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      A Paleogenomic Reconstruction of the Deep Population History of the Andes

      research-article
      1 , 2 , , 1 , 3 , 4 , 5 , 1 , 1 , 6 , 7 , 3 , 8 , 1 , 6 , 1 , 6 , 1 , 6 , 1 , 6 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 18 , 20 , 21 , 22 , 23 , 19 , 21 , 24 , 25 , 26 , 27 , 12 , 15 , 28 , 21 , 29 , 30 , 30 , 31 , 32 , 22 , 23 , 33 , 32 , 3 , 3 , 32 , 1 , 6 , 7 , 34 , 36 , ∗∗ , 8 , 35 , 36 , 37 , ∗∗∗
      Cell
      Cell Press
      Andes, population genetics, archaeology, anthropology, ancient DNA

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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.

          Summary

          There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today’s genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000–500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin.

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          Highlights

          • Ancient DNA transect reveals north-south substructure of Andean highlands by 5,800 BP

          • After 5,800 BP, gene flow mixed highland people with their neighbors

          • After 2,000 BP, striking genetic continuity through rise and fall of major cultures

          Abstract

          Genome-wide data from 89 ancient humans illuminates the changes to the genetic landscape in the Central Andes over 9,000 years, revealing large-scale gene flow and cosmopolitan societies in the Tiwanaku and Inca polities.

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          Most cited references122

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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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              MUSCLE: multiple sequence alignment with high accuracy and high throughput.

              We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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                Author and article information

                Contributors
                Journal
                Cell
                Cell
                Cell
                Cell Press
                0092-8674
                1097-4172
                28 May 2020
                28 May 2020
                : 181
                : 5
                : 1131-1145.e21
                Affiliations
                [1 ]Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
                [2 ]Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA
                [3 ]Max Planck Institute for the Science of Human History, Jena 07745, Germany
                [4 ]Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
                [5 ]Francis Crick Institute, London NW1 1AT, UK
                [6 ]Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA
                [7 ]Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
                [8 ]UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
                [9 ]Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
                [10 ]Department of Sociology, Anthropology and Social Work, Kansas State University, Manhattan, KS 66506, USA
                [11 ]Sociedad de Arqueología de La Paz, 5294 La Paz, Bolivia
                [12 ]McDonald Institute for Archaeological Research, University of Cambridge, Downing St., Cambridge, CB2 3ER, UK
                [13 ]Department of Anthropology, Yale University, New Haven, CT 06511, USA
                [14 ]Office of Scholarly Communication, Cambridge University Library, Cambridge CB3 9DR, UK
                [15 ]Centro de Genética y Biología Molecular, Facultdad de Medicina, Universidad de San Martín de Porres, Lima 15011, Peru
                [16 ]Peruvian Ministry of Culture, DDC Ica, Directos of the Nasca-Palpa Management Plan, Calle Juan Matta 880, Nasca 11401, Peru
                [17 ]Sainsbury Research Unit, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
                [18 ]Carrera de Arqueología, Universidad Mayor de San Andrés, Edificio Facultad de Ciencias Sociales 3er Piso, La Paz 1995, Bolivia
                [19 ]Harvard Peabody Museum, Harvard University, Cambridge, MA 02138, USA
                [20 ]School of Archaeology, Geography and Environmental Sciences, University of Reading, Reading, Berkshire, RG6 6AH, UK
                [21 ]INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
                [22 ]Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
                [23 ]Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
                [24 ]Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
                [25 ]Commission for Archaeology of Non-European Cultures, German Archaeological Institute, Berlin 14195, Germany
                [26 ]Universidad de Magallanes, Punta Arenas 6210427, Chile
                [27 ]Field Museum Natural History 1400 S Lake Shore Dr., Chicago, IL 60605, USA
                [28 ]Instituto de Alta Investigation, Universidad de Tarapaca, Antafogasta 1520, Arica, 1000000, Chile
                [29 ]Departamento de Antropología, Universidad de Tarapacá, Antafogasta 1520, Arica, 1000000, Chile
                [30 ]Museo de Sitio Huaca Pucllana, Calle General Borgoño, Cuadra 8, Miraflores, Lima 18, Peru
                [31 ]Department of Humanities, Pontifical Catholic University of Peru, San Miguel 15088, Peru
                [32 ]Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
                [33 ]Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
                [34 ]Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
                [35 ]UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
                Author notes
                []Corresponding author nathan_nakatsuka@ 123456hms.harvard.edu
                [∗∗ ]Corresponding author reich@ 123456genetics.med.harvard.edu
                [∗∗∗ ]Corresponding author lfehrens@ 123456ucsc.edu
                [36]

                Senior author

                [37]

                Lead Contact

                Article
                S0092-8674(20)30477-3
                10.1016/j.cell.2020.04.015
                7304944
                32386546
                fceeed0a-1a91-473b-80c3-5158942ff400
                © 2020 The Authors. Published by Elsevier Inc.

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 29 August 2019
                : 11 January 2020
                : 13 April 2020
                Categories
                Article

                Cell biology
                andes,population genetics,archaeology,anthropology,ancient dna
                Cell biology
                andes, population genetics, archaeology, anthropology, ancient dna

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