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      The genomic history and global expansion of domestic donkeys

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      American Association for the Advancement of Science (AAAS)

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.

          Donkeys’ African origins

          Donkeys have been important to humans for thousands of years, being the primary source of work and transport for many cultures. Unlike horses, little was known about the origin and domestication of donkeys. Todd et al . sequenced the genomes of modern and ancient donkeys and found evidence of an eastern African origin over 7000 years ago, with subsequent isolation and divergence of lineages in Africa and Eurasia. They also reveal the imprint of desertification on divergence among groups and specifics about donkey breeding and husbandry, including selection for large size and the practice of inbreeding. —SNV

          Abstract

          Ancient and modern genomes elucidate the origins, spread, and management practices underlying donkey domestication.

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          Is Open Access

          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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            The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

            Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS--the 1000 Genome pilot alone includes nearly five terabases--make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
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              PLINK: a tool set for whole-genome association and population-based linkage analyses.

              Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.
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                Journal
                Science
                Science
                American Association for the Advancement of Science (AAAS)
                0036-8075
                1095-9203
                September 09 2022
                September 09 2022
                : 377
                : 6611
                : 1172-1180
                Affiliations
                [1 ]Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France.
                [2 ]Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Pakistan.
                [3 ]CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.
                [4 ]BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.
                [5 ]Department of Animal Science, Sul Ross State University, Alpine, TX 79830, USA.
                [6 ]Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
                [7 ]Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.
                [8 ]Earth System Science Department, University of California, Irvine, CA 92697, USA.
                [9 ]Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, Evry 91042, France.
                [10 ]Laboratoire Archéorient, Université Lyon 2, Lyon 69007, France.
                [11 ]Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy.
                [12 ]Bioarchaeology Service, Museo delle Civiltà, Rome 00144, Italy.
                [13 ]Soprintendenza archeologia belle arti e paesaggio per le province di Verona, Rovigo e Vicenza, Verona 37121, Italy.
                [14 ]ICArEHB, Campus de Gambelas, University of Algarve, Faro 8005-139, Portugal.
                [15 ]Universidade Aberta, Lisbon 1269-001, Portugal.
                [16 ]Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro 8000-117, Portugal.
                [17 ]Centre for Research on Science and Geological Engineering, Universidade NOVA de Lisboa, Lisbon 1099-085, Portugal.
                [18 ]Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich 80539, Germany.
                [19 ]School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4DQ, United Kingdom.
                [20 ]Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.
                [21 ]Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA.
                [22 ]Institut de Paléontologie Humaine, Fondation Albert Ier, Paris / UMR 7194 HNHP, MNHN-CNRS-UPVD / EPCC Centre Européen de Recherche Préhistorique, Tautavel 66720, France.
                [23 ]Archéologie des Sociétés Méditéranéennes, Université Paul Valéry - Site Saint-Charles 2, Montpellier 34090, France.
                [24 ]National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem 9190401, Israel.
                [25 ]Archaeology Department, Ankara University, Ankara 06100, Turkey.
                [26 ]Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
                [27 ]Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul 34320, Turkey.
                [28 ]Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d’Histoire Naturelle, Paris 75005, France.
                [29 ]Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord 9416745775, Iran.
                [30 ]Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran.
                [31 ]Department of Osteology, National Museum of Iran, Tehran 1136918111, Iran.
                [32 ]GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Castaneet-Tolosan Cedex 31326, France.
                [33 ]Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
                [34 ]DGAOT, Faculty of Sciences, Universidade do Porto, Porto 4169-007, Portugal.
                [35 ]Sustainable Agrifood Production Research Centre (GreenUPorto), Universidade do Porto, Vairão 4485-646, Portugal.
                [36 ]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
                [37 ]Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
                Article
                10.1126/science.abo3503
                36074859
                13a2f866-049e-48a8-9371-4f52089e4624
                © 2022
                History

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