Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages

Proceedings of the Royal Society B: Biological Sciences

Volumn 278, Issue 1725, 2011, Pages 3662-3669

  Lee, Sean ^a   Hasegawa, Toshikazu ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Japonic languages; Linguistic evolution; Phylogenetics

Indexed keywords

AGRICULTURAL INTENSIFICATION; AGRICULTURAL WORKER; ANCESTRY; ARCHAEOLOGICAL EVIDENCE; BAYESIAN ANALYSIS; DATA SET; EVOLUTIONARY BIOLOGY; LANGUAGE; PHYLOGENETICS; PHYLOGENY; RANGE EXPANSION;

JAPAN;

EID: 80855164613     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2011.0518     Document Type: Article

References (60)

1. Diamond, J. & Bellwood, P. 2003 Farmers and their languages: the first expansions. Science 300, 597-603. (doi:10.1126/science.1078208)
2. Campbell, L. 2003 What drives linguistic diversification and language spread? In Examining the farming/language dispersal hypothesis (eds P. Bellwood & C. Renfrew), pp. 49-63. Cambridge, UK: McDonald Institute for Archaeological Research.
3. Welsch, R., Terrell, J. & Nadolski, J. 1992 Language and culture on the north coast of New Guinea. Am. Anthropol. 94, 568-600. (doi:10.1525/aa.1992.94.3. 02a00030)
4. Bergsland, K. & Vogt, H. 1962 On the validity of glottochronology. Curr. Anthropol. 3, 115-153. (doi:10.1086/200264)
5. Blust, R. 2000 Why lexicostatistics doesn't work: the 'universal constant' hypothesis and the Austronesian languages. In Time depth in historical linguistics (eds C. Renfrew, A. McMahon & L. Trask), pp. 311-332. Cambridge, UK: McDonald Institute for Archaeological Research.
6. Atkinson, Q. D. & Gray, R. D. 2005 Curious parallels and curious connections: phylogenetic thinking in biology and historical linguistics. Syst. Biol. 54, 513-526. (doi:10.1080/10635150590950317)
7. Pagel, M. 2009 Human language as a culturally transmitted replicator. Nat. Rev. Genet. 10, 405-415.(doi:10.1038/nrg2560)
8. Holden, C. J., Meade, A. & Pagel, M. 2005 Comparison of maximum parsimony and Bayesian Bantu language trees. In The evolution of cultural diversity: a phylogenetic approach (eds R. Mace, C. J. Holden & S. Shennan), pp. 53-65. London, UK: UCL Press.
9. Gray, R. D. & Atkinson, Q. D. 2003 Language-tree divergence times support the Anatolian theory of Indo-European origin. Nature 426, 435-439. (doi:10.1038/nature02029)
10. Gray, R. D., Drummond, A. J. & Greenhill, S. J. 2009 Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 323, 479-483. (doi:10.1126/science.1166858)
11. Lewis, M. P. 2009 Ethnologue: languages of the world. Dallas, TX: SIL International.
12. Hudson, M. 1999 Ruins of identity: ethnogenesis in the Japanese Islands. Honolulu, HI: University of Hawaii'i Press.
13. Dodo, Y., Doi, N. & Kondo, O. 1998 Ainu and Ryukyuan cranial nonmetric variation: evidence which disputes the Ainu-Ryukyu common origin theory. Anthropol. Sci. 106, 99-120.
14. Matsumura, H. 2001 Differentials of Yayoi immigration to Japan as derived from dental metrics. HOMO J. Compar. Hum. Biol. 52, 135-156. (doi:10.1078/0018-442X-00025)
15. Hammer, M. F., Karafet, T. M., Park, H., Omoto, K., Harihara, S., Stoneking, M. & Horai, S. 2006 Dual origins of the Japanese: common ground for hunter- gatherer and farmer Y chromosomes. J. Hum. Genet. 51, 47-58. (doi:10.1007/s10038-005-0322-0)
16. Suzuki, H. 1981 Racial history of the Japanese. Rassengeschichte der Menschheit 8, 7-69.
17. Nei, M. 1995 The origins of human populations: Genetic, linguistic, and archeological data. In The origin and past of modern humans as viewed from DNA (eds S. Brenner & K. Hanihara), pp. 71-91. Singapore, Singapore: World Scientific Publishing.
18. Greenhill, S. J., Blust, R. & Gray, R. D. 2008 The Austronesian basic vocabulary database: from bioinformatics to lexomics. Evol. Bioinfo. 4, 271-283.
19. Embleton, S. M. 1986 Statistics in historical linguistics. Bochum, Germany: Brockmeyer.
20. Jodaigo Jiten HenshuIinkai. 1967 Jidaibetsu kokugo daijiten. Jōdai hen. Tokyo, Japan: Sanseidō
21. Yasumoto, B. & Honda, M. 1978 Nihongo no Tanjyō. Tokyo, Japan: Taishūkan Shoten.
22. Muromachi Jidaigo Jiten Henshu Iinkai 2001 Jidaibetsu kokugo daijiten: Muromachi jidai hen. Tokyo, Japan: Sanseidō
23. Hirayama, T. 1988 Minami Ryukyū no Hōgenkisogoi. Tokyo, Japan: Ohfusya.
24. Hirayama, T. 1992 Gendai Nihongohōgen Daijiten. Tokyo, Japan: Meiji Shoin.
25. Frellesvig, B. & Whitman, J. 2008 Proto-Japanese: issues and prospects. Amsterdam, The Netherlands: John Benjamins Publishing Co.
26. Crowley, T. & Bowern, C. 2009 An introduction to historical linguistics. Oxford, London: Oxford University Press.
27. Hattori, S. 1961 A glottochronological study on three Okinawan dialects. Int. J. Am. Ling. 27, 52-62. (doi:10.1086/464603)
28. Hattori, S. 1978-1979 Nihon sogo ni tsuite. Gekkan gengo, vols 7-8.
29. Drummond, A. J. & Rambaut, A. 2007 BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214. (doi:10.1186/1471-2148-7-214)
30. Kitchen, A., Ehret, C., Assefa, S. & Mulligan, C. J. 2009 Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East. Proc. R. Soc. B 276, 2703-2710. (doi:10.1098/rspb.2009.0408)
31. Yang, Z. 1996 Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11, 367-372. (doi:10.1016/0169-5347(96)10041-0)
32. Penny, D., McComish, B., Charleston, M. & Hendy, M. 2001 Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J. Mol. Evol. 53, 711-723. (doi:10.1007/s002390010258)
33. Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. 2006 Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88. (doi:10.1371/journal.pbio.0040088)
34. Shapiro, B., Ho, S.Y.W., Drummond, A. J., Suchard, M.A., Pybus, O. G. & Rambaut, A. 2011 A Bayesian phylogenetic method to estimate unknown sequence ages. Mol. Biol. Evol. 28, 879-887. (doi:10.1093/molbev/msq262)
35. Clarke, H. 1989 The development of Edo language. In 18th century Japan: culture and society (ed. C. A. Gerstle), pp. 63-72. Richmond, UK: Curzon Press.
36. Twine, N. 1988 Standardizing written Japanese. A factor in modernization. Monum. Nippon 43, 429-454. (doi:10.2307/2384796)
37. Rambaut, A. & Drummond, A. J. 2007. TRACER v. 1. 5. See http://beast.bio.ed.ac.uk/Tracer.
38. Newton, M. A. & Raftery, A. E. 1994 Approximate Bayesian inference with the weighted likelihood bootstrap. J. R. Stat. Soc. B 56, 3-48.
39. Suchard, M., Weiss, R., Dorman, K., Patel, M., McCabe, E. & Sinsheimer, J. 2000 Evolutionary similarity among genes when data are sparse. In Proceedings of the Section on Bayesian Statistical Science, pp. 92-97. Alexandria, VA: American Statistical Assocation.
40. Raftery, A. 1996 Hypothesis testing and model selection. In Markov chain Monte Carlo in practice (eds W. R. Gilks, S. Richardson & D. J. Speigelhalter), pp. 163-187. New York, NY: Chapman & Hall.
41. Starostin, S. A., Dybo, A. V. & Mudrak, O. A. 2003 Etymological dictionary of the Altaic languages. Leiden, The Netherlands: Brill Academic Publishers.
42. Hock, H. H. 1986 Principles of historical linguistics. Berlin, Germany: Mouton de Gruyter.
43. Huson, D. H. & Bryant, D. 2006 Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254-267. (doi:10.1093/molbev/msj030)
44. Gray, R. D., Bryant, D. & Greenhill, S. J. 2010 On the shape and fabric of human history. Phil. Trans. R. Soc. B 365, 3923-3933. (doi:10.1098/rstb.2010.0162)
45. Garrett, A. 2006 Convergence in the formation of Indo-European subgroups: phylogeny and chronology. In Phylogenetic methods and the prehistory of languages (eds P. Forster & C. Renfrew), pp. 139-151. Cambridge, UK: McDonald Institute for Archaeological Research.
46. Koyama, S., Thomas, D. H. & Hakubutsukan, K. M. (eds) 1982 Affluent foragers: Pacific coasts east and west. Osaka, Japan: The National Museum of Ethnology.
47. Habu, J. 2004 Ancient Jomon of Japan. Cambridge, UK: Cambridge University Press.
48. Diamond, J. M. 1997 Guns, germs, and steel: the fates of human societies. New York, NY: W.W. Norton & Company.
49. Nelson, S. M. 1993 The archaeology of Korea. Cambridge, UK: Cambridge University Press.
50. Nakahashi, T. 2005 Nihonjin no kigen. Tokyo, Japan: Kodansha.
51. Benedict, P. K. 1990 Japanese/Austro-Tai. Ann Arbor, MI: Karoma.
52. The HUGO Pan-Asian SNP Consortium 2009 Mapping human genetic diversity in Asia. Science 326, 1541-1545. (doi:10.1126/science.1177074)
53. Greenhill, S. J., Currie, T. E. & Gray, R. D. 2009 Does horizontal transmission invalidate cultural phylogenies? Proc. R. Soc. B 276, 2299-2306. (doi:10.1098/rspb.2008.1944)
54. Haspelmath, M. & Tadmor, U. 2009 Loanwords in the world's languages: a comparative handbook. Berlin, Germany: Mouton de Gruyter.
55. Pagel, M. 2000 Maximum-likelihood models for glottochronology and for reconstructing linguistic phylogenies. In Time depth in historical linguistics (eds C. Renfrew, A. McMahon & L. Trask), pp. 189-207. Cambridge, UK: McDonald Institute for Archaeological Research.
56. Atkinson, Q. D., Meade, A., Venditti, C., Greenhill, S. J. & Pagel, M. 2008 Languages evolve in punctuational bursts. Science 319, 588. (doi:10.1126/science.1149683)
57. Pagel, M., Atkinson, Q. D. & Meade, A. 2007 Frequency of word-use predicts rates of lexical evolution throughout Indo-European history. Nature 449, 717-720. (doi:10.1038/nature06176)
58. Lieberman, E., Michel, J. B., Jackson, J., Tang, T. & Nowak, M. A. 2007 Quantifying the evolutionary dynamics of language. Nature 449, 713-716. (doi:10.1038/nature06137)
59. Reali, F. & Griffiths, T. L. 2010 Words as alleles: connecting language evolution with Bayesian learners to models of genetic drift. Proc. R. Soc. B 277, 429-436. (doi:10.1098/rspb.2009.1513)
60. Kirby, S., Cornish, H. & Smith, K. 2008 Cumulative cultural evolution in the laboratory: an experimental approach to the origins of structure in human language. Proc. Natl Acad. Sci. USA 105, 10 681-10 686. (doi:10.1073/pnas.0707835105)