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Garrido Marques A, Rubinacci S, Malaspinas AS, Delaneau O, Sousa da Mota B. Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA. Sci Rep 2024; 14:6227. [PMID: 38486065 PMCID: PMC10940295 DOI: 10.1038/s41598-024-56584-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Low-coverage imputation is becoming ever more present in ancient DNA (aDNA) studies. Imputation pipelines commonly used for present-day genomes have been shown to yield accurate results when applied to ancient genomes. However, post-mortem damage (PMD), in the form of C-to-T substitutions at the reads termini, and contamination with DNA from closely related species can potentially affect imputation performance in aDNA. In this study, we evaluated imputation performance (i) when using a genotype caller designed for aDNA, ATLAS, compared to bcftools, and (ii) when contamination is present. We evaluated imputation performance with principal component analyses and by calculating imputation error rates. With a particular focus on differently imputed sites, we found that using ATLAS prior to imputation substantially improved imputed genotypes for a very damaged ancient genome (42% PMD). Trimming the ends of the sequencing reads led to similar improvements in imputation accuracy. For the remaining genomes, ATLAS brought limited gains. Finally, to examine the effect of contamination on imputation, we added various amounts of reads from two present-day genomes to a previously downsampled high-coverage ancient genome. We observed that imputation accuracy drastically decreased for contamination rates above 5%. In conclusion, we recommend (i) accounting for PMD by either trimming sequencing reads or using a genotype caller such as ATLAS before imputing highly damaged genomes and (ii) only imputing genomes containing up to 5% of contamination.
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Affiliation(s)
| | - Simone Rubinacci
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
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2
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Sousa da Mota B, Rubinacci S, Cruz Dávalos DI, G Amorim CE, Sikora M, Johannsen NN, Szmyt MH, Włodarczak P, Szczepanek A, Przybyła MM, Schroeder H, Allentoft ME, Willerslev E, Malaspinas AS, Delaneau O. Imputation of ancient human genomes. Nat Commun 2023; 14:3660. [PMID: 37339987 DOI: 10.1038/s41467-023-39202-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 06/02/2023] [Indexed: 06/22/2023] Open
Abstract
Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.
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Affiliation(s)
- Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Simone Rubinacci
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Diana Ivette Cruz Dávalos
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Niels N Johannsen
- Department of Archaeology and Heritage Studies, Aarhus University, Aarhus, Denmark
| | - Marzena H Szmyt
- Institute for Eastern Research, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
- Department of Anatomy, Jagiellonian University, Medical College, Kraków, Poland
| | | | - Hannes Schroeder
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Science, Curtin University, Bentley, WA, Australia
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- MARUM, University of Bremen, Bremen, Germany
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
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3
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Neuenschwander S, Cruz Dávalos DI, Anchieri L, Sousa da Mota B, Bozzi D, Rubinacci S, Delaneau O, Rasmussen S, Malaspinas AS. Mapache: a flexible pipeline to map ancient DNA. Bioinformatics 2023; 39:6986969. [PMID: 36637197 PMCID: PMC9901408 DOI: 10.1093/bioinformatics/btad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/14/2022] [Accepted: 01/12/2023] [Indexed: 01/14/2023] Open
Abstract
SUMMARY We introduce mapache, a flexible, robust and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large datasets-such as reference panels and multiple extracts and libraries per sample - to one or several genomes. Mapache can easily be customized or combined with other Snakemake tools. AVAILABILITY AND IMPLEMENTATION Mapache is freely available on GitHub (https://github.com/sneuensc/mapache). An extensive manual is provided at https://github.com/sneuensc/mapache/wiki. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Vital-IT, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Diana I Cruz Dávalos
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Lucas Anchieri
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Davide Bozzi
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Simone Rubinacci
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
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4
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Arizmendi Cárdenas YO, Neuenschwander S, Malaspinas AS. Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study. PeerJ 2022; 10:e12784. [PMID: 35356467 PMCID: PMC8958974 DOI: 10.7717/peerj.12784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/21/2021] [Indexed: 01/10/2023] Open
Abstract
Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieve the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend that users verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest.
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Affiliation(s)
- Yami Ommar Arizmendi Cárdenas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland,Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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5
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Clemente F, Unterländer M, Dolgova O, Amorim CEG, Coroado-Santos F, Neuenschwander S, Ganiatsou E, Cruz Dávalos DI, Anchieri L, Michaud F, Winkelbach L, Blöcher J, Arizmendi Cárdenas YO, Sousa da Mota B, Kalliga E, Souleles A, Kontopoulos I, Karamitrou-Mentessidi G, Philaniotou O, Sampson A, Theodorou D, Tsipopoulou M, Akamatis I, Halstead P, Kotsakis K, Urem-Kotsou D, Panagiotopoulos D, Ziota C, Triantaphyllou S, Delaneau O, Jensen JD, Moreno-Mayar JV, Burger J, Sousa VC, Lao O, Malaspinas AS, Papageorgopoulou C. The genomic history of the Aegean palatial civilizations. Cell 2021; 184:2565-2586.e21. [PMID: 33930288 PMCID: PMC8127963 DOI: 10.1016/j.cell.2021.03.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/17/2020] [Accepted: 03/18/2021] [Indexed: 12/30/2022]
Abstract
The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.
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Affiliation(s)
- Florian Clemente
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Martina Unterländer
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece; Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Olga Dolgova
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Carlos Eduardo G Amorim
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Francisco Coroado-Santos
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Elissavet Ganiatsou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diana I Cruz Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Lucas Anchieri
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Frédéric Michaud
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Yami Ommar Arizmendi Cárdenas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Eleni Kalliga
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Angelos Souleles
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Ioannis Kontopoulos
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | - Olga Philaniotou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, 85132 Rhodes, Greece
| | - Dimitra Theodorou
- Ephorate of Antiquities of Kozani, Hellenic Ministry of Culture and Sports, 50004 Kozani, Greece
| | - Metaxia Tsipopoulou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Ioannis Akamatis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Paul Halstead
- Department of Archaeology, University of Sheffield, Minalloy House, 10-16 Regent St., Sheffield S1 3NJ, UK
| | - Kostas Kotsakis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dushka Urem-Kotsou
- Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diamantis Panagiotopoulos
- Institute of Classical Archaeology, University of Heidelberg, Marstallhof 4, 69117 Heidelberg, Germany
| | - Christina Ziota
- Ephorate of Antiquities of Florina, Hellenic Ministry of Culture and Sports, 53100 Florina, Greece
| | - Sevasti Triantaphyllou
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - J Víctor Moreno-Mayar
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark; National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Vitor C Sousa
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece.
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Abstract
Shinde et al. report the first genome-wide data from an ancient individual from the Indus Valley Civilization in South Asia. Their findings have implications for the origins and spread of farming and Indo-European languages in the region and the makings of the South Asian gene pool.
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Affiliation(s)
- Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Hannes Schroeder
- Section for Evolutionary Genomics, The Globe Institute, University of Copenhagen, 1553 Copenhagen, Denmark
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne & Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
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7
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Moreno-Mayar JV, Korneliussen TS, Dalal J, Renaud G, Albrechtsen A, Nielsen R, Malaspinas AS. A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data. Bioinformatics 2019; 36:828-841. [PMID: 31504166 PMCID: PMC8215924 DOI: 10.1093/bioinformatics/btz660] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/05/2019] [Accepted: 08/22/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION The presence of present-day human contaminating DNA fragments is one of the challenges defining ancient DNA (aDNA) research. This is especially relevant to the ancient human DNA field where it is difficult to distinguish endogenous molecules from human contaminants due to their genetic similarity. Recently, with the advent of high-throughput sequencing and new aDNA protocols, hundreds of ancient human genomes have become available. Contamination in those genomes has been measured with computational methods often developed specifically for these empirical studies. Consequently, some of these methods have not been implemented and tested for general use while few are aimed at low-depth nuclear data, a common feature in aDNA datasets. RESULTS We develop a new X-chromosome-based maximum likelihood method for estimating present-day human contamination in low-depth sequencing data from male individuals. We implement our method for general use, assess its performance under conditions typical of ancient human DNA research, and compare it to previous nuclear data-based methods through extensive simulations. For low-depth data, we show that existing methods can produce unusable estimates or substantially underestimate contamination. In contrast, our method provides accurate estimates for a depth of coverage as low as 0.5× on the X-chromosome when contamination is below 25%. Moreover, our method still yields meaningful estimates in very challenging situations, i.e. when the contaminant and the target come from closely related populations or with increased error rates. With a running time below 5 min, our method is applicable to large scale aDNA genomic studies. AVAILABILITY AND IMPLEMENTATION The method is implemented in C++ and R and is available in github.com/sapfo/contaminationX and popgen.dk/angsd.
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Affiliation(s)
| | | | - Jyoti Dalal
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen
| | - Anders Albrechtsen
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen,Department of Statistics, CA 94720, USA,Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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8
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Wright JL, Wasef S, Heupink TH, Westaway MC, Rasmussen S, Pardoe C, Fourmile GG, Young M, Johnson T, Slade J, Kennedy R, Winch P, Pappin M, Wales T, Bates W“B, Hamilton S, Whyman N, van Holst Pellekaan S, McAllister PJ, Taçon PS, Curnoe D, Li R, Millar C, Subramanian S, Willerslev E, Malaspinas AS, Sikora M, Lambert DM. Ancient nuclear genomes enable repatriation of Indigenous human remains. Sci Adv 2018; 4:eaau5064. [PMID: 30585290 PMCID: PMC6300400 DOI: 10.1126/sciadv.aau5064] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance. We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods.
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Affiliation(s)
- Joanne L. Wright
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Sally Wasef
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Tim H. Heupink
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- Global Health Institute, Epidemiology and Social Medicine, University of Antwerp, Belgium
| | - Michael C. Westaway
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Simon Rasmussen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Colin Pardoe
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia
| | | | - Michael Young
- Barkandji/Paakantyi Elder, Red Cliffs, VIC, Australia
| | - Trish Johnson
- Barkandji/Paakantyi Elder, Pooncarie, NSW, Australia
| | - Joan Slade
- Ngiyampaa Elder, Ivanhoe, NSW, Australia
| | | | - Patsy Winch
- Mutthi Mutthi Elder, Balranald, NSW, Australia
| | - Mary Pappin
- Mutthi Mutthi Elder, Broken Hill, NSW, Australia
| | - Tapij Wales
- Thanynakwith Elder, Napranum, QLD, Australia
| | | | | | | | - Sheila van Holst Pellekaan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | | | - Paul S.C. Taçon
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Darren Curnoe
- ARC Centre of Excellence for Australian Biodiversity and Heritage and Paleontology, Geobiology and Earth Archives Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Craig Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Sankar Subramanian
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Corresponding author. (M.S.); (D.M.L.)
| | - David M. Lambert
- Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
- Corresponding author. (M.S.); (D.M.L.)
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9
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Moreno-Mayar JV, Vinner L, de Barros Damgaard P, de la Fuente C, Chan J, Spence JP, Allentoft ME, Vimala T, Racimo F, Pinotti T, Rasmussen S, Margaryan A, Iraeta Orbegozo M, Mylopotamitaki D, Wooller M, Bataille C, Becerra-Valdivia L, Chivall D, Comeskey D, Devièse T, Grayson DK, George L, Harry H, Alexandersen V, Primeau C, Erlandson J, Rodrigues-Carvalho C, Reis S, Bastos MQR, Cybulski J, Vullo C, Morello F, Vilar M, Wells S, Gregersen K, Hansen KL, Lynnerup N, Mirazón Lahr M, Kjær K, Strauss A, Alfonso-Durruty M, Salas A, Schroeder H, Higham T, Malhi RS, Rasic JT, Souza L, Santos FR, Malaspinas AS, Sikora M, Nielsen R, Song YS, Meltzer DJ, Willerslev E. Early human dispersals within the Americas. Science 2018; 362:science.aav2621. [DOI: 10.1126/science.aav2621] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022]
Abstract
Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct “Paleoamericans.” We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.
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10
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Cruz-Dávalos DI, Nieves-Colón MA, Sockell A, Poznik GD, Schroeder H, Stone AC, Bustamante CD, Malaspinas AS, Ávila-Arcos MC. In-solution Y-chromosome capture-enrichment on ancient DNA libraries. BMC Genomics 2018; 19:608. [PMID: 30107783 PMCID: PMC6092841 DOI: 10.1186/s12864-018-4945-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/16/2018] [Indexed: 12/04/2022] Open
Abstract
Background As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. Results The six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1–1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12–9549 times more targeted unique Y-chromosome sequences after capture, where 0.0–6.2% (WGC + YCC) and 0.0–23.5% (YCC) of the sequence reads were on-target, compared to 0.0–0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries’ initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins. Conclusions We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round. Electronic supplementary material The online version of this article (10.1186/s12864-018-4945-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diana I Cruz-Dávalos
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - María A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, USA
| | | | | | - Hannes Schroeder
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Faculty of Archaeology, Leiden University, Leiden, Netherlands
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, USA.,Institute of Human Origins, Arizona State University, Tempe, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, Stanford, USA.,Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Anna-Sapfo Malaspinas
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico.
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11
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McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, van Driem G, Gram Wilken U, Seguin-Orlando A, de la Fuente Castro C, Wasef S, Shoocongdej R, Souksavatdy V, Sayavongkhamdy T, Saidin MM, Allentoft ME, Sato T, Malaspinas AS, Aghakhanian FA, Korneliussen T, Prohaska A, Margaryan A, de Barros Damgaard P, Kaewsutthi S, Lertrit P, Nguyen TMH, Hung HC, Minh Tran T, Nghia Truong H, Nguyen GH, Shahidan S, Wiradnyana K, Matsumae H, Shigehara N, Yoneda M, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Hanihara T, Nakagome S, Deviese T, Bacon AM, Duringer P, Ponche JL, Shackelford L, Patole-Edoumba E, Nguyen AT, Bellina-Pryce B, Galipaud JC, Kinaston R, Buckley H, Pottier C, Rasmussen S, Higham T, Foley RA, Lahr MM, Orlando L, Sikora M, Phipps ME, Oota H, Higham C, Lambert DM, Willerslev E. The prehistoric peopling of Southeast Asia. Science 2018; 361:88-92. [DOI: 10.1126/science.aat3628] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
Abstract
The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
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Affiliation(s)
- Hugh McColl
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fabrice Demeter
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- National Museum of Natural History, Ecoanthropology and Ethnobiology, Musée de l’Homme, Paris, France
| | - Takashi Gakuhari
- Center for Cultural Resource Studies, Kanazawa University, Kanazawa, Japan
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | | | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
- University of New England, Armidale, NSW, Australia
| | - Uffe Gram Wilken
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | | | - Sally Wasef
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, Thailand
| | - Viengkeo Souksavatdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Thongsa Sayavongkhamdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Mohd Mokhtar Saidin
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | - Morten E. Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Farhang A. Aghakhanian
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | | | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | | | - Supannee Kaewsutthi
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patcharee Lertrit
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thi Mai Huong Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Hsiao-chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia
| | - Thi Minh Tran
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Huu Nghia Truong
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Giang Hai Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Shaiful Shahidan
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Hiromi Matsumae
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- University Museum, University of Tokyo, Tokyo, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | | | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Thibaut Deviese
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Anne-Marie Bacon
- Laboratoire AMIS, Université Paris Descartes, Faculté de Chirurgie Dentaire, Montrouge, France
| | - Philippe Duringer
- École et Observatoire des Sciences de la Terre, Université de Strasbourg, Strasbourg, France
- Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UDS UMR 7516), Strasbourg, France
| | - Jean-Luc Ponche
- Laboratory “Image Ville et Environnement LIVE,” UMR7362, CNRS and Université de Strasbourg, Strasbourg, France
| | - Laura Shackelford
- Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | | | - Anh Tuan Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Bérénice Bellina-Pryce
- CNRS, UMR7055 “Préhistoire et Technologie,” Maison Archéologie et Ethnologie, Nanterre, France
| | - Jean-Christophe Galipaud
- Research Institute for Development, National Museum of Natural History, UMR Paloc, Paris, France
| | - Rebecca Kinaston
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hallie Buckley
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Charles Higham
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
- St. Catharine’s College, University of Cambridge, Cambridge, UK
| | - David M. Lambert
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
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12
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Wutke S, Sandoval-Castellanos E, Benecke N, Döhle HJ, Friederich S, Gonzalez J, Hofreiter M, Lõugas L, Magnell O, Malaspinas AS, Morales-Muñiz A, Orlando L, Reissmann M, Trinks A, Ludwig A. Decline of genetic diversity in ancient domestic stallions in Europe. Sci Adv 2018; 4:eaap9691. [PMID: 29675468 PMCID: PMC5906072 DOI: 10.1126/sciadv.aap9691] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/01/2018] [Indexed: 05/12/2023]
Abstract
Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.
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Affiliation(s)
- Saskia Wutke
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Department of Environmental and Biological Sciences, University of Eastern Finland, 80101 Joensuu, Finland
| | | | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, 14195 Berlin, Germany
| | - Hans-Jürgen Döhle
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt—Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt—Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Javier Gonzalez
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Michael Hofreiter
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, Rüütli 10, 10130 Tallinn, Estonia
| | - Ola Magnell
- National Historical Museums, Contract Archaeology, 226 60 Lund, Sweden
| | | | | | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
- Université de Toulouse, Université Paul Sabatier, Laboratoire Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Toulouse, France
| | - Monika Reissmann
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University Berlin, 10115 Berlin, Germany
| | - Alexandra Trinks
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Corresponding author.
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13
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Moreno-Mayar JV, Potter BA, Vinner L, Steinrücken M, Rasmussen S, Terhorst J, Kamm JA, Albrechtsen A, Malaspinas AS, Sikora M, Reuther JD, Irish JD, Malhi RS, Orlando L, Song YS, Nielsen R, Meltzer DJ, Willerslev E. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 2018; 553:203-207. [DOI: 10.1038/nature25173] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/26/2017] [Indexed: 12/30/2022]
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14
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Malaspinas AS. Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective. Mol Ecol 2015; 25:24-41. [DOI: 10.1111/mec.13492] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/08/2015] [Accepted: 11/10/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Anna-Sapfo Malaspinas
- Institute of Ecology and Evolution; University of Bern; Baltzerstrasse 6 CH-3012 Bern Switzerland
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
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15
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Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, de Barros Damgaard P, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CPE, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 2015. [PMID: 26198033 DOI: 10.1126/science.aab3884] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.
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Affiliation(s)
- Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Matthias Steinrücken
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Kelley Harris
- Department of Mathematics, University of California, Berkeley, CA 94720, USA
| | - Stephan Schiffels
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Michael DeGiorgio
- Departments of Biology and Statistics, Pennsylvania State University, 502 Wartik Laboratory, University Park, PA 16802, USA
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Cristina Valdiosera
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Integrative Systems Biology Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Julian R Homburger
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Jeff Wall
- Institute for Human Genetics, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Omar E Cornejo
- School of Biological Sciences, Washington State University, PO Box 644236, Heald 429, Pullman, Washington 99164, USA
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Tracey Pierre
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - John Lindo
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave, Urbana, IL 61801, USA
| | - Ene Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Ricardo Rodríguez-Varela
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humano, Madrid, Spain
| | - Josefina Mansilla
- Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico Mexico City, Mexico
| | - Celeste Henrickson
- University of Utah, Department of Anthropology, 270 S 1400 E, Salt Lake City, Utah 84112, USA
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Helena Malmström
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Thomas Stafford
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark
| | - Suyash S Shringarpure
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Andrés Moreno-Estrada
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA.,Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | - Monika Karmin
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Kristiina Tambets
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia
| | - Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Vera Warmuth
- UCL Genetics Institute, Gower Street, London WC1E 6BT, UK.,Evolutionsbiologiskt Centrum, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Andrew D Friend
- Department of Geography, University of Cambridge, Downing Place, Cambridge CB2 3EN, UK
| | - Joy Singarayer
- Centre for Past Climate Change and Department of Meteorology, University of Reading, Earley Gate, PO Box 243, Reading, UK
| | - Paul Valdes
- School of Geographical Sciences, University Road, Clifton, Bristol BS8 1SS, UK
| | | | - Ilán Leboreiro
- Instituto Nacional de Antropología e Historia, Moneda 13, Centro, Cuauhtémoc, 06060 Mexico Mexico City, Mexico
| | - Jose Luis Vera
- Escuela Nacional de AntropologÍa e Historia, Periférico Sur y Zapote s/n. Colonia Isidro Fabela, Tlalpan, Isidro Fabela, 14030 Mexico City, Mexico
| | | | - Davide Pettener
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Donata Luiselli
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Loren G Davis
- Department of Anthropology, Oregon State University, 238 Waldo Hall, Corvallis, OR, 97331 USA
| | - Evelyne Heyer
- Museum National d'Histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie et Ethnobiologie (UMR7206), Paris, France
| | - Christoph P E Zollikofer
- Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Marcia S Ponce de León
- Anthropological Institute and Museum, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Colin I Smith
- Department of Archaeology and History, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Vaughan Grimes
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Kelly-Anne Pike
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada
| | - Michael Deal
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada
| | - Benjamin T Fuller
- Department of Earth System Science, University of California, Irvine, Keck CCAMS Group, B321 Croul Hall, Irvine, California, 92697, USA
| | - Bernardo Arriaza
- Instituto de Alta Investigación, Universidad de Tarapacá, 18 de Septiembre 2222, Carsilla 6-D Arica, Chile
| | - Vivien Standen
- Departamento de Antropologia, Universidad de Tarapacá, 18 de Septiembre 2222. Casilla 6-D Arica, Chile
| | - Maria F Luz
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Francois Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, CNRS, Université de Toulouse, 31073 Toulouse, France
| | - Niede Guidon
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Ludmila Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
| | - Mikhail I Voevoda
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Institute of Internal Medicine, Siberian Branch of RAS, 175/1 ul. B. Bogatkova, Novosibirsk 630089, Russia.,Novosibirsk State University, Laboratory of Molecular Epidemiology and Bioinformatics, 630090 Novosibirsk, Russia
| | - Olga L Posukh
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia.,Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia.,Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia
| | | | - Yuri Bogunov
- Vavilov Institute of General Genetics, Gubkina 3, 119333 Moscow, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Zaki Validi 32, 450076 Ufa, Russia
| | - Marina Gubina
- Fundação Museu do Homem Americano, Centro Cultural Sérgio Motta, Campestre, 64770-000 Sao Raimundo Nonato, Brazil
| | - Elena Balanovska
- Research Centre for Medical Genetics, Moskvorechie 1, 115478 Moscow, Russia
| | - Sardana Fedorova
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Sergelyahskoe Shosse 4, 677010 Yakutsk, Russia.,Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, 677000 Yakutsk, Russia
| | - Sergey Litvinov
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Prospekt Oktyabrya 71, 450054 Ufa, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - M J Mosher
- Department of Anthropology, Western Washington University, Bellingham Washington 98225, USA
| | - David Archer
- Department of Anthropology, Northwest Community College, 353 Fifth Street, Prince Rupert, British Columbia V8J 3L6, Canada
| | - Jerome Cybulski
- Canadian Museum of History, 100 Rue Laurier, Gatineau, Quebec K1A 0M8, Canada.,University of Western Ontario, London, Ontario N6A 3K7, Canada.,Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Barbara Petzelt
- Metlakatla Treaty Office, PO Box 224, Prince Rupert, BC, Canada V8J 3P6
| | | | - Rosita Worl
- Sealaska Heritage Institute, 105 S. Seward Street, Juneau, Alaska 99801, USA
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, California 94305-5126, USA
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Science Building, Stanford, California 94305-5126, USA
| | - Brian M Kemp
- School of Biological Sciences, Washington State University, PO Box 644236, Heald 429, Pullman, Washington 99164, USA.,Department of Anthropology, Washington State University, Pullman Washington 99163, USA
| | - Toomas Kivisild
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Division of Biological Anthropology, University of Cambridge, Henry Wellcome Building, Fitzwilliam Street, CB2 1QH, Cambridge, UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Manjinder S Sandhu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.,Dept of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Michael Crawford
- Laboratory of Biological Anthropology, University of Kansas, 1415 Jayhawk Blvd., 622 Fraser Hall, Lawrence, Kansas 66045, USA
| | - Richard Villems
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.,Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - David Glenn Smith
- Molecular Anthropology Laboratory, 209 Young Hall, Department of Anthropology, University of California, One Shields Avenue, Davis, California 95616, USA
| | - Michael R Waters
- Center for the Study of the First Americans, Texas A&M University, College Station, Texas 77843-4352, USA.,Department of Anthropology, Texas A&M University, College Station, Texas 77843-4352, USA.,Department of Geography, Texas A&M University, College Station, Texas 77843-4352, USA
| | - Ted Goebel
- Center for the Study of the First Americans, Texas A&M University, College Station, Texas 77843-4352, USA
| | - John R Johnson
- Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave, Urbana, IL 61801, USA.,Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, USA
| | - Mattias Jakobsson
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - David J Meltzer
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.,Department of Anthropology, Southern Methodist University, Dallas, Texas 75275, USA
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Carlos D Bustamante
- Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr. Lane Bldg Room L331, Stanford, California 94305, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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16
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Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas AS, Manica A, Moltke I, Albrechtsen A, Ko A, Margaryan A, Moiseyev V, Goebel T, Westaway M, Lambert D, Khartanovich V, Wall JD, Nigst PR, Foley RA, Lahr MM, Nielsen R, Orlando L, Willerslev E. Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years. Science 2014; 346:1113-8. [PMID: 25378462 DOI: 10.1126/science.aaa0114] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal'ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.
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Affiliation(s)
- Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Ida Moltke
- Department of Human Genetics, University of Chicago, 920 East 58th Street, Cummings Life Science Center, Chicago, IL 60637, USA. The Bioinformatics Center, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark
| | - Anders Albrechtsen
- The Bioinformatics Center, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark
| | - Amy Ko
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Nathan, Brisbane, Queensland 4111, Australia
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Vyacheslav Moiseyev
- Department of Physical Anthropology, Kunstkamera, Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, 24 Srednii Prospect, Vassilievskii Island, St. Petersburg, Russia
| | - Ted Goebel
- Center for the Study of the First Americans and Department of Anthropology, Texas A&M University, TAMU-4352, College Station, Texas 77845-4352, USA
| | - Michael Westaway
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Nathan, Brisbane, Queensland 4111, Australia
| | - David Lambert
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Nathan, Brisbane, Queensland 4111, Australia
| | - Valeri Khartanovich
- Department of Physical Anthropology, Kunstkamera, Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, 24 Srednii Prospect, Vassilievskii Island, St. Petersburg, Russia
| | - Jeffrey D Wall
- Department of Epidemiology and Biostatistics, University of California San Francisco, 185 Berry Street, Lobby 5, Suite 5700, San Francisco, CA 94107, USA
| | - Philip R Nigst
- Division of Archaeology, University of Cambridge, Cambridge, Downing Street, CB2 3DZ, UK. Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Robert A Foley
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, Fitzwilliam Street, CB2 1QH, UK
| | - Marta Mirazon Lahr
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, Fitzwilliam Street, CB2 1QH, UK.
| | - Rasmus Nielsen
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Nathan, Brisbane, Queensland 4111, Australia.
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
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17
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Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Sagredo FS, Rasmussen S, Gonçalves VF, Albrechtsen A, Allentoft ME, Johnson PLF, Li M, Reis S, Bernardo DV, DeGiorgio M, Duggan AT, Bastos M, Wang Y, Stenderup J, Moreno-Mayar JV, Brunak S, Sicheritz-Ponten T, Hodges E, Hannon GJ, Orlando L, Price TD, Jensen JD, Nielsen R, Heinemeier J, Olsen J, Rodrigues-Carvalho C, Lahr MM, Neves WA, Kayser M, Higham T, Stoneking M, Pena SDJ, Willerslev E. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Curr Biol 2014; 24:R1035-7. [PMID: 25455029 PMCID: PMC4370112 DOI: 10.1016/j.cub.2014.09.078] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Understanding the peopling of the Americas remains an important and challenging question. Here, we present (14)C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as 'Botocudos'. We find that their genomic ancestry is Polynesian, with no detectable Native American component. Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century. Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport.
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Affiliation(s)
- Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Oscar Lao
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; Faculty of Archaeology, Leiden University, PO Box 9515, 2300 Leiden, The Netherlands
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Ida Moltke
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, Copenhagen 2200, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Francisca Santana Sagredo
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, South Parks Road, Dyson Perrins Building, Oxford University, OX1 3QY, UK
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby, DK-2800, Denmark
| | - Vanessa F Gonçalves
- Centre for Addiction and Mental Health, Toronto, Canada, Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, Copenhagen 2200, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Philip L F Johnson
- Department of Biology, Emory University, 1510 Clifton Rd NE, Rm 2006, Atlanta, GA 30322
| | - Mingkun Li
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Silvia Reis
- Setor de Antropologia Biológica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Danilo V Bernardo
- Instituto de Ciências Humanas e da Informação - ICHI, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, Pennsylvania 16802, USA
| | - Ana T Duggan
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Murilo Bastos
- Setor de Antropologia Biológica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yong Wang
- Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140; Ancestry.com DNA LLC, San Francisco, CA 94107, USA
| | - Jesper Stenderup
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - J Victor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby, DK-2800, Denmark
| | - Thomas Sicheritz-Ponten
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, Kgs. Lyngby, DK-2800, Denmark
| | - Emily Hodges
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA, Howard Hughes Medical Institute
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA, Howard Hughes Medical Institute
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - T Douglas Price
- Department of Anthropology 5240 W.H. Sewell Social Science Building 1180 Observatory Dr. University of Wisconsin Madison, WI 53706, USA
| | - Jeffrey D Jensen
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Station 15, CH-1015 Lausanne, Switzerland
| | - Rasmus Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140
| | - Jan Heinemeier
- AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - Jesper Olsen
- AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - Claudia Rodrigues-Carvalho
- Setor de Antropologia Biológica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marta Mirazón Lahr
- LCHES, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam St, Cambridge CB2 1QH, UK
| | - Walter A Neves
- Laboratory for Human Evolutionary Studies, Department of Genetics and Evolutionary Biology, Institute of Bioscience, University of São Paulo, Brazil
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, South Parks Road, Dyson Perrins Building, Oxford University, OX1 3QY, UK
| | - Mark Stoneking
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Deutscher Platz 6, D-04103 Leipzig, Germany.
| | - Sergio D J Pena
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil.
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.
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18
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Moreno-Mayar JV, Rasmussen S, Seguin-Orlando A, Rasmussen M, Liang M, Flåm ST, Lie BA, Gilfillan GD, Nielsen R, Thorsby E, Willerslev E, Malaspinas AS. Genome-wide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans. Curr Biol 2014; 24:2518-25. [PMID: 25447991 DOI: 10.1016/j.cub.2014.09.057] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 08/29/2014] [Accepted: 09/22/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND Rapa Nui (Easter Island), located in the easternmost corner of the Polynesian Triangle, is one of the most isolated locations on the planet inhabited by humans. Archaeological and genetic evidence suggests that the island was first colonized by Polynesians around AD 1200, during their eastward expansion. Although it remains contentious whether Polynesians reached South America, suggestive evidence has been brought forward supporting the possibility of Native American contact prior to the European "discovery" of the island in AD 1722. RESULTS We generated genome-wide data for 27 Rapanui. We found a mostly Polynesian ancestry among Rapanui and detected genome-wide patterns consistent with Native American and European admixture. By considering the distribution of local ancestry tracts of eight unrelated Rapanui, we found statistical support for Native American admixture dating to AD 1280-1495 and European admixture dating to AD 1850-1895. CONCLUSIONS These genetic results can be explained by one or more pre-European trans-Pacific contacts.
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Affiliation(s)
- J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, 1350 Copenhagen K, Denmark
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet 208, 2800 Kongens Lyngby, Denmark
| | | | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, 1350 Copenhagen K, Denmark; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mason Liang
- Center for Theoretical Evolutionary Genomics, Department of Integrative Biology and Department of Statistics, University of California, Berkeley, Berkeley, CA 94720-3140, USA
| | - Siri Tennebø Flåm
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0424 Oslo, Norway
| | - Benedicte Alexandra Lie
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0424 Oslo, Norway
| | - Gregor Duncan Gilfillan
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0424 Oslo, Norway
| | - Rasmus Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, 1350 Copenhagen K, Denmark; Center for Theoretical Evolutionary Genomics, Department of Integrative Biology and Department of Statistics, University of California, Berkeley, Berkeley, CA 94720-3140, USA
| | - Erik Thorsby
- Department of Immunology, University of Oslo and Oslo University Hospital, 0424 Oslo, Norway
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, 1350 Copenhagen K, Denmark.
| | - Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, 1350 Copenhagen K, Denmark.
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19
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Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P, Korneliussen TS, Grønnow B, Appelt M, Gulløv HC, Friesen TM, Fitzhugh W, Malmström H, Rasmussen S, Olsen J, Melchior L, Fuller BT, Fahrni SM, Stafford T, Grimes V, Renouf MAP, Cybulski J, Lynnerup N, Lahr MM, Britton K, Knecht R, Arneborg J, Metspalu M, Cornejo OE, Malaspinas AS, Wang Y, Rasmussen M, Raghavan V, Hansen TVO, Khusnutdinova E, Pierre T, Dneprovsky K, Andreasen C, Lange H, Hayes MG, Coltrain J, Spitsyn VA, Götherström A, Orlando L, Kivisild T, Villems R, Crawford MH, Nielsen FC, Dissing J, Heinemeier J, Meldgaard M, Bustamante C, O'Rourke DH, Jakobsson M, Gilbert MTP, Nielsen R, Willerslev E. The genetic prehistory of the New World Arctic. Science 2014; 345:1255832. [PMID: 25170159 DOI: 10.1126/science.1255832] [Citation(s) in RCA: 228] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.
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Affiliation(s)
- Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, 502 Wartik Laboratory, University Park, PA 16802, USA
| | - Anders Albrechtsen
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Ida Moltke
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark. Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Pontus Skoglund
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thorfinn S Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Bjarne Grønnow
- Arctic Centre at the Ethnographic Collections (SILA), National Museum of Denmark, Frederiksholms Kanal 12, 1220 Copenhagen, Denmark
| | - Martin Appelt
- Arctic Centre at the Ethnographic Collections (SILA), National Museum of Denmark, Frederiksholms Kanal 12, 1220 Copenhagen, Denmark
| | - Hans Christian Gulløv
- Arctic Centre at the Ethnographic Collections (SILA), National Museum of Denmark, Frederiksholms Kanal 12, 1220 Copenhagen, Denmark
| | - T Max Friesen
- Department of Anthropology, University of Toronto, Toronto, Ontario M5S 2S2, Canada
| | - William Fitzhugh
- Arctic Studies Center, Post Office Box 37012, Department of Anthropology, MRC 112, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Helena Malmström
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jesper Olsen
- AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Linea Melchior
- Anthropological Laboratory, Institute of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Frederik V's Vej 11, 2100 Copenhagen, Denmark
| | - Benjamin T Fuller
- Department of Earth System Science, University of California, Irvine, CA 92697, USA
| | - Simon M Fahrni
- Department of Earth System Science, University of California, Irvine, CA 92697, USA
| | - Thomas Stafford
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Vaughan Grimes
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - M A Priscilla Renouf
- Department of Archaeology, Memorial University, Queen's College, 210 Prince Philip Drive, St. John's, Newfoundland, A1C 5S7, Canada
| | - Jerome Cybulski
- Canadian Museum of History, 100 Rue Laurier, Gatineau, Quebec K1A 0M8, Canada. Department of Anthropology, University of Western Ontario, 1151 Richmond Street North, London N6A 5C2, Canada
| | - Niels Lynnerup
- Anthropological Laboratory, Institute of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Frederik V's Vej 11, 2100 Copenhagen, Denmark
| | - Marta Mirazon Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Kate Britton
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany. Department of Archaeology, University of Aberdeen, St. Mary's Building, Elphinstone Road, Aberdeen AB24 3UF, Scotland, UK
| | - Rick Knecht
- Department of Archaeology, University of Aberdeen, St. Mary's Building, Elphinstone Road, Aberdeen AB24 3UF, Scotland, UK
| | - Jette Arneborg
- National Museum of Denmark, Frederiksholms kanal 12, 1220 Copenhagen, Denmark. School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Mait Metspalu
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Omar E Cornejo
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA. School of Biological Sciences, Washington State University, Post Office Box 644236, Pullman, WA 99164, USA
| | - Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Yong Wang
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. Ancestry.com DNA LLC, San Francisco, CA 94107, USA
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Vibha Raghavan
- Informatics and Bio-computing, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, M5G 0A3, Canada
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Bashkortostan 450074, Russia
| | - Tracey Pierre
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Kirill Dneprovsky
- State Museum for Oriental Art, 12a, Nikitsky Boulevard, Moscow 119019, Russia
| | - Claus Andreasen
- Greenland National Museum and Archives, Post Office Box 145, 3900 Nuuk, Greenland
| | - Hans Lange
- Greenland National Museum and Archives, Post Office Box 145, 3900 Nuuk, Greenland
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA. Department of Anthropology, Weinberg College of Arts and Sciences, Northwestern University, Evanston, IL 60208, USA. Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joan Coltrain
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA
| | - Victor A Spitsyn
- Research Centre for Medical Genetics of Russian Academy of Medical Sciences, 1 Moskvorechie, Moscow 115478, Russia
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Toomas Kivisild
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Richard Villems
- Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Michael H Crawford
- Laboratory of Biological Anthropology, University of Kansas, Lawrence, KS 66045, USA
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Jørgen Dissing
- Anthropological Laboratory, Institute of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Frederik V's Vej 11, 2100 Copenhagen, Denmark
| | - Jan Heinemeier
- AMS 14C Dating Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Morten Meldgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Carlos Bustamante
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Dennis H O'Rourke
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
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20
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Malaspinas AS, Tange O, Moreno-Mayar JV, Rasmussen M, DeGiorgio M, Wang Y, Valdiosera CE, Politis G, Willerslev E, Nielsen R. bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS). ACTA ACUST UNITED AC 2014; 30:2962-4. [PMID: 24974206 PMCID: PMC4184259 DOI: 10.1093/bioinformatics/btu410] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Summary: We present bammds, a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of individuals (usually genotypes) using a multidimensional scaling algorithm. Our tool is aimed at determining the ancestry of unknown samples—typical of ancient DNA data—particularly when only low amounts of data are available for those samples. Availability and implementation: The software package is available under GNU General Public License v3 and is freely available together with test datasets https://savannah.nongnu.org/projects/bammds/. It is using R (http://www.r-project.org/), parallel (http://www.gnu.org/software/parallel/), samtools (https://github.com/samtools/samtools). Contact:bammds-users@nongnu.org Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
| | - Ole Tange
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
| | - José Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
| | - Michael DeGiorgio
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
| | - Yong Wang
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
| | - Cristina E Valdiosera
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
| | - Gustavo Politis
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
| | - Rasmus Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, Department of Biology, Pennsylvania State University, Wartik Laboratory, University Park, PA 16802, Centre for Theoretical Evolutionary Genomics, Departments of Integrative Biology and Statistics, University of California, Berkeley, CA 94720-3140, Ancestry.com DNA LLC, San Francisco, CA 94107, Department of Archaeology, Environment and Community Planning Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia, INCUAPA-CONICET, Universidad del Centro de la Provincia de Buenos Aires, 7600 Olavarría, Argentina and Facultad de Ciencias Naturales y Museo de La Plata, 1900 La Plata, Argentina
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21
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Foll M, Poh YP, Renzette N, Ferrer-Admetlla A, Bank C, Shim H, Malaspinas AS, Ewing G, Liu P, Wegmann D, Caffrey DR, Zeldovich KB, Bolon DN, Wang JP, Kowalik TF, Schiffer CA, Finberg RW, Jensen JD. Influenza virus drug resistance: a time-sampled population genetics perspective. PLoS Genet 2014; 10:e1004185. [PMID: 24586206 PMCID: PMC3937227 DOI: 10.1371/journal.pgen.1004185] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 01/06/2014] [Indexed: 01/01/2023] Open
Abstract
The challenge of distinguishing genetic drift from selection remains a central focus of population genetics. Time-sampled data may provide a powerful tool for distinguishing these processes, and we here propose approximate Bayesian, maximum likelihood, and analytical methods for the inference of demography and selection from time course data. Utilizing these novel statistical and computational tools, we evaluate whole-genome datasets of an influenza A H1N1 strain in the presence and absence of oseltamivir (an inhibitor of neuraminidase) collected at thirteen time points. Results reveal a striking consistency amongst the three estimation procedures developed, showing strongly increased selection pressure in the presence of drug treatment. Importantly, these approaches re-identify the known oseltamivir resistance site, successfully validating the approaches used. Enticingly, a number of previously unknown variants have also been identified as being positively selected. Results are interpreted in the light of Fisher's Geometric Model, allowing for a quantification of the increased distance to optimum exerted by the presence of drug, and theoretical predictions regarding the distribution of beneficial fitness effects of contending mutations are empirically tested. Further, given the fit to expectations of the Geometric Model, results suggest the ability to predict certain aspects of viral evolution in response to changing host environments and novel selective pressures.
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Affiliation(s)
- Matthieu Foll
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yu-Ping Poh
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Nicholas Renzette
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Anna Ferrer-Admetlla
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Department of Biology and Biochemistry, University of Fribourg, Fribourg, Switzerland
| | - Claudia Bank
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Hyunjin Shim
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Anna-Sapfo Malaspinas
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Gregory Ewing
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Ping Liu
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Daniel Wegmann
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- Department of Biology and Biochemistry, University of Fribourg, Fribourg, Switzerland
| | - Daniel R. Caffrey
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Konstantin B. Zeldovich
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Daniel N. Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jennifer P. Wang
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Timothy F. Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robert W. Finberg
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jeffrey D. Jensen
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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22
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Yang MA, Malaspinas AS, Durand EY, Slatkin M. Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity. Mol Biol Evol 2012; 29:2987-95. [PMID: 22513287 DOI: 10.1093/molbev/mss117] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Neanderthals have been shown to share more genetic variants with present-day non-Africans than Africans. Recent admixture between Neanderthals and modern humans outside of Africa was proposed as the most parsimonious explanation for this observation. However, the hypothesis of ancient population structure within Africa could not be ruled out as an alternative explanation. We use simulations to test whether the site frequency spectrum, conditioned on a derived Neanderthal and an ancestral Yoruba (African) nucleotide (the doubly conditioned site frequency spectrum [dcfs]), can distinguish between models that assume recent admixture or ancient population structure. We compare the simulations to the dcfs calculated from data taken from populations of European, Chinese, and Japanese descent in the Complete Genomics Diversity Panel. Simulations under a variety of plausible demographic parameters were used to examine the shape of the dcfs for both models. The observed shape of the dcfs cannot be explained by any set of parameter values used in the simulations of the ancient structure model. The dcfs simulations for the recent admixture model provide a good fit to the observed dcfs for non-Africans, thereby supporting the hypothesis that recent admixture with Neanderthals accounts for the greater similarity of Neanderthals to non-Africans than Africans.
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Affiliation(s)
- Melinda A Yang
- Department of Integrative Biology, University of California, Berkeley.
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Abstract
Rapid research progress in genotyping techniques have allowed large genome-wide associationstudies. Existing methods often focus on determining associations between single loci anda specic phenotype. However, a particular phenotype is usually the result of complex relationshipsbetween multiple loci and the environment. In this paper, we describe a two-stage methodfor detecting epistasis by combining the traditionally used single-locus search with a search formultiway interactions. Our method is based on an extended version of Fisher's exact test. Toperform this test, a Markov chain is constructed on the space of multidimensional contingencytables using the elements of a Markov basis as moves. We test our method on simulated data andcompare it to a two-stage logistic regression method and to a fully Bayesian method, showing thatwe are able to detect the interacting loci when other methods fail to do so. Finally, we apply ourmethod to a genome-wide data set consisting of 685 dogs and identify epistasis associated withcanine hair length for four pairs of single nucleotide polymorphisms (SNPs).
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24
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Malaspinas AS, Slatkin M, Song YS. Match probabilities in a finite, subdivided population. Theor Popul Biol 2011; 79:55-63. [PMID: 21266180 DOI: 10.1016/j.tpb.2011.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 01/12/2011] [Accepted: 01/18/2011] [Indexed: 10/18/2022]
Abstract
We generalize a recently introduced graphical framework to compute the probability that haplotypes or genotypes of two individuals drawn from a finite, subdivided population match. As in the previous work, we assume an infinite-alleles model. We focus on the case of a population divided into two subpopulations, but the underlying framework can be applied to a general model of population subdivision. We examine the effect of population subdivision on the match probabilities and the accuracy of the product rule which approximates multi-locus match probabilities as a product of one-locus match probabilities. We quantify the deviation from predictions of the product rule by R, the ratio of the multi-locus match probability to the product of the one-locus match probabilities. We carry out the computation for two loci and find that ignoring subdivision can lead to underestimation of the match probabilities if the population under consideration actually has subdivision structure and the individuals originate from the same subpopulation. On the other hand, under a given model of population subdivision, we find that the ratio R for two loci is only slightly greater than 1 for a large range of symmetric and asymmetric migration rates. Keeping in mind that the infinite-alleles model is not the appropriate mutation model for STR loci, we conclude that, for two loci and biologically reasonable parameter values, population subdivision may lead to results that disfavor innocent suspects because of an increase in identity-by-descent in finite populations. On the other hand, for the same range of parameters, population subdivision does not lead to a substantial increase in linkage disequilibrium between loci. Those results are consistent with established practice.
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Affiliation(s)
- Anna-Sapfo Malaspinas
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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25
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Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MHY, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome. Science 2010; 328:710-722. [PMID: 20448178 PMCID: PMC5100745 DOI: 10.1126/science.1188021] [Citation(s) in RCA: 2079] [Impact Index Per Article: 148.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
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Affiliation(s)
- Richard E. Green
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Johannes Krause
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Adrian W. Briggs
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Udo Stenzel
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Martin Kircher
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heng Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Weiwei Zhai
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Markus Hsi-Yang Fritz
- European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Nancy F. Hansen
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric Y. Durand
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Anna-Sapfo Malaspinas
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey D. Jensen
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Tomas Marques-Bonet
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Institute of Evolutionary Biology (UPF-CSIC), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Can Alkan
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Hernán A. Burbano
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Jeffrey M. Good
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Rigo Schultz
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Anne Butthof
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Barbara Höber
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Barbara Höffner
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Madlen Siegemund
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S. Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carsten Russ
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathaniel Novod
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Christine Verna
- Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Pavao Rudan
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | - Dejana Brajkovic
- Croatian Academy of Sciences and Arts, Institute for Quaternary Paleontology and Geology, Ante Kovacica 5, HR-10000 Zagreb, Croatia
| | - Željko Kucan
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | - Ivan Gušic
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | | | | | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marco de la Rasilla
- Área de Prehistoria Departamento de Historia Universidad de Oviedo, Oviedo, Spain
| | - Javier Fortea
- Área de Prehistoria Departamento de Historia Universidad de Oviedo, Oviedo, Spain
| | - Antonio Rosas
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Ralf W. Schmitz
- Der Landschaftverband Rheinlund–Landesmuseum Bonn, Bachstrasse 5-9, D-53115 Bonn, Germany
- Abteilung für Vor- und Frühgeschichtliche Archäologie, Universität Bonn, Germany
| | | | - Evan E. Eichler
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daniel Falush
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Ewan Birney
- European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - James C. Mullikin
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Michael Lachmann
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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26
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Ludwig A, Pruvost M, Reissmann M, Benecke N, Brockmann GA, Castaños P, Cieslak M, Lippold S, Llorente L, Malaspinas AS, Slatkin M, Hofreiter M. Coat color variation at the beginning of horse domestication. Science 2009; 324:485. [PMID: 19390039 DOI: 10.1126/science.1172750] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The transformation of wild animals into domestic ones available for human nutrition was a key prerequisite for modern human societies. However, no other domestic species has had such a substantial impact on the warfare, transportation, and communication capabilities of human societies as the horse. Here, we show that the analysis of ancient DNA targeting nuclear genes responsible for coat coloration allows us to shed light on the timing and place of horse domestication. We conclude that it is unlikely that horse domestication substantially predates the occurrence of coat color variation, which was found to begin around the third millennium before the common era.
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Affiliation(s)
- Arne Ludwig
- Leibniz Institute for Zoo and Wildlife Research, 10252 Berlin, Germany.
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27
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Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PLF, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković D, Kućan Z, Gusić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 2008; 134:416-26. [PMID: 18692465 DOI: 10.1016/j.cell.2008.06.021] [Citation(s) in RCA: 303] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 05/29/2008] [Accepted: 06/13/2008] [Indexed: 10/21/2022]
Abstract
A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from approximately 0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 +/- 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.
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Affiliation(s)
- Richard E Green
- Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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28
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Krause J, Unger T, Noçon A, Malaspinas AS, Kolokotronis SO, Stiller M, Soibelzon L, Spriggs H, Dear PH, Briggs AW, Bray SCE, O'Brien SJ, Rabeder G, Matheus P, Cooper A, Slatkin M, Pääbo S, Hofreiter M. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol 2008; 8:220. [PMID: 18662376 PMCID: PMC2518930 DOI: 10.1186/1471-2148-8-220] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 07/28/2008] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods. RESULTS We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal position within the genus Ursus. The sun bear is the sister taxon to both the American and Asian black bears, and this clade is the sister clade of cave bear, brown bear and polar bear confirming a recent study on bear mitochondrial genomes. CONCLUSION Sequences from extinct bears represent the third and fourth Pleistocene species for which complete mitochondrial genomes have been sequenced. Moreover, the cave bear specimen demonstrates that mitogenomic studies can be applied to Pleistocene fossils that have not been preserved in permafrost, and therefore have a broad application within ancient DNA research. Molecular dating of the mtDNA divergence times suggests a rapid radiation of bears in both the Old and New Worlds around 5 million years ago, at the Miocene-Pliocene boundary. This coincides with major global changes, such as the Messinian crisis and the first opening of the Bering Strait, and suggests a global influence of such events on species radiations.
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Affiliation(s)
- Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Tina Unger
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Aline Noçon
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Anna-Sapfo Malaspinas
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Sergios-Orestis Kolokotronis
- Department of Ecology, Evolution and Environmental Biology, Columbia University, 1200 Amsterdam Avenue, MC5557, New York, NY 10027, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Mathias Stiller
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Leopoldo Soibelzon
- Departamento Científico Paleontologia de Vertebrados, Museo de La Plata. Paseo del Bosque, (1900) La Plata, Buenos Aires, Argentina
| | - Helen Spriggs
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
| | - Paul H Dear
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
| | - Adrian W Briggs
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Sarah CE Bray
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Gernot Rabeder
- Department of Paleontology, University of Vienna, 1090 Vienna, Austria
| | - Paul Matheus
- Alaska Quaternary Center, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Michael Hofreiter
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
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29
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Rohland N, Malaspinas AS, Pollack JL, Slatkin M, Matheus P, Hofreiter M. Proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup. PLoS Biol 2007; 5:e207. [PMID: 17676977 PMCID: PMC1925134 DOI: 10.1371/journal.pbio.0050207] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 05/24/2007] [Indexed: 11/29/2022] Open
Abstract
We have sequenced the complete mitochondrial genome of the extinct American mastodon (Mammut americanum) from an Alaskan fossil that is between 50,000 and 130,000 y old, extending the age range of genomic analyses by almost a complete glacial cycle. The sequence we obtained is substantially different from previously reported partial mastodon mitochondrial DNA sequences. By comparing those partial sequences to other proboscidean sequences, we conclude that we have obtained the first sequence of mastodon DNA ever reported. Using the sequence of the mastodon, which diverged 24-28 million years ago (mya) from the Elephantidae lineage, as an outgroup, we infer that the ancestors of African elephants diverged from the lineage leading to mammoths and Asian elephants approximately 7.6 mya and that mammoths and Asian elephants diverged approximately 6.7 mya. We also conclude that the nuclear genomes of the African savannah and forest elephants diverged approximately 4.0 mya, supporting the view that these two groups represent different species. Finally, we found the mitochondrial mutation rate of proboscideans to be roughly half of the rate in primates during at least the last 24 million years.
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Affiliation(s)
- Nadin Rohland
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna-Sapfo Malaspinas
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
- Department of Zoology and Animal Biology, University of Geneva, Geneva, Switzerland
| | - Joshua L Pollack
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Paul Matheus
- Alaska Quaternary Center, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Michael Hofreiter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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