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

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 13, 2014, Pages 4826-4831

  Thomson, Vicki A ^a   Lebrasseur, Ophélie ^b   Austin, Jeremy J ^a,c   Hunt, Terry L ^d   Burney, David A ^e   Denham, Tim ^f   Rawlence, Nicolas J ^a,g   Wood, Jamie R ^h   Gongora, Jaime ⁱ   Flink, Linus Girdland ^b,j   Linderholm, Anna ^b   Dobney, Keith ^k   Larson, Greger ^b   Cooper, Alan ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b DURHAM UNIVERSITY   (United Kingdom)

^c MUSEUM VICTORIA   (Australia)

^d UNIVERSITY OF OREGON   (United States)

^e NATIONAL TROPICAL BOTANICAL GARDEN   (United States)

^f AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^g UNIVERSITY OF OTAGO   (New Zealand)

^h LANDCARE RESEARCH   (New Zealand)

ⁱ UNIVERSITY OF SYDNEY   (Australia)

^j DURHAM UNIVERSITY   (United Kingdom)

^k UNIVERSITY OF ABERDEEN   (United Kingdom)

more..

Author keywords

Archaeology; Lapita; Migration; Pacific colonization; Phylogeography

Indexed keywords

MITOCHONDRIAL DNA;

ARCHEOLOGY; ARTICLE; CHICKEN; DNA DETERMINATION; DNA SEQUENCE; FEDERATED STATES OF MICRONESIA; HAPLOTYPE; MITOCHONDRIAL GENOME; NONHUMAN; PACIFIC ISLANDER; POLYNESIA; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH AMERICA;

ARCHAEOLOGY; LAPITA; MIGRATION; PACIFIC COLONIZATION; PHYLOGEOGRAPHY;

ANIMAL MIGRATION; ANIMALS; BASE PAIRING; BAYES THEOREM; CHICKENS; DNA; GENOME, MITOCHONDRIAL; GEOGRAPHY; HAPLOTYPES; HUMANS; LOCUS CONTROL REGION; MOLECULAR SEQUENCE DATA; PACIFIC OCEAN; PHYLOGENY; POLYNESIA; TIME FACTORS;

EID: 84897490832     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1320412111     Document Type: Article

References (49)

1. Denham T, et al. (2012) Dating the appearance of Lapita pottery in the Bismarck Archipelago and its dispersal to Remote Oceania. Archaeology in Oceania 47(1): 39-46.
2. Green RC (1991) The Lapita Cultural Complex: Current evidence and proposed models. Indo-Pacific Prehistory Association Bulletin 11(1991):295-305.
3. Kirch P (1997) The Lapita Peoples: Ancestors of the Oceanic World (Blackwell, Oxford).
4. Spriggs M (1997) The Island Melanesians (Blackwell, Oxford).
5. Summerhayes G (2000) Lapita Interaction (Australian National Univ Press, Canberra, Australia).
6. Wilmshurst JM, Hunt TL, Lipo CP, Anderson AJ (2011) High-precision radiocarbon dating shows recent and rapid initial human colonization of East Polynesia. Proc Natl Acad Sci USA 108(5):1815-1820.
7. Clarke AC, Burtenshaw MK, McLenachan PA, Erickson DL, Penny D; SMBE Tri-National Young Investigators (2006) Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria). Mol Biol Evol 23(5):893-900.
8. Whitaker T, Carter G (1954) Oceanic drift of gourds-Experimental observations. Am J Bot 41(9):697-700.
9. Roullier C, Benoit L, McKey DB, Lebot V (2013) Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination. Proc Natl Acad Sci USA 110(6):2205-2210.
10. Larson G, et al. (2007) Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania. Proc Natl Acad Sci USA 104(12):4834-4839.
11. Larson G, et al. (2010) Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proc Natl Acad Sci USA 107(17): 7686-7691.
12. Savolainen P, Leitner T, Wilton AN, Matisoo-Smith E, Lundeberg J (2004) A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc Natl Acad Sci USA 101(33):12387-12390.
13. Matisoo-Smith E, Robins JH (2004) Origins and dispersals of Pacific peoples: Evidence from mtDNA phylogenies of the Pacific rat. Proc Natl Acad Sci USA 101(24): 9167-9172.
14. Storey AA, 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.
15. Storey AA, et al. (2010) Mitochondrial DNA from 3000-year old chickens at the Teouma site, Vanuatu. J Archaeol Sci 37(10):2459-2468.
16. Storey AA, et al. (2012) Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures. PLoS ONE 7(7):e39171.
17. Storey AA, et al. (2013) Polynesian chickens in the New World: A detailed application of a commensal approach. Archaeology in Oceania 48(2):101-119.
18. Oskarsson MCR, et al. (2012) Mitochondrial DNA data indicate an introduction through Mainland Southeast Asia for Australian dingoes and Polynesian domestic dogs. Proc Biol Sci 279(1730):967-974.
19. Muir WM, et al. (2008) Review of the initial validation and characterization of a 3K chicken SNP array. Worlds Poult Sci J 64(2):219-225.
20. Fumihito A, et al. (1996) Monophyletic origin and unique dispersal patterns of domestic fowls. Proc Natl Acad Sci USA 93(13):6792-6795.
21. Kanginakudru S, Metta M, Jakati RD, Nagaraju J (2008) Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken. BMC Evol Biol 8:174.
22. Oka T, et al. (2007) Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Anim Genet 38(3):287-293.
23. Silva P, et al. (2009) Mitochondrial DNA-based analysis of genetic variation and relatedness among Sri Lankan indigenous chickens and the Ceylon junglefowl (Gallus lafayetti). Anim Genet 40(1):1-9.
24. Liu YP, et al. (2006) Multiple maternal origins of chickens: Out of the Asian jungles. Mol Phylogenet Evol 38(1):12-19.
25. Miao YW, et al. (2013) Chicken domestication: An updated perspective based on mitochondrial genomes. Heredity (Edinb) 110(3):277-282.
26. Dancause KN, Vilar MG, Steffy R, Lum JK (2011) Characterizing genetic diversity of contemporary pacific chickens using mitochondrial DNA analyses. PLoS ONE 6(2):e16843.
27. Gongora J, et al. (2008) Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Proc Natl Acad Sci USA 105(30):10308-10313.
28. Gongora J, 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.
29. Storey AA, et al. (2008) Pre-Columbian chickens, dates, isotopes, and mtDNA. Proc Natl Acad Sci USA 105(48):E99, author reply E100.
30. Gonçalves VF, et al. (2013) Identification of Polynesian mtDNA haplogroups in remains of Botocudo Amerindians from Brazil. Proc Natl Acad Sci USA 110(16): 6465-6469.
31. Bellwood P (2007) Prehistory of the Indo-Malaysian Archipelago (Australian National Univ Press, Canberra, Australia), 3rd Ed, p 385.
32. Barker FK, Benesh MK, Vandergon AJ, Lanyon SM (2012) Contrasting evolutionary dynamics and information content of the avian mitochondrial control region and ND2 gene. PLoS ONE 7(10):e46403.
33. Champlot S, et al. (2010) An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PLoS ONE 5(9):e13042.
34. Leonard J, et al. (2007) Animal DNA in PCR reagents plagues ancient DNA research. J Archaeol Sci 34(9):1361-1366.
35. Wickler S (2004) Modelling colonisation and migration in Micronesia from a zooarchaeological perspective. Colonisation, Migration, and Marginal Areas: A Zooarchaeological Approach, eds Mondini M, Munoz S, Wickler S (Oxbow Books, Oxford), pp 28-40.
36. Carson M (2008) Refining earliest settlement in Remote Oceania: Renewed archaeological investigation at Unai Bapot, Saipan. Journal of Island & Coastal Archaeology 3(1):115-139.
37. Anderson A (2009) The rat and the octopus: Initial human colonization and the prehistoric introduction of domestic animals to Remote Oceania. Biol Invasions 11(7): 1503-1519.
38. Addison DJ, Matisoo-Smith E (2010) Rethinking Polynesians origins: A West-Polynesia Triple-I model. Archaeology in Oceania 45(1):1-12.
39. Cooper A, Poinar HN (2000) Ancient DNA: Do it right or not at all. Science 289(5482):1139.
40. Lanfear R, Calcott B, Ho SY, Guindon S (2012) Partitionfinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol 29(6):1695-1701.
41. Ronquist F, et al. (2012) MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61(3):539-542.
42. Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688-2690.
43. Adebambo A, et al. (2010) Lack of phylogeographic structure in Nigerian village chickens revealed by mitochondrial DNA D-loop sequence analysis. Int J Poult Sci 9(5): 503-507.
44. Berthouly-Salazar C, et al. (2010) Vietnamese chickens: A gate towards Asian genetic diversity. BMC Genet 11:53.
45. Muchadeyi FC, et al. (2008) Mitochondrial DNA D-loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens. Anim Genet 39(6):615-622.
46. Mwacharo JM, et al. (2011) Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa. Mol Phylogenet Evol 58(2):374-382.
47. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 6(29):29.
48. Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16(1):37-48.
49. Specht J (2007) Small islands in the big picture: The formative period of Lapita in the Bismarck Archipelago. Oceanic Explorations: Lapita and Western Pacific Settlement, Terra Australis, eds Bedford S, Sand C, Connaughton SP (Australian National Univ Press, Canberra, Australia), Vol 26, pp 51-70.