Accuracy of molecular dating with the rho statistic: Deviations from coalescent expectations under a range of demographic models

Human Biology

Volumn 81, Issue 5-6, 2009, Pages 911-933

  Cox, Murray P ^a,b  

^a UNIVERSITY OF ARIZONA   (United States)

^b SANTA FE INSTITUTE   (United States)

Author keywords

Genetic dating; Mitochondrial DNA; Molecular chronology; statistic

Indexed keywords

MITOCHONDRIAL DNA;

BIOLOGICAL MODEL; CONFIDENCE INTERVAL; DEMOGRAPHY; FEMALE; FOUNDER EFFECT; GENETIC DATABASE; GENETIC POLYMORPHISM; GENETICS; HISTORY; HUMAN; MOLECULAR BIOLOGY; MOLECULAR EPIDEMIOLOGY; POPULATION GENETICS; PROCEDURES; STATISTICAL ANALYSIS; STATISTICAL BIAS; STATISTICAL MODEL; UNITED STATES;

BIAS (EPIDEMIOLOGY); CONFIDENCE INTERVALS; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; DEMOGRAPHY; DNA, MITOCHONDRIAL; FEMALE; FOUNDER EFFECT; GENETICS, POPULATION; HISTORY, 21ST CENTURY; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR BIOLOGY; MOLECULAR EPIDEMIOLOGY; POLYMORPHISM, GENETIC; UNITED STATES;

EID: 77952893958     PISSN: 00187143     EISSN: 15346617     Source Type: Journal    
DOI: 10.3378/027.081.0631     Document Type: Article

References (47)

1. Bandelt, H.-J., and P. Forster. 1995. Network: Phylogenetic Network Software. Available at http://www. fluxus-engineering.com/netwinfo.htm
2. Basu, A., and P. Majumdar. 2003. A comparison of two popular statistical methods for estimating the time to most recent common ancestor (TMRCA) from a sample of DNA sequences. J. Genet. 82:7-12.
3. Bellwood, P. 2005. The First Farmers: The Origins of Agricultural Societies. Oxford: Blackwell.
4. Bendall, K. E., V. A. Macaulay, J. R. Baker et al. 1996. Heteroplasmic point mutations in the human mtDNA control region. Am. J. Hum. Genet. 59:1276-1287.
5. Cox, M. P. 2005. Indonesian mitochondrial DNA and its opposition to a Pleistocene era origin of proto-Polynesians in Island Southeast Asia. Hum. Biol. 77:179-188.
6. Cox, M. P., F. L. Mendez, T. M. Karafet et al. 2008a. Testing for archaic hominin admixture on the X chromosome: Model likelihoods for the modern human RRM2P4 region from summaries of genealogical topology under the structured coalescent. Genetics 178:427-437.
7. Cox, M. P.,A. J. Redd, T. M. Karafet et al. 2008b.APolynesian motif on theYchromosome: Population structure in remote Oceania. Hum. Biol. 79:525-535.
8. Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
9. Fenner, J. N. 2005. Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. Am. J. Phys. Anthropol. 128:415-423.
10. Forster, P., R. Harding, A. Torroni et al. 1996. Origin and evolution of Native American mtDNA variation: A reappraisal. Am. J. Hum. Genet. 59:935-945
11. Garrigan, D., S. B. Kingan, M. Metni Pilkington et al. 2007. Inferring human population sizes, divergence times, and rates of gene flow from mitochondrial, X, and Y chromosome resequencing data. Genetics 177:2195-2207.
12. Griffiths, R. C. 2007. Genetree v. 9.0. Available at http://www.stats.ox. ac.uk/ griff/software.html
13. Griffiths, R. C., and S. Tavaré. 1994a. Ancestral inference in population genetics. Stat. Sci. 9:307-319.
14. Griffiths, R. C., and S. Tavaré. 1994b. Simulating probability distributions in the coalescent. Theor. Popul. Biol. 46:131-159.
15. Haigh, J., and J. Maynard Smith. 1972. Population size and protein variation in man. Genet. Res. Cambridge 19:73-89.
16. Hasegawa, M., A. Di Rienzo, T. D. Kocher et al. 1993. Toward a more accurate time scale for the human mitochondrial DNA tree. J. Mol. Evol. 37:347-354.
17. Hey, J., and R. Nielsen. 2004. Multilocus methods for estimating population sizes, migration rates, and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760.
18. Hey, J., and R. Nielsen. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 104:2785-2790.
19. Hill, C., P. Soares, M. Mormina et al. 2007. A mitochondrial stratigraphy for island Southeast Asia. Am. J. Hum. Genet. 80:29-43.
20. Ho, S. Y., and G. Larson. 2006. Molecular clocks: When times are a-changin'. Tr. Genet. 22:79-83.
21. Howell, N., C. B. Smejkal, D. A. Mackey et al. 2003. The pedigree rate of sequence divergence in the human mitochondrial genome: There is a difference between phylogenetic and pedigree rates. Am. J. Hum. Genet. 72:659-670.
22. Hudson, R. R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337-338.
23. Joly, S., M. I. Stevens, and B. J. Van Vuuren. 2007. Haplotype networks can be misleading in the presence of missing data. Syst. Biol. 56:857-862.
24. Kingman, J. F. C. 1982. On the Genealogy of Large Populations. Sheffield, U.K.: Applied Probability Trust.
25. Kivisild, T., P. Shen, D. P.Wall et al. 2006. The role of selection in the evolution of human mitochondrial genomes. Genetics 172:373-387.
26. Kliman, R. M., and J. Hey. 1993. DNA sequence variation at the period locus within and among species at the Drosophila melanogaster complex. Genetics 133:375-387. (Pubitemid 23033491)
27. Malyarchuk, B. A., and M. V. Derenko. 2001. Variation of human mitochondrial DNA: Distribution of hot spots in hypervariable segment I of the major noncoding region. Russ. J. Genet. 37:823-832.
28. Nielsen, R., and J. Wakeley. 2001. Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics 158:885-896.
29. Non, A. L., A. Kitchen, and C. J. Mulligan. 2007. Identification of the most informative regions of the mitochondrial genome for phylogenetic and coalescent analyses. Mol. Phylogenet. Evol. 44:1164-1171.
30. Olivieri, A., A. Achilli, M. Pala et al. 2006. The mtDNA legacy of the Levantine early Upper Paleolithic in Africa. Science 314:1767-1770.
31. Oppenheimer, S. 2003. Austronesian spread into Southeast Asia and Oceania: Where from and when? In Pacific Archaeology: Assessments and Prospects, C. Sand (ed). Noumea, New Caledonia: Le Cahiers de l'Archéologie en Nouvelle-Calédonie, 55-70.
32. Oppenheimer, S., and M. Richards. 2001. Fast trains, slow boats, and the ancestry of the Polynesian Islanders. Sci. Prog. 84:157-181.
33. Oppenheimer, S., and M. Richards. 2002. Polynesians: Devolved Taiwanese rice farmers or Wallacean maritime traders with fishing, foraging, and horticultural skills. In Examining the Farming/ Language Dispersal Hypothesis, P. Bellwood and C. Renfrew (eds.). Cambridge, U.K.: McDonald Institute for Archaeological Research, 287-297.
34. Pulquério, M. J., and R. A. Nichols. 2007. Dates from the molecular clock: How wrong can we be? Tr. Ecol. Evol. 22:180-184.
35. Richards, M., S. Oppenheimer, and B. Sykes. 1998. MtDNA suggests Polynesian origins in eastern Indonesia. Am. J. Hum. Genet. 63:1234-1236.
36. Rosset, S. 2007. Efficient inference on known phylogenetic trees using Poisson regression. Bioinformatics 23:142-147.
37. Saillard, J., P. Forster, N. Lynnerup et al. 2000. MtDNA variation among Greenland Eskimos: The edge of the Beringian expansion. Am. J. Hum. Genet. 67:718-726.
38. Santos, C., R. Montiel, B. Sierra et al. 2005. Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: A model using families from the Azores Islands (Portugal). Mol. Biol. Evol. 22:1490-1505.
39. Saunders, I. W., S. Tavaré, and G. A. Watterson. 1984. On the genealogy of nested subsamples from a haploid population. Adv. Appl. Prob. 16:471-491.
40. Sigurdardóttir, S., A. Helgason, J. R. Gulcher et al. 2000. The mutation rate in the human mtDNA control region. Am. J. Hum. Genet. 66:1599-1609.
41. Spriggs, M. 1989. The dating of the Island Southeast Asian Neolithic: An attempt at chronometric hygiene and linguistic correlation. Antiquity 63:587-613.
42. Spriggs, M. 2003. Chronology of the Neolithic transition in Island Southeast Asia and the Western Pacific: A view from 2003. Rev. Archeol. 24:57-80.
43. Tang, H., D. O. Siegmund, P. Shen et al. 2002. Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition. Genetics 161:447-459.
44. Tavaré, S., D. Balding, R. C. Griffiths et al. 1997. Inferring coalescence times from DNA sequence data. Genetics 145:505-518.
45. Voight, B. F., A. M. Adams, L. A. Frisse et al. 2005. Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc. Natl. Acad. Sci. USA 102:18,508-18,513.
46. Wall, J. D., and M. Przeworski. 2000. When did the human population size start increasing? Genetics 155:1865-1874.
47. Wright, S. 1938. Size of a population and breeding structure in relation to evolution. Science 87:430-431.