Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania

doi:10.1073/pnas.0607753104

Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania

^aDepartment of Medical Biochemistry and Microbiology, Uppsala University Biomedical Center, Box 597, 751 24 Uppsala, Sweden;
^cDepartment of Archaeology, University of Durham, South Road, Durham DH1 3L, United Kingdom;
^eDepartment of Anthropology and Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, P.O. Box 92019, Auckland, New Zealand;
^gDepartment of Anthropology, University of Hawaii, 2424 Maile Way, Honolulu, HI 96822;
^fDepartment of Archaeology and Natural History, Research School of Pacific and Asian Studies, and
^hSchool of Archaeology and Anthropology, Faculty of Arts, The Australian National University, Canberra ACT 0200, Australia;
ⁱAustralian Centre for Ancient DNA, Earth, and Environmental Sciences, University of Adelaide, South Australia 5005, Australia;
^jAnimal Genomics Laboratory, Animal Genomics and Bioinformatics Division, National Livestock Research Institute Rural Development Administration, 564 Omockchun-Dong, Gwonseon-Gu, Suwon 441-706, Korea;
^kInstitute of Biotechnology Vietnamese Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Ha Noi, Vietnam;
^lLaboratorio di Genetica, Istituto Nazionale per la Fauna Selvatica, Via Cà Fornacetta, 9, 40064 Ozzano Emilia Bologna, Italy;
^mIndonesian Centre for Archaeology, Jl. Raya Condet Pejaten 4, Jakarta 12001, Indonesia;
ⁿDepartment of Social Research, National Museum of Ethnology, Osaka 565-8511, Japan;
^oDepartment of Anthropology, University of California, 232 Kroeber Hall, Berkeley, CA 94720;
^pInstitute of History and Philology, Academia Sinica, Nankang, Taipei 11529, Taiwan;
^qDepartment of Archaeology and Palaeoanthropology, School of Human and Environmental Studies, University of New England, Armidale, New South Wales 2351, Australia;
^rBinirayan Hills, San Jose, Antique, Panay, Philippines;
^sCentre for Palaeoecology and Evolution, Department of Archaeology, University of York, The King's Manor, York YO1 7EP, United Kingdom;
^tThe McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, United Kingdom;
^vRoyal Netherlands Institute for Sea Research, NL-1790 AB Den Burg, Texel, The Netherlands;
^wNaval Facilities Engineering Command Pacific, 258 Makalapa Drive, Pearl Harbor, HI 96860;
^xDepartment of Archaeology, Tromsø University Museum, N-9037 Tromsø, Norway;
^yResearch Centre for Archaeological Science, Institute of Archaeology, Chinese Academy of Social Sciences, Beijing 100710, China;
^u107 Dunbar Street, Mount Gravatt East, Brisbane Q4122, Australia;
^dDépartement Ecologie et Gestion de la Biodiversité, Unité Mixte de Recherche 5197, Muséum National d'Histoire Naturelle, 55 Rue Buffon, 75231 Paris Cedex 5, France; and
^zHenry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom

Edited by Barbara A. Schaal, Washington University, St. Louis, MO, and approved February 2, 2007 (received for review September 5, 2006)

Abstract

Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and Oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called “wild” pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region.

Footnotes

^bTo whom correspondence may be addressed. E-mail: greger.larson{at}imbim.uu.se or k.m.dobney{at}durham.ac.uk
Author contributions: K.D. designed research; G.L., T.C., M.F., E.M.-S., J.R., G.D., T.-H.K., N.T.D.T., E.R., A.C., and K.D. performed research; A.A., B.R., M.S., M.D., R.A.D., R.B., T.D., B.G., M.I., E.K., P.K., K.-T.L., M.M., L.M.P., P.J.P., R.J.R., P.S., G.V.d.B., E.W., S.W., and J.Y. contributed new reagents/analytic tools; G.L., T.C., M.F., E.M.-S., J.R., T.-H.K., N.T.D.T., E.R., A.C., and K.D. analyzed data; and G.L., T.C., E.M.-S., A.A., B.R., M.S., M.D., R.A.D., R.B., T.D., B.G., M.I., E.K., P.K., K.-T.L., M.M., L.M.P., P.J.P., R.J.R., P.S., G.V.d.B., E.W., S.W., J.Y., A.C., and K.D. 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. DQ779287–DQ779542, DQ779544–DQ779551, and DQ841948–DQ841949).
This article contains supporting information online at www.pnas.org/cgi/content/full/0607753104/DC1.
Abbreviations:

ISEA,

Island Southeast Asia;

HWABC,

Henry Wellcome Ancient Biomolecules Centre.