genomes Scythians

Ancient Genomes Trace the Origin and Decline of the Scythians

Ancient Genomes Trace the Origin and Decline of the Scythians

Generally thought of as fierce horse-warriors, the Scythians were a multitude of Iron Age cultures who ruled the Eurasian steppe, playing a major role in Eurasian history. A new study published in Science Advances analyzes genome-wide data for 111 ancient individuals spanning the Central Asian Steppe from the first millennia BCE and CE. The results reveal new insights into the genetic events associated with the origins, development and decline of the steppe’s legendary Scythians.

Because of their interactions and conflicts with the major contemporaneous civilizations of Eurasia, the Scythians enjoy a legendary status in historiography and popular culture. The Scythians had major influences on the cultures of their powerful neighbors, spreading new technologies such as saddles and other improvements for horse riding. The ancient Greek, Roman, Persian and Chinese empires all left a multitude of sources describing, from their perspectives, the customs and practices of the feared horse warriors that came from the interior lands of Eurasia.

An aerial view of Hun-Xianbi culture burials. Both horses and warriors can be identified. Credits: © Zainolla Samashev

Still, despite evidence from external sources, little is known about Scythian history. Without a written language or direct sources, the language or languages they spoke, where they came from and the extent to which the various cultures spread across such a huge area were in fact related to one another, remain unclear.

The Iron Age transition and the formation of the genetic profile of the Scythians

A new study published in Science Advances by an international team of geneticists, anthropologists and archeologists lead by scientists from the Archaeogenetics Department of the Max Planck Institute for the Science of Human History in Jena, Germany, helps illuminate the history of the Scythians with 111 ancient genomes from key Scythian and non-Scythian archaeological cultures of the Central Asian steppe. The results of this study reveal that substantial genetic turnovers were associated with the decline of the long-lasting Bronze Age sedentary groups and the rise of Scythian nomad cultures in the Iron Age. Their findings show that, following the relatively homogenous ancestry of the late Bronze Age herders, at the turn of the first millennium BCE, influxes from the east, west and south into the steppe formed new admixed gene pools.

Mound 4 of the Eleke Sazy necropolis in eastern Kazakhstan. Credits: © Zainolla Samashev

The diverse peoples of the Central Asian Steppe

The study goes even further, identifying at least two main sources of origin for the nomadic Iron Age groups. An eastern source likely originated from populations in the Altai Mountains that, during the course of the Iron Age, spread west and south, admixing as they moved. These genetic results match with the timing and locations found in the archeological record and suggest an expansion of populations from the Altai area, where the earliest Scythian burials are found, connecting different renowned cultures such as the Saka, the Tasmola and the Pazyryk found in southern, central and eastern Kazakhstan respectively. Surprisingly, the groups located in the western Ural Mountains descend from a second separate, but simultaneous source. Contrary to the eastern case, this western gene pool, characteristic of the early Sauromatian-Sarmatian cultures, remained largely consistent through the westward spread of the Sarmatian cultures from the Urals into the Pontic-Caspian steppe.

The decline of the Scythian cultures associated with new genetic turnovers

The study also covers the transition period after the Iron Age, revealing new genetic turnovers and admixture events. These events intensified at the turn of the first millennium CE, concurrent with the decline and then disappearance of the Scythian cultures in the Central Steppe. In this case, the new far eastern Eurasian influx is plausibly associated with the spread of the nomad empires of the Eastern steppe in the first centuries CE, such as the Xiongnu and Xianbei confederations, as well as minor influxes from Iranian sources likely linked to the expansion of Persian-related civilization from the south.

Although many of the open questions on the history of the Scythians cannot be solved by ancient DNA alone, this study demonstrates how much the populations of Eurasia have changed and intermixed through time. Future studies should continue to explore the dynamics of these trans-Eurasian connections by covering different periods and geographic regions, revealing the history of connections between west, central and east Eurasia in the remote past and their genetic legacy in present day Eurasian populations.

The burial of a social elite known as 'Golden Man' from the Eleke Sazy necropolis. Credits: © Zainolla Samashev

Press release from Max Planck Institute for the Science of Human History in Jena on the new study that helps illuminate the history of the Scythians with 111 ancient genomes from archaeological cultures of the Central Asian steppe.


ADHD neanderthals

A genomic analysis in samples of Neanderthals and modern humans shows a decrease in ADHD-associated genetic variants

A genomic analysis in samples of Neanderthals and modern humans shows a decrease in ADHD-associated genetic variants

According to the study, some features like hyperactivity or impulsiveness could have been favourably selected for survival in ancestral environments dominated by a nomad lifestyle

The frequency of genetic variants associated with attention-deficit/hyperactivity disorder (ADHD) has decreased progressively in the evolutionary human lineage from the Palaeolithic to nowadays, according to a study published in the journal Scientific Reports.

The new genomic analysis compares several ADHD-associated genetic variants described in current European populations to assess its evolution in samples of the human species (Homo sapiens), modern and ancient, and in samples of Neanderthals (Homo neanderthalensis). According to the conclusions, the low tendency observed in European populations could not be explained for the genetic mix with African populations or the introgression of Neanderthal genomic segments in our genome.

The new genomic study isled by Professor Bru Cormand, from the Faculty of Biology and the Institute of Biomedicine of the University of Barcelona (IBUB), the Research Institute Sant Joan de Déu (IRSJD) and the Rare Diseases Networking Biomedical Research Centre (CIBERER), and the researcher Oscar Lao, from the Centro Nacional de Análisis Genómico (CNAG), part of the Centre for Genomic Regulation (CRG). The study, whose first author is the CNAG-CRG researcher Paula Esteller -current doctoral student at the Institute of Evolutionary Biology (IBE, CSIC-UPF)- counts on the participation of research groups of the Aarhus University (Denmark) and the Upstate Medical University of New York (United States).

TDAH neandertales
The experts Paula Esteller, Bru Cormand and Òscar Lao

ADHD: an adaptive value in the evolutionary lineage of humans?

 The attention deficit/hyperactivity disorder (ADHD) is an alteration of the neurodevelopment which can have a large impact on the life of the affected people. Featured by hyperactivity, impulsiveness and attention deficit, it is very common in modern populations -with a prevalence of 5% in children and adolescents- and can last up to adulthood.

From an evolutionary perspective, one would expect that anything detrimental would disappear among the population. In order to explain this phenomenon, several natural hypotheses have been presented -specially focused on the context of transition from the Palaeolithic to the Neolithic-, such as the known Mismatch Theory.

“According to this theory, cultural and technological changes that occurred over the last thousands of years would have allowed us to modify our environment in order to adopt it to our physiological needs in the short term. However, in the long term, these changes would have promoted an imbalance regarding the environment in which our hunter-gatherer ancestors evolved”, note the authors.

Therefore, several traits like hyperactivity and impulsiveness -typical in people with ADHD- could have been selectively favoured in ancestral environments dominated by a nomad lifestyle. However, the same features would have become non-adaptive in other environments related to more recent times (mostly sedentary).

Why is it one of the most common disorders in children and adolescents?

 The new study, based on the study on 20,000 ADHD affected people and 35,000 controls, reveals the genetic variants and alleles associated with ADHD tend to be found in genes which are intolerant to mutations that cause loss of function, which shows the existence of a selective pressure on this phenotype.

According to the authors, the high prevalence of ADHD nowadays could be a result from a favourable selection that took place in the past. Although being an unfavourable phenotype in the new environmental context, the prevalence would still be high because much time has not passed for it to disappear. However, due to the absence of available genomic data for ADHD, none of the hypothesis has been empirically contrasted so far.

“Therefore, the analysis we conducted guarantee the presence of selective pressures that would have been acting for many years against the ADHD-associated variants. These results are compatible with the mismatch theory but they suggest negative selective pressures to have started before the transition between the Palaeolithic and the Neolithic, about 10,000 years ago”, say the authors.

Reference Article:

 Esteller-Cucala, P.; Maceda, I.; Børglum, A.D.; Demontis, D.; Faraone, S.V.; Cormand, B.; Lao, O. “Genomic analysis of the natural history of attention-deficit/hyperactivity disorder using Neanderthal and ancient Homo sapiens samples”. Scientific Reports, May,  2020. Doi: 10.1038/s41598-020-65322-4

 

Press release from the University of Barcelona

The ancient history of Neandertals in Europe

The ancient history of Neandertals in Europe

Early ancestors of the last Neandertals lived in Europe already 120,000 years ago

This is the femur of a male Neandertal from Hohlenstein-Stadel Cave, Germany. Credit: © Oleg Kuchar, Museum Ulm

Researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have retrieved nuclear genome sequences from the femur of a male Neandertal discovered in 1937 in Hohlenstein-Stadel Cave, Germany, and from the maxillary bone of a Neandertal girl found in 1993 in Scladina Cave, Belgium. Both Neandertals lived around 120,000 years ago, and therefore predate most of the Neandertals whose genomes have been sequenced to date.

Neandertals Europe
This is the Maxillary bone of a Neandertal girl from Scladina Cave, Belgium. Credit: © J. Eloy, AWEM, Archéologie andennaise

By examining the nuclear genomes of these two individuals, the researchers could show that these early Neandertals in Western Europe were more closely related to the last Neandertals who lived in the same region as much as 80,000 years later, than they were to contemporaneous Neandertals living in Siberia. "The result is truly extraordinary and a stark contrast to the turbulent history of replacements, large-scale admixtures and extinctions that is seen in modern human history", says Kay Prüfer who supervised the study.

Intriguingly, unlike the nuclear genome, the mitochondrial genome of the Neandertal from Hohlenstein-Stadel Cave in Germany is quite different from that of later Neandertals - a previous report showed that more than 70 mutations distinguish it from the mitochondrial genomes of other Neandertals. The researchers suggest that early European Neandertals may have inherited DNA from a yet undescribed population. "This unknown population could represent an isolated Neandertal population yet to be discovered, or may be from a potentially larger population in Africa related to modern humans", explains Stéphane Peyrégne who led the analysis.

 

Press release from the Max Planck Institute for Evolutionary Anthropology / Max-Planck-Institut für evolutionäre Anthropologie


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.

###

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


East Africa

Ancient DNA tells the story of the first herders and farmers in east Africa

Ancient DNA tells the story of the first herders and farmers in east Africa

A collaborative study that includes a SLU-Madrid archaeologist provides new insights on early human interaction

East Africa
Herders move goats through the Engaruka Basin in northern Tanzania's Rift Valley. Ancient DNA shows that this way of life spread to East Africa through multiple population movements. Credit: Katherine Grillo

ST. LOUIS, MO (May 30, 2019) - A collaborative study led by archaeologists, geneticists and museum curators is providing answers to previously unsolved questions about life in sub-Saharan Africa thousands of years ago. The results were published online in the journal Science Thursday, May 30.

Researchers from North American, European and African institutions analyzed ancient DNA from 41 human skeletons curated in the National Museums of Kenya and Tanzania, and the Livingstone Museum in Zambia.

"The origins of food producers in East Africa have remained elusive because of gaps in the archaeological record," said co-first author Mary Prendergast, Ph.D., professor of anthropology and chair of humanities at Saint Louis University's campus in Madrid, Spain.

"This study uses DNA to answer previously unresolvable questions about how people were moving and interacting," added Prendergast.

The research provides a look at the origins and movements of early African food producers.

The first form of food production to spread through most of Africa was the herding of cattle, sheep and goats. This way of life continues to support millions of people living on the arid grasslands that cover much of sub-Saharan Africa.

"Today, East Africa is one of the most genetically, linguistically, and culturally diverse places in the world," explains Elizabeth Sawchuk, Ph.D., a bioarchaeologist at Stony Brook University and co-first author of the study. "Our findings trace the roots of this mosaic back several millennia. Distinct peoples have coexisted in the Rift Valley for a very long time."

Previous archaeological research shows that the Great Rift Valley of Kenya and Tanzania was a key site for the transition from foraging to herding. Herders of livestock first appeared in northern Kenya around 5000 years ago, associated with elaborate monumental cemeteries, and then spread south into the Rift Valley, where Pastoral Neolithic cultures developed.

The new genetic results reveal that this spread of herding into Kenya and Tanzania involved groups with ancestry derived from northeast Africa, who appeared in East Africa and mixed with local foragers there between about 4500-3500 years ago. Previously, the origins and timing of these population shifts were unclear, and some archaeologists hypothesized that domestic animals spread through exchange networks, rather than by movement of people.

After around 3500 years ago, herders and foragers became genetically isolated in East Africa, even though they continued to live side by side. Archaeologists have hypothesized substantial interaction among foraging and herding groups, but the new results reveal that there were strong and persistent social barriers that lasted long after the initial encounters.

Another major genetic shift occurred during the Iron Age around 1200 years ago, with movement into the region of additional peoples from both northeastern and western Africa. These groups contributed to ancient ancestry profiles similar to those of many East Africans today. This genetic shift parallels two major cultural changes: farming and iron-working.

The study provided insight into the history of East Africa as an independent center of evolution of lactase persistence, which enables people to digest milk into adulthood. This genetic adaptation is found in high proportions among Kenyan and Tanzanian herders today.

Co-first author Mary Prendergast, Ph.D., is a professor of anthropology and chair of humanities at Saint Louis University's campus in Madrid, Spain. Credit: Mary Prendergast

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Uralic languages Siberia

Ancient DNA suggests that some Northern Europeans got their languages from Siberia

Ancient DNA suggests that some Northern Europeans got their languages from Siberia

Uralic languages Siberia
Estonian Grammar by Heinrich Stahl, published 1637 in Reval (Tallinn). Public Domain

Most Europeans descend from a combination of European hunter-gatherers, Anatolian early farmers, and Steppe herders. But only European speakers of Uralic languages like Estonian and Finnish also have DNA from ancient Siberians. Now, with the help of ancient DNA samples, researchers reporting in Current Biology on May 9 suggest that these languages may have arrived from Siberia by the beginning of the Iron Age, about 2,500 years ago, rather than evolving in Northern Europe.

The findings highlight the way in which a combination of genetic, archaeological, and linguistic data can converge to tell the same story about what happened in particular areas in the distant past.

"Since the transition from Bronze to Iron Age coincides with the diversification and arrival time of Finnic languages in the Eastern Baltic proposed by linguists, it is plausible that the people who brought Siberian ancestry to the region also brought Uralic languages with them," says Lehti Saag of University of Tartu, Estonia.

Although researchers knew that the Uralic-speaking people share common Siberian ancestry, its arrival time in the Eastern Baltic had remained uncertain. To characterize the genetic ancestry of people from the as-yet-unstudied cultural layers, Saag along with Kristiina Tambets and colleagues extracted DNA from the tooth roots of 56 individuals, 33 of which yielded enough DNA to include in the analysis.

"Studying ancient DNA makes it possible to pinpoint the moment in time when the genetic components that we see in modern populations reached the area since, instead of predicting past events based on modern genomes, we are analyzing the DNA of individuals who actually lived in a particular time in the past," Saag explains.

Their data suggest that the Siberian ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC--around the time of the diversification of west Uralic/Finnic languages. It also indicates an influx of people from regions with strong Western hunter-gatherer characteristics in the Bronze Age, including many traits we now associate with modern Northern Europeans, like pale skins, blue eyes, and lactose tolerance.

"The Bronze Age individuals from the Eastern Baltic show an increase in hunter-gatherer ancestry compared to Late Neolithic people and also in the frequency of light eyes, hair, and skin and lactose tolerance," Tambets says, noting that those characteristics continue amongst present-day Northern Europeans.

The researchers are now expanding their study to better understand the Iron Age migration processes in Europe. They say they will also "move forward in time and focus on the genetic structure of the medieval time period."

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horse genetic history

A genomic tour-de-force reveals the last 5,000 years of horse history

A genomic tour-de-force reveals the last 5,000 years of horse history

horse genetic history
This image shows a herd of Kazakh horses in the Pavlodar region of Kazakhstan in August 2016. Credit: Ludovic Orlando

Each year on the first Saturday in May, Thoroughbred horses reach speeds of over 40 miles per hour as they compete to win the Kentucky Derby. But the domestic horse wasn't always bred for speed. In fact, an international team now has evidence to suggest that the modern horse is genetically quite different from the horses of even just a few hundred years ago.

Their work, appearing May 2 in the journal Cell, constructs the genetic history of the domestic horse across the world over the last 5,000 years by using the largest genome collection ever generated for a non-human organism. The findings identify two new horse lineages that are now extinct and suggest that familiar traits such as speed were only selected for more recently in their history.

"The horse has impacted human history like no other animal," says Ludovic Orlando (@LudovicLorlando), a research director with CNRS and the University of Toulouse and a Professor of Molecular Archaeology at the University of Copenhagen. "If you look at the historical record from the Bronze Age onward, horses are always part of the equation up until very recent times, connecting civilizations and impacting transportation, warfare, and agriculture. Our goal was to understand how humans and their activities transformed the horse throughout history to fit their purposes--and how these changes in biology influenced human history."

The team responsible for this project consisted of 121 collaborators, including geneticists, archaeologists, and evolutionary biologists from 85 institutions around the world, and examined genome-scale data from 278 horse specimens from across Eurasia over the last 42,000 years.

"Such a large collection of data means that we can build a much more precise understanding of horse domestication and management through space and time," Orlando says. "But it was truly an interdisciplinary effort because of course it takes a lot more than just DNA to understand such a story. We had to integrate all these social, historical, and geographical aspects."

This graphical abstract summarizes horse genetic history over the last 5,000 years. Credit: Fages et al./Cell

Overall, the team's findings suggest that equine history was much more complex than was previously realized. Today, there are only two known lineages of horses, the domestic horse and the Przewalski's horse. But the researchers here identified two additional now-extinct lineages of horses, one from the Iberian Peninsula and one from Siberia, both of which still existed 4,000-4,500 years ago. "We found two lineages of horses at the far ends of Eurasia that are not related to what we call the domestic horse today, nor to the Przewalski's horse. They are a sort of horse equivalent of what Neanderthals are to modern humans," Orlando says.

The researchers also found a major shift in the genetic makeup of horses in Europe and Central Asia in the 7th to 9th centuries and say this shift probably corresponds to Islamic expansions. The horses common in Europe before that time are now only found in regions such as Iceland; the new European horses after that time were much more similar to horses found in Persia during the Sassanid Empire. When the team performed a scan to identify genes that had been selected for in these Persian horses, they found evidence of selection in genes associated with body shape.

"It was a moment in history that reshaped the landscape of horses in Europe. If you look at what we today call Arabian horses, you know that they have a different shape--and we know how popular this anatomy has been throughout history, including in racing horses. Based on the genomic evidence, we propose that this horse was so successful and influential because it brought a new anatomy and perhaps other favorable traits," he says.

The researchers found that there have been additional significant and recent changes in the domestic horse. Similar selection scans indicate that only in the last 1,500 years did traits such as ambling and speed over short distances become more actively sought. And when they looked at the overall genetic diversity of the domestic horse, the researchers found a sharp decline in the last 200 to 300 years. They believe this decline corresponds with new breeding practices that were introduced with the rise of the concept of "pure" breeds.

"What we picture as a horse today and what we picture as a horse from a thousand years ago or two thousand years ago was likely actually very different. Some of those traits that we are most familiar with are only a modern invention, and in the last few hundred years, we have actually impacted the horse genome a lot more than in the previous 4,000 years of domestication," says Orlando.

This map shows the locations of the archaeological sites where horse remains were found. Credit: Fages et al./Cell

He believes that this research can tell us a lot about both the past and the present. "Our findings show that the past is a lot more diverse than we thought it was and that it cannot be imagined or inferred through modern-day variation. But ancient DNA tells us a lot about today as well, because it teaches us about the consequences of some shifts in breeding practices," he says. And that, he believes, can also affect the way we think about conservation and modern agricultural practices.

Of course, our understanding of the domestic horse's history is far from complete. Orlando acknowledges that there are geographic and temporal gaps in his story. Perhaps mostly glaringly, we still don't know when and or where the horse was domesticated. "Horse domestication is central to human history, and in 2019, we still don't understand where it started. That's mind-blowing," he says.

He looks forward to filling in those blanks. "Whenever I'm asked about what finding I'm most excited about, I always say, the next one. Because this research opens the door for so many possibilities to be studied now."

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Inner Eurasia

Details of the history of inner Eurasia revealed by new study

Details of the history of inner Eurasia revealed by new study

Researchers combining genetics, archaeology, history and linguistics have gained new insights into the history of inner Eurasia, once a cultural and genetic crossroads connecting Europe and Asia

Inner Eurasia
Children from one of the Tajikistan communities included in the study. Credit: Elena Balanovska

An international team of researchers has combined archaeological, historical and linguistic data with genetic information from over 700 newly analyzed individuals to construct a more detailed picture of the history of inner Eurasia than ever before available. In a study published in Nature Ecology & Evolution, they found that the indigenous populations of inner Eurasia are very diverse in their genes, culture and languages, but divide into three groups that stretch across the area in east-west geographic bands.

Inner Eurasia, including areas of modern-day Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine and Uzbekistan, was once the cross-roads connecting Asia and Europe, and a major intersection for the exchange of culture, trade goods and genes in prehistory and historical periods, including the era of the famous Silk Road.

This vast area can also be divided into several distinct ecological regions that stretch in largely east-west bands across Inner Eurasia, consisting of the deserts at the southern edge of the region, the steppe in the central part, taiga forests further north, and tundra towards the Arctic region. The subsistence strategies used by indigenous groups in these regions largely correlate with the ecological zones, for example reindeer herding and hunting in the tundra region and nomadic pastoralism on the steppe.

Despite the long and important history of inner Eurasia, details about past migrations and interactions between groups are not always clear, especially in prehistory. "Inner Eurasia is a perfect place to investigate the relationship between environmental conditions and the pattern of human migration and mixture, as well as changes driven by cultural innovations such as the introduction of dairy pastoralism into the steppe," states Choongwon Jeong of the Max Planck Institute for the Science of Human History, co-first and senior author of the paper. In order to clarify our understanding of some of the nuances of the history of the region, an international team of researchers undertook an ambitious project to use modern and ancient DNA from a broad geographic range and time period, in concert with archaeological, linguistic and historical information, to clarify the relationships between the different populations. "A few ethnic groups were studied previously," comments Oleg Balanovsky from the Vavilov Institute of General Genetics in Moscow, also co-first author, "but we conducted more than a hundred field trips to study this vast region systematically, and reached communities speaking almost all of the Inner Eurasian languages".

Three distinct east-west groupings

For this study, the researchers analyzed DNA from 763 individuals from across the region as well as reanalyzed the genome-wide data from two ancient individuals from the Botai culture, and compared those results with previously published data from modern and ancient individuals. They found three distinct genetic groupings, which geographically are arranged in east-west bands stretching across the region and correlating generally to ecological zones, where populations within each band share a distinct combination of ancestries in varying proportions.

The northernmost grouping, which they term "forest-tundra", includes Russians, all Uralic language-speakers, which includes Hungarian, Finnish and Estonian, and Yeniseian-language speakers, of which only one remains today and is spoken in central Siberia. The middle grouping, which they term "steppe-forest", includes Turkic- and Mongolic-speaking populations from the Volga and the region around the Altai and Sayan mountains, near to where Russia, China, Mongolia and Kazakhstan meet. The southernmost grouping, "southern-steppe", includes the rest of Turkic- and Mongolic-speaking populations living further south, such as Kazakhs, Kyrgyzs and Uzbeks, as well as Indo-European-speaking Tajiks.

Previously unknown genetic connections revealed

Because the study includes data from a broad time period, it is able to show shifts in ancestry in the past that reveal previously unknown interactions. For example, the researchers found that the southern-steppe populations had a larger genetic component from West and South Asia than the other two groupings. This component is also widespread in the ancient populations of the region since the second half of the first millennium BC, but not found in Central Kazakhstan in earlier periods. This hints at a population movement from the southern-steppe region to the steppe-forest region that was previously unknown.

"Inner Eurasia has functioned as a conduit for human migration and cultural transfer since the first appearance of modern humans in this region. As a result, we observe deep sharing of genes between Western and Eastern Eurasian populations in multiple layers," explains Jeong. "The opportunity to find direct evidence for the hidden old layers of admixture, which is often difficult to appreciate from present-day populations, is very exciting."

"We found not only corridors, but also barriers for migrations," adds Balanovsky. "Some of them separate the historical groups of populations, while others, like the distinct barrier following the Great Caucasus mountain ridge, were obviously shaped by the geographic landscape."

Geographic locations of the Eneolithic Botai, groups including newly sampled individuals, and nearby groups with published data. The map is overlayed with ecoregional information, divided into 14 biomes downloaded from https://ecoregions2017.appspot.com/ (credited to Ecoregions 2017 © Resolve). Credit: Jeong & Balanovsky et. al. 2019. The genetic history of admixture across inner Eurasia. Nature Ecology & Evolution, http://dx.doi.org/10.1038/s41559-019-0878-2.

Two ancient individuals resequenced in this study originated from the Botai culture in Kazakhstan where the horse was initially domesticated. Analysis of the Y-chromosome (inherited along the paternal genealogical lines) revealed a genetic lineage which is typical in the Kazakh steppe up to the present day. But analysis of the autosomes, which both parents contribute to their children, show no trace of Botai ancestry left in present-day people, likely due to repeated migrations into the region both from the west and the east since the Bronze Age.

The researchers emphasize that their model of three groupings does not perfectly explain all known populations and that there are examples of both outliers and intermediate groups. "It is important to organize a future study for further sampling of sparsely populated regions between the clines, for example, Central Kazakhstan or East Siberia," states Johannes Krause, also of the Max Planck Institute for the Science of Human History, and senior author of the paper.

Researchers from the study conducting field work along the Amur River. Credit: Yuri Bogunov

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