Ancient DNA connects large-scale migration with the spread of Slavs.

The second half of the first millennium CE in Central and Eastern Europe was accompanied by fundamental cultural and political transformations. This period of change is commonly associated with the appearance of the Slavs, which is supported by textual evidence and coincides with the emergence of similar archaeological horizons. However, so far there has been no consensus on whether this archaeological horizon spread by migration, Slavicisation or a combination of both.

The genetic history of the Southern Caucasus from the Bronze Age to the Early Middle Ages: 5,000 years of genetic continuity despite high mobility.

The Caucasus was a hub for cultural and technological innovation in prehistory, yet the population history between the Greater and Lesser Caucasus remains insufficiently understood. We present genome-wide data of 205 individuals from modern Georgia and 25 from Armenia, spanning the period from the Bronze Age (BA) to the "Migration Period" (c. 3500 BCE-700 CE).

Ancient Plasmodium genomes shed light on the history of human malaria.

Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P.

Early contact between late farming and pastoralist societies in southeastern Europe.

Archaeogenetic studies have described two main genetic turnover events in prehistoric western Eurasia: one associated with the spread of farming and a sedentary lifestyle starting around 7000-6000 BC (refs. ) and a second with the expansion of pastoralist groups from the Eurasian steppes starting around 3300 BC (refs. ).

14th century Yersinia pestis genomes support emergence of pestis secunda within Europe.

Pestis secunda (1356-1366 CE) is the first of a series of plague outbreaks in Europe that followed the Black Death (1346-1353 CE). Collectively this period is called the Second Pandemic. From a genomic perspective, the majority of post-Black Death strains of Yersinia pestis thus far identified in Europe display diversity accumulated over a period of centuries that form a terminal sub-branch of the Y.

Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean.

The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean-a region fundamental to Europe's prehistory-the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans.

Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete.

During the late 3 millennium BCE, the Eastern Mediterranean and Near East witnessed societal changes in many regions, which are usually explained with a combination of social and climatic factors. However, recent archaeogenetic research forces us to rethink models regarding the role of infectious diseases in past societal trajectories. The plague bacterium Yersinia pestis, which was involved in some of the most destructive historical pandemics, circulated across Eurasia at least from the onset of the 3 millennium BCE, but the challenging preservation of ancient DNA in warmer climates has restricted the identification of Y.

Stone Age genomes shed light on the early evolution, diversity, and ecology of plague.

The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development.

Ten millennia of hepatitis B virus evolution.

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene.

Dynamic changes in genomic and social structures in third millennium BCE central Europe.

Europe's prehistory oversaw dynamic and complex interactions of diverse societies, hitherto unexplored at detailed regional scales. Studying 271 human genomes dated ~4900 to 1600 BCE from the European heartland, Bohemia, we reveal unprecedented genetic changes and social processes. Major migrations preceded the arrival of "steppe" ancestry, and at ~2800 BCE, three genetically and culturally differentiated groups coexisted.

Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe.

Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length.

Human mobility at Tell Atchana (Alalakh), Hatay, Turkey during the 2nd millennium BC: Integration of isotopic and genomic evidence.

The Middle and Late Bronze Age, a period roughly spanning the 2nd millennium BC (ca. 2000-1200 BC) in the Near East, is frequently referred to as the first 'international age', characterized by intense and far-reaching contacts between different entities from the eastern Mediterranean to the Near East and beyond. In a large-scale tandem study of stable isotopes and ancient DNA of individuals excavated at Tell Atchana (Alalakh, located in Hatay, Turkey), we explored the role of mobility at the capital of a regional kingdom, named Mukish during the Late Bronze Age, which spanned the Amuq Valley and some areas beyond.

Author Correction: Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus.

Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6 millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today's Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow.

Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia.

Modern humans have inhabited the Lake Baikal region since the Upper Paleolithic, though the precise history of its peoples over this long time span is still largely unknown. Here, we report genome-wide data from 19 Upper Paleolithic to Early Bronze Age individuals from this Siberian region. An Upper Paleolithic genome shows a direct link with the First Americans by sharing the admixed ancestry that gave rise to all non-Arctic Native Americans.

Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland.

Genetic studies of Neolithic and Bronze Age skeletons from Europe have provided evidence for strong population genetic changes at the beginning and the end of the Neolithic period. To further understand the implications of these in Southern Central Europe, we analyze 96 ancient genomes from Switzerland, Southern Germany, and the Alsace region in France, covering the Middle/Late Neolithic to Early Bronze Age. Similar to previously described genetic changes in other parts of Europe from the early 3rd millennium BCE, we detect an arrival of ancestry related to Late Neolithic pastoralists from the Pontic-Caspian steppe in Switzerland as early as 2860-2460 calBCE.

Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes.

The second plague pandemic, caused by Yersinia pestis, devastated Europe and the nearby regions between the 14 and 18 centuries AD. Here we analyse human remains from ten European archaeological sites spanning this period and reconstruct 34 ancient Y. pestis genomes.

Ancient genomes from across Western Europe reveal early diversification during the First Pandemic (541-750).

The first historically documented pandemic caused by began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as , little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for DNA and reconstructed eight genomes.

Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis.

In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity.