Levänluhta

Breakthrough in the discovery of DNA in ancient bones buried in water

Breakthrough in the discovery of DNA in ancient bones buried in water

During the Iron Age around 300 AD something extraordinary was initiated in Levänluhta area in Isokyrö, SW Finland. The deceased were buried in a lake, and this habit was continued for at least 400 years. When trenches were dug in the local fields in mid-1800's skulls and other human bones were surfacing. These bones had been preserved almost intact in the anoxic, ferrous water. Archaeologists, historians and locals have been wondering about these finds for over 150 years now.

In 2010, a multidisciplinary research group at the University of Helsinki decided to re-investigate the mystery of Levänluhta. The site, thought to be e.g. a sacrificial spring, is exceptional even in global scale and has yielded altogether c. 75 kg human bone material. The research group, led by docent Anna Wessman, had an ambitious aim: to find who the deceased buried in Levänluhta were, and why they were exceptionally buried under water so far from dwelling sites. Now, after several years of scientific work, the group reports their results in the most recent issue of Nature. The results are part of a more extensive international study shedding light on the colonization and population history of Siberia with DNA data from ancient - up to 31 000 years old - human bones.

"In our part, we wanted especially to find out the origins of the Iron Age remains found from Levänluhta," says the group leader Anna Wessman.

New results with DNA sequencing technology

This was investigated using cutting edge ancient DNA sequencing technology, which Department of Forensic Medicine is interested in due to the forensic casework performed at the department. Professor Antti Sajantila explains that the early phases of this project were demanding.

"Unability to repeat even our own results was utterly frustrating," Sajantila tells about the first experiments in the laboratory.

The methods were developing rapidly during the international co-operation, and ultimately the first Finnish results were shown to be accurate. Yet, it was surprising that the genomes of three Levänluhta individuals clearly resembled those of the modern Sámi people.

"We understood this quite early, but it took long to confirm these findings," tells docent Jukka Palo.

Locals or by-passers?

The results were suggesting that the Isokyrö region was inhabited by Sámi people in ancient times - according to carbon datings the bones belonged to individuals that had died 500 - 700 AD. This would be a concrete proof of Sámi in southern Finland in the past. But were the people locals, recent immigrants or haphazard by-passers? To find out, other techniques than DNA were needed. The solution lied in the enamel of teeth.

Curator Laura Arppe from the Finnish Museum of Natural History tells that strontium isotopes found in the enamel strongly suggest that the individuals grew up in the Levänluhta region.

The current genomes of the people in Finland carry both eastern Uralic and western Scandinavian components, and the genome of one the Levänluhta individuals examined had clear ties to present day Scandinavians. As a whole the replacement of the Sámi people in southern and central Finland reflects the replacement processes in Siberia, clarified in the present article. This has probably been a common feature in the Northern latitudes.

"The Levänluhta project demands further studies, not only to broaden the DNA data but also to understand the water burials as a phenomenon. The question "Why?" still lies unanswered," ponders the bone specialist, docent Kristiina Mannermaa.

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The project was funded primarily by the Emil Aaltonen Foundation and the participating researchers represented various disciplines and departments at the University of Helsinki. As authors of the current Nature publication were: Anna Wessman, Kristiina Mannermaa and Tarja Sundell (archaeology), Antti Sajantila, Jukka Palo and Mikko Putkonen (forensic medicine), and Laura Arppe (geosciences).

Levänluhta
Levänluhta Spring in Isokyrö, SW Finland. Credit: Anna Wessman 2019

Press release from the University of Helsinki


Ancient DNA sheds light on Arctic hunter-gatherer migration to North America ~5,000 years ago

Ancient DNA sheds light on Arctic hunter-gatherer migration to North America ~5,000 years ago

An ancient population of Arctic hunter-gatherers, known as Paleo-Eskimos, made a significant genetic contribution to populations living in Arctic North America today

New research reveals the profound impact of Arctic hunter-gathers who moved from Siberia to North America about 5000 years ago on present-day Native Americans. Although this group is well-known from archaeology and ancient DNA, previous genetic studies suggested that they may have been largely replaced by the groups that gave rise to present-day Arctic peoples such as the Inuit, Yup’ik, and Aleuts. The present study proves that many present-day North Americans derive significant heritage from this ancient population.

The first humans in North America arrived from Asia some time before 14,500 years ago. The next major stream of gene flow came about 5000 years ago, and is known to archaeologists as Paleo-Eskimos. About 800 years ago, the ancestors of the present-day Inuit and Yup'ik people replaced this population across the Arctic. By about 700 years ago, the archaeological evidence for the Paleo-Eskimo culture disappeared. Their genetic legacy in living populations has been contentious, with several genetic studies arguing that they made little contribution to later North Americans.

In the current study, researchers generated genome-wide data from 48 ancient individuals and 93 modern individuals from Siberia, Alaska, the Aleutian Islands and Canada, and compared this with previously published data. The researchers used novel analysis methods to create a comprehensive model of population history that included many ancient and modern groups to determine how they might be related to each other. "Our study is unique, not only in that it greatly expands the number of ancient genomes from this region, but because it is the first study to comprehensively describe all of these populations in one single coherent model," states Stephan Schiffels of the Max Planck Institute for the Science of Human History.

Paleo-Eskimos
An ancient population of Arctic hunter-gatherers, known as Paleo-Eskimos, made a significant genetic contribution to populations living in Arctic North America today. Credit: Illustration by Kerttu Majander, Design by Michelle O'Reilly

Paleo-Eskimos left a lasting legacy that extends across North America

The researchers were able to show that a substantial proportion of the genetic heritage of all ancient and modern American Arctic and Chukotkan populations comes from Paleo-Eskimos. This includes people speaking Eskimo-Aleut languages, such as the Yup'ik, Inuit and Aleuts, and groups speaking Na-Dene languages, such as Athabaskan and Tlingit speakers, in Canada, Alaska, and the lower 48 states of the United States.

Based on the researchers' analysis, Paleo-Eskimos interbred with people with ancestry similar to more southern Native peoples shortly after their arrival to Alaska, between 5,000 and 4,000 years ago. The ancestors of Aleutian Islanders and Athabaskans derive their genetic heritage directly from the ancient mixture between these two groups. The researchers also found that the ancestors of the Inuit and Yup'ik people crossed the Bering Strait at least three times: first as Paleo-Eskimos to Alaska, second as predecessors of the Old Bering Sea archaeological culture back to Chukotka, and third to Alaska again as bearers of the Thule culture. During their stay in Chukotka that likely lasted for more than 1000 years, Yupik and Inuit ancestors also admixed with local groups related to present-day Chukchi and local peoples from Kamchatka.

Paleo-Eskimo ancestry is particularly widespread today in Na-Dene language speakers, which includes Athabaskan and Tlingit communities from Alaska and northern Canada, the West Coast of the United States, and the southwest United States.

"For the last seven years, there has been a debate about whether Paleo-Eskimos contributed genetically to people living in North America today; our study resolves this debate and furthermore supports the theory that Paleo-Eskimos spread Na-Dene languages," explains David Reich of Harvard Medical School and the Howard Hughes Medical Institute. "One of the most striking case examples from our study is the ancient DNA we generated from the ancient Athabaskan site of Tochak McGrath in interior Alaska, where we worked in consultation with the local community to obtain data from three approximately seven hundred year old individuals. We found that these individuals, who lived after the time when the Paleo-Eskimo archaeological culture disappeared across North America, are well modeled as a mixture of the same two ancestry components as those found in Athabaskans today, and derived more than 40% of their ancestry from Paleo-Eskimos.

The excavation of the Middle Dorset individual from the Buchanan site on southeastern Victoria Island, Nunavut, Central Canadian Arctic. Credit: T. Max Friesen

A case example for how genetics can be combined with archaeology to shed new light on the past

The researchers hope that the paper will provide an example of the value of genetic data, in the context of archaeological knowledge, to resolve long-standing questions.

"Determining what happened to this population was not possible from the archaeological record alone," explains Pavel Flegontov of the University of Ostrava. "By analyzing genetic data in concert with the archaeological data, we can meaningfully improve our understanding of the prehistory of peoples of this region. We faced challenging analytical problems due to the complex sequence of gene flows that have shaped ancestries of peoples on both sides of the Bering Strait. Reconstructing this sequence of events required new modelling approaches that we hope may be useful for solving similar problems in other regions of the world."

Attu Island, Aleutian Islands, Alaska. Credit: Jason Rogers

Press release from the Max Planck Institute for the Science of Human History / Max-Planck-Instituts für Menschheitsgeschichte

 


Details of first historically recorded plague pandemic revealed by ancient genomes

Details of first historically recorded plague pandemic revealed by ancient genomes

Analysis of 8 new plague genomes from the first plague pandemic reveals previously unknown levels of plague diversity, and provides the first genetic evidence of the Justinianic Plague in the British Isles

Justinianic Plague Yersinia pestis
Map and phylogenetic tree showing the newly published (yellow) and previously published (turquoise) genomes. Shaded areas and dots represent historically recorded outbreaks of the First Pandemic. Credit: Marcel Keller

An international team of researchers has analyzed human remains from 21 archaeological sites to learn more about the impact and evolution of the plague-causing bacterium Yersinia pestis during the first plague pandemic (541-750 AD). In a study published in PNAS, the researchers reconstructed 8 plague genomes from Britain, Germany, France and Spain and uncovered a previously unknown level of diversity in Y. pestis strains. Additionally, they found the first direct genetic evidence of the Justinianic Plague in the British Isles.

The Justinianic Plague began in 541 in the Eastern Roman Empire, ruled at the time by the Emperor Justinian I, and recurrent outbreaks ravaged Europe and the Mediterranean basin for approximately 200 years. Contemporaneous records describe the extent of the pandemic, estimated to have wiped out up to 25% of the population of the Roman world at the time. Recent genetic studies revealed that the bacterium Yersinia pestis was the cause of the disease, but how it had spread and how the strains that appeared over the course of the pandemic were related to each other was previously unknown.

In the current study, an international team of researchers led by the Max Planck Institute for the Science of Human History analyzed human remains from 21 sites with multiple burials in Austria, Britain, Germany, France and Spain. They were able to reconstruct 8 new Y. pestis genomes, allowing them to compare these strains to previously published ancient and modern genomes. Additionally, the team found the earliest genetic evidence of plague in Britain, from the Anglo-Saxon site of Edix Hill. By using a combination of archaeological dating and the position of this strain of Y. pestis in its evolutionary tree, the researchers concluded that the genome is likely related to an ambiguously described pestilence in the British Isles in 544 AD.

High diversity of Y. pestis strains during the First Pandemic

The researchers found that there was a previously unknown diversity of strains of Y. pestis circulating in Europe between the 6th and 8th centuries AD. The 8 new genomes came from Britain, France, Germany and Spain. "The retrieval of genomes that span a wide geographic and temporal scope gives us the opportunity to assess Y. pestis' microdiversity present in Europe during the First Pandemic," explains co-first author Marcel Keller, PhD student at the Max Planck Institute for the Science of Human History, now working at the University of Tartu. The newly discovered genomes revealed that there were multiple, closely related strains of Y. pestis circulating during the 200 years of the First Pandemic, some possibly at the same times and in the same regions.

Despite the greatly increased number of genomes now available, the researchers were not able to clarify the onset of the Justinianic Plague. "The lineage likely emerged in Central Asia several hundred years before the First Pandemic, but we interpret the current data as insufficient to resolve the origin of the Justinianic Plague as a human epidemic, before it was first reported in Egypt in 541 AD. However, the fact that all genomes belong to the same lineage is indicative of a persistence of plague in Europe or the Mediterranean basin over this time period, instead of multiple reintroductions."

Sampling of a tooth from a suspected plague burial. Credit: Evelyn Guevara

Possible evidence of convergent evolution in strains from two independent historical pandemics

Another interesting finding of the study was that plague genomes appearing towards the end of the First Pandemic showed a big deletion in their genetic code that included two virulence factors. Plague genomes from the late stages of the Second Pandemic some 800-1000 years later show a similar deletion covering the same region of the genomes. "This is a possible example of convergent evolution, meaning that these Y. pestis strains independently evolved similar characteristics. Such changes may reflect an adaptation to a distinct ecological niche in Western Eurasia where the plague was circulating during both pandemics," explains co-first author Maria Spyrou of the Max Planck Institute for the Science of Human History.

The current study offers new insights into the first historically documented plague pandemic, and provides additional clues alongside historical, archaeological, and palaeoepidemiological evidence, helping to answer outstanding questions. "This study shows the potential of palaeogenomic research for understanding historical and modern pandemics by comparing genomes across millennia," explains senior author Johannes Krause of the Max Planck Institute for the Science of Human History. "With more extensive sampling of possible plague burials, we hope to contribute to the understanding of Y. pestis' microevolution and its impact on humans during the course of past and present pandemics."

Lunel-Viel (Languedoc-Southern France). Victim of the plague thrown into a demolition trench of a Gallo-Roman house; end of the 6th-early 7th century. Credit: 1990; CNRS - Claude Raynaud

Press release from the Max Planck Institute for the Science of Human History / Max-Planck-Instituts für Menschheitsgeschichte