Human population history revealed by a supertree approach

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Duda, Pavel ^a   Zrzavý, Jan ^b  

^a UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

^b INSTITUTE OF MATHEMATICS   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

CLADISTICS; COEVOLUTION; HUMAN; HUMAN EXPERIMENT; KHOISAN; LANGUAGE; MELANESIA; PYGMY; AFRICA SOUTH OF THE SAHARA; ALGORITHM; GENETICS; HISTORY; LINGUISTICS; PHYLOGENY; POPULATION GENETICS; WHOLE GENOME SEQUENCING; Y CHROMOSOME;

MITOCHONDRIAL DNA;

AFRICA SOUTH OF THE SAHARA; ALGORITHMS; CHROMOSOMES, HUMAN, Y; DNA, MITOCHONDRIAL; GENETICS, POPULATION; HISTORY, ANCIENT; HUMANS; LINGUISTICS; PHYLOGENY; WHOLE GENOME SEQUENCING;

EID: 84978943233     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep29890     Document Type: Article

References (60)

1. Templeton, A. R. Biological races in humans. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44, 262-271, doi: http: //dx. doi. org/10. 1016/j. shpsc. 2013. 04. 010 (2013).
2. Hellenthal, G. et al. A Genetic Atlas of Human Admixture History. Science 343, 747-751, doi: 10. 1126/science. 1243518 (2014).
3. Li, J. Z. et al. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319, 1100-1104, doi: 10. 1126/science. 1153717 (2008).
4. Tishkoff, S. A. et al. The genetic structure and history of Africans and African Americans. Science 324, 1035-1044, doi: 10. 1126/ science. 1172257 (2009).
5. Mace, R. & Holden, C. J. A phylogenetic approach to cultural evolution. Trends in ecology & evolution 20, 116-121, doi: 10. 1016/j. Tree. 2004. 12. 002 (2005).
6. Pagel, M. Human language as a culturally transmitted replicator. Nature Reviews Genetics 10, 405-415, doi: 10. 1038/nrg2560 (2009).
7. Mace, R. & Jordan, F. M. Macro-evolutionary studies of cultural diversity: A review of empirical studies of cultural transmission and cultural adaptation. Philosophical Transactions of the Royal Society B-Biological Sciences 366, 402-411, doi: 10. 1098/rstb. 2010. 0238 (2011).
8. Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLOS Genetics 8, doi: 10. 1371/journal. pgen. 1002967 (2012).
9. Lipson, M. et al. Reconstructing Austronesian population history in Island Southeast Asia. Nature Communications 5, 7, doi: 10. 1038/ncomms5689 (2014).
10. Nelson-Sathi, S. et al. Networks uncover hidden lexical borrowing in Indo-European language evolution. Proceedings of the Royal Society B-Biological Sciences 278, 1794-1803, doi: 10. 1098/rspb. 2010. 1917 (2011).
11. Veeramah, K. R. & Hammer, M. F. The impact of whole-genome sequencing on the reconstruction of human population history. Nature Reviews Genetics 15, 149-162, doi: 10. 1038/nrg3625 (2014).
12. Pemberton, T. J., DeGiorgio, M. & Rosenberg, N. A. Population structure in a comprehensive genomic data set on human microsatellite variation. G3-Genes Genomes Genetics 3, 891-907, doi: 10. 1534/g3. 113. 005728 (2013).
13. Shriner, D., Tekola-Ayele, F., Adeyemo, A. & Rotimi, C. N. Genome-wide genotype and sequence-based reconstruction of the 140, 000 year history of modern human ancestry. Scientific Reports 4, doi: 10. 1038/srep06055 (2014).
14. Currie, T. E., Meade, A., Guillon, M. & Mace, R. Cultural phylogeography of the Bantu Languages of sub-Saharan Africa. Proceedings of the Royal Society B-Biological Sciences 280, 8, doi: 10. 1098/rspb. 2013. 0695 (2013).
15. Pagel, M., Atkinson, Q. D., Calude, A. S. & Meade, A. Ultraconserved words point to deep language ancestry across Eurasia. Proceedings of the National Academy of Sciences of the United States of America 110, 8471-8476, doi: 10. 1073/pnas. 1218726110 (2013).
16. Jäger, G. Support for linguistic macrofamilies from weighted sequence alignment. Proceedings of the National Academy of Sciences 112, 12752-12757, doi: 10. 1073/pnas. 1500331112 (2015).
17. Greenberg, J. H. The Eurasiatic Language Family: Indo-European and Its Closest Relations. Volume I: Grammar. Vol. 1 (Stanford University Press, 2000).
18. Greenberg, J. H. Indo-European and its Closest Relatives: The Eurasiatic Language Family Volume II: Lexicon. Vol. 2 (Stanford University Press, 2002).
19. Bomhard, A. R. & Kerns, J. C. The Nostratic macrofamily: A study in distant linguistic relationship. Vol. 74 (Walter de Gruyter, 1994).
20. Greenberg, J. H. In Current trends in linguistics Vol. 8 (ed T. A. Sebeok) 807-871 (Mouton, 1971).
21. Greenberg, J. H. Language in the Americas. (Stanford University Press, 1987).
22. Kluge, A. G. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Systematic Zoology 38, 7-25, doi: 10. 2307/2992432 (1989).
23. Pisani, D. & Wilkinson, M. Matrix representation with parsimony, taxonomic congruence, and total evidence. Systematic Biology 51, 151-155, doi: 10. 1080/106351502753475925 (2002).
24. Bininda-Emonds, O. R. P. The evolution of supertrees. Trends in ecology & evolution 19, 315-322, doi: 10. 1016/j. Tree. 2004. 03. 015 (2004).
25. Baum, B. R. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41, 3-10, doi: 10. 2307/1222480 (1992).
26. Ragan, M. A. Phylogenetic Inference Based on Matrix Representation of Trees. Molecular Phylogenetics and Evolution 1, 53-58, doi: 10. 1016/1055-7903(92)90035-f (1992).
27. Wheeler, W. C. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Systematic Biology 44, 321-331, doi: 10. 2307/2413595 (1995).
28. Pol, D. & Escapa, I. H. Unstable taxa in cladistic analysis: identification and the assessment of relevant characters. Cladistics 25, 515-527, doi: 10. 1111/j. 1096-0031. 2009. 00258. x (2009).
29. Goloboff, P. A. & Szumik, C. A. Identifying unstable taxa: Efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok. Molecular phylogenetics and evolution 88, 93-104 (2015).
30. Nixon, K. C. & Wheeler, Q. D. In Extinction and Phylogeny (eds M. J. Novacek & Q. D. Wheeler) 119-143 (Columbia University Press, 1993).
31. Abdulla, M. A. et al. Mapping human genetic diversity in Asia. Science 326, 1541-1545, doi: 10. 1126/science. 1177074 (2009).
32. Ayub, Q. et al. Reconstruction of human evolutionary tree using polymorphic autosomal microsatellites. American Journal of Physical Anthropology 122, 259-268, doi: 10. 1002/ajpa. 10234 (2003).
33. Chaubey, G. & Endicott, P. The Andaman Islanders in a regional genetic context: Reexamining the evidence for an early peopling of the archipelago from South Asia. Human Biology 85, 153-171 (2013).
34. Macaulay, V. et al. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308, 1034-1036, doi: 10. 1126/science. 1109792 (2005).
35. Jinam, T. A. et al. Evolutionary history of continental Southeast Asians: "Early train" hypothesis based on genetic analysis of mitochondrial and autosomal DNA data. Molecular Biology and Evolution 29, 3513-3527, doi: 10. 1093/molbev/mss169 (2012).
36. Gray, R. D., Drummond, A. J. & Greenhill, S. J. Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 323, 479-483, doi: 10. 1126/science. 1166858 (2009).
37. Friedlaender, J. S. et al. The genetic structure of Pacific islanders. PLOS Genetics 4, doi: 10. 1371/journal. pgen. 0040019 (2008).
38. Reesink, G., Singer, R. & Dunn, M. Explaining the linguistic diversity of Sahul using population models. PLOS Biology 7, doi: 10. 1371/journal. pbio. 1000241 (2009).
39. Pugach, I., Delfin, F., Gunnarsdottir, E., Kayser, M. & Stoneking, M. Genome-wide data substantiate Holocene gene flow from India to Australia. Proceedings of the National Academy of Sciences of the United States of America 110, 1803-1808, doi: 10. 1073/ pnas. 1211927110 (2013).
40. Regueiro, M. et al. Austronesian genetic signature in East African Madagascar and Polynesia. Journal of Human Genetics 53, 106-120, doi: 10. 1007/s10038-007-0224-4 (2008).
41. Thangaraj, K. et al. Genetic affinities of the Andaman Islanders, a vanishing human population. Current Biology 13, 86-93, doi: 10. 1016/s0960-9822(02)01336-2 (2003).
42. Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Reconstructing Indian population history. Nature 461, 489-U450, doi: 10. 1038/nature08365 (2009).
43. Aghakhanian, F. et al. Unravelling the Genetic History of Negritos and Indigenous populations of Southeast Asia. Genome Biol. Evol. 7, 1206-1215, doi: 10. 1093/gbe/evv065 (2015).
44. Basu, A., Sarkar-Roy, N. & Majumder, P. P. Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure. Proceedings of the National Academy of Sciences, doi: 10. 1073/pnas. 1513197113 (2016).
45. Pakendorf, B. Coevolution of languages and genes. Current Opinion in Genetics & Development 29, 39-44, doi: 10. 1016/j. gde. 2014. 07. 006 (2014).
46. Creanza, N. et al. A comparison of worldwide phonemic and genetic variation in human populations. Proceedings of the National Academy of Sciences of the United States of America 112, 1265-1272, doi: 10. 1073/pnas. 1424033112 (2015).
47. Steele, J. & Kandler, A. Language trees not equal gene trees. Theory in Biosciences 129, 223-233, doi: 10. 1007/s12064-010-0096-6 (2010).
48. Lewis, M., Simons, G. & Fennig, C. Ethnologue: Languages of the World, Seventeenth Edition. (SIL international Dallas, TX, 2013).
49. Ruhlen, M. Guide to the World's Languages: Classification. Vol. 1 (Stanford University Press, 1991).
50. Greenberg, J. H. & Ruhlen, M. An Amerind Etymological Dictionary. (Stanford University, Department of Anthropological Sciences, 2007).
51. Yunusbayev, B. et al. The genetic legacy of the expansion of Turkic-speaking nomads across Eurasia. PLOS Genetics 11, 24, doi: 10. 1371/journal. pgen. 1005068 (2015).
52. Peoples, H. C., Duda, P. & Marlowe, F. W. Hunter-Gatherers and the Origins of Religion. Human Nature, 1-22, doi: 10. 1007/s12110-016-9260-0 (2016).
53. Bronzati, M., Montefeltro, F. C. & Langer, M. C. A species-level supertree of Crocodyliformes. Historical Biology 24, 598-606, doi: 10. 1080/08912963. 2012. 662680 (2012).
54. Goloboff, P. A., Farris, J. S. & Nixon, K. C. TNT, a free program for phylogenetic analysis. Cladistics 24, 774-786 (2008).
55. Bahuchet, S. Changing language, remaining pygmy. Human Biology 84, 11-43 (2012).
56. Burenhult, N., Kruspe, N. & Dunn, M. In Dynamics of Human Diversity: The Case of Mainland Southeast Asia (ed N. J. Enfield) Ch. 11, 257-275 (Pacific Linguistics, 2011).
57. Dunn, M., Kruspe, N. & Burenhult, N. Time and place in the prehistory of the Aslian languages. Human Biology 85, 383-399 (2013).
58. Reid, L. A. Who are the Philippine negritos? Evidence from language. Human Biology 85, 329-358 (2013).
59. Huson, D. H. & Scornavacca, C. Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Systematic Biology 61, 1061-1067, doi: 10. 1093/sysbio/sys062 (2012).
60. Maddison, W. P. & Maddison, D. R. Mesquite: A modular system for evolutionary analysis v. 3. 02 (2015).