Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.Introduction Results - The IA transition in the Kazakh Steppe - Admixture modeling of IA steppe populations - Post-IA genetic turnovers in the Kazakh Steppe - Dating ancient admixture - Present-day Kazakhs Discussion Material and methods - Radiocarbon dating - DNA extraction, library preparations, and sequencing - Modern DNA genotyping and quality controls - Ancient DNA data processing -- Raw data -- Authentication and contamination estimate -- Genotyping -- Sex determination -- Genetic relatedness estimation - Uniparental haplogroup assignment - Population structure analyses - Individual labeling and population grouping criteria - F-statistics and ancestry modeling - Admixture dating - CHROMOPAINTER and fineSTRUCTURE analyse

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

The bacterial pathogenYersinia pestisgave rise to devastating outbreaks throughouthuman history, and ancient DNA evidence has shown it afflicted human populations asfar back as the Neolithic.Y. pestisgenomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to itsemergence from aYersinia pseudotuberculosis-like progenitor; however, the number ofreconstructed LNBA genomes are too few to explore its diversity during this criticalperiod of development. Here, we present 17Y. pestisgenomes dating to 5,000 to 2,500y BP from a wide geographic expanse across Eurasia. This increased dataset enabled usto explore correlations between temporal, geographical, and genetic distance. Ourresults suggest a nonflea-adapted and potentially extinct single lineage that persistedover millennia without significant parallel diversification, accompanied by rapid dis-persal across continents throughout this period, a trend not observed in other pathogensfor which ancient genomes are available. A stepwise pattern of gene loss provides fur-ther clues on its early evolution and potential adaptation. We also discover the presenceof theflea-adapted form ofY. pestisin Bronze Age Iberia, previously only identified inin the Caucasus and the Volga regions, suggesting a much wider geographic spread ofthis form ofY. pestis. Together, these data reveal the dynamic nature of plague’s forma-tive years in terms of its early evolution and ecology

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. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic

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 similar to 10,500 and similar to 400 years ago. We date the most recent common ancestor of all HBV lineages to between similar to 20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for similar to 4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.Molecular Technology and Informatics for Personalised Medicine and Healt

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. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic

ЕЖЕЛГІ ПАТОГЕНДІ МИКРОАҒЗАЛАРДЫ ЗЕРТТЕУ ЕРЕКШЕЛІКТЕРІ

Infectious disease have affected humans throughout their evolution, both during acute pandemic events and through persistent morbidity and mortality. Recent advancements in the field of ancient genomics have increased our understanding of the infectious disease history and pathogen evolution though time. For the article, we used more than 300 ancient teeth samples from Central Asia, spanning the time period between the 4th century BCE and the 4th century CE, to address questions related to pathogen presence in past populations and microbial evolution through time. It focused on non-targeted metagenomic approaches for the detection of ancient pathogens in ancient human remains. Additionally, the article describes a specific case study of paleo-DNA screening for the plague pathogen, Yersinia pestis, which is known to have afflicted human populations since the Neolithic period, has caused immense mortality during the Middle Ages in Europe and continues to be prevalent across Central Asia today.1. Introduction 2. Materials and methods 3. Results and discussion Conclusio

ЕЖЕЛГІ ПАТОГЕНДІ МИКРОАҒЗАЛАРДЫ ЗЕРТТЕУ ЕРЕКШЕЛІКТЕРІ

Infectious disease have affected humans throughout their evolution, both during acute pandemic events and through persistent morbidity and mortality. Recent advancements in the field of ancient genomics have increased our understanding of the infectious disease history and pathogen evolution though time. For the article, we used more than 300 ancient teeth samples from Central Asia, spanning the time period between the 4th century BCE and the 4th century CE, to address questions related to pathogen presence in past populations and microbial evolution through time. It focused on non-targeted metagenomic approaches for the detection of ancient pathogens in ancient human remains. Additionally, the article describes a specific case study of paleo-DNA screening for the plague pathogen, Yersinia pestis, which is known to have afflicted human populations since the Neolithic period, has caused immense mortality during the Middle Ages in Europe and continues to be prevalent across Central Asia today.1. Introduction 2. Materials and methods 3. Results and discussion Conclusio

A Case History in Cooperative Biological Research: Compendium of Studies and Program Analyses in Kazakhstan

Kazakhstan and the United States have partnered since 2003 to counter the proliferation of weapons of mass destruction. The US Department of Defense (US DoD) has funded threat reduction programs to eliminate biological weapons, secure material in repositories that could be targeted for theft, and enhance surveillance systems to monitor infectious disease outbreaks that would affect national security. The cooperative biological research (CBR) program of the US DoD’s Biological Threat Reduction Program has provided financing, mentorship, infrastructure, and biologic research support to Kazakhstani scientists and research institutes since 2005. The objective of this paper is to provide a historical perspective for the CBR involvement in Kazakhstan, including project chronology, successes and challenges to allow lessons learned to be applied to future CBR endeavors. A project compendium from open source data and interviews with partner country Kazakhstani participants, project collaborators, and stakeholders was developed utilizing studies from 2004 to the present. An earlier project map was used as a basis to determine project linkages and continuations during the evolution of the CBR program. It was determined that consistent and effective networking increases the chances to collaborate especially for competitive funding opportunities. Overall, the CBR program has increased scientific capabilities in Kazakhstan while reducing their risk of biological threats. However, there is still need for increased scientific transparency and an overall strategy to develop a capability-based model to better enhance and sustain future research. Finally, we offer a living perspective that can be applied to further link related studies especially those related to One Health and zoonoses and the assessment of similar capability-building programs

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. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic

Programmable Systems for Intelligence in Automobiles (PRYSTINE): Final results after Year 3

Autonomous driving is disrupting the automotive industry as we know it today. For this, fail-operational behavior is essential in the sense, plan, and act stages of the automation chain in order to handle safety-critical situations on its own, which currently is not reached with state-of-the-art approaches.The European ECSEL research project PRYSTINE realizes Fail-operational Urban Surround perceptION (FUSION) based on robust Radar and LiDAR sensor fusion and control functions in order to enable safe automated driving in urban and rural environments. This paper showcases some of the key exploitable results (e.g., novel Radar sensors, innovative embedded control and E/E architectures, pioneering sensor fusion approaches, AI-controlled vehicle demonstrators) achieved until its final year 3