Genome of a middle Holocene hunter-gatherer from Wallacea

  • 1.

    McColl, H. et al. The prehistoric peopling of Southeast Asia. Science 361, 88–92 (2018).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 2.

    Hasanuddin. Gua Panningnge di Mallawa, Maros: kajian tentang gua hunian berdasarkan artefak batu dan sisa fauna. Naditira Widya 11, 81–96 (2017).

    Article 

    Google Scholar
     

  • 3.

    Bulbeck, D., Pasqua, M. & Di Lello, A. Culture history of the Toalean of South Sulawesi, Indonesia. Asian Perspect. 39, 71–108 (2000).

    Article 

    Google Scholar
     

  • 4.

    Perston, Y. L. et al. A standardised classification scheme for the mid-Holocene Toalean artefacts of South Sulawesi, Indonesia. PLoS ONE 16, e0251138 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 5.

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

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 6.

    Pugach, I., Delfin, F., Gunnarsdóttir, E., Kayser, M. & Stoneking, M. Genome-wide data substantiate Holocene gene flow from India to Australia. Proc. Natl Acad. Sci. USA 110, 1803–1808 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 7.

    Rasmussen, M. et al. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334, 94–98 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 8.

    Teixeira, J. C. & Cooper, A. Using hominin introgression to trace modern human dispersals. Proc. Natl Acad. Sci. USA 116, 15327–15332 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 9.

    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 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 10.

    Clarkson, C. et al. Human occupation of northern Australia by 65,000 years ago. Nature 547, 306–310 (2017).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 11.

    Brumm, A. et al. Oldest cave art found in Sulawesi. Sci. Adv. 7, eabd4648 (2021).

    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 12.

    Sutikna, T. et al. The spatio-temporal distribution of archaeological and faunal finds at Liang Bua (Flores, Indonesia) in light of the revised chronology for Homo floresiensis. J. Hum. Evol. 124, 52–74 (2018).

    PubMed 
    Article 

    Google Scholar
     

  • 13.

    Samper Carro, S. C. et al. Somewhere beyond the sea: human cranial remains from the Lesser Sunda Islands (Alor Island, Indonesia) provide insights on Late Pleistocene peopling of Island Southeast Asia. J. Hum. Evol. 134, 102638 (2019).

    PubMed 
    Article 

    Google Scholar
     

  • 14.

    Bird, M. I. et al. Early human settlement of Sahul was not an accident. Sci. Rep. 9, 8220 (2019).

    PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar
     

  • 15.

    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.e9 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 16.

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

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • 17.

    Jacobs, G. S. et al. Multiple deeply divergent Denisovan ancestries in Papuans. Cell 177, 1010–1021.e32 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 18.

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

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 19.

    Reich, D. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053–1060 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 20.

    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).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 21.

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

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 22.

    Choin, J. et al. Genomic insights into population history and biological adaptation in Oceania. Nature 592, 583–589 (2021).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 23.

    Teixeira, J. C. et al. Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture. Nat. Ecol. Evol. 5, 616–624 (2021).

    PubMed 
    Article 

    Google Scholar
     

  • 24.

    Mondal, M., Bertranpetit, J. & Lao, O. Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania. Nat. Commun. 10, 246 (2019).

    PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar
     

  • 25.

    Mondal, M. et al. Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nat. Genet. 48, 1066–1070 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 26.

    Lipson, M. et al. Reconstructing Austronesian population history in Island Southeast Asia. Nat. Commun. 5, 4689 (2014).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 27.

    Suryatman, et al. Artefak batu preneolitik situs Leang Jarie: bukti teknologi Maros Point tertua di Kawasan budaya Toalean, Sulawesi Selatan. AMERTA 37, 1–17 (2019).

    Article 

    Google Scholar
     

  • 28.

    Anggraeni, A., Simanjuntak, T., Bellwood, P. & Piper, P. Neolithic foundations in the Karama valley, West Sulawesi, Indonesia. Antiquity 88, 740–756 (2014).

    Article 

    Google Scholar
     

  • 29.

    Pawlik, A., Croxier, R., Fuentes, R., Wood, R. & Piper, P. Burial traditions in early mid-Holocene Island Southeast Asia: new evidence from Bubog-1, Ilin Island, Mindoro Occidental. Antiquity 93, 901–918 (2019).

    Article 

    Google Scholar
     

  • 30.

    Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 31.

    Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 32.

    Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 33.

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

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 34.

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

    PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar
     

  • 35.

    Kanzawa-Kiriyama, H. et al. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J. Hum. Genet. 62, 213–221 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 36.

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

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 37.

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

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 38.

    Yang, M. A. et al. 40,000-year-old individual from Asia provides insight into early population structure in Eurasia. Curr. Biol. 27, 3202–3208.e9 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 39.

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

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 40.

    Bergström, A. et al. Insights into human genetic variation and population history from 929 diverse genomes. Science 367, eaay5012 (2020).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 41.

    Peter, B. M. 100,000 years of gene flow between Neandertals and Denisovans in the Altai mountains. Preprint at doi.org/10.1101/2020.03.13.990523 (2020).

  • 42.

    Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 43.

    Sikora, M. et al. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 358, 659–662 (2017).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 44.

    Aubert, M. et al. Pleistocene cave art from Sulawesi, Indonesia. Nature 514, 223–227 (2014).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 45.

    Aubert, M. et al. Earliest hunting scene in prehistoric art. Nature 576, 442–445 (2019).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 46.

    van den Bergh, G. D. et al. Earliest hominin occupation of Sulawesi, Indonesia. Nature 529, 208–211 (2016).

    PubMed 
    Article 
    ADS 
    CAS 

    Google Scholar
     

  • 47.

    Wang, C.-C. et al. Genomic insights into the formation of human populations in East Asia. Nature 591, 413–419 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 48.

    Bellwood, P. First Islanders: Prehistory and Human Migration in Island Southeast Asia (Wiley Blackwell, 2017).

  • 49.

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

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 50.

    Fu, Q. et al. The genetic history of Ice Age Europe. Nature 534, 200–205 (2016).

  • 51.

    Scott, G. R. & Turner, C. G. II. The Anthropology of Modern Human Teeth: Dental Morphology and its Variation in Recent Human Populations (Cambridge Univ. Press, 1997).

  • 52.

    Hillson, S. Dental Anthropology (Cambridge Univ. Press, 1996).

  • 53.

    Pinhasi, R. et al. Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS ONE 10, e0129102 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 54.

    Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 55.

    Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. Lond. B 370, 20130624 (2015).

    Article 
    CAS 

    Google Scholar
     

  • 56.

    Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & Meyer, M. Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat. Protoc. 15, 2279–2300 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 57.

    Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 58.

    Peltzer, A. et al. EAGER: efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 59.

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

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 60.

    Peyrégne, S. & Peter, B. M. AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination. Genome Biol. 21, 246 (2020).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 61.

    Renaud, G., Slon, V., Duggan, A. T. & Kelso, J. Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biol. 16, 224 (2015).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 62.

    Vianello, D. et al. HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment. Hum. Mutat. 34, 1189–1194 (2013).

    PubMed 
    Article 

    Google Scholar
     

  • 63.

    Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 64.

    Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 65.

    Skoglund, P. et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl Acad. Sci. USA 111, 2229–2234 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • 66.

    Patterson, N., Richter, D. J., Gnerre, S., Lander, E. S. & Reich, D. Genetic evidence for complex speciation of humans and chimpanzees. Nature 441, 1103–1108 (2006).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • 67.

    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
     

  • 68.

    Narasimhan, V. M. et al. The formation of human populations in South and Central Asia. Science 365, eaat7487 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Read more here: Source link