November 23, 2024

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

hobi #hobi

  • 1.

    Bae, C. J., Douka, K. & Petraglia, M. D. On the origin of modern humans: Asian perspectives. Science 358, eaai9067 1–7 (2017).

    Google Scholar 

  • 2.

    Shang, H., Tong, H., Zhang, S., Chen, F. & Trinkaus, E. An early modern human from Tianyuan Cave, Zhoukoudian, China. Proc. Natl. Acad. Sci. USA 104, 6573–6578 (2007).

    CAS  PubMed  Google Scholar 

  • 3.

    Pope, K. O. & Terrell, J. E. Environmental setting of human migrations in the circum-Pacific region. J. Biogeogr. 35, 1–21 (2008).

    Google Scholar 

  • 4.

    Kaifu, Y., Izuho, M. & Goebel, T. Modern human dispersal and behavior in Paleolithic Asia. in Emergence and diversity of modern human behavior in Paleolithic Asia (eds Kaifu, Y., Izuho, M., Goebel, T., Sato, H., & Ono, A.) 535–566 (Texas A & M University Press College Station, 2015).

  • 5.

    Reyes-Centeno, H., Hubbe, M., Hanihara, T., Stringer, C. & Harvati, K. Testing modern human out-of-Africa dispersal models and implications for modern human origins. J. Hum. Evol. 87, 95–106 (2015).

    PubMed  Google Scholar 

  • 6.

    Jeong, C. et al. Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc. Proc. Natl. Acad. Sci. USA 113, 7485–7490 (2016).

    CAS  PubMed  Google Scholar 

  • 7.

    HUGO Pan-Asian SNP Consortium et al. Mapping human genetic diversity in Asia. Science 326, 1541–1545 (2009).

  • 8.

    Jeong, C., Nakagome, S. & Di Rienzo, A. Deep history of East Asian populations revealed through genetic analysis of the Ainu. Genetics 202, 261–272 (2016).

    CAS  PubMed  Google Scholar 

  • 9.

    Kaifu, Y., Izuho, M., Goebel, T., Sato, H. & Ono, A. Emergence and Diversity of Modern Human Behavior in Paleolithic Asia. (Texas A&M University Press, 2015).

  • 10.

    Habu, J. Ancient Jomon of Japan. (Cambridge University Press, 2004).

  • 11.

    Lambeck, K., Yokoyama, Y. & Purcell, T. Into and out of the Last Glacial Maximum: sea-level change during Oxygen Isotope Stages 3 and 2. Quat. Sci. Rev. 21, 343–360 (2002).

    Google Scholar 

  • 12.

    Nakagawa, T. et al. Pollen/event stratigraphy of the varved sediment of Lake Suigetsu, central Japan from 15,701 to 10,217 SG vyr BP (Suigetsu varve years before present): description, interpretation, and correlation with other regions. Quat. Sci. Rev. 24, 1691–1701 (2005).

    Google Scholar 

  • 13.

    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  Google Scholar 

  • 14.

    Hofreiter, M. Ancient DNA. Oxford Bibliographies Online Datasets. https://doi.org/10.1093/obo/9780199941728-0036 (2014).

  • 15.

    Kanzawa-Kiriyama, H. et al. Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan. Anthropol. Sci. 127, 83–108 (2019). 2019.

    Google Scholar 

  • 16.

    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  Google Scholar 

  • 17.

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

    CAS  PubMed  Google Scholar 

  • 18.

    Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. USA 104, 14616–14621 (2007).

    CAS  PubMed  Google Scholar 

  • 19.

    Orlando, L. et al. True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res. 21, 1705–1719 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 20.

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

    PubMed  PubMed Central  Google Scholar 

  • 21.

    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  Google Scholar 

  • 22.

    Adachi, N., Shinoda, K.-I., Umetsu, K. & Matsumura, H. Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American. Am. J. Phys. Anthropol. 138, 255–265 (2009).

    PubMed  Google Scholar 

  • 23.

    Kanzawa-Kiriyama, H., Saso, A., Suwa, G. & Saitou, N. Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan. Anthropol. Sci. 121, 89–103 (2013).

    Google Scholar 

  • 24.

    Gamba, C. et al. Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun. 5, 5257 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 25.

    Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014).

    PubMed  Google Scholar 

  • 26.

    Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015).

    CAS  PubMed  Google Scholar 

  • 27.

    Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 28.

    Jones, E. R. et al. Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat. Commun. 6, 8912 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 29.

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

    CAS  PubMed  Google Scholar 

  • 30.

    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  Google Scholar 

  • 31.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 32.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 33.

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

    PubMed  PubMed Central  Google Scholar 

  • 34.

    Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006).

    CAS  PubMed  Google Scholar 

  • 35.

    Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl. Acad. Sci. U. S. A. 110, 2223–2227 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 36.

    Jinam, T. et al. The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations. J. Hum. Genet. 57, 787–795 (2012).

    CAS  PubMed  Google Scholar 

  • 37.

    Hanihara, K. Dual Structure Model for the Population History of the Japanese. Japan Rev. 2, 1–33 (1991).

    Google Scholar 

  • 38.

    Hanihara, K. Reanalysis of Local Variations in the Ainu Crania. Anthropol. Sci. 106, 1–15 (1998).

    Google Scholar 

  • 39.

    Shigematsu, M., Ishida, H., Goto, M. & Hanihara, T. Morphological affinities between Jomon and Ainu: reassessment based on nonmetric cranial traits. Anthropol. Sci. 112, 161–172 (2004).

    Google Scholar 

  • 40.

    Hammer, M. F. et al. Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes. J. Hum. Genet. 51, 47–58 (2006).

    PubMed  Google Scholar 

  • 41.

    Ishida, H., Hanihara, T., Kondo, O. & Fukumine, T. Craniometric divergence history of the Japanese populations. Anthropol. Sci. 117, 147–156 (2009).

    Google Scholar 

  • 42.

    Nakagome, S. et al. Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data. Mol. Biol. Evol. 32, 1533–1543 (2015).

    CAS  PubMed  Google Scholar 

  • 43.

    Yuasa, I. et al. Investigation of Japanese-specific alleles: most are of Jomon lineage. Leg. Med. 17, 52–55 (2015).

    CAS  Google Scholar 

  • 44.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 45.

    Loh, P.-R. et al. Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193, 1233–1254 (2013).

    PubMed  PubMed Central  Google Scholar 

  • 46.

    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  Google Scholar 

  • 47.

    Damgaard, P. de B. et al. 137 ancient human genomes from across the Eurasian steppes. Nature 557, 369–374 (2018).

  • 48.

    Siska, V. et al. Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago. Sci. Adv. 3, e1601877 (2017).

    PubMed  PubMed Central  Google Scholar 

  • 49.

    Moreno-Mayar, J. V. et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 553, 203–207 (2018).

    CAS  PubMed  Google Scholar 

  • 50.

    Rasmussen, M. et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 51.

    Yamagiwa, K. et al. A possible new oldest pottery group in the Southern Ryukyu Islands, Japan: comparative analysis of elemental components of potsherds from the Shiraho-Saonetabaru Cave Site. J. Archaeological Sci.: Rep. 26, 101879 (2019).

    Google Scholar 

  • 52.

    Sato, T. et al. Genome-wide SNP analysis reveals population structure and demographic history of the ryukyu islanders in the southern part of the Japanese archipelago. Mol. Biol. Evol. 31, 2929–2940 (2014).

    CAS  PubMed  Google Scholar 

  • 53.

    Stringer, C. Palaeoanthropology. Coasting out of Africa. Nature 405, 24–5 (2000). 27.

    CAS  PubMed  Google Scholar 

  • 54.

    Cordaux, R. et al. Mitochondrial DNA analysis reveals diverse histories of tribal populations from India. Eur. J. Hum. Genet. 11, 253–264 (2003).

    CAS  PubMed  Google Scholar 

  • 55.

    Cordaux, R. & Stoneking, M. South Asia, the Andamanese, and the genetic evidence for an ‘early’ human dispersal out of Africa. Am. J. Hum. Genet. 72, 1586–1590 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 56.

    Underhill, P. A. A synopsis of extant Y chromosome diversity in East Asia and Oceania. THE PEOPLING OF EAST ASIA, (eds Sagart, L., Blench, R. and Sanchez-Mazas, A.) 297–214 (2005).

  • 57.

    Jinam, T. A., Kanzawa-Kiriyama, H. & Saitou, N. Human genetic diversity in the Japanese Archipelago: dual structure and beyond. Genes Genet. Syst. 90, 147–152 (2015).

    CAS  PubMed  Google Scholar 

  • 58.

    Ishida, H. Metric and nonmetric cranial variation of the Prehistoric Okhotsk people. Anthropol. Sci. 104, 233–258 (1996).

    Google Scholar 

  • 59.

    Komesu, A. et al. Nonmetric cranial variation in human skeletal remains associated with Okhotsk culture. Anthropol. Sci. 116, 33–47 (2008).

    Google Scholar 

  • 60.

    Kaburagi, M., Ishida, H., Goto, M. & Hanihara, T. Comparative studies of the Ainu, their ancestors, and neighbors: assessment based on metric and nonmetric dental data. Anthropol. Sci. 118, 95–106 (2010).

    Google Scholar 

  • 61.

    Sato, T. et al. Origins and genetic features of the Okhotsk people, revealed by ancient mitochondrial DNA analysis. J. Hum. Genet. 52, 618–627 (2007).

    CAS  PubMed  Google Scholar 

  • 62.

    Sato, T. et al. Mitochondrial DNA haplogrouping of the Okhotsk people based on analysis of ancient DNA: an intermediate of gene flow from the continental Sakhalin people to the Ainu. Anthropol. Sci. 117, 171–180 (2009).

    Google Scholar 

  • 63.

    Trejaut, J. A. et al. Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol. 3, e247 (2005).

    PubMed  PubMed Central  Google Scholar 

  • 64.

    Kaifu, Y. & Masuyama, T. Why humeri of the Jomon people are so thick?: Imprications from its inter-site variation. Anthropological Sci. (Jpn. Ser.) 126, 133–155 (2018).

    Google Scholar 

  • 65.

    Koganei, Y. On the ritual ablation of upper canine in the stone age people of Japan. Anthropol. Sci. 33, 31–36 (1918).

    Google Scholar 

  • 66.

    Ramsey, B. C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).

    CAS  Google Scholar 

  • 67.

    Reimer, P. J. et al. IntCal13 and Marine13 radiocarbon age calibration curves 0-50,000 years cal BP. Radiocarbon 55, 1869–1887 (2013).

    CAS  Google Scholar 

  • 68.

    Kemp, B. M. & Smith, D. G. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci. Int. 154, 53–61 (2005).

    CAS  PubMed  Google Scholar 

  • 69.

    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  Google Scholar 

  • 70.

    Lindgreen, S. AdapterRemoval: easy cleaning of next generation sequencing reads. BMC Res. Notes 5, 337 (2012).

    PubMed  PubMed Central  Google Scholar 

  • 71.

    Andrews, S. & Others. FastQC: a quality control tool for high throughput sequence data.  Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc (2010).

  • 72.

    Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    PubMed  PubMed Central  Google Scholar 

  • 73.

    Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).

    PubMed  PubMed Central  Google Scholar 

  • 74.

    Ishiya, K. & Ueda, S. MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing. PeerJ 5, e3406 (2017).

    PubMed  PubMed Central  Google Scholar 

  • 75.

    Ayub, Q. et al. The Kalash genetic isolate: ancient divergence, drift, and selection. Am. J. Hum. Genet. 96, 775–783 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 76.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 77.

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

    PubMed  Google Scholar 

  • 78.

    Raghavan, M. et al. The genetic prehistory of the New World Arctic. Science 345, 1255832 (2014).

    PubMed  Google Scholar 

  • 79.

    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  Google Scholar 

  • 80.

    Raghavan, M. et al. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 349, aab3884 (2015).

  • 81.

    Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 82.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 83.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 84.

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

    PubMed  PubMed Central  Google Scholar 

  • 85.

    Jinam, T. et al. The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations. J. Hum. Genet. 57, 787–795 (2012).

    CAS  PubMed  Google Scholar 

  • 86.

    Skoglund, P. et al. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336, 466–469 (2012).

    CAS  PubMed  Google Scholar 

  • 87.

    Behr, A. A., Liu, K. Z., Liu-Fang, G., Nakka, P. & Ramachandran, S. pong: fast analysis and visualization of latent clusters in population genetic data. Bioinformatics 32, 2817–2823 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 88.

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • 89.

    Rasmussen, M. et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • Leave a Reply