101
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Schörnig M, Taverna E. A Closer Look to the Evolution of Neurons in Humans and Apes Using Stem-Cell-Derived Model Systems. Front Cell Dev Biol 2021; 9:661113. [PMID: 33968936 PMCID: PMC8097028 DOI: 10.3389/fcell.2021.661113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/01/2021] [Indexed: 12/14/2022] Open
Abstract
The cellular, molecular and functional comparison of neurons from closely related species is crucial in evolutionary neurobiology. The access to living tissue and post-mortem brains of humans and non-human primates is limited and the state of the tissue might not allow recapitulating important species-specific differences. A valid alternative is offered by neurons derived from induced pluripotent stem cells (iPSCs) obtained from humans and non-human apes and primates. We will review herein the contribution of iPSCs-derived neuronal models to the field of evolutionary neurobiology, focusing on species-specific aspects of neuron’s cell biology and timing of maturation. In addition, we will discuss the use of iPSCs for the study of ancient human traits.
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Affiliation(s)
- Maria Schörnig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Taverna
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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102
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Vernot B, Zavala EI, Gómez-Olivencia A, Jacobs Z, Slon V, Mafessoni F, Romagné F, Pearson A, Petr M, Sala N, Pablos A, Aranburu A, de Castro JMB, Carbonell E, Li B, Krajcarz MT, Krivoshapkin AI, Kolobova KA, Kozlikin MB, Shunkov MV, Derevianko AP, Viola B, Grote S, Essel E, Herráez DL, Nagel S, Nickel B, Richter J, Schmidt A, Peter B, Kelso J, Roberts RG, Arsuaga JL, Meyer M. Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments. Science 2021; 372:science.abf1667. [PMID: 33858989 DOI: 10.1126/science.abf1667] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/31/2021] [Indexed: 12/15/2022]
Abstract
Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA (mtDNA) has been retrieved from cave sediments but provides limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments and applied them to cave deposits in western Europe and southern Siberia dated to between 200,000 and 50,000 years ago. We detected a population replacement in northern Spain about 100,000 years ago, which was accompanied by a turnover of mtDNA. We also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene. Our work lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments.
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Affiliation(s)
- Benjamin Vernot
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Elena I Zavala
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Asier Gómez-Olivencia
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain.,Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain.,Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frédéric Romagné
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alice Pearson
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Petr
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nohemi Sala
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Centro Nacional de Investigación Sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Adrián Pablos
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Centro Nacional de Investigación Sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Arantza Aranburu
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain.,Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain
| | | | - Eudald Carbonell
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Universitat Rovira i Virgili, Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili, Tarragona, Spain
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Maciej T Krajcarz
- Institute of Geological Sciences, Polish Academy of Sciences, Warszawa, Poland
| | - Andrey I Krivoshapkin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Kseniya A Kolobova
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | - Steffi Grote
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Essel
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David López Herráez
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Peter
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Juan-Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Departamento de Paleontología, Facultad Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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103
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Reinscheid RK, Mafessoni F, Lüttjohann A, Jüngling K, Pape HC, Schulz S. Neandertal introgression and accumulation of hypomorphic mutations in the neuropeptide S (NPS) system promote attenuated functionality. Peptides 2021; 138:170506. [PMID: 33556445 DOI: 10.1016/j.peptides.2021.170506] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/14/2021] [Accepted: 02/03/2021] [Indexed: 12/21/2022]
Abstract
The neuropeptide S (NPS) system plays an important role in fear and fear memory processing but has also been associated with allergic and inflammatory diseases. Genes for NPS and its receptor NPSR1 are found in all tetrapods. Compared to non-human primates, several non-synonymous single-nucleotide polymorphisms (SNPs) occur in both human genes that collectively result in functional attenuation, suggesting adaptive mechanisms in a human context. To investigate historic and geographic origins of these hypomorphic mutations and explore genetic signs of selection, we analyzed ancient genomes and worldwide genotype frequencies of four prototypic SNPs in the NPS system. Neandertal and Denisovan genomes contain exclusively ancestral alleles for NPSR1 while all derived alleles occur in ancient genomes of anatomically modern humans, indicating that they arose in modern Homo sapiens. Worldwide genotype frequencies for three hypomorphic NPSR1 SNPs show significant regional homogeneity but follow a gradient towards increasing derived allele frequencies that supports an out-of-Africa scenario. Increased density of high-frequency polymorphisms around the three NPSR1 loci suggests weak or possibly balancing selection. A hypomorphic mutation in the NPS precursor, however, was detected at high frequency in Eurasian Neandertal genomes and shows genetic signatures indicating that it was introgressed into the human gene pool, particularly in Southern Europe, by interbreeding with Neandertals. We discuss potential evolutionary scenarios including behavior and immune-based natural selection.
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Affiliation(s)
- Rainer K Reinscheid
- Institute of Pharmacology & Toxicology, Friedrich-Schiller-University, Jena, Germany; Institute of Physiology I, Westfälische-Wilhelms-University, Münster, Germany.
| | | | - Annika Lüttjohann
- Institute of Physiology I, Westfälische-Wilhelms-University, Münster, Germany
| | - Kay Jüngling
- Institute of Physiology I, Westfälische-Wilhelms-University, Münster, Germany
| | - Hans-Christian Pape
- Institute of Physiology I, Westfälische-Wilhelms-University, Münster, Germany
| | - Stefan Schulz
- Institute of Pharmacology & Toxicology, Friedrich-Schiller-University, Jena, Germany
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104
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Hajdinjak M, Mafessoni F, Skov L, Vernot B, Hübner A, Fu Q, Essel E, Nagel S, Nickel B, Richter J, Moldovan OT, Constantin S, Endarova E, Zahariev N, Spasov R, Welker F, Smith GM, Sinet-Mathiot V, Paskulin L, Fewlass H, Talamo S, Rezek Z, Sirakova S, Sirakov N, McPherron SP, Tsanova T, Hublin JJ, Peter BM, Meyer M, Skoglund P, Kelso J, Pääbo S. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature 2021; 592:253-257. [PMID: 33828320 PMCID: PMC8026394 DOI: 10.1038/s41586-021-03335-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/05/2021] [Indexed: 02/01/2023]
Abstract
Modern humans appeared in Europe by at least 45,000 years ago1-5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.
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Affiliation(s)
- Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Francis Crick Institute, London, UK.
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Laurits Skov
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Oana Teodora Moldovan
- Emil Racovita Institute of Speleology, Cluj Department, Cluj-Napoca, Romania
- Romanian Institute of Science and Technology, Cluj-Napoca, Romania
| | - Silviu Constantin
- Department of Geospeleology and Paleontology, Emil Racovita Institute of Speleology, Bucharest, Romania
- Centro Nacional de Investigación sobre la Evolución Humana, CENIEH, Burgos, Spain
| | | | - Nikolay Zahariev
- Archaeology Department, New Bulgarian University, Sofia, Bulgaria
| | - Rosen Spasov
- Archaeology Department, New Bulgarian University, Sofia, Bulgaria
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Geoff M Smith
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry 'G. Ciamician', University of Bologna, Bologna, Italy
| | - Zeljko Rezek
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- University of Pennsylvania Museum of Archaeology and Anthropology, University of Pennsylvania, Philadelphia, PA, USA
| | - Svoboda Sirakova
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Nikolay Sirakov
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Shannon P McPherron
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tsenka Tsanova
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, Collège de France, Paris, France
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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105
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Zeberg H, Pääbo S. A genomic region associated with protection against severe COVID-19 is inherited from Neandertals. Proc Natl Acad Sci U S A 2021; 118:e2026309118. [PMID: 33593941 PMCID: PMC7936282 DOI: 10.1073/pnas.2026309118] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
It was recently shown that the major genetic risk factor associated with becoming severely ill with COVID-19 when infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is inherited from Neandertals. New, larger genetic association studies now allow additional genetic risk factors to be discovered. Using data from the Genetics of Mortality in Critical Care (GenOMICC) consortium, we show that a haplotype at a region on chromosome 12 associated with requiring intensive care when infected with the virus is inherited from Neandertals. This region encodes proteins that activate enzymes that are important during infections with RNA viruses. In contrast to the previously described Neandertal haplotype that increases the risk for severe COVID-19, this Neandertal haplotype is protective against severe disease. It also differs from the risk haplotype in that it has a more moderate effect and occurs at substantial frequencies in all regions of the world outside Africa. Among ancient human genomes in western Eurasia, the frequency of the protective Neandertal haplotype may have increased between 20,000 and 10,000 y ago and again during the past 1,000 y.
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Affiliation(s)
- Hugo Zeberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany;
- Department of Neuroscience, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany;
- Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
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106
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Mora-Bermúdez F, Taverna E, Huttner WB. From stem and progenitor cells to neurons in the developing neocortex: key differences among hominids. FEBS J 2021; 289:1524-1535. [PMID: 33638923 DOI: 10.1111/febs.15793] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 01/05/2023]
Abstract
Comparing the biology of humans to that of other primates, and notably other hominids, is a useful path to learn more about what makes us human. Some of the most interesting differences among hominids are closely related to brain development and function, for example behaviour and cognition. This makes it particularly interesting to compare the hominid neural cells of the neocortex, a part of the brain that plays central roles in those processes. However, well-preserved tissue from great apes is usually extremely difficult to obtain. A variety of new alternative tools, for example brain organoids, are now beginning to make it possible to search for such differences and analyse their potential biological and biomedical meaning. Here, we present an overview of recent findings from comparisons of the neural stem and progenitor cells (NSPCs) and neurons of hominids. In addition to differences in proliferation and differentiation of NSPCs, and maturation of neurons, we highlight that the regulation of the timing of these processes is emerging as a general foundational difference in the development of the neocortex of hominids.
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Affiliation(s)
- Felipe Mora-Bermúdez
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Taverna
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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107
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Bergström A, Stringer C, Hajdinjak M, Scerri EML, Skoglund P. Origins of modern human ancestry. Nature 2021; 590:229-237. [PMID: 33568824 DOI: 10.1038/s41586-021-03244-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023]
Abstract
New finds in the palaeoanthropological and genomic records have changed our view of the origins of modern human ancestry. Here we review our current understanding of how the ancestry of modern humans around the globe can be traced into the deep past, and which ancestors it passes through during our journey back in time. We identify three key phases that are surrounded by major questions, and which will be at the frontiers of future research. The most recent phase comprises the worldwide expansion of modern humans between 40 and 60 thousand years ago (ka) and their last known contacts with archaic groups such as Neanderthals and Denisovans. The second phase is associated with a broadly construed African origin of modern human diversity between 60 and 300 ka. The oldest phase comprises the complex separation of modern human ancestors from archaic human groups from 0.3 to 1 million years ago. We argue that no specific point in time can currently be identified at which modern human ancestry was confined to a limited birthplace, and that patterns of the first appearance of anatomical or behavioural traits that are used to define Homo sapiens are consistent with a range of evolutionary histories.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Chris Stringer
- Department of Earth Sciences, Natural History Museum, London, UK.
| | - Mateja Hajdinjak
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK
| | - Eleanor M L Scerri
- Pan-African Evolution Research Group, Max Planck Institute for Science of Human History, Jena, Germany.,Department of Classics and Archaeology, University of Malta, Msida, Malta.,Institute of Prehistoric Archaeology, University of Cologne, Cologne, Germany
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
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108
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Böck J, Krogsaeter E, Passon M, Chao YK, Sharma S, Grallert H, Peters A, Grimm C. Human genome diversity data reveal that L564P is the predominant TPC2 variant and a prerequisite for the blond hair associated M484L gain-of-function effect. PLoS Genet 2021; 17:e1009236. [PMID: 33465068 PMCID: PMC7845996 DOI: 10.1371/journal.pgen.1009236] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 01/29/2021] [Accepted: 10/29/2020] [Indexed: 12/29/2022] Open
Abstract
The endo-lysosomal two-pore channel (TPC2) has been established as an intracellular cation channel of significant physiological and pathophysiological relevance in recent years. For example, TPC2-/- mice show defects in cholesterol degradation, leading to hypercholesterinemia; TPC2 absence also results in mature-onset obesity, and a role in glucagon secretion and diabetes has been proposed. Infections with bacterial toxins or viruses e.g., cholera toxin or Ebola virus result in reduced infectivity rates in the absence of TPC2 or after pharmacological blockage, and TPC2-/- cancer cells lose their ability to migrate and metastasize efficiently. Finally, melanin production is affected by changes in hTPC2 activity, resulting in pigmentation defects and hair color variation. Here, we analyzed several publicly available genome variation data sets and identified multiple variations in the TPC2 protein in distinct human populations. Surprisingly, one variation, L564P, was found to be the predominant TPC2 isoform on a global scale. By applying endo-lysosomal patch-clamp electrophysiology, we found that L564P is a prerequisite for the previously described M484L gain-of-function effect that is associated with blond hair. Additionally, other gain-of-function variants with distinct geographical and ethnic distribution were discovered and functionally characterized. A meta-analysis of genome-wide association studies was performed, finding the polymorphisms to be associated with both distinct and overlapping traits. In sum, we present the first systematic analysis of variations in TPC2. We functionally characterized the most common variations and assessed their association with various disease traits. With TPC2 emerging as a novel drug target for the treatment of various diseases, this study provides valuable insights into ethnic and geographical distribution of TPC2 polymorphisms and their effects on channel activity.
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Affiliation(s)
- Julia Böck
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Einar Krogsaeter
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Marcel Passon
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Yu-Kai Chao
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sapna Sharma
- Helmholtz Zentrum–Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epidemiology, Neuherberg, Germany
| | - Harald Grallert
- Helmholtz Zentrum–Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epidemiology, Neuherberg, Germany
| | - Annette Peters
- Helmholtz Zentrum–Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epidemiology, Neuherberg, Germany
| | - Christian Grimm
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
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109
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The structure, function and evolution of a complete human chromosome 8. Nature 2021; 593:101-107. [PMID: 33828295 PMCID: PMC8099727 DOI: 10.1038/s41586-021-03420-7] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/04/2021] [Indexed: 02/07/2023]
Abstract
The complete assembly of each human chromosome is essential for understanding human biology and evolution1,2. Here we use complementary long-read sequencing technologies to complete the linear assembly of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08-Mb centromeric α-satellite array, a 644-kb copy number polymorphism in the β-defensin gene cluster that is important for disease risk, and an 863-kb variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73-kb hypomethylated region of diverse higher-order α-satellites enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. In addition, we confirm the overall organization and methylation pattern of the centromere in a diploid human genome. Using a dual long-read sequencing approach, we complete high-quality draft assemblies of the orthologous centromere from chromosome 8 in chimpanzee, orangutan and macaque to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved in the great ape ancestor with a layered symmetry, in which more ancient higher-order repeats locate peripherally to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated by more than 2.2-fold compared to the unique portions of the genome, and this acceleration extends into the flanking sequence.
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Global Picture of Genetic Relatedness and the Evolution of Humankind. BIOLOGY 2020; 9:biology9110392. [PMID: 33182715 PMCID: PMC7696950 DOI: 10.3390/biology9110392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/20/2022]
Abstract
Simple Summary The intricacies of human ancestry are buried deep within our DNA. For years, scientists have been working to piece together a vast picture of our genetic lineage. The purpose of this study was to further reveal this global picture of human genetic relatedness using identical-by-descent (IBD) genomic fragments. We processed over 65 million very rare single nucleotide polymorphic (SNP) alleles and detected over 17 million shared IBD fragments, including very short IBD fragments that allowed us to trace common ancestors back to 200,000 years ago. We also determined nine geographical regions representing nine unique genetic components for mankind: East and West Africa, Northern Europe, Arctica, East Asia, Oceania, South Asia, Middle East, and South America. The levels of admixture in every studied population could be assigned to one of these regions and long-term neighboring populations are strikingly similar, despite any political, religious, and cultural differences. Additionally, we observed the topmost admixture to be in central Eurasia. The entire picture of relatedness of all the studied populations presents itself in the form of shared number/size of IBDs, providing novel insights into geographical admixtures and genetic contributions that shaped human ancestry into what it is today. Abstract We performed an exhaustive pairwise comparison of whole-genome sequences of 3120 individuals, representing 232 populations from all continents and seven prehistoric people including archaic and modern humans. In order to reveal an intricate picture of worldwide human genetic relatedness, 65 million very rare single nucleotide polymorphic (SNP) alleles have been bioinformatically processed. The number and size of shared identical-by-descent (IBD) genomic fragments for every pair of 3127 individuals have been revealed. Over 17 million shared IBD fragments have been described. Our approach allowed detection of very short IBD fragments (<20 kb) that trace common ancestors who lived up to 200,000 years ago. We detected nine distinct geographical regions within which individuals had strong genetic relatedness, but with negligible relatedness between the populations of these regions. The regions, comprising nine unique genetic components for mankind, are the following: East and West Africa, Northern Europe, Arctica, East Asia, Oceania, South Asia, Middle East, and South America. The level of admixture in every studied population has been apportioned among these nine genetic components. Genetically, long-term neighboring populations are strikingly similar to each other in spite of any political, religious, and cultural differences. The topmost admixture has been observed at the center of Eurasia. These admixed populations (including Uyghurs, Azerbaijanis, Uzbeks, and Iranians) have roughly equal genetic contributions from the Middle East, Europe, China, and India, with additional significant traces from Africa and Arctic. The entire picture of relatedness of all the studied populations unfolds and presents itself in the form of shared number/size of IBDs.
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Massilani D, Skov L, Hajdinjak M, Gunchinsuren B, Tseveendorj D, Yi S, Lee J, Nagel S, Nickel B, Devièse T, Higham T, Meyer M, Kelso J, Peter BM, Pääbo S. Denisovan ancestry and population history of early East Asians. Science 2020; 370:579-583. [DOI: 10.1126/science.abc1166] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Diyendo Massilani
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Laurits Skov
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
- Francis Crick Institute, London NW1 1AT, UK
| | - Byambaa Gunchinsuren
- Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar 13343, Mongolia
| | | | - Seonbok Yi
- Department of Archaeology, Seoul National University, Gwanak-gu, Seoul 08826, Korea
| | - Jungeun Lee
- Department of Archaeology, Seoul National University, Gwanak-gu, Seoul 08826, Korea
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Birgit Nickel
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Thibaut Devièse
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Benjamin M. Peter
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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Zeberg H, Pääbo S. The major genetic risk factor for severe COVID-19 is inherited from Neanderthals. Nature 2020; 587:610-612. [PMID: 32998156 DOI: 10.1038/s41586-020-2818-3] [Citation(s) in RCA: 330] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/22/2020] [Indexed: 11/09/2022]
Abstract
A recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A separate study (COVID-19 Host Genetics Initiative)2 comprising 3,199 hospitalized patients with coronavirus disease 2019 (COVID-19) and control individuals showed that this cluster is the major genetic risk factor for severe symptoms after SARS-CoV-2 infection and hospitalization. Here we show that the risk is conferred by a genomic segment of around 50 kilobases in size that is inherited from Neanderthals and is carried by around 50% of people in south Asia and around 16% of people in Europe.
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Affiliation(s)
- Hugo Zeberg
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Okinawa Institute of Science and Technology, Onna-son, Japan.
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Bokelmann L, Glocke I, Meyer M. Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples. Genome Res 2020; 30:1449-1457. [PMID: 32963029 PMCID: PMC7605269 DOI: 10.1101/gr.263863.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
Abstract
Extensive manipulations involved in the preparation of DNA samples for sequencing have hitherto made it impossible to determine the precise structure of double-stranded DNA fragments being sequenced, such as the presence of blunt ends, single-stranded overhangs, or single-strand breaks. We here describe MatchSeq, a method that combines single-stranded DNA library preparation from diluted DNA samples with computational sequence matching, allowing the reconstruction of double-stranded DNA fragments on a single-molecule level. The application of MatchSeq to Neanderthal DNA, a particularly complex source of degraded DNA, reveals that 1- or 2-nt overhangs and blunt ends dominate the ends of ancient DNA molecules and that short gaps exist, which are predominantly caused by the loss of individual purines. We further show that deamination of cytosine to uracil occurs in both single- and double-stranded contexts close to the ends of molecules, and that single-stranded parts of DNA fragments are enriched in pyrimidines. MatchSeq provides unprecedented resolution for interrogating the structures of fragmented double-stranded DNA and can be applied to fragmented double-stranded DNA isolated from any biological source. The method relies on well-established laboratory techniques and can easily be integrated into routine data generation. This possibility is shown by the successful reconstruction of double-stranded DNA fragments from previously published single-stranded sequence data, allowing a more comprehensive characterization of the biochemical properties not only of ancient DNA but also of cell-free DNA from human blood plasma, a clinically relevant marker for the diagnosis and monitoring of disease.
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Affiliation(s)
- Lukas Bokelmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Isabelle Glocke
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland). Sci Rep 2020; 10:14778. [PMID: 32901061 PMCID: PMC7479612 DOI: 10.1038/s41598-020-71504-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/17/2020] [Indexed: 02/03/2023] Open
Abstract
The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus.
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Lodewijk GA, Fernandes DP, Vretzakis I, Savage JE, Jacobs FMJ. Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels. Mol Biol Evol 2020; 37:2531-2548. [PMID: 32330268 PMCID: PMC7475042 DOI: 10.1093/molbev/msaa104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ever since the availability of genomes from Neanderthals, Denisovans, and ancient humans, the field of evolutionary genomics has been searching for protein-coding variants that may hold clues to how our species evolved over the last ∼600,000 years. In this study, we identify such variants in the human-specific NOTCH2NL gene family, which were recently identified as possible contributors to the evolutionary expansion of the human brain. We find evidence for the existence of unique protein-coding NOTCH2NL variants in Neanderthals and Denisovans which could affect their ability to activate Notch signaling. Furthermore, in the Neanderthal and Denisovan genomes, we find unusual NOTCH2NL configurations, not found in any of the modern human genomes analyzed. Finally, genetic analysis of archaic and modern humans reveals ongoing adaptive evolution of modern human NOTCH2NL genes, identifying three structural variants acting complementary to drive our genome to produce a lower dosage of NOTCH2NL protein. Because copy-number variations of the 1q21.1 locus, encompassing NOTCH2NL genes, are associated with severe neurological disorders, this seemingly contradicting drive toward low levels of NOTCH2NL protein indicates that the optimal dosage of NOTCH2NL may have not yet been settled in the human population.
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Affiliation(s)
- Gerrald A Lodewijk
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Diana P Fernandes
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Iraklis Vretzakis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics
| | - Frank M J Jacobs
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics
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Delpiano D, Uthmeier T. Techno-functional and 3D shape analysis applied for investigating the variability of backed tools in the Late Middle Paleolithic of Central Europe. PLoS One 2020; 15:e0236548. [PMID: 32813722 PMCID: PMC7446931 DOI: 10.1371/journal.pone.0236548] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/01/2020] [Indexed: 11/21/2022] Open
Abstract
In the Late Middle Paleolithic of Central Europe, two main cultural complexes have been distinguished: the Micoquian or Keilmessergruppe (KMG), and the Mousterian. Their differences mainly consist in the frequence of some retouched tools and the presence of bifacial technology. When these industries coexist, one element of discussion is the application of different concepts to manufacture tools with the same techno-functionality. This is particularly true for backed artifacts, such as Keilmesser (backed, asymmetrical bifacially-shaped knives) opposed to flake-tools equipped with a natural or knapped back. We conducted a techno-functional analysis of the backed tools from the G-Layer-Complex of Sesselfelsgrotte, one of the main Late Middle Paleolithic sequences in Central Europe, characterized by a combination of KMG and Mousterian aspects. In order to better understand the morpho-metrical data, 3D scans were used for recording technical features and performing semi-automatic geometric morphometrics. Results indicate that the techno-functional schemes of Keilmesser show a moderate variability and often overlap with the schemes of other typological groups. Within bifacial backed knives, a process of imitation of unifacial flake tools' functionaly was recognized particularly in the cutting edge manufacturing. Keilmesser proved to be the long-life, versatile version of backed flake-tools, also due to the recurrent valence as both tool and core. This is why Keilmesser represent an ideal strategic blank when a mobile and multi-functional tool is needed. Based on these data, it is assumed that the relationship between Mousterian and KMG is deeply rooted and the emergence of KMG aspects could be related to constrained situations characterizing the long cold stages of the Early Weichselian. A higher regional mobility caused by the comparably low predictability of resources characterized the subsistence tactics of Neanderthal groups especially at the borders of their overall distribution. For this reason, Keilmesser could have represented an ecological answer before possibly becoming a marker of cultural identity.
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Affiliation(s)
- Davide Delpiano
- Dipartimento di Studi Umanistici, Sezione di Scienze Preistoriche e Antropologiche, Università degli Studi di Ferrara, Ferrara, Italy
| | - Thorsten Uthmeier
- Department of the Old World and Asian Studies, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
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