential contamination from soil, the researchers analyzed sediment control samples, revealing significantly fewer starch and fungal remains in these samples than in pottery residues.
This finding reinforces the conclusion that the residues were directly associated with fermentation activities. Modern fermentation experiments using rice, Monascus, and yeast further validated the findings by demonstrating morphological consistency with the fungal remains identified on Shangshan pottery.
“These alcoholic beverages likely played a pivotal role in ceremonial feasting, highlighting their ritual importance as a potential driving force behind the intensified utilization and widespread cultivation of rice in Neolithic China,” said Prof. LIU.
The evidence of rice alcohol fermentation at Shangshan represents the earliest known occurrence of this technology in East Asia, offering new insights into the complex interplay between rice domestication, alcoholic beverage production, and social formation during the early Holocene in China.
The research was supported by the Min Kwaan Chinese Archaeology Program at Stanford University and the National Natural Science Foundation of China.
