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      Homo sapiens reached the higher latitudes of Europe by 45,000 years ago

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      1 , 2 , 2 , 3 , , 2 , 4 , 2 , 5 , 6 , 2 , 2 , 2 , 7 , 1 , 2 , 2 , 8 , 2 , 9 , 2 , 10 , 11 , 12 , 13 , 14 , 2 , 15 , 2 , 16 , 2 , 17 , 18 , 2 , 19 , 20 , 21 , 21 , 21 , 10 , 2 , 22 , 2 , 2 , 2 , 12 , 2 , 23 , 1 , 2 ,
      Nature
      Nature Publishing Group UK
      Population genetics, Archaeology, Anthropology

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          Abstract

          The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H.sapiens in eastern Europe 1 . Local hybridization between the two groups occurred 2 , but not on all occasions 3 . Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups 4 . One such technocomplex for which the makers are unknown is the Lincombian–Ranisian–Jerzmanowician (LRJ), which has been described in northwestern and central Europe 58 . Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H.sapiens remains in Eurasia. We show that early H.sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.

          Abstract

          Through archaeological excavation, morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains, a study reports the presence of Homo sapiens in Germany north of the Alps more than 45,000 years ago.

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          The Sequence Alignment/Map format and SAMtools

          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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            MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

            We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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              The PRIDE database and related tools and resources in 2019: improving support for quantification data

              Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.
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                Author and article information

                Contributors
                marcel.weiss@fau.de
                hublin@eva.mpg.de
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                31 January 2024
                31 January 2024
                2024
                : 626
                : 7998
                : 341-346
                Affiliations
                [1 ]Chair of Paleoanthropology, CIRB (UMR 7241–U1050), Collège de France, ( https://ror.org/04ex24z53) Paris, France
                [2 ]Max Planck Institute for Evolutionary Anthropology, ( https://ror.org/02a33b393) Leipzig, Germany
                [3 ]Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Ur- und Frühgeschichte, ( https://ror.org/00f7hpc57) Erlangen, Germany
                [4 ]Ancient Genomics Lab, Francis Crick Institute, ( https://ror.org/04tnbqb63) London, UK
                [5 ]Department of Molecular and Cell Biology, University of California Berkeley, ( https://ror.org/01an7q238) Berkeley, CA USA
                [6 ]Department of Anthropology, California State University Northridge, ( https://ror.org/005f5hv41) Northridge, CA USA
                [7 ]School of Anthropology and Conservation, University of Kent, ( https://ror.org/00xkeyj56) Canterbury, UK
                [8 ]GRID grid.412041.2, ISNI 0000 0001 2106 639X, Univ. Bordeaux, CNRS, Ministère de la Culture, PACEA, UMR 5199, ; Bordeaux, France
                [9 ]Archaeological Micromorphology and Biomarker Lab, University of La Laguna, ( https://ror.org/01r9z8p25) San Cristóbal de La Laguna, Spain
                [10 ]Center for Protein Research, University of Copenhagen, ( https://ror.org/035b05819) Copenhagen, Denmark
                [11 ]College of Earth and Environmental Sciences, Lanzhou University, ( https://ror.org/01mkqqe32) Lanzhou, China
                [12 ]Globe Institute, University of Copenhagen, ( https://ror.org/035b05819) Copenhagen, Denmark
                [13 ]Departament de Prehistòria, Universitat Autònoma de Barcelona, ( https://ror.org/052g8jq94) Barcelona, Spain
                [14 ]GRID grid.425754.5, ISNI 0000 0004 0622 6158, Department of Soil Protection and Soil Survey, State Authority for Mining, , Energy and Geology of Lower Saxony (LBEG), ; Hannover, Germany
                [15 ]Terrestrial Sedimentology, Department of Geosciences, University of Tübingen, ( https://ror.org/03a1kwz48) Tübingen, Germany
                [16 ]Department of Evolutionary Anthropology and Human Evolution and Archaeological Sciences (HEAS), University of Vienna, ( https://ror.org/03prydq77) Vienna, Austria
                [17 ]Institute of Ecology, Leuphana University, ( https://ror.org/02w2y2t16) Lüneburg, Germany
                [18 ]Historical Anthropospheres Working Group, Leipzig Lab, Leipzig University, ( https://ror.org/03s7gtk40) Leipzig, Germany
                [19 ]Department of Chemistry G. Ciamician, Bologna University, ( https://ror.org/01111rn36) Bologna, Italy
                [20 ]Ion Beam Physics, ETH Zurich, ( https://ror.org/05a28rw58) Zurich, Switzerland
                [21 ]Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt – Landesmuseum für Vorgeschichte, ( https://ror.org/01ybxp914) Halle, Germany
                [22 ]Department of Physiology and Pharmacology, Karolinska Institutet, ( https://ror.org/056d84691) Stockholm, Sweden
                [23 ]Thuringian State Office for the Preservation of Historical Monuments and Archaeology, Weimar, Germany
                Author information
                http://orcid.org/0000-0002-0778-5520
                http://orcid.org/0000-0002-9093-3490
                http://orcid.org/0000-0001-7687-5370
                http://orcid.org/0000-0003-0358-0285
                http://orcid.org/0000-0002-4064-0331
                http://orcid.org/0000-0001-7155-5140
                http://orcid.org/0000-0002-5621-5786
                http://orcid.org/0000-0002-2642-8043
                http://orcid.org/0000-0001-5553-1421
                http://orcid.org/0000-0002-4171-4427
                http://orcid.org/0000-0002-6124-8021
                http://orcid.org/0000-0002-2406-3132
                http://orcid.org/0000-0002-8215-2678
                http://orcid.org/0000-0003-3629-8251
                http://orcid.org/0000-0002-4747-4938
                http://orcid.org/0000-0001-7118-1249
                http://orcid.org/0000-0001-6242-3058
                http://orcid.org/0000-0001-9144-3920
                http://orcid.org/0000-0002-4760-558X
                http://orcid.org/0000-0002-2063-468X
                http://orcid.org/0000-0001-9190-8054
                http://orcid.org/0000-0001-6283-8114
                Article
                6923
                10.1038/s41586-023-06923-7
                10849966
                38297117
                9aaff1fc-d692-40e0-bb62-946093b9f919
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 27 June 2023
                : 30 November 2023
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                © Springer Nature Limited 2024

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                population genetics,archaeology,anthropology
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                population genetics, archaeology, anthropology

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