Liivi Varul | University of Tartu (original) (raw)

Papers by Liivi Varul

SummaryHuman herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today ... more SummaryHuman herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1’s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 × 10-7 - 1.13 × 10-6 for non-African diversity leading to an estimated age of sampled...

Transition from the Stone to the Bronze Age in Central and Western Europe was a period of major p... more Transition from the Stone to the Bronze Age in Central and Western Europe was a period of major population movements originating from the Ponto-Caspian Steppe. Here, we report new genome-wide sequence data from 28 individuals from the territory north of this source area – from the under-studied Western part of present-day Russia, including Stone Age hunter-gatherers (10,800–4,250 cal BC) and Bronze Age farmers from the Corded Ware complex called Fatyanovo Culture (2,900–2,050 cal BC). We show that Eastern hunter-gatherer ancestry was present in Northwestern Russia already from around 10,000 BC. Furthermore, we see a clear change in ancestry with the arrival of farming – the Fatyanovo Culture individuals were genetically similar to other Corded Ware cultures, carrying a mixture of Steppe and European early farmer ancestry and thus likely originating from a fast migration towards the northeast from somewhere in the vicinity of modern-day Ukraine, which is the closest area where these ...

Current Biology, 2019

Highlights d Increase in hunter-gatherer ancestry in Bronze Age Eastern Baltic genomes d Genetic ... more Highlights d Increase in hunter-gatherer ancestry in Bronze Age Eastern Baltic genomes d Genetic input from Siberia to the Eastern Baltic during the transition to Iron Age d Arrival of Siberian ancestry coincides with proposed arrival of Uralic languages d Light eyes, hair, and skin and lactose tolerance become frequent in the Bronze Age

SSRN Electronic Journal, 2019

Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and ... more Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance Highlights d 31 new ancient genomes help compare the Scythians to preand postdating cultures d Scythian dominance brought along an increase of eastern ancestry across the steppe d Results imply some demic diffusion in the spread of the Scythian culture d Genetic makeup agrees with the Gothic source of post-Scythian Chernyakhiv culture

Journal of Archaeological Science: Reports, 2018

Journal of forensic sciences, Jan 12, 2018

Determining maximum heating temperatures of burnt bones is a long-standing problem in forensic sc... more Determining maximum heating temperatures of burnt bones is a long-standing problem in forensic science and archaeology. In this pilot study, controlled experiments were used to heat 14 fleshed and defleshed pig vertebrae (wet bones) and archaeological human vertebrae (dry bones) to temperatures of 400, 600, 800, and 1000°C. Specular component included (SCI) color values were recorded from the bone surfaces with a Konica-Minolta cm-2600d spectrophotometer. These color values were regressed onto heating temperature, using both a traditional linear model and the k-nearest neighbor (k-NN) machine-learning algorithm. Mean absolute errors (MAE) were computed for 1000 rounds of temperature prediction. With the k-NN approach, the median MAE prediction errors were 41.6°C for the entire sample, and 20.9°C for the subsample of wet bones. These results indicate that spectrophotometric color measurements combined with machine learning methods can be a viable tool for estimating bone heating temp...

Ecology and evolution, Mar 1, 2018

Recent ancient DNA (aDNA) studies of human pathogens have provided invaluable insights into their... more Recent ancient DNA (aDNA) studies of human pathogens have provided invaluable insights into their evolutionary history and prevalence in space and time. Most of these studies were based on DNA extracted from teeth or postcranial bones. In contrast, no pathogen DNA has been reported from the petrous bone which has become the most desired skeletal element in ancient DNA research due to its high endogenous DNA content. To compare the potential for pathogenic aDNA retrieval from teeth and petrous bones, we sampled these elements from five ancient skeletons, previously shown to be carrying . Based on shotgun sequencing data, four of these five plague victims showed clearly detectable levels of DNA in the teeth, whereas all the petrous bones failed to produce DNA above baseline levels. A broader comparative metagenomic analysis of teeth and petrous bones from 10 historical skeletons corroborated these results, showing a much higher microbial diversity in teeth than petrous bones, includin...

Estonian Journal of Archaeology, 2016

There have been various explanations in archaeological literature about whether the earliest Bron... more There have been various explanations in archaeological literature about whether the earliest Bronze Age stone-cist graves and the first Pre-Roman Iron Age tarand graves in Estonia were built by locals or non-locals. As to possible immigrations, the stone-cist graves have been often related to Scandinavian populations, whilst early tarand graves allegedly had roots in eastern directions. The oldest known examples of these cemetery types are at Jõelähtme and Muuksi for stone-cist graves, and at Ilmandu and Kunda for early tarand graves, in the coastal zone of northern Estonia. In order to test the migration hypothesis we carried out a bioarchaeological study, measuring and mapping local biologically available Sr and O isotope ratios and analysing stable isotope signals of altogether eight individuals from these early stone-cist and tarand graves. The study material was chosen on the basis of the oldest AMS dates of skeletons available so far, or according to the earliest burial constructions in the cemeteries. Based on the comparison of local biologically available Sr and O isotopic baseline results and the results obtained from the individuals, we can talk about migrants in the case of two persons from Kunda and perhaps one from Muuksi, whilst most of the individuals analysed are of local origin. Thus, the idea of Early Metal Period migrations to Estonia from the surrounding regions is supported to some extent. However, the discussion of these migrations might turn out to be surprisingly different from what is expected on the basis of material culture. We also emphasise the importance of further analysis, especially mapping isotopic baseline data in the eastern Baltics, in order to draw further conclusions about the directions and extent of prehistoric migration in this region.

Cell, 2015

Highlights d Yersinia pestis was common across Eurasia in the Bronze Age d The most recent common... more Highlights d Yersinia pestis was common across Eurasia in the Bronze Age d The most recent common ancestor of all Y. pestis was 5,783 years ago d The ymt gene was acquired before 951 cal BC, giving rise to transmission via fleas d Bronze Age Y. pestis was not capable of causing bubonic plague

Farming-based economies appear relatively late in Northeast Europe and the extent to which they i... more Farming-based economies appear relatively late in Northeast Europe and the extent to which they involve genetic ancestry change is still poorly understood. Here we present the analyses of low coverage whole genome sequence data from five hunter-gatherers and five farmers of Estonia dated to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic Culture are closest to Eastern hunter-gatherers. The Estonian first farmers of Corded Ware Culture show high similarity in their autosomes with Steppe Belt Late Neolithic/Bronze Age individuals, Caucasus hunter-gatherers and Iranian farmers while their X chromosomes are most closely related with the European Early Farmers of Anatolian descent. These findings suggest that the shift to intensive cultivation and animal husbandry in Estonia was triggered by the arr...

Journal of Archaeological Science: Reports, 2019

We present an individual biography of an adult woman from the 3rd millennium BC from the Eastern ... more We present an individual biography of an adult woman from the 3rd millennium BC from the Eastern Baltic. Being a representative of a Corded Ware Culture she is considered one of the first documented cases carrying the early plague bacteria, Yersina pestis. The appearance, life, and death of this individual from Sope, NE Estonia, is provided through an application of a range of osteological and biomolecular analyses. The mortuary practices that accompanied her death are revealed through post-excavation archaeothanatological analysis. The position of bones within the grave indicates that her remains were handled differently from the known contemporary Corded Ware Culture inhumations. The mortuary treatment consisted of at least two phases that resulted in an imitation of a 'proper' flexed burial. Probably, the reburial of bones was undertaken during the Corded Ware period.

Nature

The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, ... more The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Journal of Archaeological Science: Reports, 2019

We present an individual biography of an adult woman from the 3rd millennium BC from the Eastern ... more We present an individual biography of an adult woman from the 3rd millennium BC from the Eastern Baltic.
Being a representative of a Corded Ware Culture she is considered one of the first documented cases carrying the
early plague bacteria, Yersina pestis. The appearance, life, and death of this individual from Sope, NE Estonia, is
provided through an application of a range of osteological and biomolecular analyses. The mortuary practices
that accompanied her death are revealed through post-excavation archaeothanatological analysis. The position
of bones within the grave indicates that her remains were handled differently from the known contemporary
Corded Ware Culture inhumations. The mortuary treatment consisted of at least two phases that resulted in an
imitation of a ‘proper’ flexed burial. Probably, the reburial of bones was undertaken during the Corded Ware
period.

Graphical Abstract Highlights d Yersinia pestis was common across Eurasia in the Bronze Age d The... more Graphical Abstract Highlights d Yersinia pestis was common across Eurasia in the Bronze Age d The most recent common ancestor of all Y. pestis was 5,783 years ago

The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics wi... more The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

Current Biology, 2019

SSRN Electronic Journal, 2019

Journal of Archaeological Science: Reports, 2018

Journal of forensic sciences, Jan 12, 2018

Ecology and evolution, Mar 1, 2018

Estonian Journal of Archaeology, 2016

Cell, 2015

Journal of Archaeological Science: Reports, 2019

Nature

Journal of Archaeological Science: Reports, 2019

We present an individual biography of an adult woman from the 3rd millennium BC from the Eastern ... more We present an individual biography of an adult woman from the 3rd millennium BC from the Eastern Baltic.
Being a representative of a Corded Ware Culture she is considered one of the first documented cases carrying the
early plague bacteria, Yersina pestis. The appearance, life, and death of this individual from Sope, NE Estonia, is
provided through an application of a range of osteological and biomolecular analyses. The mortuary practices
that accompanied her death are revealed through post-excavation archaeothanatological analysis. The position
of bones within the grave indicates that her remains were handled differently from the known contemporary
Corded Ware Culture inhumations. The mortuary treatment consisted of at least two phases that resulted in an
imitation of a ‘proper’ flexed burial. Probably, the reburial of bones was undertaken during the Corded Ware
period.

Several Corded Ware culture (in Eastern Baltic 2800–2000 cal BC) burial sites are known from Esto... more Several Corded Ware culture (in Eastern Baltic 2800–2000 cal BC) burial sites are known from Estonia. As majority of the sites has been destroyed by plowing or construction works, only four of them have been archaeologically excavated. Therefore we solely have scattered pieces of information regarding the burial customs and people of the Corded Ware complexes.
The preserved osteological material reveals around ten individuals from both sexes and various age groups. The corpses were buried mainly in crouched positions in pit graves, accompanied by grave goods (e.g. ceramic vessels, items of stone, flint and bone and probably meat). It is also assumed that the dead were treated differently, based on their sex e.g. variations in the placement of the body or the type of grave goods interred with the deceased. However, the recent osteological analyses contradict few of the previous notions. For example, a female was buried with a shaft-hole stone axe – an item usually associated with “males”. Additionally there appears to be evidence of either a secondary deposition of the remains or a disturbed grave.

Abstracts. 19th Annual Meeting of the European Association of Archaeologists. 2013 Pilsen - Czech Republic. Pilsen, University of West Bohemia, p. 429.

"The first above-ground grave type that appeared in Estonia is the stone-cist grave (used from La... more "The first above-ground grave type that appeared in Estonia is the stone-cist grave (used from Late Bronze Age to Early Iron Ages). In 1980’s due to rescue excavations in Jõelähtme in Northern Estonia, 36 stone-cist graves were fully excavated. Current case study focuses on the grave no 19. Our aim is to find out to what extent the events regarding this grave can be reconstructed, if we can rely only on inconsistent, yet sufficient documentation and fragmented osteological material.

Based on the material it is possible to determine the number of species and individuals, also age, sex, pathologies and taphonomical features. At least, three individuals were buried in grave No 19 but only one of them had a complete skeleton. Additionally, many animal and bird species were present; bones from three dogs among them. Since the documentation shows mostly general location of the remains, the contexts of single finds cannot be assessed. Still, we provide a discussion on how do the human remains relate to each other, why there are numerous animal and bird species, and, based on 14C datings, how are human and animal bones correlated."

Stone-cist graves are round structures with central cist(s) and one or more exterior circular wal... more Stone-cist graves are round structures with central cist(s) and one or more exterior circular walls. They were used throughout the Late Bronze Age (around 1200–500 BC) in coastal regions of Estonia. Although the graves appear to be meant for a single burial, usually remains of multiple individuals are found within them. In 1980s 36 graves in Jõelähtme in Northern Estonia were fully excavated. We have approached the bone material using osteological and taphonomic methods, together with contextual analysis. The fragmented nature of the bones and problematic documentation has made the study challenging but fruitful. Some examples of the results: minimum number of human individuals in graves varies from zero to six, all age groups are represented; there are several mammal and bird species; none of the human or animal skeletons are complete or articulated, even though bones preserve well in that environment. Our presentation tackles various questions such as why are numerous skeletons represented only by few bone fragments? Why were human remains often commingled with animal bones? How do we explain different taphonomic features e.g. heavy fragmentation and only a few cut-marks? Which animal bones can be associated with the burial customs? Why does the number of individuals per grave vary so extensively?

Stone-cist graves are round structures with central cist(s) and one or more exterior circular wal... more Stone-cist graves are round structures with central cist(s) and one or more exterior circular walls. They have been used throughout Late Bronze Age (around 1200–500 BC) in coastal regions of Estonia. Although the graves appear to be meant for a single burial, usually remains of multiple individuals are found. In 1980’s 36 graves in Jõelähtme in Northern Estonia were fully excavated.
We have approached the bone material using osteological and taphonomic methods together with contextual analysis. Fragmented nature of the bones and problematic documentation has made the study challenging but fruitful. Some examples of the results: minimum number of human individuals in graves varies from zero to six, all age groups are represented; there are several mammal and bird species; none of the human or animal skeletons are complete or articulated, even though bones preserve well in that environment.
Our presentation tackles various questions like why are numerous skeletons represented only by few bone fragments? Why were human remains often commingled with animal bones? How to explain different taphonomic features e.g. heavy fragmentation and only few cut-marks? Which animal bones can be associated with the burial customs? Why does the number of individuals per grave vary so extensively?