Author
Dalia Pokutta
Other affiliations: University of Gothenburg
Bio: Dalia Pokutta is an academic researcher from Stockholm University. The author has contributed to research in topics: Bronze Age & Population. The author has an hindex of 6, co-authored 17 publications receiving 1347 citations. Previous affiliations of Dalia Pokutta include University of Gothenburg.
Topics: Bronze Age, Population, Radiocarbon dating, Archaeological science, δ13C
Papers
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University of Copenhagen1, University of Gothenburg2, Technical University of Denmark3, Leiden University4, Lund University5, University of Oxford6, University of Wrocław7, University of Zurich8, Wrocław Medical University9, University of Toronto10, Gorno-Altaisk State University11, South Ural State University12, Polish Academy of Sciences13, Ludwig Maximilian University of Munich14, Hungarian Natural History Museum15, Eötvös Loránd University16, Hungarian Academy of Sciences17, Academy of Sciences of the Czech Republic18, Masaryk University19, University of Tartu20, Yerevan State University21, Hungarian National Museum22, University of Szeged23, University of Wisconsin-Madison24, Russian Academy of Sciences25, First Faculty of Medicine, Charles University in Prague26, Armenian National Academy of Sciences27, Moscow State University28, University of California, Berkeley29
TL;DR: It is shown 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.
Abstract: 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.
1,088 citations
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TL;DR: 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 is reported and is found to be at least two times older than previous estimates.
367 citations
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University of Cambridge1, Charité2, University of Copenhagen3, Karagandy State University4, University of Arizona5, National University of Mongolia6, Mongolian State University of Agriculture7, National Academy of Sciences8, First Faculty of Medicine, Charles University in Prague9, Russian Academy of Sciences10, South Ural State University11, Stockholm University12, University of Gothenburg13, Paul Sabatier University14, Technical University of Denmark15, University of Veterinary Medicine Vienna16, University of Giessen17, Erasmus University Rotterdam18, Wellcome Trust Sanger Institute19
TL;DR: Phylogenies reconstructed using 12 hepatitis B virus genomes, which were recovered from ancient human genome data, reveal a complex history of hepatitis B evolution that is not evident when using only modern samples.
Abstract: 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 × 10−6–1.51 × 10−5 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 Ages1,2. 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. Phylogenies reconstructed using 12 hepatitis B virus genomes, which were recovered from ancient human genome data, reveal a complex history of hepatitis B evolution that is not evident when using only modern samples.
148 citations
29 Aug 2013
14 citations
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12 Jul 2016
TL;DR: In this paper, the role and character of ritual activities, diversity and variety of religious orientations in the Eneolithic period and the question of how and for what reason this particular cave was modified from a natural space to a sacred place are investigated.
Abstract: In Eneolithic Europe, the complexity of mortuary differentiation increased with the complexity of the society at large. Human remains from the Verteba Cave provide a unique opportunity to study the lives, deaths and cultural practices of the Cucuteni-Trypillia culture in Western Ukraine. The subterranean sanctuary of Verteba was without a doubt a rallying point of both religious and social significance. Therefore, this investigation focuses on the role and character of ritual activities, the diversity and variety of religious orientations in the Eneolithic period and the question of how and for what reason this particular cave was modified from a natural space to a sacred place. We also seek to clarify the research potential of the site in relation to highly developed and relatively wide-spread religion with direct implications for the Cucuteni-Trypillia social structure.
10 citations
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
10,124 citations
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TL;DR: Some of the key events in the peopling of the world in the light of the findings of work on ancient DNA are reviewed.
Abstract: Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.
1,365 citations
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Harvard University1, Broad Institute2, Howard Hughes Medical Institute3, University College Dublin4, Emory University5, University of Copenhagen6, Trinity College, Dublin7, University of Adelaide8, Russian Academy of Sciences9, Complutense University of Madrid10, Rovira i Virgili University11, University of Valladolid12, Max Planck Society13, University of Tübingen14, University of Basel15, Danube Private University16, Hartwick College17, Pompeu Fabra University18
TL;DR: A genome-wide scan for selection using ancient DNA is reported, 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.
Abstract: 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.
1,083 citations
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Broad Institute1, Whitman College2, Simon Fraser University3, Howard Hughes Medical Institute4, University of Coimbra5, University College Dublin6, Emory University7, Chinese Academy of Sciences8, University of Ferrara9, University of Miskolc10, Armenian National Academy of Sciences11, University of Pennsylvania12, University of Winnipeg13, Alexandru Ioan Cuza University14, University of Edinburgh15, Royal College of Surgeons in Ireland16, Spanish National Research Council17, Imperial College London18, Max Planck Society19, Binghamton University20, University of Huddersfield21, University of Pavia22, Yerevan State University23
TL;DR: This paper reported genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers, showing that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other.
Abstract: We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
695 citations
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TL;DR: This work focuses on four major phases that witnessed broad anthropogenic alterations to biodiversity—the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks.
Abstract: The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity—the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.
516 citations