Ancient nuclear genomes enable repatriation of Indigenous human remains

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Abstract

Ancient DNA facilitates the return of remains to Indigenous tribal groups, resolving a long-standing concern.

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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Most cited references 45

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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.

Heng Li (2011)

Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty. We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors. http://samtools.sourceforge.net. hengli@broadinstitute.org.

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Ancient human genomes suggest three ancestral populations for present-day Europeans

Iosif Lazaridis, Nick Patterson, Nick Patterson … (2015)

We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.

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Genomic insights into the origin of farming in the ancient Near East

Iosif Lazaridis, Dani Nadel, Gary Rollefson … (2016)

We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

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Author and article information

Journal

Journal ID (nlm-ta): Sci Adv

Journal ID (iso-abbrev): Sci Adv

Journal ID (publisher-id): SciAdv

Journal ID (hwp): advances

Title: Science Advances

Publisher: American Association for the Advancement of Science

ISSN (Electronic): 2375-2548

Publication date Collection: December 2018

Publication date (Electronic): 19 December 2018

Volume: 4

Issue: 12

Electronic Location Identifier: eaau5064

Affiliations

[1 ]Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia.

[2 ]Global Health Institute, Epidemiology and Social Medicine, University of Antwerp, Belgium.

[3 ]DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.

[4 ]Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia.

[5 ]Gimuy Yidniji Elder, Cairns, QLD, Australia.

[6 ]Barkandji/Paakantyi Elder, Red Cliffs, VIC, Australia.

[7 ]Barkandji/Paakantyi Elder, Pooncarie, NSW, Australia.

[8 ]Ngiyampaa Elder, Ivanhoe, NSW, Australia.

[9 ]Ngiyampaa Elder, Hay, NSW, Australia.

[10 ]Mutthi Mutthi Elder, Balranald, NSW, Australia.

[11 ]Mutthi Mutthi Elder, Broken Hill, NSW, Australia.

[12 ]Thanynakwith Elder, Napranum, QLD, Australia.

[13 ]Barkandji/Paakantyi Elder, Mildura, VIC, Australia.

[14 ]Barapa Barapa Nation, Barham, NSW, Australia.

[15 ]School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.

[16 ]School of Biological Sciences, University of Sydney, Sydney, NSW, Australia.

[17 ]Springbrook, QLD, Australia.

[18 ]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.

[19 ]Novogene Bioinformatics Institute, Beijing, China.

[20 ]School of Biological Sciences, University of Auckland, Auckland, New Zealand.

[21 ]GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia.

[22 ]Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

[23 ]Department of Zoology, University of Cambridge, Cambridge, UK.

[24 ]Wellcome Trust Sanger Institute, Hinxton, UK.

[25 ]Department of Computational Biology, University of Lausanne, Switzerland.

[26 ]SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Author notes

[*]

Deceased.

[†]

These authors contributed equally to this work.

[‡ ]Corresponding author. Email: martin.sikora@ 123456snm.ku.dk (M.S.); d.lambert@ 123456griffith.edu.au (D.M.L.)

Author information

Joanne L. Wright http://orcid.org/0000-0002-2829-6400

Sally Wasef http://orcid.org/0000-0002-7207-7395

Tim H. Heupink http://orcid.org/0000-0001-6237-3898

Simon Rasmussen http://orcid.org/0000-0001-6323-9041

Colin Pardoe http://orcid.org/0000-0002-6288-6375

Darren Curnoe http://orcid.org/0000-0001-8622-4141

Ruiqiang Li http://orcid.org/0000-0003-4760-1535

Craig Millar http://orcid.org/0000-0002-1918-8248

Sankar Subramanian http://orcid.org/0000-0002-2375-3254

Eske Willerslev http://orcid.org/0000-0002-7081-6748

Martin Sikora http://orcid.org/0000-0003-2818-8319

David M. Lambert http://orcid.org/0000-0002-5821-3637

Article

Publisher ID: aau5064

DOI: 10.1126/sciadv.aau5064

PMC ID: 6300400

PubMed ID: 30585290

SO-VID: 2aeca163-8058-450e-befe-bb632c7c7c72

Copyright © Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

License:

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