A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea

New Guinea shows human occupation since ~50 thousand years ago (ka), independent adoption of plant cultivation ~10 ka, and great cultural and linguistic diversity today.We performed genome-wide single-nucleotide polymorphism genotyping on 381 individuals from 85 language groups in Papua New Guinea and find a sharp divide originating 10 to 20 ka between lowland and highland groups and a lack of non–New Guinean admixture in the latter. All highlanders share ancestry within the last 10 thousand years, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition. However, genetic differentiation between groups in Papua New Guinea is much stronger than in comparable regions in Eurasia, demonstrating that such a transition does not necessarily limit the genetic and linguistic diversity of human societies.We thank all sample donors who contributed to this study; T. Parks, A. V. Hill, J. B. Clegg, D. Higgs, D. J. Weatherall, O. Bunari, A. Spencer, J. Barker, R. Spark, and P. Sill for assistance in sample collection and discussion; J. Friedlaender for background information on the HGDP-CEPH samples; and the Wellcome Trust Sanger Institute genotyping and sequencing facilities for generating data, especially M. Quail, D. Jackson, and S. Leonard for generating 10x Genomics data. A.B., Y.X., M.S.S., and C.T.-S. were supported by the Wellcome Trust (grant 098051). A.J.M. was supported by a Wellcome Trust Clinical Research Training grant (106289/Z/14/ Z). S.J.O., A.J.M., and K.A. were supported by a Wellcome Trust Core Award (090532/Z/09/Z), and K.A. was supported by a European Research Council Advanced Grant to A. V. S. Hill (294557). The array genotypes are available for population history studies (EGA accession EGAS00001001587). The 10x Genomics sequencing data are available as two sets, the HGDP-CEPH samples with no restrictions (ENA accession ERP015796) and the others for population history studies (EGA accession EGAS00001001853)