Publications by authors named "Vyacheslav Moiseyev"

23 Publications

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Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age.

Science 2020 07;369(6502)

Lundbeck Foundation GeoGenetics Center, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark.

Smallpox, one of the most devastating human diseases, killed between 300 million and 500 million people in the 20th century alone. We recovered viral sequences from 13 northern European individuals, including 11 dated to ~600-1050 CE, overlapping the Viking Age, and reconstructed near-complete variola virus genomes for four of them. The samples predate the earliest confirmed smallpox cases by ~1000 years, and the sequences reveal a now-extinct sister clade of the modern variola viruses that were in circulation before the eradication of smallpox. We date the most recent common ancestor of variola virus to ~1700 years ago. Distinct patterns of gene inactivation in the four near-complete sequences show that different evolutionary paths of genotypic host adaptation resulted in variola viruses that circulated widely among humans.
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http://dx.doi.org/10.1126/science.aaw8977DOI Listing
July 2020

Human auditory ossicles as an alternative optimal source of ancient DNA.

Genome Res 2020 03 25;30(3):427-436. Epub 2020 Feb 25.

Institute of Archaeological Sciences, Eötvös Loránd University, H-1088 Budapest, Hungary.

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.
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http://dx.doi.org/10.1101/gr.260141.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111520PMC
March 2020

The formation of human populations in South and Central Asia.

Science 2019 09;365(6457)

Earth Institute, University College Dublin, Dublin 4, Ireland.

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.
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http://dx.doi.org/10.1126/science.aat7487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822619PMC
September 2019

The population history of northeastern Siberia since the Pleistocene.

Nature 2019 06 5;570(7760):182-188. Epub 2019 Jun 5.

Institute of Archaeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
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http://dx.doi.org/10.1038/s41586-019-1279-zDOI Listing
June 2019

Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe.

Nat Commun 2018 11 27;9(1):5018. Epub 2018 Nov 27.

Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.

European population history has been shaped by migrations of people, and their subsequent admixture. Recently, ancient DNA has brought new insights into European migration events linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and north-western Russia. We show that the genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago. This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today. Additionally, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age, which adds to the historical and linguistic information about the population history of Finland.
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http://dx.doi.org/10.1038/s41467-018-07483-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258758PMC
November 2018

Co-morbidity with hypertrophic osteoarthropathy: A possible Iron Age Sarmatian case from the Volga steppe of Russia.

Int J Paleopathol 2019 03 5;24:66-78. Epub 2018 Oct 5.

Department of Electronic Devices, St. Petersburg State Electrotechnical University «LETI», 5 Professora Popova street, St. Petersburg, Russia. Electronic address:

Purpose: Hypertrophic osteoarthropathy (HOA) is a condition that can be inherited or acquired. It causes diffuse periosteal new bone formation on the long bones, with a predilection for the appendicular skeleton. When acquired, it is a nonspecific indicator of systemic disease that arises following a primary condition. This paper reviews the palaeopathological literature associated with this rare condition. It also describes the first possible case of co-morbidity associated with hypertrophic osteoarthropathy in an adult skeleton (cal. BC 170 - 1 cal. AD) from the mobile pastoralist Sarmatian culture of the Volga steppes of Russia.

Methods: Macroscopic and radiological examination provide differential diagnoses of the lesions, while clinical and bioarchaeological analyses offer insights into the possible experience of disease and social implications of care among the nomadic populations of Iron Age Russia.

Results: The analysis of Sk. 6524.102 displays lesions that may be due to both hypertrophic osteoarthropathy and osteomalacia. The man was physically impaired and his participation in physically challenging activities would have been limited.

Conclusions: The study stresses that co-morbidity is a key parameter when interpreting disease in past populations, particularly when the diagnosis involves hypertrophic osteoarthropathy.

Significance: This is the first case of hypertrophic osteoarthropathy identified in Eurasian prehistoric populations. The research emphasises the significance of co-morbidity in the past.

Limitations: The diagnosis of co-morbid diseases in human remains is extremely complex and the conditions were identified as most probable by a process of elimination.

Suggestions For Further Research: Further studies should be dedicated to understanding co-morbidity in the past.
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http://dx.doi.org/10.1016/j.ijpp.2018.09.007DOI Listing
March 2019

Ancient hepatitis B viruses from the Bronze Age to the Medieval period.

Nature 2018 05 9;557(7705):418-423. Epub 2018 May 9.

Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands.

Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient sequences group either within or in a sister relationship with extant human or other ape HBV clades. Generally, the genome properties follow those of modern HBV. The root of the HBV tree is projected to between 8.6 and 20.9 thousand years ago, and we estimate a substitution rate of 8.04 × 10-1.51 × 10 nucleotide substitutions per site per year. In several cases, the geographical locations of the ancient genotypes do not match present-day distributions. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are shown to have an early Eurasian presence. The geographical and temporal patterns that we observe in ancient and modern HBV genotypes are compatible with well-documented human migrations during the Bronze and Iron Ages. We provide evidence for the creation of HBV genotype A via recombination, and for a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. These data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
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http://dx.doi.org/10.1038/s41586-018-0097-zDOI Listing
May 2018

The first horse herders and the impact of early Bronze Age steppe expansions into Asia.

Science 2018 06 9;360(6396). Epub 2018 May 9.

Institute for the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia.

The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.
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http://dx.doi.org/10.1126/science.aar7711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748862PMC
June 2018

Author Correction: The genetic prehistory of the Baltic Sea region.

Nat Commun 2018 04 11;9(1):1494. Epub 2018 Apr 11.

Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.

The original version of this Article omitted references to previous work, which are detailed in the associated Author Correction. These omissions have been corrected in both the PDF and HTML versions of the Article.
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http://dx.doi.org/10.1038/s41467-018-03872-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895581PMC
April 2018

Ancient pathogen DNA in human teeth and petrous bones.

Ecol Evol 2018 03 26;8(6):3534-3542. Epub 2018 Feb 26.

Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark.

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, 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.
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http://dx.doi.org/10.1002/ece3.3924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869295PMC
March 2018

The genomic history of southeastern Europe.

Nature 2018 03 21;555(7695):197-203. Epub 2018 Feb 21.

Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy.

Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west-east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.
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http://dx.doi.org/10.1038/nature25778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6091220PMC
March 2018

The genetic prehistory of the Baltic Sea region.

Nat Commun 2018 01 30;9(1):442. Epub 2018 Jan 30.

Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.

While the series of events that shaped the transition between foraging societies and food producers are well described for Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here, we report genome-wide DNA data from 38 ancient North Europeans ranging from ~9500 to 2200 years before present. Our analysis provides genetic evidence that hunter-gatherers settled Scandinavia via two routes. We reveal that the first Scandinavian farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Mesolithic Western hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers during the Early and Middle Neolithic. The arrival of steppe pastoralists in the Late Neolithic introduced a major shift in economy and mediated the spread of a new ancestry associated with the Corded Ware Complex in Northern Europe.
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http://dx.doi.org/10.1038/s41467-018-02825-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789860PMC
January 2018

The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers.

Curr Biol 2017 Feb 2;27(4):576-582. Epub 2017 Feb 2.

Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland. Electronic address:

The Neolithic transition was a dynamic time in European prehistory of cultural, social, and technological change. Although this period has been well explored in central Europe using ancient nuclear DNA [1, 2], its genetic impact on northern and eastern parts of this continent has not been as extensively studied. To broaden our understanding of the Neolithic transition across Europe, we analyzed eight ancient genomes: six samples (four to ∼1- to 4-fold coverage) from a 3,500 year temporal transect (∼8,300-4,800 calibrated years before present) through the Baltic region dating from the Mesolithic to the Late Neolithic and two samples spanning the Mesolithic-Neolithic boundary from the Dnieper Rapids region of Ukraine. We find evidence that some hunter-gatherer ancestry persisted across the Neolithic transition in both regions. However, we also find signals consistent with influxes of non-local people, most likely from northern Eurasia and the Pontic Steppe. During the Late Neolithic, this Steppe-related impact coincides with the proposed emergence of Indo-European languages in the Baltic region [3, 4]. These influences are distinct from the early farmer admixture that transformed the genetic landscape of central Europe, suggesting that changes associated with the Neolithic package in the Baltic were not driven by the same Anatolian-sourced genetic exchange.
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http://dx.doi.org/10.1016/j.cub.2016.12.060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321670PMC
February 2017

The genetic history of Ice Age Europe.

Nature 2016 06 2;534(7606):200-5. Epub 2016 May 2.

Instituto Internacional de Investigaciones Prehistóricas, Universidad de Cantabria, 39005 Santander, Spain.

Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3-6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.
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http://dx.doi.org/10.1038/nature17993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943878PMC
June 2016

Genome-wide patterns of selection in 230 ancient Eurasians.

Nature 2015 Dec 23;528(7583):499-503. Epub 2015 Nov 23.

Max Planck Institute for the Science of Human History, D-07745 Jena, Germany.

Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.
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http://dx.doi.org/10.1038/nature16152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918750PMC
December 2015

Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.

Cell 2015 Oct 22;163(3):571-82. Epub 2015 Oct 22.

Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden.

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.
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http://dx.doi.org/10.1016/j.cell.2015.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644222PMC
October 2015

Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.

PLoS One 2015 18;10(6):e0129102. Epub 2015 Jun 18.

Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknechtstr. 24-25, 14476 Potsdam Golm, Germany; Department of Biology, University of York, Wentworth Way, Heslington, York, United Kingdom.

The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129102PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472748PMC
April 2016

Population genomics of Bronze Age Eurasia.

Nature 2015 Jun;522(7555):167-72

The Archaeological Museum of Wrocław, 50-077 Wrocław, Poland.

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.
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http://dx.doi.org/10.1038/nature14507DOI Listing
June 2015

Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years.

Science 2014 Nov 6;346(6213):1113-8. Epub 2014 Nov 6.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal'ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.
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http://dx.doi.org/10.1126/science.aaa0114DOI Listing
November 2014

Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1.

PLoS One 2014 4;9(2):e87612. Epub 2014 Feb 4.

Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia.

The human mitochondrial haplogroup C1 has a broad global distribution but is extremely rare in Europe today. Recent ancient DNA evidence has demonstrated its presence in European Mesolithic individuals. Three individuals from the 7,500 year old Mesolithic site of Yuzhnyy Oleni Ostrov, Western Russia, could be assigned to haplogroup C1 based on mitochondrial hypervariable region I sequences. However, hypervariable region I data alone could not provide enough resolution to establish the phylogenetic relationship of these Mesolithic haplotypes with haplogroup C1 mitochondrial DNA sequences found today in populations of Europe, Asia and the Americas. In order to obtain high-resolution data and shed light on the origin of this European Mesolithic C1 haplotype, we target-enriched and sequenced the complete mitochondrial genome of one Yuzhnyy Oleni Ostrov C1 individual. The updated phylogeny of C1 haplogroups indicated that the Yuzhnyy Oleni Ostrov haplotype represents a new distinct clade, provisionally coined "C1f". We show that all three C1 carriers of Yuzhnyy Oleni Ostrov belong to this clade. No haplotype closely related to the C1f sequence could be found in the large current database of ancient and present-day mitochondrial genomes. Hence, we have discovered past human mitochondrial diversity that has not been observed in modern-day populations so far. The lack of positive matches in modern populations may be explained by under-sampling of rare modern C1 carriers or by demographic processes, population extinction or replacement, that may have impacted on populations of Northeast Europe since prehistoric times.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087612PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3913659PMC
December 2014

Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

PLoS Genet 2013 14;9(2):e1003296. Epub 2013 Feb 14.

Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia.

North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans.
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http://dx.doi.org/10.1371/journal.pgen.1003296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3573127PMC
June 2013
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