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Research Article

Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific

Vicki A. Thomson, Ophélie Lebrasseur, Jeremy J. Austin, Terry L. Hunt, David A. Burney, Tim Denham, Nicolas J. Rawlence, Jamie R. Wood, Jaime Gongora, Linus Girdland Flink, Anna Linderholm, Keith Dobney, Greger Larson, and Alan Cooper
PNAS first published March 17, 2014; https://doi.org/10.1073/pnas.1320412111
Vicki A. Thomson
aAustralian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
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Ophélie Lebrasseur
bDurham Evolution and Ancient DNA, Department of Archaeology, and
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Jeremy J. Austin
aAustralian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
cSciences Department, Museum Victoria, Melbourne, VIC 3001, Australia;
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  • For correspondence: alan.cooper@adelaide.edu.au jeremy.austin@adelaide.edu.au
Terry L. Hunt
dClark Honors College and
eDepartment of Anthropology, University of Oregon, Eugene, OR 97403;
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David A. Burney
fNational Tropical Botanical Garden, Kalaheo, HI 96741;
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Tim Denham
gSchool of Archaeology and Anthropology, ANU College of Arts and Social Sciences, The Australian National University, Canberra, ACT 0200, Australia;
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Nicolas J. Rawlence
aAustralian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
hAllan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin 9016, New Zealand;
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Jamie R. Wood
iLandcare Research, Lincoln 7640, New Zealand;
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Jaime Gongora
jFaculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia; and
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Linus Girdland Flink
bDurham Evolution and Ancient DNA, Department of Archaeology, and
kSchool of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom;
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Anna Linderholm
bDurham Evolution and Ancient DNA, Department of Archaeology, and
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Keith Dobney
lDepartment of Archaeology, University of Aberdeen, Aberdeen AB24 3UF, Scotland
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Greger Larson
bDurham Evolution and Ancient DNA, Department of Archaeology, and
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Alan Cooper
aAustralian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia;
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  • For correspondence: alan.cooper@adelaide.edu.au jeremy.austin@adelaide.edu.au
  1. Edited by David J. Meltzer, Southern Methodist University, Dallas, TX, and approved February 20, 2014 (received for review October 31, 2013)

This article has Letters. Please see:

  • No evidence against Polynesian dispersal of chickens to pre-Columbian South America - August 13, 2014
  • Statistical flaws undermine pre-Columbian chicken debate - August 13, 2014
  • No evidence for sample contamination or diet offset for pre-Columbian chicken dates from El Arenal - August 13, 2014

See related content:

  • Ancestral Polynesian “D” lineages
    - Aug 13, 2014
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Significance

Ancient DNA sequences from chickens provide an opportunity to study their human-mediated dispersal across the Pacific due to the significant genetic diversity and range of archaeological material available. We analyze ancient and modern material and reveal that previous studies have been impacted by contamination with modern chicken DNA and, that as a result, there is no evidence for Polynesian dispersal of chickens to pre-Columbian South America. We identify genetic markers of authentic ancient Polynesian chickens and use them to model early chicken dispersals across the Pacific. We find connections between chickens in the Micronesian and Bismarck Islands, but no evidence these were involved in dispersals further east. We also find clues about the origins of Polynesian chickens in the Philippines.

Abstract

The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.

  • Lapita
  • Pacific colonization
  • phylogeography
  • archaeology
  • migration

Footnotes

  • ↵1To whom correspondence may be addressed. E-mail: alan.cooper{at}adelaide.edu.au or jeremy.austin{at}adelaide.edu.au.
  • Author contributions: V.A.T., J.J.A., J.G., and A.C. designed research; V.A.T., O.L., N.J.R., J.R.W., L.G.F., and A.L. performed research; T.L.H., D.A.B., and K.D. contributed new reagents/analytic tools; V.A.T., J.J.A., and A.C. analyzed data; and V.A.T., J.J.A., T.D., G.L., and A.C. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. KJ000585–KJ000642).

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1320412111/-/DCSupplemental.

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Origins and dispersal of Polynesian chickens
Vicki A. Thomson, Ophélie Lebrasseur, Jeremy J. Austin, Terry L. Hunt, David A. Burney, Tim Denham, Nicolas J. Rawlence, Jamie R. Wood, Jaime Gongora, Linus Girdland Flink, Anna Linderholm, Keith Dobney, Greger Larson, Alan Cooper
Proceedings of the National Academy of Sciences Mar 2014, 201320412; DOI: 10.1073/pnas.1320412111

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Origins and dispersal of Polynesian chickens
Vicki A. Thomson, Ophélie Lebrasseur, Jeremy J. Austin, Terry L. Hunt, David A. Burney, Tim Denham, Nicolas J. Rawlence, Jamie R. Wood, Jaime Gongora, Linus Girdland Flink, Anna Linderholm, Keith Dobney, Greger Larson, Alan Cooper
Proceedings of the National Academy of Sciences Mar 2014, 201320412; DOI: 10.1073/pnas.1320412111
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