Cited by 98Forensic and Genetic ResearchGenetic diversity and population structureForensic Anthropology and Bioarchaeology Studies

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

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Malaspinas, Anna-Sapfo, Lao, Oscar, Schroeder, Hannes, Rasmussen, Morten, Raghavan, Maanasa, Moltke, Ida, Campos, Paula F., Sagredo, Francisca Santana +32 more·2014·Current Biology

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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Written from the paper’s full text.

TL;DR

Two ancient Botocudo skulls from Minas Gerais, Brazil, yielded whole-genome data showing Polynesian ancestry with no detectable Native American component. Radiocarbon dates place them before the 19th century, leaving Polynesian voyaging or European-mediated transport as possible explanations.

Key findings

  • Only Bot15 and Bot17 had >1% endogenous human DNA (5.6% and 12.5%, respectively); whole-genome shotgun sequencing reached average depths of 1.2X and 1.5X. Genetic analyses placed both within Polynesian populations, and at K = 7 more than 99.9% of their genomes were assigned to the Polynesian cluster, with no detectable Native American ancestry.
  • AMS radiocarbon dating of five teeth from four Botocudo individuals gave Southern Hemisphere-calibrated 95% HPDs of 1452–1510 AD and 1579–1620 AD for Bot15 (bimodal), and 1419–1477 AD for Bot17. Marine-corrected, described as highly conservative, 95% HPDs were 1479–1708 AD and 1730–1804 AD for Bot15, and 1496–1842 AD for Bot17.
  • The Peru–Polynesia slave trade was excluded because the calibrated dates predate 1862–1864 AD. The Madagascar–Brazil slave trade was excluded because Malagasy ancestors admixed with African populations prior to the slave trade, no such ancestry was detected in the Botocudo sample, and Madagascar was peopled by Southeast Asian rather than Polynesian populations.
  • European ship trade after 1760 AD was considered unlikely because Bot15 and Bot17 were already deceased by 1760 with probabilities of 0.92 and 0.81, respectively, but the authors state they cannot exclude this scenario; Polynesian voyaging also cannot be excluded.

Methods

  • Archival review at the Museu Nacional in Rio de Janeiro selected four Botocudo crania (Bot13, Bot15, Bot17, Bot65), corroborated by labels on the skulls.
  • DNA screening by shotgun sequencing of the four individuals was followed by whole-genome sequencing for Bot15 and Bot17, mtDNA capture for Bot15, and SNP capture for 6,000 ancestry informative markers for Bot15. Analyses included multidimensional scaling on identity-by-state distances and clustering analyses.
  • AMS radiocarbon dating of five teeth from the four individuals was performed in two independent laboratories and calibrated with the Southern Hemisphere curve; δ13C, δ15N and δ34S values were compared with Brazilian fauna and flora and archaeological and modern human bone samples, with strontium analysis and craniometry detailed in the Supplemental information.

Limitations

  • Stated: there is a general lack of baseline isotope data for the relevant areas and archaeological remains; a marine reservoir effect cannot be fully excluded, so the marine-corrected age estimates must be considered highly conservative, and more work on foodwebs and carbon cycling in Minas Gerais is needed.
  • Stated: the European-mediated transport scenario cannot be excluded, and the Polynesian expansion scenario cannot be excluded; the authors also note it is hard to explain why the first possible genomic evidence of Polynesian contact with South America would be found in Brazil rather than on the west coast, and they call for further sampling.
  • Evident from the text: only two of the four screened individuals yielded sufficient endogenous DNA, so the genomic conclusions rest on two genomes, and the dating intervals are broad and depend on whether a marine correction is applied.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/j.cub.2014.09.078

Cites

8 of 8 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 14 cited sources checked · 0 supported · 0 flagged

  • Findingown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Only Bot15 and Bot17 yielded endogenous human DNA content higher than 1% (5.6% and 12.5%, respectively).

    “We performed an initial DNA screening by shotgun sequencing the four individuals, finding that only Bot15 and Bot17 yielded a endogenous human DNA content higher than 1% (5.6% and 12.5%, respectively), thus allowing for whole genome sequencing (Supplemental information).”
    Quote in the paperSubstantial claim
  • Findingown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    The two Botocudo individuals (Bot15 and Bot17) died prior to the beginning of the 19th century.

    “Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century.”
    Quote in the paperSubstantial claim
  • Findingown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    In MDS analysis of IBS distances, the ancient Botocudo genomes fall within Polynesian populations.

    “when conducting a classical multidimensional scaling (MDS) analysis on identity-by-state (IBS) distance-of-genotype data of worldwide populations, including the Botocudo whole genome data, we found that the ancient genomes fall within the Polynesian populations (Figure 1C).”
    Quote in the paperSubstantial claim
  • Findingown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    No African ancestry (such as that from Malagasy ancestors) was detected in the Botocudo sample.

    “no such ancestry is detected in our Botocudo sample”
    Quote in the paperSubstantial claim
  • Study design and conductown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    The four Botocudo individuals analyzed were confirmed as bona fide Botocudo by archival study and skull labels.

    “We confined our analyses to four Botocudo individuals (Bot13, Bot15, Bot17 and Bot65; Supplemental information) after careful review of all available records at the Museu Nacional in Rio de Janeiro, Brazil, including an extensive archival study that pointed to the four crania being bona fide Botocudo, a designation which is also corroborated by the labels on the skulls (Figure 1A).”
    Quote in the paperSubstantial claim
  • May combine two claims. 12
  • Classified as probably not a substantial claim. 8
  • May combine two claims.

    Findingown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    The 95% HPDs of the marine-corrected dates are 1479-1708 AD and 1730-1804 AD for Bot15, and 1496-1842 AD for Bot17.

    “The 95% HPDs of the marine corrected dates are 1479–1708 AD and 1730–1804 AD for Bot15, and 1496–1842 AD for Bot17 (Figure 1B).”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Two Botocudo individuals (Bot15 and Bot17) have Polynesian ancestry for both mitochondrial and nuclear genomes, with no detectable Native American component.

    “We find that their genomic ancestry is Polynesian, with no detectable Native American component.”
    • Also stated in: § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil · boosted
      “All the genetic data point towards two individuals with Polynesian ancestry and no detectable Native American ancestry.”
    • Also stated in: § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil · plain
      “our result that two Botocudo individuals have Polynesian ancestry for both the mitochondrial and nuclear genomes [1]”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Bot15 and Bot17 were already deceased by 1760 AD with probabilities 0.92 and 0.81, respectively.

    “By 1760 AD, Bot15 and Bot17 were already deceased with a probability of 0.92 and 0.81, respectively (Supplemental information)”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Calibrated 14C dates for Bot15 are 1452-1510 AD and 1579-1620 AD (bimodal), and for Bot17 1419-1477 AD.

    “When calibrating the 14C dates with the Southern Hemisphere curve [3], the 95% highest posterior density regions (HPD) were 1452–1510 AD and 1579–1620 AD for Bot15 (bimodal distribution), and 1419–1477AD for Bot17.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [3] McCormac, 2004, SHCal04 Southern Hemisphere calibration, 0-11.0 cal kyr BP, Radiocarbon source

      Not checked in the free run.

  • May combine two claims.

    Findingown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    When assuming seven ancestral populations (K=7), the Polynesians form their own cluster and more than 99.9% of the genomes of Bot15 and Bot17 were assigned to this Polynesian cluster.

    “When assuming seven ancestral populations (K = 7), the Polynesians form their own cluster and more than 99.9% of the genomes of Bot15 and Bot17 were assigned to this Polynesian cluster (Figure 1D).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Study design and conductreasoning
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    A marine reservoir effect cannot be fully excluded, so the marine-corrected age estimates are highly conservative.

    “While there is a general lack of baseline isotope data for the relevant areas and from archaeological remains, the combined evidence from the δ13C, δ15N and δ34S values when compared to Brazilian fauna and flora, as well as archaeological and modern human bone samples, suggests that a marine reservoir effect cannot be fully excluded (Supplemental information).”
    • Also stated in: § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil · plain
      “More work on foodwebs and carbon cycling in the Minas Gerais area is needed to determine if a marine reservoir correction for the 14C dates is indeed required; hence, the marine-corrected age estimates presented must be considered highly conservative.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    The Polynesian Pacific expansion from Southeast Asia covered thousands of kilometers, reaching New Zealand, Hawaii and Easter Island between ca. 1200 and 1300 AD.

    “It has been established that the Polynesian Pacific expansion from Southeast Asia covered distances of thousands of kilometers, reaching New Zealand, Hawaii and Easter Island — an area approximately the size of North America — between ca. 1200 and 1300 AD [10].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [10] Wilmshurst, 2011, High-precision radiocarbon dating shows recent and rapid initial human colonization of East Polynesia, Proc. Natl. Acad. Sci. USA source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    The Madagascar-Brazil slave trade hypothesis can be excluded because Malagasy ancestors admixed with African populations prior to the slave trade and no such African ancestry is detected in the Botocudo sample.

    “However, we can further exclude this hypothesis as recent genomic data have demonstrated that the Malagasy ancestors admixed with African populations prior to the slave trade [5], and no such ancestry is detected in our Botocudo sample (Supplemental information).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [5] Pierron, 2014, Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar, Proc. Natl. Acad. Sci. USA

      Not checked in the free run.

  • May combine two claims.

    Premisecitation
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Many Polynesian islands were not visited by Europeans again for at least 200 years after Magellan's 1521 sighting, due to lack of precise navigational techniques and war between European nations.

    “While Fernão de Magalhães (Magellan) first spotted some seemingly uninhabited Polynesian islands in 1521 AD, the lack of precise navigational techniques [6], as well as war between European nations, meant that many of those islands were not visited by Europeans again for at least another 200 years.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [6] Maude, 1959, Spanish discoveries In the Pacific, J. Polynesian Soc.

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Several scenarios have been previously proposed to explain Polynesian ancestry in Botocudos: the Polynesia-Peru slave trade, the Madagascar-Brazil slave trade, voyaging on European ships, and Polynesian voyaging.

    “Several scenarios have been previously proposed that are of potential relevance for explaining our result that two Botocudo individuals have Polynesian ancestry for both the mitochondrial and nuclear genomes [1]: the Polynesia–Peru slave trade [4], the Madagascar–Brazil slave trade, voyaging on European ships either as crew, passengers, or stowaways, and Polynesian voyaging.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [1] Gonçalves, 2013, Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil, Proc. Natl. Acad. Sci. USA source

      Not checked in the free run.

    • cites [4] Maude, 1981

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisereasoning
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    The previous suggestion that Oceanian mtDNA variants in Botocudos came from runaway slaves was not supported by direct dating or genomic analyses.

    “Although it was argued that these genetic traits were likely to be derived from runaway slaves brought to Brazil by Europeans, no direct-dating or genomic analyses were used to support this conclusion.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [1] Gonçalves, 2013, Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil, Proc. Natl. Acad. Sci. USA source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    The scenario explaining Polynesian ancestry in the Botocudos must invoke more than two Polynesian migrants, because Polynesian ancestry was detected in two out of 35 Botocudo individuals in the Museu Nacional collection.

    “Regardless, the scenario must necessarily invoke a certain number of Polynesian migrants — presumably more than two, as we detected Polynesian ancestry in two out of 35 Botocudo individuals in the Museu Nacional collection.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Evidence has accumulated in favor of Polynesian and South American contact, though the issue remains controversial.

    “In recent years, evidence has continued to accumulate in favor of a Polynesian and South American contact [8], although the issue has remained mired in controversy (e.g., [9]).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [8] Jones, 2011

      Not checked in the free run.

    • cites [9] Gongora, 2008, Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA, Proc. Natl. Acad. Sci. USA source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    The genetic data showed features characteristic of ancient DNA.

    “We found features in the data characteristic of ancient DNA (Supplemental information).”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Interpretationreasoning
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    The Polynesian voyaging scenario cannot be excluded.

    “It is hard to explain how the first possible genomic evidence of such Polynesian contact with South America would be found in Brazil rather than on the west coast of South America, yet we cannot exclude this scenario either.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    Radiocarbon dating was carried out in two independent laboratories.

    “Accelerator mass spectrometry (AMS) radiocarbon dating of five teeth from the four Botocudo individuals was carried out in two independent laboratories.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning
    § Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

    The European ship trade scenario cannot be excluded.

    “Although improbable also because it would involve both individuals making it to the interior of Brazil, we cannot exclude this scenario.”
    Quote in the paperNot a substantial claim
17 of 17

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Human skulls in Brazilian collections attributed to the Botocudo have mtDNA lineages B4a1a1a and B4a1a1 and nuclear DNA typical of Polynesians.

    “Recent ancient DNA studies of human skulls in the collections of the National Museum of Brazil (Museu Nacional)/Universidade Federal do Rio de Janeiro (UFRJ), attributed to a Native American group in Eastern-Central Brazil called the Botocudo have been shown to have mtDNA linages (B4a1a1a and B4a1a1) [103] and nuclear DNA typical of Polynesians [131].”

Cites

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Research works printed but not linked: 1

  1. Maude, 1959, Spanish discoveries In the Pacific, J. Polynesian Soc., 68, 285

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Authors
Malaspinas, A.-S., Lao, O., Schroeder, H., Rasmussen, M., Raghavan, M., Moltke, I., Campos, P. F., Sagredo, F. S., Rasmussen, S., Gonçalves, V. F., Albrechtsen, A., Allentoft, M. E., Johnson, P. L. F., Li, M., Reis, S., Bernardo, D. V., DeGiorgio, M., Duggan, A. T., Bastos, M., Wang, Y., Stenderup, J., Moreno-Mayar, J. V., Brunak, S., Sicheritz-Ponten, T., Hodges, E., Hannon, G. J., Orlando, L., Price, T. D., Jensen, J. D., Nielsen, R., Heinemeier, J., Olsen, J., Rodrigues-Carvalho, C., Lahr, M. M., Neves, W. A., Kayser, M., Higham, T., Stoneking, M., Pena, S. D. J., & Willerslev, E.
Affiliations
  • Natural History Museum of Denmark (DK)
  • Leiden University (NL)
  • Stanford Medicine (US)
  • University of Copenhagen (DK)
  • Technical University of Denmark (DK)
  • Centre for Addiction and Mental Health (CA)
  • Emory University (US)
  • Max Planck Institute for Evolutionary Anthropology (DE)
  • Universidade Federal do Rio de Janeiro (BR)
  • Universidade Federal do Rio Grande (BR)
  • Pennsylvania State University (US)
  • University of California, Berkeley (US)
  • Howard Hughes Medical Institute (US)
  • University of Wisconsin–Madison (US)
  • École Polytechnique Fédérale de Lausanne (CH)
  • Aarhus University (DK)
  • Universidade de São Paulo (BR)
  • Erasmus MC (NL)
  • University of Oxford (GB)
Corresponding author
  • Stoneking, Mark
  • Willerslev, Eske
Venue
Current Biology
Publisher
Elsevier BV
Published
2014-11
Volume
24
Issue
21
Pages
R1035-R1037
ISSN
0960-9822 (ISSN-L)
OpenAlex
W2083402207
Cited by
98
References
8
Citations by year
2026: 3 · 2025: 3 · 2024: 20 · 2023: 2 · 2022: 15 · 2021: 9 · 2020: 8 · 2019: 12 · 2018: 6 · 2017: 7 · 2016: 6 · 2015: 6 · 2014: 1
FWCI
4.37
Type
journal article
Language
en
Open access
Locations
  • Current Biology (publishedVersion, other-oa)
  • PubMed (publishedVersion)
  • EUR Research Repository (Erasmus University Rotterdam) (publishedVersion, other-oa)
  • SERVAL (Université de Lausanne) (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
  • IRIS (submittedVersion, cc-by-nc-sa)
  • EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, other-oa)
  • RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
  • eScholarship (California Digital Library) (submittedVersion)
  • Max Planck Digital Library (submittedVersion)
  • Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
  • Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
  • Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
  • Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion)
  • RePub (Erasmus University Rotterdam) (submittedVersion)
  • Griffith Research Online (submittedVersion)
  • Apollo (University of Cambridge) (submittedVersion, cc-by-nc-nd)
Funders
  • National Science Foundation (FP7/2007-2013, 1103639)
  • Emory University
  • University of Chicago
  • Aarhus Universitet
  • Villum Fonden (00007171)
  • Wellcome Trust (FP7/2007–2013)
  • Cancer Research UK (21143)
  • National Institute for Health and Care Research (FP7/2007–2013)
  • University of Oxford
  • European Commission (2007–2013, FP7 2007-2013, 319209, FP7/2007, 317184)
  • National Research Foundation (94107)
  • École Polytechnique Fédérale de Lausanne
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (FP7/2007-2013, 143529, 31270, 53706)
  • Danmarks Grundforskningsfond (DNRF94)
  • Lundbeckfonden (R109-2012-9995, R70-2010-6286, R155-2013-16338, R38-2008-3048, R24-2008-2527)
  • University of Toronto
  • Danmarks Tekniske Universitet
  • Universidade de São Paulo
  • Copenhagen Graduate School for Nanoscience and Nanotechnology
  • Universidade Federal de Minas Gerais
  • Max-Planck-Institut für Evolutionäre Anthropologie
  • Universidade Federal do Rio de Janeiro
  • H. Lundbeck A/S
  • National Institutes of Health (FP7/2007-2013)
  • Directorate for Biological Sciences
  • Department of Psychiatry, University of Toronto
  • Medical Research Council (FP7/20072013)
  • National Health and Medical Research Council
  • National Cancer Institute (P01CA013106)
  • National Institute of General Medical Sciences (K99GM104158)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Social Sciences › Arts and Humanities › Archeology › Forensic Anthropology and Bioarchaeology Studies
Keywords
Botocudos, Polynesian ancestry, ancient human genomes, peopling of the Americas, radiocarbon dating, human skull, isotopic analysis, genetic ancestry, Minas Gerais, indigenous peoples of Brazil
MeSH terms
Brazil, DNA, Mitochondrial, Humans, Indians, South American, Genome, Human, Radiometric Dating

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