Cited by 48

The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.

Papuan mitochondrial genomes and the settlement of Sahul

Pedro, Nicole, Brucato, Nicolas, Fernandes, Veronica, André, Mathilde, Saag, Lauri, Pomat, William, Besse, Céline, Boland, Anne, Deleuze, Jean-François, Clarkson, Chris, Sudoyo, Herawati, Metspalu, Mait, Stoneking, Mark, Cox, Murray P., Leavesley, Matthew, Pereira, Luisa, Ricaut, François-Xavier·2020·Journal of Human Genetics

Abstract

New Guineans represent one of the oldest locally continuous populations outside Africa, harboring among the greatest linguistic and genetic diversity on the planet. Archeological and genetic evidence suggest that their ancestors reached Sahul (present day New Guinea and Australia) by at least 55,000 years ago (kya). However, little is known about this early settlement phase or subsequent dispersal and population structuring over the subsequent period of time. Here we report 379 complete Papuan mitochondrial genomes from across Papua New Guinea, which allow us to reconstruct the phylogenetic and phylogeographic history of northern Sahul. Our results support the arrival of two groups of settlers in Sahul within the same broad time window (50–65 kya), each carrying a different set of maternal lineages and settling Northern and Southern Sahul separately. Strong geographic structure in northern Sahul remains visible today, indicating limited dispersal over time despite major climatic, cultural, and historical changes. However, following a period of isolation lasting nearly 20 ky after initial settlement, environmental changes postdating the Last Glacial Maximum stimulated diversification of mtDNA lineages and greater interactions within and beyond Northern Sahul, to Southern Sahul, Wallacea and beyond. Later, in the Holocene, populations from New Guinea, in contrast to those of Australia, participated in early interactions with incoming Asian populations from Island Southeast Asia and continuing into Oceania.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s10038-020-0781-3

Cites

15 of 15 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Show all 15 references

Research works printed but not linked: 43

  1. Loh J, Harmon D. A global index of biocultural diversity. Ecol Indic. 2005;5:231–41. · DOI
  2. Clarkson C, Jacobs Z, Marwick B, Fullagar R, Wallis L, Smith M, et al. Human occupation of northern Australia by 65,000 years ago. Nature. 2017;547:306–10. · DOI · Paper page
  3. Lewis SE, Sloss CR, Murray-Wallace CV, Woodroffe CD, Smithers SG. Post-glacial sea-level changes around the Australian margin: a review. Quat Sci Rev. 2013;74:115–38. · DOI
  4. Norman K, Inglis J, Clarkson C, Faith JT, Shulmeister J, Harris D. An early colonisation pathway into northwest Australia 70-60,000 years ago. Quat Sci Rev. 2018;180:229e239. · DOI · Paper page
  5. Bradshaw CJA, Ulm S, Williams AN, Bird MI, Roberts RG, Jacobs Z, et al. Minimum founding populations for the first peopling of Sahul. Nat Ecol Evol. 2019;3:1057–63. · DOI · Paper page
  6. Summerhayes GR, Leavesley M, Fairbairn A, Mandui H, Field J, Ford A, et al. Human adaptation and use of plants in highland New Guinea 49,000–44,000 years ago. Science. 2010;330:78e81. · DOI · Paper page
  7. Leavesley M, Chappell J. Buang Merabak: additional early radiocarbon evidence of the colonisation of the Bismarck Archipelago, Papua New Guinea. Antiquity. 2004;78:301.
  8. Wickler S. Prehistoric Melanesian exchange and interaction: recent evidence from the Northern Solomon Islands. Asian Perspect. 1990;29:135e154.
  9. Haberle SG, Lentfer CI, Denham T. Palaeoecology. In: Golson J, Denham T, Hughes P, Swadling P, Muke J, editors. Ten thousand years of cultivation at kuk swamp in the highlands of Papua New Guinea. The Australian National University, Canberra, Australia: ANU Press; 2017, p. 145–62. · DOI
  10. Donohue M, Tim Denham. Farming and language in island Southeast Asia reframing Austronesian history. Curr Anthropol. 2010;51:223. · DOI
  11. Schapper A. Farming and the trans-new Guinea family: a consideration chapter. In: Robbeets M, Savelyev A, editors. Language dispersal beyond farming. Amsterdam: John Benjamins Publishing Compagny; 2017, p. 155–82. · DOI
  12. Bergstrom A, Oppenheimer SJ, Mentzer AJ, Auckland K, Robson K, Attenborough R, et al. A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea. Science. 2017;357:1160–3. · DOI
  13. Mona S, Grunz KE, Brauer S, Pakendorf B, Castrì L, Sudoyo H, et al. Genetic admixture history of Eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis. Mol Biol Evol. 2009;26:1865–77. · DOI
  14. Bergström A, Nagle N, Chen Y, McCarthy S, Pollard MO, Ayub Q, et al. Deep roots for Aboriginal Australian Y chromosomes. Curr Biol. 2016;26:809–13. · DOI
  15. Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, et al. Genomic analyses inform on migration events during the peopling of Eurasia. Nature. 2016;538:238–42. · DOI
  16. Summerhayes GR, Field JH, Shaw B, Gaffney D. The archaeology of forest exploitation and change in the tropics during the Pleistocene: the case of Northern Sahul (Pleistocene New Guinea). Quat Int. 2017;448:14e30. · DOI
  17. Nagle N, van Oven M, Wilcox S, van Holst Pellekaan S, Tyler-Smith C, Xue Y, et al. Genographic Consortium. Aboriginal Australian mitochondrial genome variation—an increased understanding of population antiquity and diversity. Sci Rep. 2017;7:43041. · DOI
  18. Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Wilcox S, et al. Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania. J Hum Genet. 2016;62:343–53. · DOI
  19. Tobler R, Rohrlach A, Soubrier J, Bover P, Llamas B, Tuke J, et al. Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia. Nature. 2017;544:180–4. · DOI
  20. Brucato N, Fernandes V, Mazières S, Kusuma P, Cox MP, Ng’ang’a JW, et al. The Comoros shows the earliest Austronesian gene flow in East Africa. Am J Hum Genet. 2018;102:58–68. · DOI
  21. Maricic T, Whitten M, Pääbo S. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS ONE. 2010;5:e14004. · DOI
  22. Arias L, Barbieri C, Barreto G, Stoneking M, Pakendorf B. High resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwest Amazonia. Am J Phys Anthropol. 2018;165:238–55. · DOI
  23. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet. 1999;23:147. · DOI · Paper page
  24. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. · DOI · Paper page
  25. Kloss-Brandstätter A, Pacher D, Schönherr S, Weissensteiner H, Binna R, Specht G, et al. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Hum Mutat. 2011;32:25–32. · DOI
  26. Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, et al. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet. 2009;84:740–59. · DOI
  27. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS. 1997;13:555–6.
  28. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005;22:1185–92. · DOI
  29. Friedlaender JS, Friedlaender FR, Hodgson JA, Stoltz M, Koki G, Horvat G, et al. Melanesian mtDNA complexity. PLoS ONE. 2007;2:e248. · DOI
  30. Duggan AT, Evans B, Friedlaender FR, Friedlaender JS, Koki G, Merriwether DA, et al. Maternal history of Oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion. Am J Hum Genet. 2014;94:721–33. · DOI
  31. Brandão A, Eng KK, Rito T, Cavadas B, Bulbeck D, Gandini F, et al. Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia. Hum Genet. 2016;135:363–76. · DOI
  32. Soares P, Rito T, Trejaut J, Mormina M, Hill C, Tinkler-Hundal E, et al. Ancient voyaging and Polynesian origins. Am J Hum Genet. 2011;88:239–47. · DOI
  33. Stoneking M, Jorde LB, Bhatia K, Wilson AC. Geographic variation in human mitochondrial DNA from Papua New Guinea. Genetics. 1990;124:717–33. · DOI
  34. Friedlaender J, Schurr T, Gentz F, Koki G, Friedlaender F, Horvat G, et al. Expanding Southwest Pacific mitochondrial haplogroups P and Q. Mol Biol Evol. 2005;22:1506–17. · DOI · Paper page
  35. Vilar MG, Kaneko A, Hombhanje FG, Tsukahara T, Hwaihwanje I, Lum JK. Reconstructing the origin of the Lapita Cultural Complex: mtDNA analyses of East Sepik Province, PNG. J Hum Genet. 2008;53:698–708. · DOI
  36. Hudjashov G, Kivisild T, Underhill PA, Endicott P, Sanchez JJ, Lin AA. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc Natl Acad Sci USA. 2007;104:8726–30. · DOI
  37. Gomes SM, Bodner M, Souto L, Zimmermann B, Huber G, Strobl C, et al. Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity. BMC Genomics. 2015;14:16.70.
  38. Ricaut FX, Thomas T, Mormina M, Cox MP, Bellatti M, Foley RA, et al. Ancient Solomon Islands mtDNA: Assessing Holocene settlement and the impact of European contact. J Archaeol Sci. 2010;37:1161–17. · DOI
  39. Hope G. The sensitivity of the high mountain ecosystems of New Guinea to climatic change and anthropogenic impact. Arct Antarct Alp Res. 2014;46:777e786. · DOI
  40. Pavlides C, Gosden C. 35,000 year-old sites in the rainforests of West New Britain, Papua New Guinea. Antiquity. 1994;69:604–10. · DOI
  41. Wurster CM, Bird MI. Barriers and bridges: early human dispersals in equatorial SE Asia. In: Harff J, Bailey G, Lüth F, editors. Geology and Archaeology: submerged landscapes of the continental shelf. Special Publications (411). London, UK: Geological Society of London; 2016, p. 235–50. · DOI
  42. Irwin G, editors. The prehistoric exploration and colonization of the Pacific. Cambridge, UK: University Press; 1992. · DOI
  43. Solheim WGII, Bulbeck D, Flavel A, editors. Archaeology and culture in Southeast Asia: unraveling the Nusantao. Diliman, Quezon City: University of Philippines Press, Philippines; 2006.

Cited by

Sorted by citations

See all 48

Metadata

Authors
Pedro, N., Brucato, N., Fernandes, V., André, M., Saag, L., Pomat, W., Besse, C., Boland, A., Deleuze, J.-F., Clarkson, C., Sudoyo, H., Metspalu, M., Stoneking, M., Cox, M. P., Leavesley, M., Pereira, L., & Ricaut, F.-X.
Venue
Journal of Human Genetics
Published
2020-06-01
Volume
65
Issue
10
Pages
875-887
ISSN
  • 1434-5161
  • 1435-232X
Cited by
48
References
15
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review