CoChat
Sign Up
Cited by 41

The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.

Evolutionary history of modern Samoans

Harris, Daniel N., Kessler, Michael D., Shetty, Amol C., Weeks, Daniel E., Minster, Ryan L., Browning, Sharon, Cochrane, Ethan E., Deka, Ranjan, Hawley, Nicola L., Reupena, Muagututi‘a Sefuiva, Naseri, Take, Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Population Genetics Working Group, McGarvey, Stephen T., O’Connor, Timothy D.·2020·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1913157117PMC PMC7196816
Open this paper in CoChat — free account

Abstract

Archaeological studies estimate the initial settlement of Samoa at 2,750 to 2,880 y ago and identify only limited settlement and human modification to the landscape until about 1,000 to 1,500 y ago. At this point, a complex history of migration is thought to have begun with the arrival of people sharing ancestry with Near Oceanic groups (i.e., Austronesian-speaking and Papuan-speaking groups), and was then followed by the arrival of non-Oceanic groups during European colonialism. However, the specifics of this peopling are not entirely clear from the archaeological and anthropological records, and is therefore a focus of continued debate. To shed additional light on the Samoan population history that this peopling reflects, we employ a population genetic approach to analyze 1,197 Samoan high-coverage whole genomes. We identify population splits between the major Samoan islands and detect asymmetrical gene flow to the capital city. We also find an extreme bottleneck until about 1,000 y ago, which is followed by distinct expansions across the islands and subsequent bottlenecks consistent with European colonization. These results provide for an increased understanding of Samoan population history and the dynamics that inform it, and also demonstrate how rapid demographic processes can shape modern genomes.

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 · 10.1073/pnas.1913157117

Cites

12 of 12 references verified0 citation errors · 0 not checkable

Statistics

Figures

Fig. 1. Increased admixture in urban regions. (A) Global ancestry proportions estimated by ADMIXTURE (34, 35) analysis for each Samoan individual. (B) Source of African, East Asian, and European admixture. Proportion of the AUA, NWU, and ROU admixed individuals’ genomes attributed to the different source populations as determined by ChromoPainter (36) and Globetrotter (37). Our interpretation of each ancestry cluster is included in Lower Right.
Fig. 1. Increased admixture in urban regions. (A) Global ancestry proportions estimated by ADMIXTURE (34, 35) analysis for each Samoan individual. (B) Source of African, East Asian, and European admixture. Proportion of the AUA, NWU, and ROU admixed individuals’ genomes attributed to the different source populations as determined by ChromoPainter (36) and Globetrotter (37). Our interpretation of each ancestry cluster is included in Lower Right.CC BY-NC-ND · PubMed Central
Fig. 2. Denisovan ancestry is correlated to Papuan ancestry. The x axis represents f4 ratio-estimated Papuan ancestry proportions, and the y axis represents the D-statistic test for Denisovan admixture in Samoan and other modern Austronesian individuals. Samoans are represented by black points, and other Austronesian individuals are represented by blue points. Polynesian and Polynesian outlier individuals are represented by red squares.
Fig. 2. Denisovan ancestry is correlated to Papuan ancestry. The x axis represents f4 ratio-estimated Papuan ancestry proportions, and the y axis represents the D-statistic test for Denisovan admixture in Samoan and other modern Austronesian individuals. Samoans are represented by black points, and other Austronesian individuals are represented by blue points. Polynesian and Polynesian outlier individuals are represented by red squares.CC BY-NC-ND · PubMed Central
Fig. 3. Samoan population structure is strongly influenced by urbanization. Map of Samoan census regions, with arrows indicating the between-region rare variant sharing and the white numbers representing within-region rare variant sharing. Red arrows represent the following comparisons with P < 0.05: SAV shares more with AUA than with ROU (P = 0.044), ROU shares more with NWU than with SAV (P = 0.043), ROU shares more with AUA than with SAV (P = 0.001), and ROU shares more with AUA than with NWU (P = 0.048) (SI Appendix, Fig. S8). Shaded geographical regions represent their corresponding census regions (SI Appendix, Fig. S2). Each value represents the average number of rare variants shared between all pairs of individuals, and all values were multiplied by 10,000 for visualization.
Fig. 3. Samoan population structure is strongly influenced by urbanization. Map of Samoan census regions, with arrows indicating the between-region rare variant sharing and the white numbers representing within-region rare variant sharing. Red arrows represent the following comparisons with P < 0.05: SAV shares more with AUA than with ROU (P = 0.044), ROU shares more with NWU than with SAV (P = 0.043), ROU shares more with AUA than with SAV (P = 0.001), and ROU shares more with AUA than with NWU (P = 0.048) (SI Appendix, Fig. S8). Shaded geographical regions represent their corresponding census regions (SI Appendix, Fig. S2). Each value represents the average number of rare variants shared between all pairs of individuals, and all values were multiplied by 10,000 for visualization.CC BY-NC-ND · PubMed Central
Fig. 4. Samoan population history. The colored lines represent the Ne history from IBDNe (43) of SAV and Upolu. The lighter-shaded polygons around the lines represent the 95% CI. All Ne values are plotted on a log10 scale. The icons below the Ne results represent a summary of known events in Samoan history from archaeological and historical records, assuming a 30-y human generation time (8). European sustained contact, rise of Samoan chiefdoms, Samoan interarchipelago voyages increase, pottery disappears, potential migration into Samoa, sparse peopling of all Samoan islands, and initial settlement of Upolu are shown from left to right. The icons are derived from Samoan and Polynesian archaeology, material culture, and ethnohistoric accounts. The Lapita pottery sherd is copied from a similar sherd found at the Mulifanua archaeological site (14). The triangular shape of the human icons is modeled after rock art pictographs in Polynesia (e.g., Tonga and Hawaii), although no anthropomorphic rock art is known for Samoa. The Samoan chief icon holds a to’oto’o, the staff associated with tulafale or orator-chiefs. The Tongan maritime chiefdom icon depicts some items exchanged between Samoa, Tonga, and Fiji: basalt for adzes and other tools, bird feathers (particularly red colored), and timber and mats for canoe building (SI Appendix, Table S5).
Fig. 4. Samoan population history. The colored lines represent the Ne history from IBDNe (43) of SAV and Upolu. The lighter-shaded polygons around the lines represent the 95% CI. All Ne values are plotted on a log10 scale. The icons below the Ne results represent a summary of known events in Samoan history from archaeological and historical records, assuming a 30-y human generation time (8). European sustained contact, rise of Samoan chiefdoms, Samoan interarchipelago voyages increase, pottery disappears, potential migration into Samoa, sparse peopling of all Samoan islands, and initial settlement of Upolu are shown from left to right. The icons are derived from Samoan and Polynesian archaeology, material culture, and ethnohistoric accounts. The Lapita pottery sherd is copied from a similar sherd found at the Mulifanua archaeological site (14). The triangular shape of the human icons is modeled after rock art pictographs in Polynesia (e.g., Tonga and Hawaii), although no anthropomorphic rock art is known for Samoa. The Samoan chief icon holds a to’oto’o, the staff associated with tulafale or orator-chiefs. The Tongan maritime chiefdom icon depicts some items exchanged between Samoa, Tonga, and Fiji: basalt for adzes and other tools, bird feathers (particularly red colored), and timber and mats for canoe building (SI Appendix, Table S5).CC BY-NC-ND · PubMed Central

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

Show all 12 references

Research works printed but not linked: 49

  1. E. Matisoo-Smith, Ancient DNA and the human settlement of the Pacific: A review. J. Hum. Evol. 79, 93–104 (2015). · DOI
  2. J. F. O’Connell, J. Allen, The process, biotic impact, and global implications of the human colonization of Sahul about 47,000 years ago. J. Archaeol. Sci. 56, 73–84 (2015). · DOI · Paper page
  3. R. D. Gray, A. J. Drummond, S. J. Greenhill, Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 323, 479–483 (2009). · DOI · Paper page
  4. M. Lipson ., Population turnover in Remote Oceania shortly after initial settlement. Curr. Biol. 28, 1157–1165.e7 (2018). · DOI
  5. I. Pugach ., The gateway from near into Remote Oceania: New insights from genome-wide data. Mol. Biol. Evol. 35, 871–886 (2018). · DOI
  6. K. E. Langergraber ., Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proc. Natl. Acad. Sci. U.S.A. 109, 15716–15721 (2012). · DOI
  7. D. V. Burley, D. J. Addison, “Tonga and Sāmoa in Oceanic prehistory: Contemporary debates and personal perspectives” in The Oxford Handbook of Prehistoric Oceania, E. E. Cochrane, T. L. Hunt, Eds. (Oxford University Press, New York, NY, 2018), pp. 231–251.
  8. F. J. Petchey, Radiocarbon determinations from the Mulifanua Lapita site, Upolu, Western Samoa. Radiocarbon 43, 63–68 (2001). · DOI
  9. J. T. Clark ., Refining the chronology for west polynesian colonization: New data from the Samoan archipelago. J. Archaeol. Sci. Rep. 6, 266–274 (2016).
  10. T. M. Rieth, A. E. Morrison, D. J. Addison, The temporal and spatial patterning of the initial settlement of Sāmoa. J. Island Coast. Archaeol. 3, 214–239 (2008). · DOI
  11. E. E. Cochrane, T. M. Rieth, W. R. Dickinson, Plainware ceramics from Sāmoa: Insights into ceramic chronology, cultural transmission, and selection among colonizing populations. J. Anthropol. Archaeol. 32, 499–510 (2013). · DOI
  12. E. E. Cochrane, T. M. Rieth, Sāmoan artefact provenance reveals limited artefact transfer within and beyond the archipelago. Archaeol. Ocean. 51, 150–157 (2016). · DOI · Paper page
  13. E. E. Cochrane ., Lack of suitable coastal plains likely influenced Lapita (∼2800 cal. BP) settlement of Sāmoa: Evidence from south-eastern ‘Upolu. Holocene 26, 126–135 (2016). · DOI
  14. W. R. Dickinson, R. C. Green, Geoarchaeological context of Holocene subsidence at the ferry berth Lapita site, Mulifanua, Upolu, Samoa. Geoarchaeology 13, 239–263 (1998). · DOI
  15. R. C. Green, “A retrospective view of settlement pattern studies in Samoa” in Pacific Landscapes: Archaeological Approaches, T. Ladefoged, M. Graves, Eds. (The Easter Island Foundation, 2002), pp. 125–152.
  16. J. T. Clark, “Samoan prehistory in review” in Oceanic Culture History: Essays in Honour of Roger Green, J. Davidson, G. Irwin, F. Leach, A. K. Pawley, D. Brown, Eds. (New Zealand Archaeological Association, Dunedin, New Zealand, 1996), pp. 445–460.
  17. S. J. Quintus, E. E. Cochrane, Pre-contact Samoan cultivation practices in regional and theoretical perspective. J. Island Coast. Archaeol. 13, 474–500 (2017). · DOI
  18. L. D. Holmes, Factors contributing to the cultural stability of Samoa. Anthropol. Q. 53, 188–197 (1980). · DOI
  19. P. S. Meleisea, Lagaga: A Short History of Western Samoa (University of the South Pacific, 1987).
  20. J. A. Moses, The coolie labour question and German colonial policy in Samoa, 1900-1914. J. Pac. Hist. 8, 101–124 (1973). · DOI
  21. P. Pirie, “Population growth in the Pacific Islands: The example of Western Samoa” in Man in the Pacific Islands: Essays on Geographical Change in the Pacific Island, R. G. Ward, Eds. (Oxford University Press, Oxford, UK, 1972), pp. 189–218.
  22. P. N. D. Pirie “The geography of population in Western Samoa ” PhD thesis Australian National University Canberra Australia (1963).
  23. Samoa Bureau of Statistics, 2016 CENSUS Brief No. 1 (Samoa Bureau of Statistics, 2017).
  24. D. Taliun . Sequencing of 53 831 diverse genomes from the NHLBI TOPMed program. bioRxiv:563866 (6 March 2019).
  25. R. L. Minster ., A thrifty variant in CREBRF strongly influences body mass index in Samoans. Nat. Genet. 48, 1049–1054 (2016). · DOI
  26. N. L. Hawley ., Prevalence of adiposity and associated cardiometabolic risk factors in the Samoan genome-wide association study. Am. J. Hum. Biol. 26, 491–501 (2014). · DOI
  27. R. C. Green, Linguistic, biological and cultural origins of the initial inhabitants of Remote Oceania. N. Z. J. Archaeol. 17, 5–27 (1997).
  28. D. H. Alexander, J. Novembre, K. Lange, Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009). · DOI · Paper page
  29. H. Zhou, D. Alexander, K. Lange, A quasi-Newton acceleration for high-dimensional optimization algorithms. Stat. Comput. 21, 261–273 (2011). · DOI
  30. G. Hellenthal ., A genetic atlas of human admixture history. Science 343, 747–751 (2014). · DOI · Paper page
  31. W. Fu .; NHLBI Exome Sequencing Project, Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493, 216–220 (2013). · DOI
  32. T. D. O’Connor .; NHLBI GO Exome Sequencing Project; ESP Population Genetics and Statistical Analysis Working Group, Emily Turner, Rare variation facilitates inferences of fine-scale population structure in humans. Mol. Biol. Evol. 32, 653–660 (2015). · DOI
  33. S. R. Browning, B. L. Browning, Accurate non-parametric estimation of recent effective population size from segments of identity by descent. Am. J. Hum. Genet. 97, 404–418 (2015). · DOI
  34. P. O’Brien, Tautai: Sāmoa, World History, and the Life of Taʻisi O. F. Nelson (University of Hawaiʻi Press, Honolulu, HI, 2017). · DOI
  35. R. C. Green, “Pottery from the Lagoon at Mulifanua, Upolu (Report 33)” in Archaeology in Western Samoa, R. C. Green, J. M. Davidson, Eds. (Auckland Institute and Museum, Auckland, New Zealand, 1974), vol. II, pp. 170–175.
  36. F. J. Petchey “The archaeology of Kudon: Archaeological analysis of Lapita ceramics from Mulifanua Samoa and Sigatoka Fiji " MA thesis University of Auckland Auckland New Zealand (1995).
  37. P. V. Kirch, J.-L. Rallu, The Growth and Collapse of Pacific Island Societies: Archaeological and Demographic Perspectives (University of Hawaiʻi Press, Honolulu, HI, 2007). · DOI
  38. D. V. Burley, “Archaeological demography and population growth in the Kingdom of Tonga 950 BC to the historic era” in Long Term Demographic History in the Pacific Islands, P. Kirch, J.-L. Rallu, Eds. (University of Hawaiʻi Press, Honolulu, HI, 2007), pp. 177–202.
  39. M. T. Carson, Recent Developments in Prehistory. Perspectives on Settlement Chronology, Inter-Community Relations, and Identity Formation, Polynesian Outliers: The State of the Art (University of Pittsburgh, Pittsburgh, PA, 2012).
  40. E. E. Cochrane, The evolution of migration: The case of Lapita in the Southwest Pacific. J. Archaeol. Method Theory 25, 520–558 (2018). · DOI
  41. A. Gusev ., Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population. Genetics 190, 679–689 (2012). · DOI
  42. H. Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011). · DOI
  43. C. C. Chang ., Second-generation PLINK: Rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015). · DOI · Paper page
  44. S. R. Browning, B. L. Browning, Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084–1097 (2007). · DOI
  45. International HapMap Consortium, The International HapMap project. Nature 426, 789–796 (2003). · DOI · Paper page
  46. D. Petkova, J. Novembre, M. Stephens, Visualizing spatial population structure with estimated effective migration surfaces. Nat. Genet. 48, 94–100 (2016). · DOI
  47. D. Prokopenko ., Utilizing the Jaccard index to reveal population stratification in sequencing data: A simulation study and an application to the 1000 genomes project. Bioinformatics 32, 1366–1372 (2016). · DOI
  48. B. L. Browning, S. R. Browning, Improving the accuracy and efficiency of identity by descent detection in population data. Genetics 194, 459–471 (2013). · DOI
  49. ESRI, ArcGIS Desktop: Release 10.6 (Environmental Systems Research Institute, Redlands, CA, 2017).

Cited by

Sorted by citations

Metadata

Authors
Harris, D. N., Kessler, M. D., Shetty, A. C., Weeks, D. E., Minster, R. L., Browning, S., Cochrane, E. E., Deka, R., Hawley, N. L., Reupena, M. S., Naseri, T., Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Population Genetics Working Group, McGarvey, S. T., & O’Connor, T. D.
Affiliations
  • Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201;
  • Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261;
  • Department of Biostatistics, University of Washington, Seattle, WA 98195;
  • Anthropology, The University of Auckland, Auckland 1010, New Zealand;
  • Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267;
  • Department of Epidemiology (Chronic Disease), Yale University School of Public Health, New Haven, CT 06520;
  • Lutia i Puava ae Mapu i Fagalele, Apia, Samoa 663030;
  • Ministry of Health, Government of Samoa, Apia, Samoa 663030;
  • International Health Institute, Department of Epidemiology, Brown University School of Public Health, Providence, RI 02912;
ORCID
Cochrane, Ethan E.
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2020-04-14
Volume
117
Issue
17
Pages
9458-9465
ISSN
  • 0027-8424
  • 1091-6490
DOI
10.1073/pnas.1913157117
PMC
PMC7196816
Cited by
41
References
12
Language
en
Licence
creativecommons.org/licenses/by-nc-nd/4.0/ (vor)
Funders
  • Royal Society of New Zealand (UOA1709)
  • HHS | NIH | National Cancer Institute (T32CA154274)
  • HHS | NIH | National Human Genome Research Institute (R35-HG010692-01)
  • HHS | NIH | National Heart, Lung, and Blood Institute (U01 HL137181-01)
  • NIH (R01-HL133040, R01-HL093093)

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