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      The source of the Black Death in fourteenth-century central Eurasia

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          Abstract

          The origin of the medieval Black Death pandemic ( ad 1346–1353) has been a topic of continuous investigation because of the pandemic’s extensive demographic impact and long-lasting consequences 1, 2 . Until now, the most debated archaeological evidence potentially associated with the pandemic’s initiation derives from cemeteries located near Lake Issyk-Kul of modern-day Kyrgyzstan 1, 39 . These sites are thought to have housed victims of a fourteenth-century epidemic as tombstone inscriptions directly dated to 1338–1339 state ‘pestilence’ as the cause of death for the buried individuals 9 . Here we report ancient DNA data from seven individuals exhumed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium Yersinia pestis in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic’s emergence, here dated to the first half of the fourteenth century. Comparisons with present-day diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early fourteenth-century source of the second plague pandemic in central Eurasia.

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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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            MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

            We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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              RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

              Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                maria.spyrou@ifu.uni-tuebingen.de
                philip.slavin@stir.ac.uk
                krause@eva.mpg.de
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                15 June 2022
                15 June 2022
                2022
                : 606
                : 7915
                : 718-724
                Affiliations
                [1 ]GRID grid.10392.39, ISNI 0000 0001 2190 1447, Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, ; Tübingen, Germany
                [2 ]GRID grid.419518.0, ISNI 0000 0001 2159 1813, Department of Archaeogenetics, , Max Planck Institute for Evolutionary Anthropology, ; Leipzig, Germany
                [3 ]GRID grid.469873.7, ISNI 0000 0004 4914 1197, Department of Archaeogenetics, , Max Planck Institute for the Science of Human History, ; Jena, Germany
                [4 ]Laboratory of Population Genetics, Institute of Genetics and Physiology, Almaty, Kazakhstan
                [5 ]GRID grid.77184.3d, ISNI 0000 0000 8887 5266, Kazakh National University by al-Farabi, ; Almaty, Kazakhstan
                [6 ]GRID grid.469873.7, ISNI 0000 0004 4914 1197, Transmission, Infection, Diversification & Evolution Group, , Max Planck Institute for the Science of Human History, ; Jena, Germany
                [7 ]GRID grid.5395.a, ISNI 0000 0004 1757 3729, Department of Civilisations and Forms of Knowledge, , University of Pisa, ; Pisa, Italy
                [8 ]GRID grid.4886.2, ISNI 0000 0001 2192 9124, Department of Physical Anthropology, , Kunstkamera, Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, ; St Petersburg, Russian Federation
                [9 ]GRID grid.14476.30, ISNI 0000 0001 2342 9668, Research Institute and Museum of Anthropology, Lomonosov Moscow State University, ; Moscow, Russian Federation
                [10 ]GRID grid.9613.d, ISNI 0000 0001 1939 2794, European Virus Bioinformatics Center (EVBC), ; Jena, Germany
                [11 ]GRID grid.11918.30, ISNI 0000 0001 2248 4331, Division of History, Heritage and Politics, , University of Stirling, ; Stirling, UK
                Author information
                http://orcid.org/0000-0002-3615-3936
                http://orcid.org/0000-0002-6490-8101
                http://orcid.org/0000-0002-9499-6472
                http://orcid.org/0000-0002-5533-0686
                http://orcid.org/0000-0001-6398-2177
                http://orcid.org/0000-0002-6745-9903
                http://orcid.org/0000-0003-2937-3006
                http://orcid.org/0000-0002-5657-018X
                http://orcid.org/0000-0003-2475-2007
                http://orcid.org/0000-0002-6460-145X
                http://orcid.org/0000-0001-9144-3920
                Article
                4800
                10.1038/s41586-022-04800-3
                9217749
                35705810
                68fc19aa-89ac-407b-9ae5-a2c23e6d6ea5
                © The Author(s) 2022

                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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 19 July 2021
                : 25 April 2022
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                © The Author(s), under exclusive licence to Springer Nature Limited 2022

                Uncategorized
                evolutionary genetics,archaeology,pathogens
                Uncategorized
                evolutionary genetics, archaeology, pathogens

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