mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory

Molecular Biology and Evolution

Volumn 25, Issue 2, 2008, Pages 468-474

  Atkinson, Quentin D ^a   Gray, Russell D ^b   Drummond, Alexei J ^b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

Anthropology; Bayesian skyline plot; Human evolution; Mitochondrial DNA; Population genetics

Indexed keywords

MITOCHONDRIAL DNA;

ANTHROPOLOGY; ARTICLE; ASIA; BAYES THEOREM; EVOLUTION; GENETIC PARAMETERS; GENETIC VARIABILITY; HISTORY; HUMAN; MONTE CARLO METHOD; POPULATION; POPULATION GENETICS; POPULATION GROWTH; PREDICTION;

ASIA; BAYES THEOREM; DNA, MITOCHONDRIAL; GENETICS, POPULATION; HUMANS; POPULATION DENSITY; VARIATION (GENETICS);

EID: 38949133420     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msm277     Document Type: Article

References (51)

1. Achilli A, Rengo C, Battaglia V, et al. (13 co-authors). 2005. Saami and Berbers-an unexpected mitochondrial DNA link. Am J Hum Genet. 76:883-886.
2. Alonso S, Armour JA. 2001. A highly variable segment of human subterminal 16p reveals a history of population growth for modern humans outstide Africa. Proc Natl Acad Sci USA. 98:864-869.
3. Bazin E, Glemin S, Galtier N. 2006. Population size does not influence mitochondrial genetic diversity in animals. Science. 312:570-572.
4. Biraben JN. 1979. Essay on the evolution of numbers of mankind. Population. 34:13-25.
5. Birdsell JB. 1993. Microevolutionary patterns in aboriginal Australia: a gradient analysis of clines. New York: Oxford University Press.
6. Cann RL, Stoneking M, Wilson AC. 1987. Mitochondrial DNA and human evolution. Nature. 325:31-36.
7. Cavalli-Sforza LL, Menozzi P, Piazza A. 1994. The history and geography of human genes. Princeton (NJ): Princeton University Press.
8. Drummond AJ, Rambaut A. 2003. BEAST. Version 1.3, Oxford University Press, Oxford [computer programme]. Available from: http://beast.bio.ed.ac.uk/. Accessed 20 January 2007.
9. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 22:1185-1192.
10. Elson JL, Andrews RM, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. 2001. Analysis of European mtDNAs for recombination. Am J Hum Genet. 68:145-153.
11. Eyre-Walker A. 2006. Evolution - size does not matter for mitochondrial DNA. Science. 312:537-538.
12. Forster P. 2004. Ice ages and the mitochondrial DNA chronology of human dispersals: a review. Philos Trans R Soc Lond B Biol Sci. 359:255-264; discussion 264.
13. Forster P, Matsumura S. 2005. Evolution. Did early humans go north or south? Science. 308:965-966.
14. Friedlaender J, Schurr T, Gentz F, et al. (13 co-authors). 2005. Expanding southwest pacific mitochondrial haplogroups P and Q. Mol Biol Evol. 22:1506-1517.
15. Gkiasta M, Russell T, Shennan S, Steele J. 2003. Neolithic transition in Europe: the radiocarbon record revisited. Antiquity. 77:45-62.
16. Goebel T. 2007. Anthropology. The missing years for modern humans. Science. 315:194-196.
17. Gonser R, Donnelly P, Nicholson G, Di Rienzo A. 2000. Microsatellite mutations and inferences about human demography. Genetics. 154:1793-1807.
18. Gray RD, Atkinson QD. 2003. Language-tree divergence times support the Anatolian theory of Indo-European origin. Nature. 426:435-439.
19. Harpending HC, Sherry ST, Rogers AR, Stoneking M. 1993. The genetic-structure of ancient human-populations. Curr Anthropol. 34:483-496.
20. Ho SY, Phillips MJ, Cooper A, Drummond AJ. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 22: 1561-1568.
21. Housley RA, Gamble CS, Street M, Pettitt P. 1997. Radiocarbon evidence for the Lateglacial human recolonisation of northern Europe. Proc Prehistoric Soc. 63:25-26.
22. Howell N, Kubacka I, Mackey DA. 1996. How rapidly does the human mitochondrial genome evolve? Am J Hum Genet. 59: 501-509.
23. Hudson RR. 1990. Gene genealogies and the coalescent process. Oxf Surv Evol Biol. 7:1-14.
24. Huoponen K, Schurr TG, Chen Y, Wallace DC. 2001. Mitochondrial DNA variation in an aboriginal Australian population: evidence for genetic isolation and regional differentiation. Hum Immunol. 62:954-969.
25. Ingman M, Gyllensten U. 2003. Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Res. 13:1600-1606.
26. Ingman M, Kaessmann H, Paabo S, Gyllensten U. 2000. Mitochondrial genome variation and the origin of modern humans. Nature. 408:708-713.
27. Kivisild T, Rootsi S, Metspalu M, et al. (18 co-authors). 2003. The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet. 72:313-332.
28. Kivisild T, Shen P, Wall DP, et al. (17 co-authors). 2006. The role of selection in the evolution of human mitochondrial genomes. Genetics. 172:373-387.
29. Larsen CS. 2006. The agricultural revolution as environmental catastrophe: implications for health and lifestyle in the Holocene. Quatern Int. 150:12-20.
30. Macaulay V, Hill C, Achilli A, et al. (21 co-authors). 2005. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science. 308:1034-1036.
31. Marth GT, Czabarka E, Murvai J, Sherry ST. 2004. The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics. 166:351-372.
32. Mellars P. 2006a. Going east: new genetic and archaeological perspectives on the modern human colonization of Eurasia. Science. 313:796-800.
33. Mellars P. 2006b. A new radiocarbon revolution and the dispersal of modern humans in Eurasia. Nature. 439:931-935.
34. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. 1953. Equations of state calculations by fast computing machines. J Chem Phy. 21:1087-1091.
35. Mishmar D, Ruiz-Pesini E, Golik P, et al. (13 co-authors). 2003. Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci USA. 100:171-176.
36. Newton MA, Raftery AE, Davison AC, et al. (33 co-authors). 1994. Approximate bayesian-inference with the weighted likelihood bootstrap. J R Stat Soc Ser B Methodol. 56:3-48.
37. O'Connell JF, Allen J. 2004. Dating the colonization of Sahul (Pleistocene Australia-New Guinea): a review of recent research. J Arch Sci. 31:835-853.
38. Olivieri A, Achilli A, Pala M, et al. (15 co-authors). 2006. The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science. 314:1767-1770.
39. Richards M, Macaulay V, Hickey E, et al. (37 co-authors). 2000. Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet. 67:1251-1276.
40. Rogers AR. 1995. Genetic-evidence for a pleistocene population explosion. Evolution. 49:608-615.
41. Rogers AR. 2001. Order emerging from chaos in human evolutionary genetics. Proc Natl Acad Sci USA. 98:779-780.
42. Sherry ST, Rogers AR, Harpending H, Soodyall H, Jenkins T, Stoneking M. 1994. Mismatch distributions of mtDNA reveal recent human population expansions. Hum Biol. 66:761-775.
43. Steel MA, Hendy MD, Penny D. 1988. Loss of information in genetic distances. Nature. 336:118.
44. Sun C, Kong QP, Palanichamy MG, Agrawal S, Bandelt HJ, Yao YG, Khan F, Zhu CL, Chaudhuri TK, Zhang YP. 2006. The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. Mol Biol Evol. 23:683-690.
45. Thangaraj K, Chaubey G, Kivisild T, Reddy AG, Singh VK, Rasalkar AA, Singh L. 2005. Reconstructing the origin of Andaman Islanders. Science. 308:996.
46. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
47. van Holst Pellekaan SM, Ingman M, Roberts-Thomson J, Harding RM. 2006. Mitochondrial genomics identifies major haplogroups in Aboriginal Australians. Am J Phys Anthropol. 131:282-294.
48. Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson AC. 1991. African populations and the evolution of human mitochondrial DNA. Science. 253:1503-1507.
49. Wakeley J. 2000. The effects of subdivision on the genetic divergence of populations and species. Evol Int J Org Evol. 54:1092-1101.
50. Watson E, Forster P, Richards M, Bandelt HJ. 1997. Mitochondrial footprints of human expansions in Africa. Am J Hum Genet. 61:691-704.
51. Zhivotovsky LA, Bennett L, Bowcock AM, Feldman MW. 2000. Human population expansion and microsatellite variation. Mol Biol Evol. 17:757-767.