Genomic insights into population history and biological adaptation in Oceania

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  • 1.

    Gosling, A. L. & Matisoo-Smith, E. A. The evolutionary history and human settlement of Australia and the Pacific. Curr. Opin. Genet. Dev. 53, 53–59 (2018).

    PubMed 
    Article 
    CAS 

    Google Scholar
     

  • 2.

    Hung, H.-C. & Carson, M. T. Foragers, fishers and farmers: origins of the Taiwanese Neolithic. Antiquity 88, 1115–1131 (2014).

    Article 

    Google Scholar
     

  • 3.

    Gray, R. D., Drummond, A. J. & Greenhill, S. J. Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 323, 479–483 (2009).

    ADS 
    PubMed 
    Article 
    CAS 

    Google Scholar
     

  • 4.

    Bellwood, P. First Farmers: the Origins of Agricultural Societies (Blackwell, 2005).

  • 5.

    O’Connell, J. F. et al. When did Homo sapiens first reach Southeast Asia and Sahul? Proc. Natl Acad. Sci. USA 115, 8482–8490 (2018).

    PubMed 
    Article 
    CAS 

    Google Scholar
     

  • 6.

    Kirch, P. V. On the Road of the Winds: An Archeological History of the Pacific Islands before European Contact (Univ. California Press, 2017).

  • 7.

    Wollstein, A. et al. Demographic history of Oceania inferred from genome-wide data. Curr. Biol. 20, 1983–1992 (2010).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 8.

    Lipson, M. et al. Population turnover in Remote Oceania shortly after initial settlement. Curr. Biol. 28, 1157–1165 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 9.

    Skoglund, P. et al. Genomic insights into the peopling of the Southwest Pacific. Nature 538, 510–513 (2016).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 10.

    Posth, C. et al. Language continuity despite population replacement in Remote Oceania. Nat. Ecol. Evol. 2, 731–740 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 11.

    Pugach, I. et al. The gateway from Near into Remote Oceania: new insights from genome-wide data. Mol. Biol. Evol. 35, 871–886 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 12.

    Bergström, A. et al. A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea. Science 357, 1160–1163 (2017).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 13.

    Ioannidis, A. G. et al. Native American gene flow into Polynesia predating Easter Island settlement. Nature 583, 572–577 (2020).

    ADS 
    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 14.

    Qin, P. & Stoneking, M. Denisovan ancestry in East Eurasian and Native American populations. Mol. Biol. Evol. 32, 2665–2674 (2015).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 15.

    Reich, D. et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am. J. Hum. Genet. 89, 516–528 (2011).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 16.

    Vernot, B. et al. Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science 352, 235–239 (2016).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 17.

    Sankararaman, S., Mallick, S., Patterson, N. & Reich, D. The combined landscape of Denisovan and Neanderthal ancestry in present-day humans. Curr. Biol. 26, 1241–1247 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 18.

    Malaspinas, A. S. et al. A genomic history of Aboriginal Australia. Nature 538, 207–214 (2016).

    ADS 
    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 19.

    Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 20.

    Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).

    ADS 
    Article 
    CAS 

    Google Scholar
     

  • 21.

    Prüfer, K. et al. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358, 655–658 (2017).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 22.

    Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 23.

    Lipson, M. et al. Three phases of ancient migration shaped the ancestry of human populations in Vanuatu. Curr. Biol. 30, 4846–4856 (2020).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 24.

    Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V. C. & Foll, M. Robust demographic inference from genomic and SNP data. PLoS Genet. 9, e1003905 (2013).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 25.

    Larena, M. et al. Multiple migrations to the Philippines during the last 50,000 years. Proc. Natl Acad. Sci. USA, https://doi.org/10.1073/pnas.2026132118 (2021).

  • 26.

    Yang, M. A. et al. Ancient DNA indicates human population shifts and admixture in northern and southern China. Science 369, 282–288 (2020).

    ADS 
    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 27.

    Rieth, T. M. & Athens, J. S. Late Holocene human expansion into Near and Remote Oceania: a Bayesian model of the chronologies of the Mariana Islands and Bismarck Archipelago. J. Island Coast. Archaeol. 14, 5–16 (2019).

    Article 

    Google Scholar
     

  • 28.

    Browning, S. R., Browning, B. L., Zhou, Y., Tucci, S. & Akey, J. M. Analysis of human sequence data reveals two pulses of archaic Denisovan admixture. Cell 173, 53–61 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 29.

    Jacobs, G. S. et al. Multiple deeply divergent Denisovan ancestries in Papuans. Cell 177, 1010–1021 (2019).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 30.

    Détroit, F. et al. A new species of Homo from the Late Pleistocene of the Philippines. Nature 568, 181–186 (2019).

    ADS 
    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 31.

    Gittelman, R. M. et al. Archaic hominin admixture facilitated adaptation to out-of-Africa environments. Curr. Biol. 26, 3375–3382 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 32.

    Racimo, F., Marnetto, D. & Huerta-Sánchez, E. Signatures of archaic adaptive introgression in present-day human populations. Mol. Biol. Evol. 34, 296–317 (2017).

    PubMed 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 33.

    Simonti, C. N. et al. The phenotypic legacy of admixture between modern humans and Neandertals. Science 351, 737–741 (2016).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 34.

    Vitale, C. et al. Surface expression and function of p75/AIRM-1 or CD33 in acute myeloid leukemias: engagement of CD33 induces apoptosis of leukemic cells. Proc. Natl Acad. Sci. USA 98, 5764–5769 (2001).

    ADS 
    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 35.

    Negishi, H. et al. Negative regulation of Toll-like-receptor signaling by IRF-4. Proc. Natl Acad. Sci. USA 102, 15989–15994 (2005).

    ADS 
    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 36.

    Hedblom, E. & Kirkness, E. F. A novel class of GABAA receptor subunit in tissues of the reproductive system. J. Biol. Chem. 272, 15346–15350 (1997).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 37.

    Hoffmann, T. J. et al. A large multiethnic genome-wide association study of adult body mass index identifies novel loci. Genetics 210, 499–515 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 38.

    Lee, I. H. et al. Atg7 modulates p53 activity to regulate cell cycle and survival during metabolic stress. Science 336, 225–228 (2012).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 39.

    Giri, A. et al. Trans-ethnic association study of blood pressure determinants in over 750,000 individuals. Nat. Genet. 51, 51–62 (2019).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 40.

    Sakaue, S. et al. Functional variants in ADH1B and ALDH2 are non-additively associated with all-cause mortality in Japanese population. Eur. J. Hum. Genet. 28, 378–382 (2020).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 41.

    Perttilä, J. et al. OSBPL10, a novel candidate gene for high triglyceride trait in dyslipidemic Finnish subjects, regulates cellular lipid metabolism. J. Mol. Med. 87, 825–835 (2009).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 42.

    Sierra, B. et al. OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans. PLoS Pathog. 13, e1006220 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 43.

    Gao, X. R., Huang, H. & Kim, H. Genome-wide association analyses identify 139 loci associated with macular thickness in the UK Biobank cohort. Hum. Mol. Genet. 28, 1162–1172 (2019).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 44.

    Sella, G. & Barton, N. H. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annu. Rev. Genomics Hum. Genet. 20, 461–493 (2019).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 45.

    Bycroft, C. et al. The UK Biobank resource with deep phenotyping and genomic data. Nature 562, 203–209 (2018).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 46.

    Field, Y. et al. Detection of human adaptation during the past 2000 years. Science 354, 760–764 (2016).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 47.

    Berg, J. J. et al. Reduced signal for polygenic adaptation of height in UK Biobank. eLife 8, e39725 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 48.

    Brown, P. et al. A new small-bodied hominin from the Late Pleistocene of Flores, Indonesia. Nature 431, 1055–1061 (2004).

    ADS 
    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 49.

    Gouy, A. & Excoffier, L. Polygenic patterns of adaptive introgression in modern humans are mainly shaped by response to pathogens. Mol. Biol. Evol. 37, 1420–1433 (2020).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 50.

    Gosling, A. L., Buckley, H. R., Matisoo-Smith, E. & Merriman, T. R. Pacific populations, metabolic disease and ‘just-so stories’: a critique of the ‘thrifty genotype’ hypothesis in Oceania. Ann. Hum. Genet. 79, 470–480 (2015).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 51.

    R Core Team. R: A language and environment for statistical computing. http://www.R-project.org/ (R Foundation for Statistical Computing, 2013).

  • 52.

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 53.

    DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 54.

    McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 55.

    Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 56.

    Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 57.

    Manichaikul, A. et al. Robust relationship inference in genome-wide association studies. Bioinformatics 26, 2867–2873 (2010).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 58.

    Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 59.

    Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 60.

    Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 61.

    Barrett, J. C., Fry, B., Maller, J. & Daly, M. J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265 (2005).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 62.

    1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015).

    Article 
    CAS 

    Google Scholar
     

  • 63.

    Excoffier, L., Smouse, P. E. & Quattro, J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479–491 (1992).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 64.

    Meyer, L. R. et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 41, D64–D69 (2013).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 65.

    de Manuel, M. et al. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 354, 477–481 (2016).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 66.

    Sikora, M. et al. The population history of northeastern Siberia since the Pleistocene. Nature 570, 182–188 (2019).

    ADS 
    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 67.

    Schiffels, S. & Durbin, R. Inferring human population size and separation history from multiple genome sequences. Nat. Genet. 46, 919–925 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 68.

    Fenner, J. N. Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. Am. J. Phys. Anthropol. 128, 415–423 (2005).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 69.

    Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 70.

    Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 71.

    Excoffier, L. & Lischer, H. E. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567 (2010).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 72.

    Beaumont, M. A., Zhang, W. & Balding, D. J. Approximate Bayesian computation in population genetics. Genetics 162, 2025–2035 (2002).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 73.

    Tavaré, S., Balding, D. J., Griffiths, R. C. & Donnelly, P. Inferring coalescence times from DNA sequence data. Genetics 145, 505–518 (1997).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 74.

    Fortes-Lima, C. A., Laurent, L., Thouzeau, V., Toupance, B. & Verdu, P. Complex genetic admixture histories reconstructed with approximate Bayesian computations. Mol. Ecol. Resour. https://doi.org/10.1111/1755-0998.13325 (2021).

  • 75.

    Verdu, P. & Rosenberg, N. A. A general mechanistic model for admixture histories of hybrid populations. Genetics 189, 1413–1426 (2011).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 76.

    Gravel, S. Population genetics models of local ancestry. Genetics 191, 607–619 (2012).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 77.

    Liang, M. & Nielsen, R. The lengths of admixture tracts. Genetics 197, 953–967 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 78.

    Csilléry, K., François, O. & Blum, M. G. B. abc: an R package for approximate Bayesian computation (ABC). Methods Ecol. Evol. 3, 475–479 (2012).

    Article 

    Google Scholar
     

  • 79.

    Pudlo, P. et al. Reliable ABC model choice via random forests. Bioinformatics 32, 859–866 (2016).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 80.

    Maples, B. K., Gravel, S., Kenny, E. E. & Bustamante, C. D. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. Am. J. Hum. Genet. 93, 278–288 (2013).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 81.

    Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 82.

    Sankararaman, S. et al. The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507, 354–357 (2014).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 83.

    Delaneau, O., Marchini, J. & Zagury, J. F. A linear complexity phasing method for thousands of genomes. Nat. Methods 9, 179–181 (2012).

    Article 
    CAS 

    Google Scholar
     

  • 84.

    Delaneau, O., Zagury, J. F. & Marchini, J. Improved whole-chromosome phasing for disease and population genetic studies. Nat. Methods 10, 5–6 (2013).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 85.

    Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 86.

    Kutmon, M. et al. WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res. 44, D488–D494 (2016).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 87.

    Buniello, A. et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47, D1005–D1012 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 88.

    The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29 (2000).

    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 89.

    Deschamps, M. et al. genomic signatures of selective pressures and introgression from archaic hominins at human innate immunity genes. Am. J. Hum. Genet. 98, 5–21 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 90.

    Enard, D. & Petrov, D. A. Evidence that RNA viruses drove adaptive introgression between Neanderthals and modern humans. Cell 175, 360–371 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 91.

    Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 92.

    Rentzsch, P., Witten, D., Cooper, G. M., Shendure, J. & Kircher, M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 47, D886–D894 (2019).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 93.

    ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).

    ADS 
    Article 
    CAS 

    Google Scholar
     

  • 94.

    Shriver, M. D. et al. The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum. Genomics 1, 274–286 (2004).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 95.

    Sabeti, P. C. et al. Genome-wide detection and characterization of positive selection in human populations. Nature 449, 913–918 (2007).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 96.

    Speidel, L., Forest, M., Shi, S. & Myers, S. R. A method for genome-wide genealogy estimation for thousands of samples. Nat. Genet. 51, 1321–1329 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 97.

    GenomeAsia100K Consortium. The GenomeAsia 100K Project enables genetic discoveries across Asia. Nature 576, 106–111 (2019).

    ADS 
    Article 
    CAS 

    Google Scholar
     



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