Kathrin Nägele | Max Planck Institute for Evolutionary Anthropology (original) (raw)

Drafts by Kathrin Nägele

bioRxiv, 2018

The first historically documented pandemic caused by Yersinia pestis started as the Justinianic P... more The first historically documented pandemic caused by Yersinia pestis started as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although palaeogenomic studies have previously identified the causative agent as Y. pestis, 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 20 sites in Austria, Britain, Germany, France and Spain for Y. pestis DNA and reconstructed six new genomes. We present a novel methodological approach assessing SNPs in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis reveals the existence of previously undocumented Y. pestis diversity during the 6th-7th centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as southern France and Spain, and that southern Germany seems to have been affected by at least two distinct Y. pestis strains. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45 kb genomic region in the most recent First Pandemic strain affecting two virulence factors, intriguingly overlapping with a deletion found in 17th-18th-century genomes of the Second Pandemic.

Papers by Kathrin Nägele

The Pacific islands have experienced multiple waves of human migrations, providing a case study f... more The Pacific islands have experienced multiple waves of human migrations, providing a case study for exploring the potential of using the microbiome to study human migration. We performed a metagenomic study of archaeological dental calculus from 103 ancient individuals, originating from 12 Pacific islands and spanning a time range of ∼3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone from the Pacific, and comparable to that seen in calculus from temperate regions. Variation in the microbial community composition was minimally driven by time period and geography within the Pacific, while comparison with samples from Europe, Africa, and Asia reveal the microbial communities of Pacific calculus samples to be distinctive. Phylogenies of individual bacterial species in Pacific calculus reflect geography. Archaeological dental calculus shows potential to yield information about past human migrations, complementing studies ...

Journal of Anthropological Sciences, Dec 30, 2022

Nature

Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic r... more Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdal...

HAL (Le Centre pour la Communication Scientifique Directe), Nov 1, 2022

Nature Ecology & Evolution

Sambaqui (shellmound) societies are among the most intriguing archaeological phenomena in pre-col... more Sambaqui (shellmound) societies are among the most intriguing archaeological phenomena in pre-colonial South America, extending from approximately 8,000 to 1,000 years before present (yr bp) across 3,000 km on the Atlantic coast. However, little is known about their connection to early Holocene hunter-gatherers, how this may have contributed to different historical pathways and the processes through which late Holocene ceramists came to rule the coast shortly before European contact. To contribute to our understanding of the population history of indigenous societies on the eastern coast of South America, we produced genome-wide data from 34 ancient individuals as early as 10,000 yr bp from four different regions in Brazil. Early Holocene hunter-gatherers were found to lack shared genetic drift among themselves and with later populations from eastern South America, suggesting that they derived from a common radiation and did not contribute substantially to later coastal groups. Our ...

Dissertation ist gesperrt bis zum 09.06.2023 !!

116 Farming was first introduced to southeastern Europe in the mid-7 millennium BCE – 117 brought... more 116 Farming was first introduced to southeastern Europe in the mid-7 millennium BCE – 117 brought by migrants from Anatolia who settled in the region before spreading 118 throughout Europe. To clarify the dynamics of the interaction between the first farmers 119 and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient 120 DNA data from 223 individuals who lived in southeastern Europe and surrounding 121 regions between 12000 and 500 BCE. We document previously uncharacterized genetic 122 structure, showing a West-East cline of ancestry in hunter-gatherers, and show that 123 some Aegean farmers had ancestry from a different lineage than the northwestern 124 Anatolian lineage that formed the overwhelming ancestry of other European farmers. 125 We show that the first farmers of northern and western Europe passed through 126 southeastern Europe with limited admixture with local hunter-gatherers, but that some 127 groups mixed extensively, with relatively sex-...

replacement in Remote Oceania 2 3 Cosimo Posth1,*,§, Kathrin Nägele1,§, Heidi Colleran2,‡, Frédér... more replacement in Remote Oceania 2 3 Cosimo Posth1,*,§, Kathrin Nägele1,§, Heidi Colleran2,‡, Frédérique Valentin3, Stuart Bedford4,2, 4 Kaitip W. Kami5,2, Richard Shing5, Hallie Buckley6, Rebecca Kinaston1, Mary Walworth2, Geoffrey 5 R. Clark7, Christian Reepmeyer8, James Flexner9, Tamara Maric10, Johannes Moser11,12, Julia 6 Gresky12, Lawrence Kiko13,12, Kathryn J. Robson14, Kathryn Auckland15, Stephen J. Oppenheimer16, 7 Adrian VS Hill15, Alexander J. Mentzer15, Jana Zech17, Fiona Petchey18, Patrick Roberts17, 8 Choongwon Jeong1, Russell D. Gray2, Johannes Krause1,* & Adam Powell2,1,* 9 10 1 Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straβe 10, Jena 07745, 11 Germany 12 2 Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Kahlaische Straβe 10, 13 Jena 07745, Germany 14 3 Maison de l’Archéologie et de l’Ethnologie, CNRS, UMR 7041, 92023 Nanterre, France 15 4 School of Culture, H...

Previous research indicates that the human genetic diversity found in Wallacea - islands in prese... more Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this region’s demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estim...

Science, 2021

Ancient DNA traces the history of hepatitis B Hepatitis B virus (HBV) infections represent a worl... more Ancient DNA traces the history of hepatitis B Hepatitis B virus (HBV) infections represent a worldwide human health concern. To study the history of this pathogen, Kocher et al . identified 137 human remains with detectable levels of virus dating between 400 and 10,000 years ago. Sequencing and analyses of these ancient viruses suggested a common ancestor between 12,000 and 20,000 years ago. There is no evidence indicating that HBV was present in the earliest humans as they spread out of Africa; however, HBV was likely present in human populations before farming. Furthermore, the virus was present in the Americas by about 9000 years ago, representing a lineage sister to the viral strains found in Eurasia that diverged about 20,000 years ago. —LMZ

Science Advances, 2021

Steppe ancestry among the non–Indo-European–speaking Etruscans challenges previous hypotheses on ... more Steppe ancestry among the non–Indo-European–speaking Etruscans challenges previous hypotheses on their recent Anatolian origin.

Proceedings of the National Academy of Sciences, 2021

The oral microbiome plays key roles in human biology, health, and disease, but little is known ab... more The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Re...

Nature, 2021

Much remains unknown about the population history of early modern humans in southeast Asia, where... more Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939–7751 calibrated years before present (yr cal bp; present taken as ad 1950), and Gua Cha in Malaysia (4.4–4.2 kyr cal bp)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia–New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3–7.2 kyr cal bp at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic...

Quaternary Science Reviews, 2021

Abstract The interior of the Iberian Peninsula has orographic conditions that make this territory... more Abstract The interior of the Iberian Peninsula has orographic conditions that make this territory especially vulnerable to Quaternary climate oscillations and which actually could have made it decisive for Paleolithic human populations at critical points. For this reason, the information provided by paleontological sites is important for reconstructing climatic and environmental conditions during the Late Pleistocene and understanding how they influenced the species that inhabited them, including humans. Nevertheless, the archaeo-paleontological record is scarce in central Iberia for the Late Pleistocene. A central Iberian site that is key to addressing this issue is Cueva de los Torrejones, which was discovered and excavated during the nineties. Clues indicating the presence of Neandertal populations near the cave site were announced during prior field excavations, including Neandertal remains, Middle Paleolithic artifacts, and evidence of anthropic exploitation of faunal resources at the site. Here we report the new results from the recent excavations and research, including detailed studies on stratigraphy, micromorphology, macro and microvertebrate paleontology, physical and molecular anthropology, taphonomy and zooarchaeology, and analysis of lithic and pottery remains. Our research has led to the detection of three Prehistoric chronologies recorded at the site. The oldest episode corresponds to between MIS 5 and MIS 4 in which the cave was used by carnivores. The second episode is represented by a faunal association dated to 30.0 ka cal BP and is indicative of cooler and more arid environmental conditions and, therefore, compatible with the worsening climate detected previously for MIS 3 in this area. The last episode corresponds to the Chalcolithic, directly dated to ∼5000 cal BP in which humans used the cavity for funerary purposes. The DNA analysis of the human remain was assigned to mtDNA haplogroup K, which was originated in the Near East and reached western Europe through the Neolithic expansion. Human occupation during the Paleolithic has been ruled out, including Paleolithic human remains and any kind of anthropic intervention on the Hermann’s tortoise and leopard as was previously proposed at the site.

Archaeology in Oceania, 2019

The first historically documented pandemic caused byYersinia pestisstarted as the Justinianic Pla... more The first historically documented pandemic caused byYersinia pestisstarted as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although palaeogenomic studies have previously identified the causative agent asY. pestis, 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 20 sites in Austria, Britain, Germany, France and Spain forY. pestisDNA and reconstructed six new genomes. We present a novel methodological approach assessing SNPs in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis reveals the existence of previously undocumentedY. pestisdiversity during the 6th–7thcenturies, and provides evidence for the presence of multiple distinctY. pestisstrains in Europe. We offer geneti...

Nature ecology & evolution, Jan 27, 2018

Recent genomic analyses show that the earliest peoples reaching Remote Oceania-associated with Au... more Recent genomic analyses show that the earliest peoples reaching Remote Oceania-associated with Austronesian-speaking Lapita culture-were almost completely East Asian, without detectable Papuan ancestry. However, Papuan-related genetic ancestry is found across present-day Pacific populations, indicating that peoples from Near Oceania have played a significant, but largely unknown, ancestral role. Here, new genome-wide data from 19 ancient South Pacific individuals provide direct evidence of a so-far undescribed Papuan expansion into Remote Oceania starting ~2,500 yr BP, far earlier than previously estimated and supporting a model from historical linguistics. New genome-wide data from 27 contemporary ni-Vanuatu demonstrate a subsequent and almost complete replacement of Lapita-Austronesian by Near Oceanian ancestry. Despite this massive demographic change, incoming Papuan languages did not replace Austronesian languages. Population replacement with language continuity is extremely rar...

bioRxiv, 2018

The first historically documented pandemic caused by Yersinia pestis started as the Justinianic P... more The first historically documented pandemic caused by Yersinia pestis started as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although palaeogenomic studies have previously identified the causative agent as Y. pestis, 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 20 sites in Austria, Britain, Germany, France and Spain for Y. pestis DNA and reconstructed six new genomes. We present a novel methodological approach assessing SNPs in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis reveals the existence of previously undocumented Y. pestis diversity during the 6th-7th centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as southern France and Spain, and that southern Germany seems to have been affected by at least two distinct Y. pestis strains. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45 kb genomic region in the most recent First Pandemic strain affecting two virulence factors, intriguingly overlapping with a deletion found in 17th-18th-century genomes of the Second Pandemic.

The Pacific islands have experienced multiple waves of human migrations, providing a case study f... more The Pacific islands have experienced multiple waves of human migrations, providing a case study for exploring the potential of using the microbiome to study human migration. We performed a metagenomic study of archaeological dental calculus from 103 ancient individuals, originating from 12 Pacific islands and spanning a time range of ∼3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone from the Pacific, and comparable to that seen in calculus from temperate regions. Variation in the microbial community composition was minimally driven by time period and geography within the Pacific, while comparison with samples from Europe, Africa, and Asia reveal the microbial communities of Pacific calculus samples to be distinctive. Phylogenies of individual bacterial species in Pacific calculus reflect geography. Archaeological dental calculus shows potential to yield information about past human migrations, complementing studies ...

Journal of Anthropological Sciences, Dec 30, 2022

Nature

Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic r... more Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdal...

HAL (Le Centre pour la Communication Scientifique Directe), Nov 1, 2022

Nature Ecology & Evolution

Sambaqui (shellmound) societies are among the most intriguing archaeological phenomena in pre-col... more Sambaqui (shellmound) societies are among the most intriguing archaeological phenomena in pre-colonial South America, extending from approximately 8,000 to 1,000 years before present (yr bp) across 3,000 km on the Atlantic coast. However, little is known about their connection to early Holocene hunter-gatherers, how this may have contributed to different historical pathways and the processes through which late Holocene ceramists came to rule the coast shortly before European contact. To contribute to our understanding of the population history of indigenous societies on the eastern coast of South America, we produced genome-wide data from 34 ancient individuals as early as 10,000 yr bp from four different regions in Brazil. Early Holocene hunter-gatherers were found to lack shared genetic drift among themselves and with later populations from eastern South America, suggesting that they derived from a common radiation and did not contribute substantially to later coastal groups. Our ...

Dissertation ist gesperrt bis zum 09.06.2023 !!

116 Farming was first introduced to southeastern Europe in the mid-7 millennium BCE – 117 brought... more 116 Farming was first introduced to southeastern Europe in the mid-7 millennium BCE – 117 brought by migrants from Anatolia who settled in the region before spreading 118 throughout Europe. To clarify the dynamics of the interaction between the first farmers 119 and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient 120 DNA data from 223 individuals who lived in southeastern Europe and surrounding 121 regions between 12000 and 500 BCE. We document previously uncharacterized genetic 122 structure, showing a West-East cline of ancestry in hunter-gatherers, and show that 123 some Aegean farmers had ancestry from a different lineage than the northwestern 124 Anatolian lineage that formed the overwhelming ancestry of other European farmers. 125 We show that the first farmers of northern and western Europe passed through 126 southeastern Europe with limited admixture with local hunter-gatherers, but that some 127 groups mixed extensively, with relatively sex-...

replacement in Remote Oceania 2 3 Cosimo Posth1,*,§, Kathrin Nägele1,§, Heidi Colleran2,‡, Frédér... more replacement in Remote Oceania 2 3 Cosimo Posth1,*,§, Kathrin Nägele1,§, Heidi Colleran2,‡, Frédérique Valentin3, Stuart Bedford4,2, 4 Kaitip W. Kami5,2, Richard Shing5, Hallie Buckley6, Rebecca Kinaston1, Mary Walworth2, Geoffrey 5 R. Clark7, Christian Reepmeyer8, James Flexner9, Tamara Maric10, Johannes Moser11,12, Julia 6 Gresky12, Lawrence Kiko13,12, Kathryn J. Robson14, Kathryn Auckland15, Stephen J. Oppenheimer16, 7 Adrian VS Hill15, Alexander J. Mentzer15, Jana Zech17, Fiona Petchey18, Patrick Roberts17, 8 Choongwon Jeong1, Russell D. Gray2, Johannes Krause1,* & Adam Powell2,1,* 9 10 1 Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straβe 10, Jena 07745, 11 Germany 12 2 Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Kahlaische Straβe 10, 13 Jena 07745, Germany 14 3 Maison de l’Archéologie et de l’Ethnologie, CNRS, UMR 7041, 92023 Nanterre, France 15 4 School of Culture, H...

Previous research indicates that the human genetic diversity found in Wallacea - islands in prese... more Previous research indicates that the human genetic diversity found in Wallacea - islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves - has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Here, we provide new insights into this region’s demographic history based on genome-wide data from 16 ancient individuals (2600-250 yrs BP) from islands of the North Moluccas, Sulawesi, and East Nusa Tenggara. While the ancestry of individuals from the northern islands fit earlier views of contact between groups related to the Austronesian expansion and the first colonization of Sahul, the ancestry of individuals from the southern islands revealed additional contributions from Mainland Southeast Asia, which seems to predate the Austronesian admixture in the region. Admixture time estimates for the oldest individuals of Wallacea are closer to archaeological estim...

Science, 2021

Ancient DNA traces the history of hepatitis B Hepatitis B virus (HBV) infections represent a worl... more Ancient DNA traces the history of hepatitis B Hepatitis B virus (HBV) infections represent a worldwide human health concern. To study the history of this pathogen, Kocher et al . identified 137 human remains with detectable levels of virus dating between 400 and 10,000 years ago. Sequencing and analyses of these ancient viruses suggested a common ancestor between 12,000 and 20,000 years ago. There is no evidence indicating that HBV was present in the earliest humans as they spread out of Africa; however, HBV was likely present in human populations before farming. Furthermore, the virus was present in the Americas by about 9000 years ago, representing a lineage sister to the viral strains found in Eurasia that diverged about 20,000 years ago. —LMZ

Science Advances, 2021

Steppe ancestry among the non–Indo-European–speaking Etruscans challenges previous hypotheses on ... more Steppe ancestry among the non–Indo-European–speaking Etruscans challenges previous hypotheses on their recent Anatolian origin.

Proceedings of the National Academy of Sciences, 2021

The oral microbiome plays key roles in human biology, health, and disease, but little is known ab... more The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Re...

Nature, 2021

Much remains unknown about the population history of early modern humans in southeast Asia, where... more Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939–7751 calibrated years before present (yr cal bp; present taken as ad 1950), and Gua Cha in Malaysia (4.4–4.2 kyr cal bp)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia–New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3–7.2 kyr cal bp at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic...

Quaternary Science Reviews, 2021

Abstract The interior of the Iberian Peninsula has orographic conditions that make this territory... more Abstract The interior of the Iberian Peninsula has orographic conditions that make this territory especially vulnerable to Quaternary climate oscillations and which actually could have made it decisive for Paleolithic human populations at critical points. For this reason, the information provided by paleontological sites is important for reconstructing climatic and environmental conditions during the Late Pleistocene and understanding how they influenced the species that inhabited them, including humans. Nevertheless, the archaeo-paleontological record is scarce in central Iberia for the Late Pleistocene. A central Iberian site that is key to addressing this issue is Cueva de los Torrejones, which was discovered and excavated during the nineties. Clues indicating the presence of Neandertal populations near the cave site were announced during prior field excavations, including Neandertal remains, Middle Paleolithic artifacts, and evidence of anthropic exploitation of faunal resources at the site. Here we report the new results from the recent excavations and research, including detailed studies on stratigraphy, micromorphology, macro and microvertebrate paleontology, physical and molecular anthropology, taphonomy and zooarchaeology, and analysis of lithic and pottery remains. Our research has led to the detection of three Prehistoric chronologies recorded at the site. The oldest episode corresponds to between MIS 5 and MIS 4 in which the cave was used by carnivores. The second episode is represented by a faunal association dated to 30.0 ka cal BP and is indicative of cooler and more arid environmental conditions and, therefore, compatible with the worsening climate detected previously for MIS 3 in this area. The last episode corresponds to the Chalcolithic, directly dated to ∼5000 cal BP in which humans used the cavity for funerary purposes. The DNA analysis of the human remain was assigned to mtDNA haplogroup K, which was originated in the Near East and reached western Europe through the Neolithic expansion. Human occupation during the Paleolithic has been ruled out, including Paleolithic human remains and any kind of anthropic intervention on the Hermann’s tortoise and leopard as was previously proposed at the site.

Archaeology in Oceania, 2019

The first historically documented pandemic caused byYersinia pestisstarted as the Justinianic Pla... more The first historically documented pandemic caused byYersinia pestisstarted as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although palaeogenomic studies have previously identified the causative agent asY. pestis, 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 20 sites in Austria, Britain, Germany, France and Spain forY. pestisDNA and reconstructed six new genomes. We present a novel methodological approach assessing SNPs in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis reveals the existence of previously undocumentedY. pestisdiversity during the 6th–7thcenturies, and provides evidence for the presence of multiple distinctY. pestisstrains in Europe. We offer geneti...

Nature ecology & evolution, Jan 27, 2018

Recent genomic analyses show that the earliest peoples reaching Remote Oceania-associated with Au... more Recent genomic analyses show that the earliest peoples reaching Remote Oceania-associated with Austronesian-speaking Lapita culture-were almost completely East Asian, without detectable Papuan ancestry. However, Papuan-related genetic ancestry is found across present-day Pacific populations, indicating that peoples from Near Oceania have played a significant, but largely unknown, ancestral role. Here, new genome-wide data from 19 ancient South Pacific individuals provide direct evidence of a so-far undescribed Papuan expansion into Remote Oceania starting ~2,500 yr BP, far earlier than previously estimated and supporting a model from historical linguistics. New genome-wide data from 27 contemporary ni-Vanuatu demonstrate a subsequent and almost complete replacement of Lapita-Austronesian by Near Oceanian ancestry. Despite this massive demographic change, incoming Papuan languages did not replace Austronesian languages. Population replacement with language continuity is extremely rar...

Farming was first introduced to southeastern Europe in the mid-7thmillennium BCE – brought by mig... more Farming was first introduced to southeastern Europe in the mid-7thmillennium BCE – brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased...