First prehistoric person with Turner syndrome identified from ancient DNA

     

• First prehistoric person with Turner syndrome identified from the Iron Age
• Earliest known person with Jacob’s syndrome identified from Early Medieval Period
• Individuals with Klinefelter syndrome identified across a range of time periods
• New technique developed to measure number of chromosomes in ancient genomes more precisely

Researchers at the Francis Crick Institute, working with University of Oxford, University of York and Oxford Archaeology, have developed a new technique to measure the number of chromosomes in ancient genomes more precisely, using it to identify the first prehistoric person with mosaic Turner syndrome (characterised by one X chromosome instead of two [XX]), who lived about 2500 years ago.

As part of their research published today in Communications Biology, they also identified the earliest known person with Jacob’s syndrome (characterised by an extra Y chromosome - XYY) in the Early Medieval Period, three people with Klinefelter syndrome (characterised by an extra X chromosome - XXY) across a range of time periods and an infant with Down Syndrome from the Iron Age.

Most cells in the human body have 23 pairs of DNA molecules called chromosomes, and the sex chromosomes are typically XX (female) or XY (male), although there are differences in sexual development. ‘Aneuploidy’ occurs when a person’s cells have an extra or missing chromosome. If this occurs in the sex chromosomes, a few differences like delayed development or changes in height can be seen around puberty.

Ancient DNA samples can erode over time and can be contaminated by DNA from other ancient samples or from people handling them. This makes it difficult to accurately capture differences in the number of sex chromosomes.

The team at the Crick developed a computational method which aims to pick up more variation in sex chromosomes. For the sex chromosomes, it involves counting the number of copies of X and Y chromosomes, and comparing the outcome to a predicted baseline (what you would expect to see).

The team used the new method to analyse ancient DNA from a large dataset of individuals collected as part of their Thousand Ancient British Genomes project across British history, identifying six individuals with aneuploidies across five sites in Somerset, Yorkshire, Oxford and Lincoln2. The individuals lived across a range of time periods, from the Iron Age (2500 years ago) up to the Post-Medieval Period (about 250 years ago).

They identified five people who had sex chromosomes which fell outside of the XX or XY categories. All were buried according to their society’s customs although no possessions were found with them to shed more light on their lives.

The three individuals with Klinefelter syndrome lived across very different time periods, but they shared some similarities - all were slightly taller than average and showed signs of delayed development in puberty.

By investigating details on the bones, the research team could see that it was unlikely that the individual with Turner syndrome had gone through puberty and started menstruation, despite their estimated age of 18-22. Their syndrome was shown to be mosaic -some cells had one copy of chromosome X and some had two.

Kakia Anastasiadou, PhD student in the Ancient Genomics Laboratory at the Crick, and first author of the study, said: “Through precisely measuring sex chromosomes, we were able to show the first prehistoric evidence of Turner syndrome 2500 years ago, and the earliest known incidence of Jacob’s syndrome around 1200 years ago. It’s hard to see a full picture of how these individuals lived and interacted with their society, as they weren’t found with possessions or in unusual graves, but it can allow some insight into how perceptions of gender identity have evolved over time.”

Pontus Skoglund, Group Leader of the Ancient Genomics Laboratory at the Crick, said: “Our      method is also able to classify DNA contamination in many cases, and can help to analyse incomplete ancient DNA, so it could be applied to archaeological remains which have been difficult to analyse.

“Combining this data with burial context and possessions can allow for a historical perspective of how sex, gender and diversity were perceived in past societies. I hope this type of approach will be applied as the common resource of ancient DNA data continues to grow.”

The team worked with archaeologists from the University of Oxford, the Wells and Mendip Museum, University of York, University of Bradford, Oxford Archaeology, York Osteoarchaeology and Network Archaeology, acknowledging support from Lincolnshire County Council, Magdalen College and Balfour Beatty for National Highways.

Rick Schulting, Professor of Scientific and Prehistoric Archaeology at the University of Oxford, said: “The results of this study open up exciting new possibilities for the study of sex in the past, moving beyond binary categories in a way that would be impossible without the advances being made in ancient DNA analysis.”

Discovered in the Upper Amazon: evidence for early urbanism in the region

A dense system of pre-Hispanic urban centers, characterized by constructed platforms and plazas and connected by large, straight roads, has been discovered in the upper Amazon, according to a new study. The research, based on more than 20 years of interdisciplinary research, suggests that this original 2500-year-old society constitutes the earliest and largest low-density agrarian urbanism documented in the Amazon thus far. Such extensive early development in the Upper Amazon resembles similar Maya urban systems in Central America. 

Although a growing body of research has begun to highlight the scope and scale of pre-Hispanic occupation of the Amazon, evidence for large-scale urbanism has remained elusive. Stéphen Rostain and colleagues present evidence for an agrarian-based civilization that began more than 2500 years ago in the Upano Valley of Amazonian Ecuador, a region in the eastern foothills of the Andes. 

Based on more than 20 years of interdisciplinary research that included fieldwork and light detection and ranging (LIDAR) mapping, Rostain et al. describe urbanism at a scale never before documented in Amazonia, consisting of more than 6000 anthropogenic rectangular earthen platforms and plaza structures connected by footpaths and roads and surrounded by expansive agricultural landscapes and river drainages within the 300 square kilometer survey area. 

The authors identified at least 15 distinct settlement sites of various sizes based on clusters of structures. However, according to Rostain et al., the most notable elements of this built environment are the extensive and complex regional-scale road network connecting urban centers and the surrounding hinterland. 

Archaeological excavations indicate that the construction and occupation of the platforms and roads occurred between ~500 BCE and 300 to 600 CE and was carried out by groups from the Kilamope and later Upano cultures. Rostain et al. note that the Upano sites are different from other monumental sites discovered in Amazonia, which are more recent and less extensive. 

“Such a discovery is another vivid example of the underestimation of Amazonia’s twofold heritage: environmental but also cultural, and therefore Indigenous,” write Rostain et al. “…we believe that it is crucial to thoroughly revise our preconceptions of the Amazonian world and, in doing so, to reinterpret contexts and concepts in the necessary light of an inclusive and participatory science.”

Discovery of immense fortifications dating back 4,000 years in north-western Arabia

 

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DIGITAL RECONSTRUCTION OF THE RAMPART NETWORK FROM THE NORTHERN SECTION OF THE KHAYBAR WALLED OASIS 4,000 YEARS AGO.

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CREDIT: © KHAYBAR LONGUE DURÉE ARCHAEOLOGICAL PROJECT, M. BUSSY & G. CHARLOUX

The North Arabian Desert oases were inhabited by sedentary populations in the 4th and 3rd millennia BCE. A fortification enclosing the Khaybar Oasis—one of the longest known going back to this period—was just revealed by a team of scientists from the CNRS1 and the Royal Commission for AlUla (RCU). This new walled oasis is, along with that of Tayma, one of the two largest in Saudi Arabia. While a number of walled oases dating back to the Bronze Age had already been documented, this major discovery sheds new light on human occupation in north-western Arabia, and provides a better grasp of local social complexity during the pre-Islamic period.

Cross-referencing field surveys and remote sensing data with architectural studies, the team estimated the original dimensions of the fortifications at 14.5 kilometres in length, between 1.70 and 2.40 metres in thickness, and approximately 5 metres in height. Preserved today over a little less than half of its original length (41%, 5.9 km and 74 bastions), this colossal edifice enclosed a rural and sedentary territory of nearly 1,100 hectares. The fortification’s date of construction is estimated between 2250 and 1950 BCE, on the basis of radiocarbon dating of samples collected during excavations.

While the study confirms that the Khaybar Oasis clearly belonged to a network of walled oases in north-western Arabia, the discovery of this rampart also raises questions regarding why it was built as well as the nature of the populations that built it, in particular their relations with populations outside the oasis.

This archaeological discovery, whose results will be published on 10 January in the Journal of Archaeological Science: Reports (JASREP), paves the way for major advances in understanding the prehistoric, pre-Islamic, and Islamic past of the north-western Arabian Peninsula.

 

Notes

1 – From the Orient and Mediterranean Laboratory (CNRS/Collège de France/EPHE-PSL/Sorbonne Université/Université Panthéon-Sorbonne) and the Archéorient – Environments and Societies of the Ancient East Laboratory (CNRS/Université Lumière Lyon 2), in connection with the Khaybar Longue Durée Archaeological Project commissioned by the French Agency for AlUla Development (AFALULA) for the Royal Commission for AlUla (RCU).

Ancient DNA reveals reason for high multiple sclerosis and Alzheimer’s rates in Europe

 

Researchers have created the world’s largest ancient human gene bank by analysing the bones and teeth of almost 5,000 humans who lived across western Europe and Asia up to 34,000 years ago.

By sequencing ancient human DNA and comparing it to modern-day samples, the international team of experts mapped the historical spread of genes – and diseases – over time as populations migrated. They found:

• The startling origins of neurodegenerative diseases including multiple sclerosis
• Why northern Europeans today are taller than people from southern Europe
• How major migration around 5,000 years ago introduced risk genes into the population in north-western Europe – leaving a legacy of higher rates of MS today
• Carrying the MS gene was an advantage at the time as it protected ancient farmers from catching infectious diseases from their sheep and cattle
• Genes known to increase the risk of diseases such as Alzheimer’s and type 2 diabetes were traced back to hunter gatherers
• Future analysis is hoped to reveal more about the genetic markers of autism, ADHD, schizophrenia, bipolar disorder, and depression

New research identifies renowned rock art sites ‘chosen’ for vantage

 

 

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MAP OF THE STUDY AREA WITHIN THE LARGER REGION, SHOWING THE ALLIGATOR RIVERS, FLOODPLAINS, KAKADU NATIONAL PARK AND ARNHEM LAND ALONG WITH THE ARNHEM PLATEAU. 

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CREDIT: DR JARRAD KOWLESSAR, FLINDERS UNIVERSITY.

New research has uncovered internationally significant rock art sites in Arnhem Land were far from random and instead “chosen” for the critical vantage points they provided.

The Flinders University research team, working in collaboration with the Njanjma Rangers and Erre Traditional Owners, used aerial and drone surveys, subsurface imaging and elevation data to create the first high-resolution palaeolandscape modelling to help understand 103 separate rock art sites in the region’s rich Red Lily Lagoon area.

What this innovative research has done is statistically model what the environmental conditions were like 15,000-28,000 years ago – when even the floodplain floor was 7-15 metres lower than where it sits today.

Flinders Associate Professor Ian Moffat says the research findings better informs how the sites would have been used, their accessibility and visibility – what the Traditional Owner artists would have been looking at, watching out for and why.

“When archaeologists interpret rock art, they often assume the landscape hasn’t changed since the art was first inscribed which certainly isn’t the case at Red Lily Lagoon,” he explains.

“This landscape has changed dramatically from being on the coast, a swamp, woodlands and freshwater – and sometimes in just one lifetime.

“Our innovative research approach adds new information to understand the rock art in a fundamentally different way.

“Modelling the changes in environmental conditions over time sheds new light on the locations, where they were in in these landscapes, how they were selected and used, and the roles they held in community and clan life.”

This area of western Arnhem Land contains internationally renowned archaeological records, including Australia's oldest known archaeological site, and at the same time it has experienced colossal environmental landscape changes generated mostly by changing sea levels.

Associate Professor Moffat says the research identifies these changes include the coastline moving from 100s of kilometres away to coming right up against the cliffs in the Red Lily region, before retreating northwards, about 50kms to its current position.

He says the Flinders research traces the transformational impact rising sea levels had on the sandstone cliffs and flat floodplains terrain – changing its open savanna to mudflats, to mangrove swamp, before evolving into the seasonally inundated freshwater wetlands of today. These changes would have had profound implications for people, how they moved, interacted and what they recorded at these locations.

“Our research has enabled a clearer understanding of the placement of rock art sites that goes beyond relying on today’s landscape as a reference point which is significant.

Flinders College of Humanities Research Associate Dr Jarrad Kowlessar says this research identifies rock art production was most active, diverse in style, and covered most of the plateau area during a period when mangroves completely covered the floodplains – approximately 6,000 years ago.

“This may be because the mangroves provided abundant resources to sustain a large and stable human population at the time, or because the land had simply contracted so much due to the rising sea level that more people were in closer proximity,” says Dr Kowlessar.

“Interestingly most sites during this time were selected with views specifically overlooking mangrove areas.

“We also identify that during the period when the sea level was rising, rock art was preferentially made in areas with long distance views over areas that had open woodlands at the time. So we can suggest these views may helped facilitate hunting, or even to more closely watch areas at a time when many people were being displaced by the rising water.

“Without doubt the research demonstrates rock art site locations were intentionally selected, with nuanced relationships to the local landscape, and there is potential to use our modelling into the future to tell us much more about the rich and significant archaeology of Arnhem Land.”

Were pigs ferried across the channel during the Medieval era?

 

The island of Madagascar separated from the African mainland around 160 million years ago, resulting in a largely unique flora and fauna. Remarkably, the bushpig is the only large, wild terrestrial mammal species that has somehow historically crossed the 400-kilometer-wide Mozambique Channel and made it from mainland Africa to the island of Madagascar.

- “Our study establishes that the bushpig was introduced to Madagascar ≈1,000-5,000 years ago from South/South-East Africa”, Rasmus states. Their arrival therefore coincides with the arrival of humans to Madagascar from a region around southern Africa. Rasmus continues: “The likely explanation for this is that people transported these bushpigs across the channel. These results contradict previously published studies which dated the arrival of bushpigs ≈480,000 years ago, well before humans were present on the island”. It has been suggested that some endemic Madagascar species might have arrived by rafting as passengers on floats of vegetation.

- “Intriguingly, our results raise a host of new questions: was the bushpig actually brought to Madagascar as a somewhat domesticated species? There is no archaeological or other evidence of bushpig domestication ever occurring, despite them being an important source of protein for many rural communities. And who was it that transported these animals to Madagascar? Was it Bantu-speakers, Austronesian-speakers or both? These questions and others still remain to be explored,” explains Renzo F. Balboa, postdoc at the Department of Biology and one of the leading authors of the study.

 

Ancestors of primates lived in pairs

A study carried out by CNRS1 scientists working with an international team has revealed that around 70 million years ago, when dinosaurs existed, the ancestors of primates most commonly lived in pairs. Only 15% of them opted for a solitary lifestyle. This discovery — that our ancestors adopted variable forms of social organization — challenges the hitherto commonly accepted hypothesis that at the time of dinosaurs, the ancestors of primates lived alone, and that pair living evolved much later. Most likely, pair living offered significant benefits, such as easier reproduction and reduced costs of thermoregulation by huddling in pairs.

While several studies have already been conducted on the social organisation of primate ancestors, this is the first one to use only currently available field observations. By studying 498 populations from 223 species, the research team has built the most accurate database of primates to date. The information obtained was then coupled with innovative statistical analysis. This research, published in the Vol. 121, no.1 issue of PNAS, paves the way for a better understanding of the social evolution of the human species.