Tarim Basin mummies genomic study genetics

The surprising origins of the Tarim Basin mummies

The surprising origins of the Tarim Basin mummies

Genomic study of the Tarim Basin mummies in western China reveals an indigenous Bronze Age population that was genetically isolated but culturally cosmopolitan

In a new study, an international team of researchers has determined the genetic origins of Asia’s most enigmatic mummies - the Tarim Basin mummies in western China. Once thought to be Indo-European speaking migrants from the West, the Bronze Age Tarim Basin mummies are revealed to be a local indigenous population with deep Asian roots and taste for far-flung cuisine.

Tarim Basin mummies genomic study genetics
Aerial view of the Xiaohe cemetery. Credits: Wenying Li, Xinjiang Institute of Cultural Relics and Archaeology

As part of the Silk Road and located at the geographical intersection of Eastern and Western cultures, the Xinjiang Uyghur Autonomous Region has long served as a major crossroads for trans-Eurasian exchanges of people, cultures, agriculture, and languages. Since the late 1990s, the discovery of hundreds of naturally mummified human remains dating to circa 2,000 BCE to 200 CE in the region’s Tarim Basin has attracted international attention due to their so-called ‘Western’ physical appearance, their felted and woven woolen clothing, and their agropastoral economy that included cattle, sheep and goat, wheat, barley, millet, and even kefir cheese. Buried in boat coffins in an otherwise barren desert, the Tarim Basin mummies have long puzzled scientists and inspired numerous theories as to their enigmatic origins.

Excavation of burial M75 at the Xiaohe cemetery. Credits: Wenying Li, Xinjiang Institute of Cultural Relics and Archaeology

The Tarim Basin mummies’ cattle-focused economy and unusual physical appearance had led some scholars to speculate that they were the descendants of migrating Yamnaya herders, a highly mobile Bronze Age society from the steppes of the Black Sea region of southern Russia. Others have placed their origins among the Central Asian desert oasis cultures of the Bactria-Margiana Archaeological Complex (BMAC), a group with strong genetic ties to early farmers on the Iranian Plateau.

To better understand the origin of the Tarim Basin mummies’ founding population, who first settled the region at sites such as Xiaohe and Gumugou circa 2,000 BCE, a team of international researchers from Jilin University, the Institute of Vertebrate Paleontology and Paleoanthropology, the Max Planck Institute for Evolutionary Anthropology, Seoul National University of Korea, and Harvard University generated and analyzed genome-wide data from thirteen of the earliest known Tarim Basin mummies, dating to circa 2,100 to 1,700 BCE, together with five individuals dating to circa 3,000 to 2,800 BCE in the neighboring Dzungarian Basin. This is the first genomic-scale study of prehistoric populations in the Xinjiang Uyghur Autonomous Region, and it includes the earliest yet discovered human remains from the region.

The Tarim Basin mummies were not newcomers to the region

Typical Xiaohe boat coffin with oar. The coffin is covered with a cattle hide. Credits: Wenying Li, Xinjiang Institute of Cultural Relics and Archaeology

To their great surprise, the researchers found that the Tarim Basin mummies were not newcomers to the region at all, but rather appear to be direct descendants of a once widespread Pleistocene population that had largely disappeared by the end of the last Ice Age. This population, known as the Ancient North Eurasians (ANE), survives only fractionally in the genomes of present-day populations, with Indigenous populations in Siberia and the Americas having the highest known proportions, at about 40 percent. In contrast to populations today, the Tarim Basin mummies show no evidence of admixture with any other Holocene groups, forming instead a previously unknown genetic isolate that likely underwent an extreme and prolonged genetic bottleneck prior to settling the Tarim Basin.

“Archaeogeneticists have long searched for Holocene ANE populations in order to better understand the genetic history of Inner Eurasia. We have found one in the most unexpected place,” says Choongwon Jeong, a senior author of the study and a professor of Biological Sciences at Seoul National University.

In contrast to the Tarim Basin, the earliest inhabitants of the neighboring Dzungarian Basin descended not only from local populations but also from Western steppe herders, namely the Afanasievo, a pastoralist group with strong genetic links to the Early Bronze Age Yamanya. The genetic characterization of the Early Bronze Age Dzungarians also helped to clarify the ancestry of other pastoralist groups known as the Chemurchek, who later spread northwards to the Altai mountains and into Mongolia. Chemurchek groups appear to be the descendants of Early Bronze Age Dzungarians and Central Asian groups the from Inner Asian Mountain Corridor (IAMC), who derive their ancestry from both local populations and BMAC agropastoralists.

“These findings add to our understanding of the eastward dispersal of Yamnaya ancestry and the scenarios under which admixture occurred when they first met the populations of Inner Asia,” says Chao Ning, co-lead author the study and a professor of School of Archaeology and Museology at Peking University.

The Tarim Basin groups were genetically but not culturally isolated

Tarim Basin mummies genomic study genetics
A naturally mummified woman from burial M11 of the Xiaohe cemetery. Credits: Wenying Li, Xinjiang Institute of Cultural Relics and Archaeology

These findings of extensive genetic mixing all around the Tarim Basin throughout the Bronze Age make it all the more remarkable that the Tarim Basin mummies exhibited no evidence of genetic admixture at all. Nevertheless, while the Tarim Basin groups were genetically isolated, they were not culturally isolated. Proteomic analysis of their dental calculus confirmed that cattle, sheep, and goat dairying was already practiced by the founding population, and that they were well aware of the different cultures, cuisines, and technologies all around them.

“Despite being genetically isolated, the Bronze Age peoples of the Tarim Basin were remarkably culturally cosmopolitan – they built their cuisine around wheat and dairy from the West Asia, millet from East Asia, and medicinal plants like Ephedra from Central Asia,” says Christina Warinner, a senior author of the study, a professor of Anthropology at Harvard University, and a research group leader at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

“Reconstructing the origins of the Tarim Basin mummies has had a transformative effect on our understanding of the region, and we will continue the study of ancient human genomes in other eras to gain a deeper understanding of the human migration history in the Eurasian steppes,” adds Yinquiu Cui, a senior author of the study and professor in the School of Life Sciences at Jilin University.

Tarim Basin mummies genomic study genetics
A profile view of the burial M13 from the Xiaohe cemetery. Credits: Wenying Li, Xinjiang Institute of Cultural Relics and Archaeology

References:

The genomic origins of the Bronze Age Tarim Basin mummies, Nature, DOI: 10.1038/s41586-021-04052-7

 

Press release from the Max Planck Institute for Evolutionary Anthropology.


Origin of domestic horses finally established

Origin of domestic horses finally established

origin domestic horses domestic horse
Origin of domestic horses finally established. Farmer catching horses in north-central Kazakhstan. © Ludovic ORLANDO / CAGT / CNRS Photothèque

Horses were first domesticated in the Pontic-Caspian steppes, northern Caucasus, before conquering the rest of Eurasia within a few centuries. These are the results of a study led by paleogeneticist Ludovic Orlando, CNRS, who headed an international team including l’Université Toulouse III - Paul Sabatier, the CEA and l’Université d’Évry. Answering a decades-old enigma, the study is published in Nature on 20 October 2021.

By whom and where were modern horses first domesticated? When did they conquer the rest of the world? And how did they supplant the myriad of other types of horses that existed at that time? This long-standing archaeological mystery finally comes to an end thanks to a team of 162 scientists specialising in archaeology, palaeogenetics and linguistics.

A few years ago, Ludovic Orlando's team looked at the site of Botai, Central Asia, which had provided the oldest archaeological evidence of domestic horses. The DNA results, however, were not compliant: these 5500-year-old horses were not the ancestors of modern domestic horses1. Besides the steppes of Central Asia, all other presumed foci of domestication, such as Anatolia, Siberia and the Iberian Peninsula, had turned out to be false.

We knew that the time period between 4,000 to 6,000 years ago was critical but no smoking guns could ever be found” says CNRS research professor Orlando.

The scientific team, therefore, decided to extend their study to the whole of Eurasia by analysing the genomes of 273 horses that lived between 50,000 and 200 years BC. This information was sequenced at the Centre for Anthropobiology and Genomics of Toulouse (CNRS/Université Toulouse III - Paul Sabatier) and Genoscope2 (CNRS/CEA/Université d’Évry) before being compared with the genomes of modern domestic horses.

This strategy paid off: although Eurasia was once populated by genetically distinct horse populations, a dramatic change had occurred between 2000 and 2200 BC.

That was a chance: the horses living in Anatolia, Europe, Central Asia and Siberia used to be genetically quite distinct” notes Dr Pablo Librado, first author of the study.

Then, a single genetic profile, previously confined to the Pontic steppes (North Caucasus)3, began to spread beyond its native region, replacing all the wild horse populations from the Atlantic to Mongolia within a few centuries.

The genetic data also point to an explosive demography at the time, with no equivalent in the last 100,000 years” adds Orlando. “This is when we took control over the reproduction of the animal and produced them in astronomic numbers.”

But how can this rapid population growth be explained? Interestingly, scientists found two striking differences between the genome of this horse and those of the populations it replaced: one is linked to a more docile behaviour and the second indicates a stronger backbone. The researchers suggest that these characteristics ensured the animals’ success at a time when horse travel was becoming “global”.

The study also reveals that the horse spread throughout Asia at the same time as spoke-wheeled chariots and Indo-Iranian languages. However, the migrations of Indo-European populations, from the steppes to Europe during the third millennium BC4 could not have been based on the horse, as its domestication and diffusion came later. This demonstrates the importance of incorporating the history of animals when studying human migrations and encounters between cultures.

origine cheval
Origin of domestic horses finally established. Horse mandible excavated from the Ginnerup archaeological site, Denmark, June 2021. (This site was included in the study.) © Lutz Klassen, East Jutland Museum

This study was directed by the the Centre for Anthropobiology and Genomics of Toulouse (CNRS/ Université Toulouse III – Paul Sabatier) with help from Genoscope (CNRS/CEA/Université d’Évry). The French laboratories Archéologies et sciences de l'Antiquité (CNRS/Université Paris 1 Panthéon Sorbonne/Université Paris Nanterre/Ministère de la Culture), De la Préhistoire à l'actuel: culture, environnement et anthropologie (CNRS/Université de Bordeaux/Ministère de la Culture) and Archéozoologie, archéobotanique : sociétés, pratiques et environnements (CNRS/MNHN) also contributed, as did 114 other research institutions throughout the world. The study was primarily funded by the European Research Council (Pegasus project) and France Genomique (Bucéphale project).

Some previous results of the Pegasus project:

Notes

1 Read this press release: Unsaddling old theory on origin of horses, 22 February 2018.
2 Genoscope is a department of CEA-Jacob.
3 The Pontic steppe is the western part of the Eurasian steppe. The home of the modern domestic horse is thought to be in the Don and Volga basins, east of the Dnieper.
4 For example, see this press release: 7,000 years of demographic history in France, 25 May 2020.

 

Press release from CNRS on the study, published on Nature, concerning the origin of domestic horses.

The new study on the origin of domestic horses, references:

Librado, P., (...), Orlando, Ludovic (2021). "The origins and spread of domestic horses from the Western Eurasian steppes". Nature, 20/10/2021. DOI: 10.1038/s41586-021-04018-9

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Horses were domesticated in the Northern Caucasus steppes and then spread across Asia and Europe

 

A large group of researchers have conducted the largest genetic study carried out to date, which has made it possible to determine that the horses from which all current domestic horses descend were first domesticated in the steppes north of the Caucasus and, from there, spread to other regions of Asia and Europe.

Researchers from the Milá y Fontanals Institution (IMF) and the Institute of Archaeology (IAM) of the Spanish National Research Council (CSIC), together with scientists from the Museum of Human Evolution (MEH), the Faculty of Veterinary Medicine of the University of Extremadura (UEx), the UCM-ISCIII Joint Centre for Human Evolution and Behaviour in Madrid, the Laboratory of Prehistoric Archaeology of the University Jaume I of Castellón (UJI) and the Faculty of Geological Sciences of the Complutense University of Madrid (UCM)have participated in the largest genetic study carried out to date, which has made it possible to determine that the horses from which all current domestic horses descend were first domesticated in the steppes north of the Caucasus and, from there, spread to other regions of Asia and Europe.

This study brings to an end a long-standing debate about the location and chronology of the earliest documented evidence of domestication of the horses that gave rise to today's populations, as well as aswering questions about when this domestication process began to spread to other regions of the world, thus replacing other types of horses that existed at the time. The results have been published in the October issue of prestigious international journal Nature.

This conclusion was reached by a team of 114 institutions and 162 researchers specialising in archaeology, palaeogenetics and linguistics, led by Professor Ludovic Orlando, CNRS researcher and principal investigator of the ERC-PEGASUS project, which, together with France Genomique-Projet Bucéphale, financed the research. The study involved sequencing the genomes of 273 remains of horses that inhabited various regions of Eurasia in a chronological arc extending from 50,000 to 200 BC. All the genetic information was sequenced at the Centre for Anthropobiology and Genomics of Toulouse, CAGT (CNRS/University of Toulouse III-Paul Sabatier) and Genoscope (CNRS/CEA/University of Évry), before being compared to the genomes of modern domestic horses. Thanks to the large battery of statistical analyses carried out, it has been possible to establish that between 2,200 and 2,000 BC, a drastic change took place in which the genetic profile existing in the Pontic steppes began to spread beyond its region of origin, thus replacing in a few centuries all wild horse populations from the Atlantic to Mongolia.

According to L. Orlando, "this replacement in the genetic composition of Eurasian populations is associated with significant genomic differences between this new type of horse and the horses of the populations that disappeared. On the one hand, this new type of horse from the steppes of the northern Caucasus had a more docile behaviour and, on the other hand, a more robust constitution in the vertebral skeleton".

The researchers suggest that these characteristics triggered the successful selection of these animals, at a time when horse travel was becoming widespread in Eurasia.

According to Pablo Librado (CNRS), first author of this research, "this study has also shown that the distribution of this new type of horse in Asia coincides with the appearance of light carts and the spread of Indo-Iranian languages. In contrast, the migration of Indo-European populations from the steppe zone to the heart of Europe during the third millennium BC did not use this new type of horse as a vector for its expansion. This result demonstrates the importance of also incorporating the genetic history of animals when analysing the dimension of human migrations and intercultural contacts".

The individuals analysed include equids from various sites on the Iberian Peninsula, including Casas del Turuñuelo (Guareña, Badajoz) and Cova Fosca (Alt Maestrat, Castelló).

The Cova Fosca was excavated by Francesc Gusi and Carmen Olaria. According to C. Olaria, professor of Prehistory at the UJI and co-author of this study,

"Cova Fosca has a very rich Holocene archaeozoological record. We were able to identify horse remains in ancient Neolithic levels, a very rare taxon in Iberian sites from this period. This uniqueness allowed us to publish years ago, together with Jaime Lira Garrido and Juan Luis Arsuaga, the first mitochondrial sequences of horses from this site".

According to J. L. Arsuaga, scientific director of the Museum of Human Evolution, professor of Palaeontology at the UCM, director of the UCM-ISCIII Joint Centre and co-author of this study,

"in Cova Fosca we found a unique mitochondrial lineage exclusive to Iberia that currently appears in very few horses, all of which are Iberian or of Iberian origin. In this new study we aimed to unveil the genomic secrets of the Cova Fosca".

Building Tartessos and Casas del Turuñuelo

origin domestic horses horse
A new study on the origin of domestic horses.View of animal slaughter documented in the courtyard of the building at Casas del Turuñuelo

Casas del Turuñuelo is one of the most impressive discoveries in peninsular archaeology in recent years. Its excavations are being carried out under a project directed by the IAM-CSIC and are being co-directed by Esther Rodríguez González and Sebastián Celestino, also researchers at the IAM-CSIC.

According to Esther Rodríguez González, co-author of this new study, "Turuñuelo is an architectural complex from the middle of the first millennium BC belonging to the Tartessos culture where we have found the largest hecatomb documented to date in a site of Mediterranean protohistory. This mass slaughter is notable for the large number of equids that have been differentiated in the courtyard of this site. For this study we selected Equid 4".According to Sebastián Celestino, also co-author of this research, "a multidisciplinary team of specialists from the humanities and biosciences has been created around Turuñuelo, which is generating a constant exchange of information and ideas, thus offering a great multidisciplinary approach to the study of this site".

Among the lines of research of "Construyendo Tartessos" [Building Tartessos], the genetic study of these slaughtered equids stands out. Jaime Lira Garrido (UEx/Centro Mixto UCM-ISCIII), who is a co-author of this study, explains that

"this latest work led by Professor Orlando has also allowed us to delve deeper into the evolutionary history of Iberian horses. In a previous study, Orlando and his team discovered that a genomic lineage developed on the Iberian Peninsula that is now extinct and very different from the rest of the ancient and modern Eurasian horse lineages described to date. The evolutionary origin of this lineage and the causes that led to its disappearance are still unknown. However, we have been able to identify in the Neolithic sample from the Cova Fosca the oldest evidence of this extinct lineage and that the Turuñuelo Equid 4 was, nevertheless, a descendant of this new type of horse that was so rapidly distributed throughout the known world some 4.000 years ago".

This study has been funded mainly by the European Research Council (PEGASUS project) and France Genomique (Bucéphale project).

 

Press release from Asociación RUVID on the new study on the origin of domestic horses.

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South Ural State University (SUSU) scientists and their foreign colleagues have continued study devoted to the time and place of horse domestication. A research group has established where exactly the focus of domestication is located in Eurasia. The results of the work have been published in the highly rated journal “Nature” (Top 10%).

The identical signs have been found in the genomes of domesticated horses in Eurasia. Specialists have noticed that remains of these animals have a strong spine. Probably, this is the reason for domesticated horses popularity and global spreading of horse travels.

The research group which includes PhD, SUSU professor Andrey Epimakhov has established the Pontic-Caspian steppes, northern Caucasus, is the centre of horse domestication. The process has occurred between 2000 and 2200 BC (the Bronze Age). Horses are distinct i n different presumed foci of domestication such as Anatolia, Siberia and the Iberian Peninsula, but several ages later the common genome has spreaded from the Atlantic to Mongolia within a few centuries.

Our research group that is led by paleo-geneticist Ludovic Orlando, National Center for Scientific Research (France), has analysed the genomes of 273 horses that lived between 50,000 and 200 years BC. The study has covered the whole of Eurasia to research presumed territories to be considered as primary foci of domestication. However, all of the territories have turned out to be false. For instance, the site of Botai, Central Asia, has provided the oldest archaeological evidence of domestic horses. Nevertheless, the DNA results are not compliant: these 5500-year-old horses are not the ancestors of modern domestic horses. On the contrary, the Ural 4000 years old samples don’t raise doubts in horse exploitation and chariot teams,” Andrey Epimakhov explained.

Research has also demonstrated that the horse spread throughout Asia at the same time as spoke-wheeled chariots and Indo-Iranian languages.

Remind that dental calculus research has helped scientists to determine the time and place of horse domestication. There are dairy diet markers that have been detected in samples found in the Volga region. Milk has been a part of people's ration since animal domestication.

 

Press release from the South Ural State University on the new study on the origin of domestic horses.


Native American Japan debunked Jomon

Popular theory of Native American origins coming from Japan debunked

Popular theory of Native American origins debunked by genetics and skeletal biology

Latest scientific findings suggest the ancestral Native American population does not originate in Japan, as believed by many archeologists

Native American Japan debunked Jomon
Popular theory of Native American origins coming from Japan, debunked by genetics and skeletal biology. Jomon teeth vs Native American teeth. Photo credits: G. Richard Scott, University of Nevada Reno

A widely accepted theory of Native American origins coming from Japan has been attacked in a new scientific study, which shows that the genetics and skeletal biology “simply does not match-up”.

The findings, published today in the peer-reviewed journal PaleoAmerica, are likely to have a major impact on how we understand Indigenous Americans’ arrival to the Western Hemisphere.

Based on similarities in stone artifacts, many archaeologists currently believe that Indigenous Americans, or ‘First Peoples’, migrated to the Americas from Japan about 15,000 years ago.

It is thought they moved along the northern rim of the Pacific Ocean, which included the Bering Land Bridge, until they reached the northwest coast of North America.

From there the First Peoples fanned out across the interior parts of the continent and farther south, reaching the southern tip of South America within less than two thousand years.

The theory is based, in part, on similarities in stone tools made by the ‘Jomon’ people (an early inhabitant of Japan, 15,000 years ago), and those found in some of the earliest known archaeological sites inhabited by ancient First Peoples.

But this new study, out today in PaleoAmerica – the flagship journal of the Center for the Study of the First Americans at Texas A&M University – suggests otherwise.

Carried out by one of the world’s foremost experts in the study of human teeth and a team of Ice-Age human genetics experts, the paper analysed the biology and genetic coding of teeth samples from multiple continents and looked directly at the Jomon people.

“We found that the human biology simply doesn’t match up with the archaeological theory,” states lead author Professor Richard Scott, a recognized expert in the study of human teeth, who led a team of multidisciplinary researchers.

“We do not dispute the idea that ancient Native Americans arrived via the Northwest Pacific coast—only the theory that they originated with the Jomon people in Japan.

“These people (the Jomon) who lived in Japan 15,000 years ago are an unlikely source for Indigenous Americans. Neither the skeletal biology or the genetics indicate a connection between Japan and the America. The most likely source of the Native American population appears to be Siberia.”

In a career spanning almost half a century, Scott – a professor of anthropology at the University of Nevada-Reno – has traveled across the globe, collecting an enormous body of information on human teeth worldwide, both ancient and modern.  He is the author of numerous scientific papers and several books on the subject.

This latest paper applied multivariate statistical techniques to a large sample of teeth from the Americas, Asia, and the Pacific, showing that quantitative comparison of the teeth reveals little relationship between the Jomon people and Native Americans. In fact, only 7% of the teeth samples were linked to the non-Arctic Native Americans (recognized as the First Peoples).

And, the genetics show the same pattern as the teeth—little relationship between the Jomon people and Native Americans.

“This is particularly clear in the distribution of maternal and paternal lineages, which do not overlap between the early Jomon and American populations,” states co-author Professor Dennis O’Rourke, who was joined by fellow human geneticists – and expert of the genetics of Indigenous Americans – at the University of Kansas, Jennifer Raff.

“Plus, recent studies of ancient DNA from Asia reveal that the two peoples split from a common ancestor at a much earlier time,” adds Professor O’Rourke.

Together with their colleague and co-author Justin Tackney, O’Rourke and Raff reported the first analysis of ancient DNA from Ice-Age human remains in Alaska in 2016.

Other co-authors include specialists in Ice-Age archaeology and ecology.

Shortly before publication of the paper, two other new studies on related topics were released.

A new genetics paper on the modern Japanese population concluded that it represents three separate migrations into Japan, rather than two, as previously believed. It offered more support to the authors’ conclusions, however, about the lack of a biological relationship between the Jomon people and Indigenous Americans.

And, in late September, archaeologists reported in another paper the startling discovery of ancient footprints in New Mexico dating to 23,000 years ago, described as “definitive evidence” of people in North America before the Last Glacial Maximum—before expanding glaciers probably cut off access from the Bering Land Bridge to the Western Hemisphere. It remains unclear who made the footprints and how they are related to living Native Americans, but the new paper provides no evidence that the latter are derived from Japan.

Professor Scott concludes that “the Incipient Jomon population represents one of the least likely sources for Native American peoples of any of the non-African populations.”

Limitations of the study include that available samples of both teeth and ancient DNA for the Jomon population are less than 10,000 years old, i.e., do not antedate the early Holocene (when the First Peoples are understood to arrive in America).

“We assume,” the authors explain however, “that they are valid proxies for the Incipient Jomon population or the people who made stemmed points in Japan 16,000–15,000 years ago.”

 

Peopling the Americas: Not “Out of Japan”, PaleoAmerica
(13-Oct-2021), DOI: 10.1080/20555563.2021.1940440

 

Press release from Taylor & Francis Group on the popular theory of Native American origins coming from Japan, debunked by genetics and skeletal biology.


hepatitis B

New research analyses the evolution of the last ten thousand years of the hepatitis B virus

The University of Valencia participates in a research on the evolution of the last ten thousand years of the hepatitis B virus

A study published in the journal Science traces the evolution of the hepatitis B virus from prehistory to the present, revealing dissemination routes and changes in viral diversity. Domingo Carlos Salazar García, researcher from the Prehistory, Archeology and Ancient History Department of the University of Valencia, has participated in this study led by the Max Planck Institute for the Science of Human History (Germany). The research uncovers the evolution of the hepatitis B virus since the Early Holocene by analyzing the largest dataset of ancient viral genomes produced to date.

hepatitis B
Domingo Carlos Salazar García, researcher from the Prehistory, Archeology and Ancient History Department of the University of Valencia

“This research puts upfront a reality many times ignored but obvious, that viruses have been linked to humans since prehistoric times”, highlighted Salazar, graduated in Medicine and in History, researcher of excellence of the Valencian Community at the University of Valencia. “If SARS-COV-2 has been able to put human societies in check worldwide during the twenty-first century, we can only begin to imagine how viral diseases influenced life in prehistoric times”, he explains. “Historians and archaeologists must start considering more the influence of viruses and other agents that until now have been invisible on the archaeological record when reconstructing past lifestyles”, he says.

The hepatitis B virus (HBV) is a major health problem worldwide, causing close to one million deaths each year. Recent ancient DNA studies have shown that HBV has been infecting humans for millennia, but its past diversity and dispersal routes remain largely unknown. A new study conducted by a large team of researchers from all around the world provides major insights into the evolutionary history of HBV by examining the virus’ genomes from 137 ancient Eurasians and Native Americans dated between ~10,500 and ~400 years ago. Their results highlight dissemination routes and shifts in viral diversity that mirror well-known human migrations and demographic events, as well as unexpected patterns and connections to the present.

Present-day HBV strains are classified into nine genotypes, two of which are found predominantly in populations of Native American ancestry. The study provides strong evidence that these strains descend from an HBV lineage that diverged around the end of the Pleistocene and was carried by some of the first inhabitants of the Americas.

“Our data suggest that all known HBV genotypes descend from a strain that was infecting the ancestors of the First Americans and their closest Eurasian relatives around the time these populations diverged”, says Denise Kühnert, leader of the research group.

 

HBV in prehistoric Europe

The study also shows that the virus was present in large parts of Europe as early as 10,000 years ago, before the spread of agriculture to the continent. “Many human pathogens are thought to have emerged after the introduction of agriculture, but HBV was clearly already affecting prehistoric hunter-gatherer populations”, says Johannes Krause, director of the Department of Archaeogenetics at the Max Planck Institute for Evolutionary Anthropology and co-supervisor of the study.

After the Neolithic transition in Europe, the HBV strains carried by hunter-gatherers were replaced by new strains that were likely spread by the continent’s first farmers, mirroring the large genetic influx associated with the expansion of farming groups across the region. These new viral lineages continued to prevail throughout western Eurasia for around 4,000 years. The dominance of these strains lasted through the expansion of Western Steppe Herders around 5,000 years ago, which dramatically altered the genetic profile of Europeans but remarkably was not associated with the spread of new HBV variants.

 

The collapse and re-emergence of pre-historic HBV

One of the most surprising findings of the study is a sudden decline of HBV diversity in western Eurasia during the second half of the 2nd millennium BCE, a time of major cultural shifts, including the collapse of large Bronze Age state societies in the eastern Mediterranean region.

“This could point to important changes in epidemiological dynamics over a very large region during this period, but we will need more research to understand what happened”, says Arthur Kocher, lead author and researcher in the group.

All ancient HBV strains recovered in western Eurasia after this period belonged to new viral lineages that still prevail in the region today. However, it appears that one variant related to the previous prehistoric diversity of the region has persisted to the present. This prehistoric variant has evolved into a rare genotype that seems to have emerged recently during the HIV pandemic, for reasons that remain to be understood.

 

Article: Kocher et al. “Ten millennia of hepatitis B virus evolution”, Science, 2021. DOI: https://www.science.org/doi/10.1126/science.abi5658

Press release from the University of Valencia and Asociación RUVID.


Oldest Acheulean North Africa Oued Boucherit

The oldest Acheulean evidence in North Africa

The oldest Acheulean evidence in North Africa

The CENIEH in collaboration with CNRPAH leads a study reporting the discovery of the oldest Acheulean lithic assemblage found in North Africa, dated to about 1.7 million years
Oldest Acheulean North Africa Oued Boucherit
View of the valley of Oued Boucherit (Algeria). Photo credits: Mathieu Duval

A new work published in the journal Quaternary Science Reviews, led by the Centro Nacional de Investigación sobre la Evolución Humana (CENIEH) in collaboration with the Centre National de Recherches Préhistoriques, Anthropologiques et Historiques (CNRPAH) (Algeria), describes the most recent advances in the current investigation performed in the valley of Oued Boucherit, located about 20 km east of the city of Sétif (Algeria).

There, the sedimentary deposits hosts a unique succession of fossiliferous and archaeological levels ranging from 3.9 Ma to 1.7 Ma. Perhaps the most noticeable outcome of this work is the discovery of the oldest evidence of Acheulean lithic industries in North Africa. Dated to 1.7 million years (Ma), it is about 400,000 years older than those recently reported at Thomas Quarry locality (Casablanca, Morocco).

'This is an exceptional discovery', indicates Dr Mathieu Duval, Ramón y Cajal Researcher at CENIEH and lead author of the work, 'because it could drastically modify our vision and understanding of early human origins and migrations throughout the African continent'.

While the French paleontologist Camille Arambourg already mentioned in the 1950s the presence of Acheulean lithic industries (typically characterized by the presence of tools like handaxes or picks) in that area, their exact origin has remained unclear until now. Field prospections carried out over the last years have allowed to find new lithic pieces, and more importantly, to define a clear stratigraphic context and provide an age.

In 2018, another important discovery from this same area was published in the journal Science: the oldest lithic industries (Oldowan-like; typically characterized by small flakes and pebble tools) in North Africa, dated to 2.4 Ma. ‘Now, Oued Boucherit hosts the oldest Oldowan and Acheulean lithic assemblages found in North Africa’ says Prof. Mohamed Sahnouni, coordinator of the Archaeology Program at CENIEH and co-author of the work. ‘This area allows us to precisely study the emergence and evolution of Acheulean and Oldowan lithic industries, like perhaps very few other localities in Africa,’ adds the researcher who has been actively working in the area since the 1990s.

These discoveries drastically change our current vision about the origin and dispersion of the first lithic industries within Africa. Currently, the oldest Oldowan and Acheulean evidence are located in East Africa, dating to about 2.6 million years (Ma) and 1.8 Ma, respectively. Less than 5 years ago, the evidence was more than half a million years older than those found in North Africa.

Oldest Acheulean North Africa
Biface stone tool from Oued Boucherit (Algeria) dated to 1.7 million years. Photo credits: Mohamed Sahnouni

Now, the recent discoveries made at Oued Boucherit indicate instead that these industries appear in North Africa very close in time to those in East Africa. While these results may suggest in first instance a much faster dispersion of these lithic industries from East Africa than previously anticipated, the plausibility of a multiple African origin scenario for stone tool manufacture and use cannot be discarded.

At the forefront of geochronology

‘This work perfectly illustrates the reason why the Geochronology and Geology Program was designed’ explains Prof. J.M. Parés, Coordinator of this Program and co-author of the article. ‘Thanks to a combination of various dating methods applied at CENIEH, namely palaeomagnetism and Electron Spin Resonance dating, we have been able to provide a solid chronological framework to such an old site, something perhaps unthinkable 20 years ago,’ concludes the researcher.

The Geochronology and Geology Program at CENIEH, Spain, hosts a unique combination of world-class facilities and international researchers fully dedicated to Human Evolutionary studies. One of the main research lines of the program consists in of refining the chronology of the early human occupations in the Mediterranean area, with a special emphasis on the combination of different dating methods in order to obtain more robust chronologies. The work at Oued Boucherit is just the latest example of this investigation carried out for more than a decade since the inauguration of the Centre in 2009.

Full bibliographic information:
Duval M., Sahnouni M., Parés J.M., van der Made J., Abdessadok S., Harichane Z., Chelli Cheheb R., Boulaghraif K., Pérez-González A. (2021). The Plio-Pleistocene sequence of Oued Boucherit (Algeria): a unique chronologically-constrained archaeological and paleontological record in North Africa. Quaternary Science Reviews 271. https://doi.org/10.1016/j.quascirev.2021.107116.
Press release from CENIEH

Bronze Age Scandinavia's trading networks for copper settled

Bronze Age Scandinavia's trading networks for copper settled

Crossing the North Sea before crossing the Alps!

trading bronze age Scandinavia's
Shafthole axe type Fårdrup. This axe is of Nordic craftsmanship and hides information on the first attempt to establish trading networks with societies across the Alps. A small group of these Nordic crafted axes is made of northern Italian copper, so called AATV-copper (from the Alto Adige, Trentino and Veneto mining region in the Italian Alps) while the majority of these axes is made of British and Welsh or eastern Alpine metal. Photo credits: Heide W. Nørgaard, by permission of the National Museum, Copenhagen

New research presents over 300 new analyses of bronze objects, raising the total number to 550 in 'the archaeological fingerprint project'. This is roughly two thirds of the entire metal inventory of the early Bronze Age in southern Scandinavia. For the first time, it was possible to map the trade networks for metals and to identify changes in the supply routes, coinciding with other socio-economic changes detectable in the rich metal-dependent societies of Bronze Age southern Scandinavia.

The magnificent Bronze Age in southern Scandinavia rose from copper traded from the British Isles and Slovakia 4000 years ago. 500 years later these established trade networks collapsed and fresh copper was then traded from the southern Alps, the so-called Italian Alps. This large-scale study could show that during the first 700 years of the Nordic Bronze Age the metal supplying networks and trade routes changed several times. These 700 years of establishment and change led to a highly specialised metalwork culture boasting beautiful artwork such as the Trundholm Sun wagon and spiral decorated belt plates branding high-ranking women; even depicted on today's Danish banknotes.

The lead isotope plot of the over 65 shafthole axes analyzed in this study dating to the end of the first Bronze Age period 1600 BC. This amount of data exceeds the previous analyses by ten times and for the first time allows to compare both axe types and understand their development

The study by H. Nørgaard, Moesgaard Museum and her colleagues H. Vandkilde from Aarhus University and E. Pernicka from the Curt-Engelhorn Centre in Mannheim built on the so far largest dataset of chemical and isotope data of ancient bronze artefacts. In total 550 objects were used to model the changes that took place: These changes correlate with major shifts in social organisation, settlements, housing, burial rites and long distance mobility.

trading bronze age Scandinavia's
Shafthole axe of Valsømagle type. Only a few axes of this type are known, and they are only distributed in northern Europe. These axes seem to be contemporary with the Fårdrup type axes as they are made of the same metal and not, if they would be slightly later, of the new Italian metal that is the main metal used in the period from 1500 BC. Photo credits: Heide W. Nørgaard, by permission of the National Museum, Copenhagen

"Now, this multi-disciplinary approach - based jointly on conventional archaeological methods and novel scientific methodologies processing large data quantities - allows us to detect these correlating changes and identify contemporaneity with societal changes recognised by colleague researchers", says Heide Nørgaard the project´s PI.

"It is highly likely that both people and technologies arrived to Scandinavia and that Scandinavians travelled abroad to acquire copper by means of the Nordic amber, highly valued by European trading partners".

###

Citation: Nørgaard HW, Pernicka E, Vandkilde H (2021) Shifting networks and mixing metals: changing metal trade routes to Scandinavia correlate with Neolithic and Bronze Age transformations. PLOS ONEhttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0252376

 

Bronze Age Scandinavia's trading networks for copper settled: press release from Aarhus University.


Homo sapiens "Linya" lived in the northeast of the Iberian Peninsula 14,000 years ago

Homo sapiens "Linya" lived in the northeast of the Iberian Peninsula 14,000 years ago

Researchers from the Centre for the Study of Archaeological Heritage (CEPARQ-UAB) working at the Cova Gran de Santa Linya have discovered the remains of a Homo sapiens female living in the eastern Pre-Pyrennees during the Upper Palaeolithic period, around 14,000 years ago. There is a scarcity of prehistoric remains of modern humans in the Iberian Peninsula. The study of Linya, as she has been named, will allow delving deeper into what is known about them and how hunter-gatherers lived in the northeastern part of the peninsula.

Homo sapiens Linya
Homo sapiens "Linya" lived in the northeast of the Iberian Peninsula 14,000 years ago. Photo Credits: CEPARQ-UAB

16/06/2021 The cave known as Cova Gran (Avellanes-Santa Linya, Noguera) preserves countless vestiges within its sediments, which allows researchers to reconstruct over 50,000 years of history of those living in the Pre-Pyrennean region (Lleida province), from the Neanderthals to the the first Homo sapiens as well as the hunther-gatherer-lifestyle to the first farmers and herders.

The research team at the Centre for the Study of Archaeological Heritage of the Universitat Autònoma de Barcelona (CEPARQ-UAB) studying the Cova Gran since 2002 has found remains dating back from 45,000 to 4,000 years ago. But no bones of those living there had ever been discovered. Until last year’s dig campaign, in which the skeletal remains of a human, in partial anatomic connection, were found two meters below ground in a lateral excavation area. A location in which researchers would not have imagined finding these types of remains.

The set ofrecovered remains, which has been made public today, corresponds to a woman who has been given the name of “Linya, the woman from Noguera”. The bones include two femurs, one of them connected to the pelvis, as well as the long bones of the upper extremities (hummerus, radius/cubitus) and lower extremities (tibia and fibula), the metapodia and several phalanges. The skull and axial skeleton (vertebrates and ribs), although present, had little representation.

The dating of the stratum in which the remains were found and the dating of one of the bones have narrowed down the period in which she lived to around 14,350 and 14,100 years ago, which corresponds to the end of the Upper Paleolithic period, which also corresponds to the end of the Pleistocene.

“The remains of Linya open a new door that brings us closer to discovering the circumstances in which she died, but also details about her life and that of those she lived with in the region. And at the same time, she is a key figure in learning about the anatomy and genetic heritage of hunter-gatherer societies at the end of the Pleistocene in the northeastern part of the Iberian Peninsula”, highlights Rafael Mora, Chair Professor at the UAB Department of Prehistory and researcher at the CEPARQ. “The combination of different paleoanthropological, forensic, genomic and archaeological analyses currently underway will provide indicators which will enrich and rectify the current perspective of a discovery we only have preliminary information on thanks to the digs we are conducting”.

The state of conservation of the bones has made it necessary to apply stabilizing and preservation processes in views of future studies. These processes are being conducted now at the Catalan Institute of Human Paleoecology and Social Evolution (IPHES).

Placed in a natural receptacle

The remains were found within what is considered to be a natural receptacle, delimited by various blocks of large dimensions fallen from the rockshelter. Researchers are currently investigating whether the extremities were moved towards the cubicle, while the axial skeleton and skull were protected under these large rocks. What researchers have been able to determine is that the location is where the person was lain once she was dead. According to the position of the femurs, she was lain directly on the ground in a supine position. The first paleoanthropological characterization conducted indicates that the pelvic girdle corresponds to an adult female, possibly of small stature.

The skeleton appeared at the base of an archaeological sequencing of 7 consecutive archaeological levels containing an abundance of lithic tools, faunal and carbon remains, all of which point to the use of the site as a living space. But the bed on which the body was lain did not contain any of those elements. Currently, the research team is looking for possible funerary offerings, which were very common in the burials of Homo sapiens. The sediment of the space marked out by the large blocks is now being sampled to recover micro residue that could indicate that the body was covered with animal skins or plant fibers. This would justify the way the body was lain on the ground, without the need of digging a burial space.

“We are aware of the need to be cautious when affirming that this is an intended burial site”, researcher at the CEPARQ Jorge Martinez-Moreno points out. He goes on to say that, “mortuary practices among hunter-gatherers point to different possibilities, ranging from an intentional burial to a secondary burial, the burial of part of the body, cannibalism, or an accidental death. We will need to evaluate these scenarios depending on the results of what we dig up in the area in which these remains appeared”.

Carbon-14 dating using fragments of the carbon found in the archaeological levels in which the remains appeared indicate that the sediment was formed in less than a millennium, from around 14,400 to 13,500 years ago. The explanation for why this sediment grew so much, and which was accompanied by the detachment of several massive blocks from the cave’s cornice, is being analyzed through the geomorphology and material that make up this part of the mountain’s slope.

A moment of ecological change

The time period in which Linya and her people lived was critical in climatic terms. Some 14,700 years ago, the world’s extremely cold and harsh climate conditions characteristic of the Last Glacial Maximum (approximately 30,000 to 15,000 years ago) suddenly changed and in a period of less than 100 years, transformed into a new climate regime similar to the one existing now. This event, known as the Bölling/Allerød warming, occurring some 14,700 to 12,900 years before the present, and was characterized by a rise in temperatures and rainfall, which produced relevant ecological changes.

Despite the fact that the impact of this event on the Pre-Pyrennees is not greatly known, some indicators recovered at the Cova Gran have allowed researchers to analyze this incident. Carbon dating analysis indicates that the human species living there during the Last Glacial Maximum only used European red pine (Pynus sylvestris) timber for fuel. In the sequence now being dug, in which the remains of Linya were discovered, other new taxon’s in addition to red pine carbon were identified, such the common juniper (Juniperus), cherry trees (Prunus) and buckthorn (Rhamus catharticus/saxatilis), a set of trees and shrubs belonging to milder climates, different to the harshness of the forests of the Last Glacial Maximum.

Very few remains of Homo sapiens in the Iberian Peninsula

The amount of human remains discovered in the Iberian Peninsula and corresponding to the Upper Paleolithic period (20,000 to 12,000 years ago) is scarce. In this sense, the Cova Gran will be key to learning more about their anatomy and where the Hunter-gatherer societies came from at the end of the Pleistocene.

A recent paleogenetic study conducted by the Max Planck Institute on remains recovered from the El Mirón Cave in Santander and the Balma Guilanyà rock shelter in Lleida indicates that the genome sequencing of the “Red Lady of El Mirón”, dating back 20,000 years, reveals close ties to human populations of Western Europe. A situation which changes in the remains found at the Balma Guilanyà rock shelter, dating 1,000 years later than the remains found at the Cova Gran, in which there is a continuation of genetic markers common to European populations, but also new markers which are present in the populations of the Italian Peninsula.

Therefore, in the interval of 20,000 to 13,000 years, the genome of Pyrenean populations registers contacts with populations from the Mediterranean. “Maybe the new climate conditions of the Bölling/Allerød warming facilitated regular contacts between these geographic areas?” researchers wonder. “The human remains at the Cova Gran will be key to evaluating the solidity of this interesting intuition”, they point out.

The CEPARQ team is convinced that the unexpected discovery of Linya will help to modulate the notions now sustained of the anatomy of those Homo sapiens, “of whom we have less precise knowledge than we do of Neanderthals”, researchers state. They also mention the fact that “the causes leading to the appearance of a space created by large blocks will aid us in learning about the behavior and decisions taken by those people regarding a transcendental and common event such as death: what ritual was followed by these people who are part of our collective, but are no longer present? The remains of Linya now pose several challenges, and we hope to solve them in the coming years”, they conclude.

The archaeological importance of the Cova Gran de Santa Linya

The Cova Gran de Santa Linya, discovered in 2002, is a site measuring over 2,500 square meters, considered key to the study of the presence of humans in the northeastern Iberian Peninsula.

It is one of the few sites of the Mediterranean region in which vestiges of a moment of “transition” have been found, such as those of the last Neanderthals (approximately 45,000 years ago) and the appearance of modern humans (some 37,000 to 30,000 years), their survival during the Last Glacial Maximum (20,000 to 15,000 years), and the appearance of the first farmers and herders (7,000 to 4,000 years ago).

The research conducted by the CEPARQ-UAB team at the Cova Gran de Santa Linya includes the financial support of the Spanish Ministry for Science and Innovation, the Archaeology and Palaecology Service of the Ministry for Culture of the Government of Catalonia, the Institute for Lleida Studies (IEI) of the Lleida Provincial Council, the Palarq Foundation, the Leakey Foundation and the City Council of Les Avellanes i Santa Linya.

Press release from Universitat Autònoma de Barcelona


The shoulders of 'Homo antecessor' and modern humans are similar

The shoulders of 'Homo antecessor' and modern humans are similar

The CENIEH has published a paper in the journal Scientific Reports which concludes that Homo antecessor had a shoulder development analogous to that in H. sapiens, although its growth was faster
Homo antecessor shoulders
Homo antecessor scapulae. Credits: D. Garcia Martínez et al

The shape of our shoulders was already present in the Lower Pleistocene, according to a pioneering study published today in the journal Scientific Reports, carried out by Daniel García Martínez and José María Bermúdez de Castro, paleoanthropologists at the Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), in collaboration with David Green of Campbell University (USA).

Studying the shoulder (technically known as the "shoulder girdle") furnishes information on points significant for human evolution such as locomotion, body shape, the possibility of climbing with ease or the ability to launch objects like stones or spears with high accuracy.

The authors of this work were able to study for the first time shoulder growth and development in the species Homo antecessor, dated to 850,000 years old, using tools from virtual anthropology and 3D geometric morphometry. The results show that the course of development of the shoulder in this species was very similar to that in H. sapiens, although the growth might have been faster.

Almost one million years ago, our evolution had already attained almost all the biomechanical capacities characterizing the shoulder in modern humans, and it had definitively parted ways from the abilities still then retained by the more archaic species of the human phylogeny, including climbing with great agility.

 To verify the changes undergone by this part of our anatomy, we need a flat bone: the shoulder blade or scapula. But, as the authors of this study state, “The fossil record of our phylogeny contains barely a handful of these highly delicate bones, which has posed enormous difficulties to studying the growth and development of the shoulders during human evolution”.

Two key fossils

By good luck, at level TD6 of the Gran Dolina site, situated in the Sierra de Atapuerca (Burgos), two scapulae have been conserved: one from a child and the other from an individual of age equivalent to a modern adolescent. These fossils were recovered during the excavation in the first decade of the twenty-first century and belonged to the species H. antecessor.

“In an earlier study of these two fossils, it had been noticed that the morphology of the scapulae was similar to our own. But until now, the growth and development model for the shoulders had remained unknown, and this work has now allowed us to check that our shoulder girdle bones have undergone modifications in accordance with different capacities”, says Bermúdez de Castro.

Comparative study

With the scant information available, it was known that the scapulae of Australopithecus species were similar in some ways to those of chimpanzees or gorillas but were different from our own. “We know that the development of our most archaic ancestors was very similar to that of the anthropoid apes, and the morphology of their shoulders shows that they still retained the capacity to climb with ease. We, on the contrary, have lost this ability”, explains García Martínez.

Comparative of scapulae. Credits: D.García Martínez et al

To determine when our anatomical peculiarities arose, in addition to virtual anthropology and 3D geometric morphometry, the researchers used complex statistical methods to study the development of the shoulder girdle in the species H. antecessor, comparing it with other species from the Pliocene and Lower Pleistocene, such as Australopithecus sediba and A. afarensis. A very broad sample from H. sapiens and chimpanzees (Pan troglodytes) was also used.

“This study shows that although there exist slight morphological differences between the scapulae of H. antecessor and H. sapiens, the former were much more similar to modern humans, to H. erectus and even to Australopithecus than to chimpanzees”, comments García Martínez.

With regard to how the scapulae grew, it was also seen that this was very different from what happens in chimpanzees, and comparable with H. sapiens. “However, it is true that the data seem to point to growth being more rapid in H. antecessor, as highlighted by the CENIEH research team on the basis of dental evidence”, emphasizes Bermúdez de Castro.

This paper lays the foundations for how the shoulder girdle developed in Lower Pleistocene species, and opens the door to new research studying shoulder development in fossil species, as it may become possible to expand the timeframe and study this development even in Pliocene species like the genus Australopithecus.

Full bibliographic information

García-Martínez, D., Green, D., Bermúdez de Castro, J.M. 2021. Evolutionary development of the Homo antecessor scapulae (Gran Dolina site, Atapuerca) suggests a modern-like development for Lower Pleistocene Homo. Scientific Reports. DOI: 10.1038/s41598-021-83039

 

Press release from CENIEH


DNA antico Caraibi

Ancient DNA retells story of Caribbean’s first people

Ancient DNA retells story of Caribbean’s first people

DNA antico Caraibi
Long Journey's End, (c) Merald Clark, for SIBA: Stone Interchanges in the Bahama Archipelago

The history of the Caribbean’s original islanders comes into sharper focus in a new Nature study that combines decades of archaeological work with advancements in genetic technology.

An international team led by Harvard Medical School’s David Reich analyzed the genomes of 263 individuals in the largest study of ancient human DNA in the Americas to date. The genetics trace two major migratory waves in the Caribbean by two distinct groups, thousands of years apart, revealing an archipelago settled by highly mobile people, with distant relatives often living on different islands.

Reich’s lab also developed a new genetic technique for estimating past population size, showing the number of people living in the Caribbean when Europeans arrived was far smaller than previously thought – likely in the tens of thousands, rather than the million or more reported by Columbus and his successors.

For archaeologist William Keegan, whose work in the Caribbean spans more than 40 years, ancient DNA offers a powerful new tool to help resolve longstanding debates, confirm hypotheses and spotlight remaining mysteries.

This “moves our understanding of the Caribbean forward dramatically in one fell swoop,” said Keegan, curator at the Florida Museum of Natural History and co-senior author of the study. “The methods David’s team developed helped address questions I didn’t even know we could address.”

Archaeologists often rely on the remnants of domestic life – pottery, tools, bone and shell discards – to piece together the past. Now, technological breakthroughs in the study of ancient DNA are shedding new light on the movement of animals and humans, particularly in the Caribbean where each island can be a unique microcosm of life.

While the heat and humidity of the tropics can quickly break down organic matter, the human body contains a lockbox of genetic material: a small, unusually dense part of the bone protecting the inner ear. Primarily using this structure, researchers extracted and analyzed DNA from 174 people who lived in the Caribbean and Venezuela between 400 and 3,100 years ago, combining the data with 89 previously sequenced individuals.

The team, which includes Caribbean-based scholars, received permission to carry out the genetic analysis from local governments and cultural institutions that acted as caretakers for the human remains. The authors also engaged representatives of Caribbean Indigenous communities in a discussion of their findings.

Two waves of people, thousands of years apart

The genetic evidence offers new insights into the peopling of the Caribbean. The islands’ first inhabitants, a group of stone tool-users, boated to Cuba about 6,000 years ago, gradually expanding eastward to other islands during the region’s Archaic Age. Where they came from remains unclear – while they are more closely related to Central and South Americans than to North Americans, their genetics do not match any particular Indigenous group. However, similar artifacts found in Belize and Cuba may suggest a Central American origin, Keegan said.

About 2,500-3,000 years ago, farmers and potters related to the Arawak-speakers of northeast South America established a second pathway into the Caribbean. Using the fingers of South America’s Orinoco River Basin like highways, they travelled from the interior to coastal Venezuela and pushed north into the Caribbean Sea, settling Puerto Rico and eventually moving westward. Their arrival ushered in the region’s Ceramic Age, marked by agriculture and the widespread production and use of pottery.

Over time, nearly all genetic traces of Archaic Age people vanished, except for a holdout community in western Cuba that persisted as late as European arrival. Intermarriage between the two groups was rare, with only three individuals in the study showing mixed ancestry.

Many present-day Cubans, Dominicans and Puerto Ricans are the descendants of Ceramic Age people, as well as European immigrants and enslaved Africans. But researchers noted only marginal evidence of Archaic Age ancestry in modern individuals.

“That’s a big mystery,” Keegan said. “For Cuba, it’s especially curious that we don’t see more Archaic ancestry.”

Changes in pottery styles not linked to new migrations

Some archaeologists pointed to dramatic shifts in Caribbean pottery styles as evidence of new migrations. But genetics show all of the styles were created by one group of people over time. These effigy vessels belong to the Saladoid pottery type, ornate and difficult to shape. Credits: Corinne Hofman and Menno Hoogland

During the Ceramic Age, Caribbean pottery underwent at least five marked shifts in style over 2,000 years. Ornate red pottery decorated with white painted designs gave way to simple, buff-colored vessels, while other pots were punctuated with tiny dots and incisions or bore sculpted animal faces that likely doubled as handles.

Some archaeologists pointed to these transitions as evidence for new migrations to the islands. But DNA tells a different story, suggesting all of the styles were developed by descendants of the people who arrived in the Caribbean 2,500-3,000 years ago, though they may have interacted with and taken inspiration from outsiders.

“That was a question we might not have known to ask had we not had an archaeological expert on our team,” said co-first author Kendra Sirak, a postdoctoral fellow in the Reich Lab. “We document this remarkable genetic continuity across changes in ceramic style. We talk about ‘pots vs. people,’ and to our knowledge, it’s just pots.”

Ancient DNA Caribbean Caribbeans
Archaeological research and ancient DNA technology can work hand in hand to illuminate past history in the Caribbean. This vessel, made between AD 1200-1500 in present-day Dominican Republic, shows a frog figure, associated with the goddess of fertility in Taino culture. Credits: Kristen Grace/Florida Museum

Genetics reveal family connections across islands

Highlighting the region’s interconnectivity, a study of male X chromosomes uncovered 19 pairs of “genetic cousins” living on different islands – people who share the same amount of DNA as biological cousins but may be separated by generations. In the most striking example, one man was buried in the Bahamas while his relative was laid to rest about 600 miles away in the Dominican Republic.

“Showing relationships across different islands is really an amazing step forward,” said Keegan, who added that shifting winds and currents can make passage between islands difficult. “I was really surprised to see these cousin pairings between islands.”

Uncovering such a high proportion of genetic cousins in a sample of fewer than 100 men is another indicator that the region’s total population size was small, said Reich, professor of genetics in the Blavatnik Institute at HMS and professor of human evolutionary biology at Harvard.

“When you sample two modern individuals, you don’t often find that they’re close relatives,” he said. “Here, we’re finding relatives all over the place.”

Revising estimates of Caribbean population size

A technique developed by study co-author Harald Ringbauer, a postdoctoral fellow in the Reich Lab, used shared segments of DNA to estimate past population size, a method that could also be applied to future studies of ancient people. Ringbauer’s technique showed about 10,000 to 50,000 people were living on two of the Caribbean’s largest islands, Hispaniola and Puerto Rico, shortly before European arrival. This falls far short of the million inhabitants Columbus described to his patrons, likely to impress them, Keegan said.

 

Later, 16th-century historian Bartolomé de las Casas claimed the region had been home to 3 million people before being decimated by European enslavement and disease. While this, too, was an exaggeration, the number of people who died as a result of colonization remains an atrocity, Reich said.

“This was a systematic program of cultural erasure. The fact that the number was not 1 million or millions of people, but rather tens of thousands, does not make that erasure any less significant,” he said.

For Keegan, collaborating with geneticists gave him the ability to prove some hypotheses he has argued for years – while upending others.

“At this point, I don’t care if I’m wrong or right,” he said. “It’s just exciting to have a firmer basis for reevaluating how we look at the past in the Caribbean. One of the most significant outcomes of this study is that it demonstrates just how important culture is in understanding human societies. Genes may be discrete, measurable units, but the human genome is culturally created.”


Daniel Fernandes of the University of Vienna and the University of Coimbra in Portugal was also co-first author of the study. Other co-senior authors are Alfredo Coppa of the Sapienza University of Rome, Mark Lipson of HMS and Harvard and Ron Pinhasi of the University of Vienna.

This work was funded by the National Geographic Society, National Science Foundation, National Institutes of Health/National Institute of General Medical Sciences, Paul Allen Foundation, John Templeton Foundation and Howard Hughes Medical Institute.

 

Press release by Natalie van Hoose, from the Florida Museum of Natural History on ancient DNA shedding light on the first people in the Caribbean.


molar size hominins

New study of molar size regulation in hominins

New study of molar size regulation in hominins

The Dental Anthropology Group at the CENIEH has tested the inhibitory cascade model to see whether it explains the size relationships and differences in shape between the different kinds of teeth, in the molar sample from the individuals identified at the Sima de los Huesos site in the Sierra de Atapuerca.
Mandíbula AT-1 de la Sima de los Huesos. Credits: Mario Modesto

The molar size relationship is one of the peculiar characteristics of the different species of hominins and various theories have been proposed to account for this, as well as the differences in shape between the different kinds of teeth (incisors, canines, premolars and molars). The latest theory, called the inhibitory cascade model, arose out of experiments with mice embryos, and in 2016 it was applied theoretically to fossil hominins, with satisfactory results.

It appeared that all hominins satisfy the inhibitory cascade model. In a paper by the Dental Anthropology Group at the Centro Nacional de Investigación sobre la evolución Humana (CENIEH), published recently in the Journal of Anatomy, this model was tested on the molar sample from the individuals identified at the Sima de los Huesos site, situated in the Sierra de Atapuerca (Burgos).

The results match the model generated in mice extraordinarily well, thus confirming the theory's utility once more. “Nevertheless, our conclusions have brought out an anomaly in the model, when it is applied to the oldest species of the genus Homo”, explains José María Bermúdez de Castro, Paleobiology Program Coordinator at the CENIEH and lead author of this work.

Increasing and decreasing patterns

In the genera Ardipithecus, Australopithecus and Paranthropus, as well as in Homo habilis, the size pattern is increasing and fits the premises of the inhibitory cascade model perfectly. The same thing happens in Homo sapiens, except that the pattern is decreasing, with the first molar larger than the second, which in turn is bigger than the third one (wisdom tooth).

Application of the inhibitory cascade model had led to the assumption that the switch from increasing to decreasing pattern would have arisen a little under two million years ago, perhaps coinciding with the transition between the genera Australopithecus and Homo. “However, in our work we noticed that this change could have required at least a million years to take place”, states Bermúdez de Castro.

The hominins from the Sima de los Huesos, which are around 430,000 years old, are a good example of that transition, whereas most specimens of Homo ergaster, Homo erectus, Homo antecessor and Homo heidelbergensis, as well as other species, do not fit the inhibitory cascade model. “Our idea is to continue our research to determine which genetic mechanisms lie behind this anomaly in the model”, says Bermúdez de Castro.

Full bibliographic information

Bermúdez de Castro et al. 2020. Testing the inhibitory cascade model in the Middle Pleistocene Sima de los Huesos (Sierra de Atapuerca, Spain) hominin sample. Journal of Anatomy. DOI: 10.1111/joa.13292
Press release from CENIEH.