Aivar Kriiska

Population genomics of Bronze Age Eurasia

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.

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago

Summary 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.

Palaeogeographic Model for the SW Estonian Coastal Zone of the Baltic Sea

The authors combined geological, geodetic and archaeological shore displacement evidence to create a temporal and spatial water-level change model for the SW Estonian coast of the Baltic Sea since 13,300 cal. years BP. The Baltic Sea shoreline database for Estonian territory was used for the modelling work and contained about 1,200 sites from the Baltic Ice Lake, Ancylus Lake and Littorina Sea stages. This database was combined with a shore displacement curve from the Parnu area (in SW Estonia) and with geodetic relative sea-level data for the last century. The curve was reconstructed on the basis of palaeocoastline elevations and radiocarbon-dated peat and soil sequences and ecofacts from archaeological sites recording three regressive phases of the past Baltic Sea, interrupted by Ancylus Lake and Littorina Sea transgressions with magnitudes of 12 and 10 m, respectively. A water-level change model was applied together with a digital terrain model in order to reconstruct coastline change in the region and to examine the relationships between coastline change and displacement of the Stone Age human settlements that moved in connection with transgressions and regressions on the shifting coastline of the Baltic Sea.

Sea level changes and Neolithic hunter-fisher-gatherers in the centre of Tallinn, southern coast of the Gulf of Finland, Baltic Sea

Relative sea level (RSL) changes and the palaeogeography of a Neolithic hunter-fisher-gatherer settlement site on the former shore of the Gulf of Finland in the city centre of Tallinn were reconstructed by implementing GIS in landscape modelling based on archaeological, sedimentary and shore displacement data. AMS radiocarbon dating of mammal bones from the cultural layer suggests the existence of the hunter-fisher-gatherer settlement around 5.1–4.8 cal. ka BP on a seaward inclining sandy beach of Tallinn palaeo-bay c. 100 m from the Litorina Sea shoreline and at about 2.4 m above the coeval sea level. The shoreline passed the study site at about 5.8 cal. ka BP and retreated towards northeast with an average speed of 13 m per century, while the RSL lowered by c. 2.5 mm annually. Combining radiocarbon dates of terrestrial and marine mammal bones from the Neolithic cultural layer, a marine reservoir effect of 350 14C years for the brackish-water Baltic Sea was calculated. By using high-resolution archaeological data in combination with RSL and other geological proxies, we demonstrate new possibilities to reconstruct the palaeoenvironment of deeply buried coastal settlement sites and to predict a possible continuation of the cultural layer in heavily built-up areas.

Ancient pathogen DNA in human teeth and petrous bones

Abstract 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 Yersinia pestis. Based on shotgun sequencing data, four of these five plague victims showed clearly detectable levels of Y. pestis DNA in the teeth, whereas all the petrous bones failed to produce Y. pestis 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, including pathogenic and oral microbial taxa. Our results imply that although petrous bones are highly valuable for ancient genomic analyses as an excellent source of endogenous DNA, the metagenomic potential of these dense skeletal elements is highly limited. This trade‐off must be considered when designing the sampling strategy for an aDNA project.