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      The Anglo-Saxon migration and the formation of the early English gene pool

      research-article
      1 , 2 , , 3 , 4 , 3 , 3 , 54 , 3 , 5 , 6 , 1 , 7 , 8 , 1 , 9 , 10 , 9 , 1 , 11 , 12 , 8 , 13 , 14 , 1 , 13 , 15 , 13 , 15 , 13 , 13 , 15 , 13 , 15 , 1 , 13 , 15 , 13 , 15 , 13 , 15 , 13 , 14 , 16 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 21 , 21 , 24 , 25 , 26 , 27 , 28 , 16 , 29 , 30 , 31 , 12 , 32 , 32 , 33 , 34 , 35 , 35 , 35 , 35 , 35 , 55 , 36 , 37 , 2 , 38 , 39 , 40 , 20 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 48 , 49 , 50 , 1 , 51 , 8 , 52 , 9 , 10 , 3 , 13 , 14 , 15 , 53 , 1 , 1 ,
      Nature
      Nature Publishing Group UK
      Population genetics, Archaeology, Evolutionary genetics, Cultural evolution

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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

          The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture 1 . The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate 24 . Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans—including 278 individuals from England—alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France 5, 6 .

          Abstract

          Archaeogenetic study of ancient DNA from medieval northwestern Europeans reveals substantial increase of continental northern European ancestry in Britain, suggesting mass migration across the North Sea during the Early Middle Ages.

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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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            Fast and accurate short read alignment with Burrows–Wheeler transform

            Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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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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                Author and article information

                Contributors
                dsayer@uclan.ac.uk
                stephan_schiffels@eva.mpg.de
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                21 September 2022
                21 September 2022
                2022
                : 610
                : 7930
                : 112-119
                Affiliations
                [1 ]GRID grid.419518.0, ISNI 0000 0001 2159 1813, Max Planck Institute for Evolutionary Anthropology, ; Leipzig, Germany
                [2 ]GRID grid.7943.9, ISNI 0000 0001 2167 3843, University of Central Lancashire, ; Preston, UK
                [3 ]GRID grid.15751.37, ISNI 0000 0001 0719 6059, University of Huddersfield, ; Huddersfield, UK
                [4 ]GRID grid.5132.5, ISNI 0000 0001 2312 1970, Leiden University, ; Leiden, Netherlands
                [5 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, University of Oxford, ; Oxford, UK
                [6 ]GRID grid.10392.39, ISNI 0000 0001 2190 1447, University of Tübingen, ; Tübingen, Germany
                [7 ]GRID grid.215654.1, ISNI 0000 0001 2151 2636, Center for Evolution and Medicine, , Arizona State University, ; Tempe, AZ USA
                [8 ]GRID grid.5254.6, ISNI 0000 0001 0674 042X, Globe Institute, Faculty of Health and Medical Sciences, , University of Copenhagen, ; Copenhagen, Denmark
                [9 ]GRID grid.421812.c, ISNI 0000 0004 0618 6889, deCODE Genetics/AMGEN Inc., ; Reykjavík, Iceland
                [10 ]GRID grid.14013.37, ISNI 0000 0004 0640 0021, Department of Anthropology, School of Social Sciences, , University of Iceland, ; Reykjavík, Iceland
                [11 ]GRID grid.5949.1, ISNI 0000 0001 2172 9288, University of Münster, ; Münster, Germany
                [12 ]GRID grid.35937.3b, ISNI 0000 0001 2270 9879, Department of Earth Sciences, , Natural History Museum, ; London, UK
                [13 ]GRID grid.38142.3c, ISNI 000000041936754X, Department of Genetics, , Harvard Medical School, ; Boston, MA USA
                [14 ]GRID grid.66859.34, ISNI 0000 0004 0546 1623, Broad Institute of Harvard and MIT, ; Cambridge, MA USA
                [15 ]GRID grid.38142.3c, ISNI 000000041936754X, Howard Hughes Medical Institute, , Harvard Medical School, ; Boston, MA USA
                [16 ]Landesmuseum Natur und Mensch, Oldenburg, Germany
                [17 ]GRID grid.10493.3f, ISNI 0000000121858338, University of Rostock, ; Rostock, Germany
                [18 ]GRID grid.461754.5, ISNI 0000 0001 2182 7603, Lower Saxony State Museum, ; Hanover, Germany
                [19 ]GRID grid.507510.6, ISNI 0000 0001 2179 7432, Landesamt für Kultur und Denkmalpflege Mecklenburg-Vorpommern, ; Schwerin, Germany
                [20 ]Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
                [21 ]Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
                [22 ]GRID grid.12026.37, ISNI 0000 0001 0679 2190, Cranfield Forensic Institute, Cranfield Defence and Security, , Cranfield University, ; Cranfield, UK
                [23 ]GRID grid.1008.9, ISNI 0000 0001 2179 088X, Melbourne Dental School, , University of Melbourne, ; Melbourne, Victoria Australia
                [24 ]The Atlantic Technological University, Sligo, Ireland
                [25 ]Milton Keynes Museum, Milton Keyes, UK
                [26 ]Cotswold Archaeology, Needham Market, UK
                [27 ]GRID grid.5600.3, ISNI 0000 0001 0807 5670, Cardiff University, ; Cardiff, UK
                [28 ]GRID grid.9764.c, ISNI 0000 0001 2153 9986, University of Kiel, ; Kiel, Germany
                [29 ]GRID grid.7400.3, ISNI 0000 0004 1937 0650, University of Zurich, ; Zurich, Switzerland
                [30 ]GRID grid.10420.37, ISNI 0000 0001 2286 1424, Department of Evolutionary Anthropology, , University of Vienna, ; Vienna, Austria
                [31 ]GRID grid.10420.37, ISNI 0000 0001 2286 1424, Human Evolution and Archaeological Sciences, , University of Vienna, ; Vienna, Austria
                [32 ]Museum of Copenhagen, Copenhagen, Denmark
                [33 ]GRID grid.499812.f, ISNI 0000 0001 2154 534X, Canterbury Archaeological Trust, ; Canterbury, UK
                [34 ]Isle Heritage CIC, Sandgate, UK
                [35 ]GRID grid.511213.5, ISNI 0000 0001 0681 2497, Oxford Archaeology East, ; Cambridge, UK
                [36 ]GRID grid.6572.6, ISNI 0000 0004 1936 7486, University of Birmingham, ; Birmingham, UK
                [37 ]GRID grid.8241.f, ISNI 0000 0004 0397 2876, Centre for Anatomy and Human Identification (CAHID), , University of Dundee, ; Dundee, UK
                [38 ]The Landscape Research Centre Ltd, Yedingham, UK
                [39 ]East Dorset Antiquarian Society (EDAS), West Bexington, UK
                [40 ]GRID grid.17236.31, ISNI 0000 0001 0728 4630, Department of Archaeology and Anthropology, , Bournemouth University, ; Poole, UK
                [41 ]Ossatura–Wilhelm-Börker, Braunschweig, Germany
                [42 ]GRID grid.5685.e, ISNI 0000 0004 1936 9668, University of York, ; York, UK
                [43 ]Tees Archaeology, Hartlepool, UK
                [44 ]FAS Heritage, York, UK
                [45 ]Royal Cornwall Museum, Truro, UK
                [46 ]Cornwall Archaeological Unit, Truro, UK
                [47 ]The Novium Museum, Chichester, UK
                [48 ]Fishbourne Roman Palace, Fishbourne, UK
                [49 ]South Downs Centre, Midhurst, UK
                [50 ]GRID grid.437963.c, ISNI 0000 0001 1349 5098, South Australian Museum, ; Adelaide, South Australia Australia
                [51 ]GRID grid.35937.3b, ISNI 0000 0001 2270 9879, Natural History Museum, ; London, UK
                [52 ]GRID grid.83440.3b, ISNI 0000000121901201, University College London, ; London, UK
                [53 ]GRID grid.38142.3c, ISNI 000000041936754X, Department of Human Evolutionary Biology, , Harvard University, ; Cambridge, MA USA
                [54 ]GRID grid.6738.a, ISNI 0000 0001 1090 0254, Present Address: Institute of Geosystems and Bioindication, , Technische Universität Braunschweig, ; Braunschweig, Germany
                [55 ]Present Address: Cotswold Archaeology, Needham Market, UK
                Author information
                http://orcid.org/0000-0002-2769-1281
                http://orcid.org/0000-0001-8911-7771
                http://orcid.org/0000-0001-9202-8331
                http://orcid.org/0000-0001-9126-1377
                http://orcid.org/0000-0003-2475-2007
                http://orcid.org/0000-0001-5912-4401
                http://orcid.org/0000-0002-9579-4362
                http://orcid.org/0000-0003-1651-6119
                http://orcid.org/0000-0003-2126-6732
                http://orcid.org/0000-0002-6772-3831
                http://orcid.org/0000-0001-5350-1608
                http://orcid.org/0000-0003-3170-8514
                http://orcid.org/0000-0003-0990-2329
                http://orcid.org/0000-0002-3533-7987
                http://orcid.org/0000-0002-5997-8631
                http://orcid.org/0000-0001-9435-2872
                http://orcid.org/0000-0001-8322-6918
                http://orcid.org/0000-0002-7979-6798
                http://orcid.org/0000-0003-0935-0739
                http://orcid.org/0000-0002-1706-3396
                http://orcid.org/0000-0001-9349-7818
                http://orcid.org/0000-0002-2452-981X
                http://orcid.org/0000-0003-3118-0967
                http://orcid.org/0000-0002-7037-5292
                http://orcid.org/0000-0001-9144-3920
                http://orcid.org/0000-0002-1017-9150
                Article
                5247
                10.1038/s41586-022-05247-2
                9534755
                36131019
                7636ed53-e579-4a4d-bf81-b76add1f4d2f
                © 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
                : 12 December 2021
                : 17 August 2022
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                population genetics,archaeology,evolutionary genetics,cultural evolution
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                population genetics, archaeology, evolutionary genetics, cultural evolution

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