Publications by authors named "Saskia Pfrengle"

12 Publications

  • Page 1 of 1

2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.

BMC Biol 2020 08 28;18(1):108. Epub 2020 Aug 28.

Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.

Background: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging.

Results: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed.

Conclusions: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.
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http://dx.doi.org/10.1186/s12915-020-00839-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7456089PMC
August 2020

Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe.

Curr Biol 2020 Oct 13;30(19):3788-3803.e10. Epub 2020 Aug 13.

Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP), University of Tübingen, Tübingen, Germany. Electronic address:

Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15 century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood.
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http://dx.doi.org/10.1016/j.cub.2020.07.058DOI Listing
October 2020

Human mitochondrial DNA lineages in Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry.

Sci Rep 2019 11 15;9(1):16883. Epub 2019 Nov 15.

Department of Biosciences, University of Helsinki, Helsinki, Finland.

Human ancient DNA studies have revealed high mobility in Europe's past, and have helped to decode the human history on the Eurasian continent. Northeastern Europe, especially north of the Baltic Sea, however, remains less well understood largely due to the lack of preserved human remains. Finland, with a divergent population history from most of Europe, offers a unique perspective to hunter-gatherer way of life, but thus far genetic information on prehistoric human groups in Finland is nearly absent. Here we report 103 complete ancient mitochondrial genomes from human remains dated to AD 300-1800, and explore mtDNA diversity associated with hunter-gatherers and Neolithic farmers. The results indicate largely unadmixed mtDNA pools of differing ancestries from Iron-Age on, suggesting a rather late genetic shift from hunter-gatherers towards farmers in North-East Europe. Furthermore, the data suggest eastern introduction of farmer-related haplogroups into Finland, contradicting contemporary genetic patterns in Finns.
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http://dx.doi.org/10.1038/s41598-019-51045-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858343PMC
November 2019

Kinship-based social inequality in Bronze Age Europe.

Science 2019 11 10;366(6466):731-734. Epub 2019 Oct 10.

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

Revealing and understanding the mechanisms behind social inequality in prehistoric societies is a major challenge. By combining genome-wide data, isotopic evidence, and anthropological and archaeological data, we have gone beyond the dominating supraregional approaches in archaeogenetics to shed light on the complexity of social status, inheritance rules, and mobility during the Bronze Age. We applied a deep microregional approach and analyzed genome-wide data of 104 human individuals deriving from farmstead-related cemeteries from the Late Neolithic to the Middle Bronze Age in southern Germany. Our results reveal individual households, lasting several generations, that consisted of a high-status core family and unrelated low-status individuals; a social organization accompanied by patrilocality and female exogamy; and the stability of this system over 700 years.
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http://dx.doi.org/10.1126/science.aax6219DOI Listing
November 2019

Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear.

Sci Rep 2019 08 15;9(1):10700. Epub 2019 Aug 15.

Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.

The cave bear (Ursus spelaeus) is one of the Late Pleistocene megafauna species that faced extinction at the end of the last ice age. Although it is represented by one of the largest fossil records in Europe and has been subject to several interdisciplinary studies including palaeogenetic research, its fate remains highly controversial. Here, we used a combination of hybridisation capture and next generation sequencing to reconstruct 59 new complete cave bear mitochondrial genomes (mtDNA) from 14 sites in Western, Central and Eastern Europe. In a Bayesian phylogenetic analysis, we compared them to 64 published cave bear mtDNA sequences to reconstruct the population dynamics and phylogeography during the Late Pleistocene. We found five major mitochondrial DNA lineages resulting in a noticeably more complex biogeography of the European lineages during the last 50,000 years than previously assumed. Furthermore, our calculated effective female population sizes suggest a drastic cave bear population decline starting around 40,000 years ago at the onset of the Aurignacian, coinciding with the spread of anatomically modern humans in Europe. Thus, our study supports a potential significant human role in the general extinction and local extirpation of the European cave bear and illuminates the fate of this megafauna species.
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http://dx.doi.org/10.1038/s41598-019-47073-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6695494PMC
August 2019

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

Erratum: The Beaker phenomenon and the genomic transformation of northwest Europe.

Authors:
Iñigo Olalde Selina Brace Morten E Allentoft Ian Armit Kristian Kristiansen Thomas Booth Nadin Rohland Swapan Mallick Anna Szécsényi-Nagy Alissa Mittnik Eveline Altena Mark Lipson Iosif Lazaridis Thomas K Harper Nick Patterson Nasreen Broomandkhoshbacht Yoan Diekmann Zuzana Faltyskova Daniel Fernandes Matthew Ferry Eadaoin Harney Peter de Knijff Megan Michel Jonas Oppenheimer Kristin Stewardson Alistair Barclay Kurt Werner Alt Corina Liesau Patricia Ríos Concepción Blasco Jorge Vega Miguel Roberto Menduiña García Azucena Avilés Fernández Eszter Bánffy Maria Bernabò-Brea David Billoin Clive Bonsall Laura Bonsall Tim Allen Lindsey Büster Sophie Carver Laura Castells Navarro Oliver E Craig Gordon T Cook Barry Cunliffe Anthony Denaire Kirsten Egging Dinwiddy Natasha Dodwell Michal Ernée Christopher Evans Milan Kuchařík Joan Francès Farré Chris Fowler Michiel Gazenbeek Rafael Garrido Pena María Haber-Uriarte Elżbieta Haduch Gill Hey Nick Jowett Timothy Knowles Ken Massy Saskia Pfrengle Philippe Lefranc Olivier Lemercier Arnaud Lefebvre César Heras Martínez Virginia Galera Olmo Ana Bastida Ramírez Joaquín Lomba Maurandi Tona Majó Jacqueline I McKinley Kathleen McSweeney Balázs Gusztáv Mende Alessandra Modi Gabriella Kulcsár Viktória Kiss András Czene Róbert Patay Anna Endrődi Kitti Köhler Tamás Hajdu Tamás Szeniczey János Dani Zsolt Bernert Maya Hoole Olivia Cheronet Denise Keating Petr Velemínský Miroslav Dobeš Francesca Candilio Fraser Brown Raúl Flores Fernández Ana-Mercedes Herrero-Corral Sebastiano Tusa Emiliano Carnieri Luigi Lentini Antonella Valenti Alessandro Zanini Clive Waddington Germán Delibes Elisa Guerra-Doce Benjamin Neil Marcus Brittain Mike Luke Richard Mortimer Jocelyne Desideri Marie Besse Günter Brücken Mirosław Furmanek Agata Hałuszko Maksym Mackiewicz Artur Rapiński Stephany Leach Ignacio Soriano Katina T Lillios João Luís Cardoso Michael Parker Pearson Piotr Włodarczak T Douglas Price Pilar Prieto Pierre-Jérôme Rey Roberto Risch Manuel A Rojo Guerra Aurore Schmitt Joël Serralongue Ana Maria Silva Václav Smrčka Luc Vergnaud João Zilhão David Caramelli Thomas Higham Mark G Thomas Douglas J Kennett Harry Fokkens Volker Heyd Alison Sheridan Karl-Göran Sjögren Philipp W Stockhammer Johannes Krause Ron Pinhasi Wolfgang Haak Ian Barnes Carles Lalueza-Fox David Reich

Nature 2018 03;555(7697):543

This corrects the article DOI: 10.1038/nature25738.
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http://dx.doi.org/10.1038/nature26164DOI Listing
March 2018

The Beaker phenomenon and the genomic transformation of northwest Europe.

Authors:
Iñigo Olalde Selina Brace Morten E Allentoft Ian Armit Kristian Kristiansen Thomas Booth Nadin Rohland Swapan Mallick Anna Szécsényi-Nagy Alissa Mittnik Eveline Altena Mark Lipson Iosif Lazaridis Thomas K Harper Nick Patterson Nasreen Broomandkhoshbacht Yoan Diekmann Zuzana Faltyskova Daniel Fernandes Matthew Ferry Eadaoin Harney Peter de Knijff Megan Michel Jonas Oppenheimer Kristin Stewardson Alistair Barclay Kurt Werner Alt Corina Liesau Patricia Ríos Concepción Blasco Jorge Vega Miguel Roberto Menduiña García Azucena Avilés Fernández Eszter Bánffy Maria Bernabò-Brea David Billoin Clive Bonsall Laura Bonsall Tim Allen Lindsey Büster Sophie Carver Laura Castells Navarro Oliver E Craig Gordon T Cook Barry Cunliffe Anthony Denaire Kirsten Egging Dinwiddy Natasha Dodwell Michal Ernée Christopher Evans Milan Kuchařík Joan Francès Farré Chris Fowler Michiel Gazenbeek Rafael Garrido Pena María Haber-Uriarte Elżbieta Haduch Gill Hey Nick Jowett Timothy Knowles Ken Massy Saskia Pfrengle Philippe Lefranc Olivier Lemercier Arnaud Lefebvre César Heras Martínez Virginia Galera Olmo Ana Bastida Ramírez Joaquín Lomba Maurandi Tona Majó Jacqueline I McKinley Kathleen McSweeney Balázs Gusztáv Mende Alessandra Modi Gabriella Kulcsár Viktória Kiss András Czene Róbert Patay Anna Endrődi Kitti Köhler Tamás Hajdu Tamás Szeniczey János Dani Zsolt Bernert Maya Hoole Olivia Cheronet Denise Keating Petr Velemínský Miroslav Dobeš Francesca Candilio Fraser Brown Raúl Flores Fernández Ana-Mercedes Herrero-Corral Sebastiano Tusa Emiliano Carnieri Luigi Lentini Antonella Valenti Alessandro Zanini Clive Waddington Germán Delibes Elisa Guerra-Doce Benjamin Neil Marcus Brittain Mike Luke Richard Mortimer Jocelyne Desideri Marie Besse Günter Brücken Mirosław Furmanek Agata Hałuszko Maksym Mackiewicz Artur Rapiński Stephany Leach Ignacio Soriano Katina T Lillios João Luís Cardoso Michael Parker Pearson Piotr Włodarczak T Douglas Price Pilar Prieto Pierre-Jérôme Rey Roberto Risch Manuel A Rojo Guerra Aurore Schmitt Joël Serralongue Ana Maria Silva Václav Smrčka Luc Vergnaud João Zilhão David Caramelli Thomas Higham Mark G Thomas Douglas J Kennett Harry Fokkens Volker Heyd Alison Sheridan Karl-Göran Sjögren Philipp W Stockhammer Johannes Krause Ron Pinhasi Wolfgang Haak Ian Barnes Carles Lalueza-Fox David Reich

Nature 2018 03 21;555(7695):190-196. Epub 2018 Feb 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain's gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.
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http://dx.doi.org/10.1038/nature25738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5973796PMC
March 2018

The genomic history of southeastern Europe.

Authors:
Iain Mathieson Songül Alpaslan-Roodenberg Cosimo Posth Anna Szécsényi-Nagy Nadin Rohland Swapan Mallick Iñigo Olalde Nasreen Broomandkhoshbacht Francesca Candilio Olivia Cheronet Daniel Fernandes Matthew Ferry Beatriz Gamarra Gloria González Fortes Wolfgang Haak Eadaoin Harney Eppie Jones Denise Keating Ben Krause-Kyora Isil Kucukkalipci Megan Michel Alissa Mittnik Kathrin Nägele Mario Novak Jonas Oppenheimer Nick Patterson Saskia Pfrengle Kendra Sirak Kristin Stewardson Stefania Vai Stefan Alexandrov Kurt W Alt Radian Andreescu Dragana Antonović Abigail Ash Nadezhda Atanassova Krum Bacvarov Mende Balázs Gusztáv Hervé Bocherens Michael Bolus Adina Boroneanţ Yavor Boyadzhiev Alicja Budnik Josip Burmaz Stefan Chohadzhiev Nicholas J Conard Richard Cottiaux Maja Čuka Christophe Cupillard Dorothée G Drucker Nedko Elenski Michael Francken Borislava Galabova Georgi Ganetsovski Bernard Gély Tamás Hajdu Veneta Handzhyiska Katerina Harvati Thomas Higham Stanislav Iliev Ivor Janković Ivor Karavanić Douglas J Kennett Darko Komšo Alexandra Kozak Damian Labuda Martina Lari Catalin Lazar Maleen Leppek Krassimir Leshtakov Domenico Lo Vetro Dženi Los Ivaylo Lozanov Maria Malina Fabio Martini Kath McSweeney Harald Meller Marko Menđušić Pavel Mirea Vyacheslav Moiseyev Vanya Petrova T Douglas Price Angela Simalcsik Luca Sineo Mario Šlaus Vladimir Slavchev Petar Stanev Andrej Starović Tamás Szeniczey Sahra Talamo Maria Teschler-Nicola Corinne Thevenet Ivan Valchev Frédérique Valentin Sergey Vasilyev Fanica Veljanovska Svetlana Venelinova Elizaveta Veselovskaya Bence Viola Cristian Virag Joško Zaninović Steve Zäuner Philipp W Stockhammer Giulio Catalano Raiko Krauß David Caramelli Gunita Zariņa Bisserka Gaydarska Malcolm Lillie Alexey G Nikitin Inna Potekhina Anastasia Papathanasiou Dušan Borić Clive Bonsall Johannes Krause Ron Pinhasi David Reich

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

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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 Stone Age Plague and Its Persistence in Eurasia.

Curr Biol 2017 Dec 22;27(23):3683-3691.e8. Epub 2017 Nov 22.

Max Planck Institute for the Science of Human History, Jena, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. Electronic address:

Yersinia pestis, the etiologic agent of plague, is a bacterium associated with wild rodents and their fleas. Historically it was responsible for three pandemics: the Plague of Justinian in the 6 century AD, which persisted until the 8 century [1]; the renowned Black Death of the 14 century [2, 3], with recurrent outbreaks until the 18 century [4]; and the most recent 19 century pandemic, in which Y. pestis spread worldwide [5] and became endemic in several regions [6]. The discovery of molecular signatures of Y. pestis in prehistoric Eurasian individuals and two genomes from Southern Siberia suggest that Y. pestis caused some form of disease in humans prior to the first historically documented pandemic [7]. Here, we present six new European Y. pestis genomes spanning the Late Neolithic to the Bronze Age (LNBA; 4,800 to 3,700 calibrated years before present). This time period is characterized by major transformative cultural and social changes that led to cross-European networks of contact and exchange [8, 9]. We show that all known LNBA strains form a single putatively extinct clade in the Y. pestis phylogeny. Interpreting our data within the context of recent ancient human genomic evidence that suggests an increase in human mobility during the LNBA, we propose a possible scenario for the early spread of Y. pestis: the pathogen may have entered Europe from Central Eurasia following an expansion of people from the steppe, persisted within Europe until the mid-Bronze Age, and moved back toward Central Eurasia in parallel with human populations.
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http://dx.doi.org/10.1016/j.cub.2017.10.025DOI Listing
December 2017

Genetic origins of the Minoans and Mycenaeans.

Nature 2017 08 2;548(7666):214-218. Epub 2017 Aug 2.

Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA.

The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We have assembled genome-wide data from 19 ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. Here we show that Minoans and Mycenaeans were genetically similar, having at least three-quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean, and most of the remainder from ancient populations related to those of the Caucasus and Iran. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter-gatherers of eastern Europe and Siberia, introduced via a proximal source related to the inhabitants of either the Eurasian steppe or Armenia. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the Early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.
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http://dx.doi.org/10.1038/nature23310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5565772PMC
August 2017