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      Early contact between late farming and pastoralist societies in southeastern Europe

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      1 , , 1 , 2 , 1 , 1 , 1 , 1 , 3 , 1 , 4 , 5 , 6 , 6 , 7 , 8 , 8 , 5 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 1 , 1 , 10 , 5 , 1 , 1 ,
      Nature
      Nature Publishing Group UK
      Evolutionary genetics, Comparative genomics, Archaeology, Biological anthropology, Population genetics

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          Abstract

          Archaeogenetic studies have described two main genetic turnover events in prehistoric western Eurasia: one associated with the spread of farming and a sedentary lifestyle starting around 7000–6000  bc (refs. 13 ) and a second with the expansion of pastoralist groups from the Eurasian steppes starting around 3300  bc (refs. 4, 5 ). The period between these events saw new economies emerging on the basis of key innovations, including metallurgy, wheel and wagon and horse domestication 69 . However, what happened between the demise of the Copper Age settlements around 4250  bc and the expansion of pastoralists remains poorly understood. To address this question, we analysed genome-wide data from 135 ancient individuals from the contact zone between southeastern Europe and the northwestern Black Sea region spanning this critical time period. While we observe genetic continuity between Neolithic and Copper Age groups from major sites in the same region, from around 4500  bc on, groups from the northwestern Black Sea region carried varying amounts of mixed ancestries derived from Copper Age groups and those from the forest/steppe zones, indicating genetic and cultural contact over a period of around 1,000 years earlier than anticipated. We propose that the transfer of critical innovations between farmers and transitional foragers/herders from different ecogeographic zones during this early contact was integral to the formation, rise and expansion of pastoralist groups around 3300  bc.

          Abstract

          Archaeogenetic analysis of 135 individuals from the zone between southeastern Europe and the northwestern Black Sea region indicates contacts between farming and pastoralist populations at the end of the Copper Age.

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          Most cited references75

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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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            A global reference for human genetic variation

            The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.
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              Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

              Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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                Author and article information

                Contributors
                sandra_ellen_penske@eva.mpg.de
                wolfgang_haak@eva.mpg.de
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                19 July 2023
                19 July 2023
                2023
                : 620
                : 7973
                : 358-365
                Affiliations
                [1 ]GRID grid.419518.0, ISNI 0000 0001 2159 1813, Department of Archaeogenetics, , Max Planck Institute for Evolutionary Anthropology, ; Leipzig, Germany
                [2 ]GRID grid.1010.0, ISNI 0000 0004 1936 7304, School of Computer and Mathematical Sciences, , University of Adelaide, ; Adelaide, South Australia Australia
                [3 ]GRID grid.10392.39, ISNI 0000 0001 2190 1447, Institute for Archaeological Sciences, , Eberhard Karls University of Tübingen, ; Tübingen, Germany
                [4 ]GRID grid.410344.6, ISNI 0000 0001 2097 3094, Institute of Experimental Morphology, Pathology and Anthropology with Museum, , Bulgarian Academy of Sciences, ; Sofia, Bulgaria
                [5 ]GRID grid.424195.f, ISNI 0000 0001 2106 6832, Eurasia Department, , German Archaeological Institute, ; Berlin, Germany
                [6 ]GRID grid.410344.6, ISNI 0000 0001 2097 3094, National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, ; Sofia, Bulgaria
                [7 ]Odesa Archaeological Museum, Odesa, Ukraine
                [8 ]Regional History Museum, Veliko Tarnovo, Bulgaria
                [9 ]Institute for Prehistory, Early History and Medieval Archaeology, Tübingen, Germany
                [10 ]GRID grid.5252.0, ISNI 0000 0004 1936 973X, Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, , Ludwig Maximilian University Munich, ; Munich, Germany
                [11 ]National Museum of History of Moldova, Chişinău, Republic of Moldova
                [12 ]GRID grid.1005.4, ISNI 0000 0004 4902 0432, Electron Microscope Unit, Mark Wainwright Analytical Centre, , University of New South Wales, ; Sydney, New South Wales Australia
                [13 ]GRID grid.1005.4, ISNI 0000 0004 4902 0432, Earth and Sustainability Science Research Centre, , School of Biological, Earth and Environmental Sciences, University of New South Wales, ; Sydney, New South Wales Australia
                [14 ]GRID grid.1004.5, ISNI 0000 0001 2158 5405, Department of History and Archaeology, , Macquarie University, ; Sydney, New South Wales Australia
                [15 ]Varna Regional Historical Museum, Varna, Bulgaria
                [16 ]GRID grid.7048.b, ISNI 0000 0001 1956 2722, Aarhus University, ; Aarhus, Denmark
                [17 ]GRID grid.418333.e, ISNI 0000 0004 1937 1389, Institutul de Arheologie “Vasile Pârvan” Academia Română, ; Bucharest, Romania
                [18 ]Yambol Regional Historical Museum, Yambol, Bulgaria
                Author information
                http://orcid.org/0000-0003-2800-0371
                http://orcid.org/0000-0002-4204-5018
                http://orcid.org/0000-0002-3144-6481
                http://orcid.org/0000-0002-6490-8101
                http://orcid.org/0000-0003-3448-5715
                http://orcid.org/0000-0002-3615-3936
                http://orcid.org/0000-0003-3825-8536
                http://orcid.org/0009-0000-9670-4296
                http://orcid.org/0000-0003-0342-5648
                http://orcid.org/0000-0002-6311-0990
                http://orcid.org/0000-0002-6369-4527
                http://orcid.org/0000-0002-4884-9682
                http://orcid.org/0000-0003-4702-9372
                http://orcid.org/0000-0001-9144-3920
                http://orcid.org/0000-0003-2475-2007
                Article
                6334
                10.1038/s41586-023-06334-8
                10412445
                37468624
                dc1f3b9b-c752-4ad1-822a-95617a800f96
                © The Author(s) 2023

                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
                : 18 August 2022
                : 16 June 2023
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                © Springer Nature Limited 2023

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                evolutionary genetics,comparative genomics,archaeology,biological anthropology,population genetics

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