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Reply

Reply to Beavan, Bryant, and Storey and Matisoo-Smith: Ancestral Polynesian “D” haplotypes reflect authentic Pacific chicken lineages

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 September 2, 2014 111 (35) E3585-E3586; first published August 13, 2014; https://doi.org/10.1073/pnas.1411566111
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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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, Australian National University College of Arts and Social Sciences, 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

This article has Letters. Please see:

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

See related content:

  • Origins and dispersal of Polynesian chickens
    - Mar 17, 2014

See related content:

  • Statistical flaws undermine chicken debate
    - Aug 13, 2014
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None of the letters in response to Thomson et al. (1) undermine our conclusions. However, several issues have been raised, which we address in this reply. Beavan (2) dismisses some of the concerns that have been raised about the accuracy of the radiocarbon dates of the El Arenal-1 chicken bones, which are immediately pre-Columbian. Although procedures, such as ultrafiltration of amino acids, are common practice for suboptimal bone samples, such as the oldest El Arenal-1 sample, further complex issues, including dietary sources and the potential for indirect marine carbon input (3), mean that a detailed assessment of the site through multiple further dates would be required to exclude the possibility that the specimens might actually be post-Columbian. This approach seems particularly advisable given that analogous issues were raised about a surprisingly early date for New Zealand colonization based on Pacific rat bone dates generated at the same laboratory using similar procedures (4), which were subsequently shown to be erroneously old (5).

Storey and Matisoo-Smith (6) raise the issue of potential contamination of laboratory components with modern DNA, including domestic animal DNA, which is well recognized in ancient DNA research (7, 8). Multiple control reactions are acknowledged to be necessary but insufficient to detect low levels or sporadic contamination, and issues such as the “carrier effect” (7, 8) can mask the true frequency of contamination. Storey and Matisoo-Smith (6) do not dispute that we have demonstrated that at least a proportion of the results reported in Storey et al. (9) were contaminated with the common chicken haplogroup E. Unfortunately, it is impossible to demonstrate the full extent of this problem within the study, as it was not possible to reanalyze most of the samples, the details of the reported independent replication were not given, and the results are not available. However, it is important to note that in tropical sites only recent samples (500–1,400 y old) are predicted to yield DNA via PCR (10), and all of the chicken specimens older than this [>1410 cal B.P. (9, 11)] yielded a likely laboratory contaminant (haplogroup E). This result is perhaps more consistent with increased rates of laboratory contamination because authentic DNA levels diminish below detectability, than with two waves of chicken introductions across the Pacific (9).

Bryant (12) questions two aspects of the statistical analyses conducted in Thomson et al. (1). The first issue concerns the Bayesian Serial Simcoal and approximate Bayesian computation analysis. We thank the author for identifying an error in the figure legend of figure S11 in ref. 1. This legend should read: “Eight alternate scenarios were also tested: route from Europe–South America with or without migration, H3 or H1 respectively, with each model having two variations…and a route from Pacific-South America with or without migration, H4 or H2 respectively” (1). The figure itself is correct and shows that the Europe–South America model without the migration matrix was the more likely model.

We applied the suggested two-sample proportion test (Fisher’s exact test) (12), and found that the detection of the two different reported levels of E haplogroups in the Pacific remains unlikely (0/22 and 15/31; P = 8.67 × 10−5). Although it is true that the statistical tests assume random sampling from a naturally occurring distribution, the temporal and geographic mixing in the island archaeological sites analyzed seem likely to reflect an approximate sample of the chicken diversity present on any island. Although it is possible that combining chicken samples from different islands in an analysis may obscure interisland variability in the proportion of “D”s vs. “E”s, there is only a single site common to both studies (Anakena on Rapa Nui), and the limited number of samples prevents statistical analysis. However, given that haplogroup E chickens are found worldwide, whereas the ancient D haplotypes we identified are specific to the Pacific, we maintain that the latter are likely to be authentic, but at least some—if not all—of the reported E haplotypes (9, 11) represent contamination.

Footnotes

  • ↵1To whom correspondence should be addressed. Email: alan.cooper{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., A.L., and A.C. performed research; T.L.H. and D.A.B. contributed new reagents/analytic tools; V.A.T. and A.C. analyzed data; and V.A.T., J.J.A., T.D., N.J.R., J.R.W., J.G., L.G.F., K.D., G.L., and A.C. wrote the paper.

  • The authors declare no conflict of interest.

View Abstract

References

  1. ↵
    1. Thomson VA,
    2. et al.
    (2014) Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific. Proc Natl Acad Sci USA 111(13):4826–4831.
    OpenUrlAbstract/FREE Full Text
  2. ↵
    1. Beavan N
    (2014) No evidence for sample contamination or diet offset for pre-Columbian chicken dates from El Arenal. Proc Natl Acad Sci USA 111:E3582.
    OpenUrlFREE Full Text
  3. ↵
    1. Gongora J,
    2. et al.
    (2008) Reply to Storey et al.: More DNA and dating studies needed for ancient El Arenal-1 chickens. Proc Natl Acad Sci USA 105(48):E100.
    OpenUrlFREE Full Text
  4. ↵
    1. Beavan Athfield N
    (2006) Comment on “Diet-derived variations in radiocarbon and stable isotopes: A case study from Shag River Mouth, New Zealand” Radiocarbon 48(1):117–121.
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    1. Wilmshurst JM,
    2. Anderson AJ,
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    4. Worthy TH
    (2008) Dating the late prehistoric dispersal of Polynesians to New Zealand using the commensal Pacific rat. Proc Natl Acad Sci USA 105(22):7676–7680.
    OpenUrlAbstract/FREE Full Text
  6. ↵
    1. Storey AA,
    2. Matisoo-Smith EA
    (2014) No evidence against Polynesian dispersal of chickens to pre-Columbian South America. Proc Natl Acad Sci USA 111:E3583.
    OpenUrlFREE Full Text
  7. ↵
    1. Cooper A,
    2. Poinar HN
    (2000) Ancient DNA: Do it right or not at all. Science 289(5482):1139.
    OpenUrlCrossRefPubMed
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    1. Leonard JA,
    2. et al.
    (2007) Animal DNA in PCR reagents plagues ancient DNA research. J Archaeol Sci 34(9):1361–1366.
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    1. Storey AA,
    2. et al.
    (2007) Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile. Proc Natl Acad Sci USA 104(25):10335–10339.
    OpenUrlAbstract/FREE Full Text
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    1. Reed FA,
    2. Kontanis EJ,
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    (2003) Brief communication: Ancient DNA prospects from Sri Lankan highland dry caves support an emerging global pattern. Am J Phys Anthropol 121(2):112–116.
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    1. Storey AA,
    2. et al.
    (2010) Mitochondrial DNA from 3000-year old chickens at the Teouma site, Vanuatu. J Archaeol Sci 37(10):2459–2468.
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  12. ↵
    1. Bryant D
    (2014) Statistical flaws undermine pre-Columbian chicken debate. Proc Natl Acad Sci USA 111:E3584.
    OpenUrlFREE Full Text
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Ancestral Polynesian “D” lineages
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 Sep 2014, 111 (35) E3585-E3586; DOI: 10.1073/pnas.1411566111

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Ancestral Polynesian “D” lineages
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 Sep 2014, 111 (35) E3585-E3586; DOI: 10.1073/pnas.1411566111
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