The Crucial Role of Calibration in Molecular Date Estimates for the Peopling of the Americas

American Journal of Human Genetics

Volumn 83, Issue 1, 2008, Pages 142-146

  Ho, Simon Y W ^a   Endicott, Phillip ^b  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b MAGDALEN COLLEGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

AMERICAN INDIAN; ANALYTIC METHOD; ARCHEOLOGY; BAYES THEOREM; CALIBRATION; COMPUTER PROGRAM; FOSSIL; GENE SEQUENCE; GENETIC CODE; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; INFORMATION PROCESSING; LETTER; MITOCHONDRIAL GENE; MONTE CARLO METHOD; PHYLOGENY; POPULATION DYNAMICS; POPULATION GENETIC STRUCTURE; POPULATION GENETICS; PRIORITY JOURNAL; PROBABILITY; WESTERN HEMISPHERE;

AMERICAS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMALS; BASE SEQUENCE; BAYES THEOREM; CALIBRATION; CHRONOLOGY AS TOPIC; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; HAPLOTYPES; HUMANS; KINETICS; MARKOV CHAINS; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; NORTH AMERICA; PHYLOGENY; PRIMATES; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 46149098443     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2008.06.014     Document Type: Letter

References (25)

1. Fagundes N.J., Kanitz R., Eckert R., Valls A.C., Bogo M.R., Salzano F.M., Smith D.G., Silva Jr. W.A., Zago M.A., Ribeiro-dos-Santos A.K., et al. Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am. J. Hum. Genet. 82 (2008) 583-592
2. Goebel T., Waters M.R., and O'Rourke D.H. The late Pleistocene dispersal of modern humans in the Americas. Science 319 (2008) 1497-1502
3. Drummond A.J., and Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7 (2007) 214
4. Achilli A., Perego U.A., Bravi C.M., Coble M.D., Kong Q.P., Woodward S.R., Salas A., Torroni A., and Bandelt H.J. The phylogeny of the four pan-American MtDNA haplogroups: Implications for evolutionary and disease studies. PLoS ONE 3 (2008) e1764
5. Dillehay T.D. Monte Verde: A Late Pleistocene Settlement in Chile: Archeological Context (1997), Smithsonian Institute Press, Washington, DC
6. Gilbert M.T., Jenkins D.L., Gotherstrom A., Naveran N., Sanchez J.J., Hofreiter M., Thomsen P.F., Binladen J., Higham T.F., Yohe II R.M., et al. DNA from pre-Clovis human coprolites in Oregon, North America. Science 320 (2008) 786-789
7. Mishmar D., Ruiz-Pesini E., Golik P., Macaulay V., Clark A.G., Hosseini S., Brandon M., Easley K., Chen E., Brown M.D., et al. Natural selection shaped regional mtDNA variation in humans. Proc. Natl. Acad. Sci. USA 100 (2003) 171-176
8. Kivisild T., Shen P., Wall D.P., Do B., Sung R., Davis K., Passarino G., Underhill P.A., Scharfe C., Torroni A., et al. The role of selection in the evolution of human mitochondrial genomes. Genetics 172 (2006) 373-387
9. Bandelt H.-J., Kong Q.P., Richards M., and Macaulay V. Estimation of mutation rates and coalescence times: Some caveats. In: Bandelt H.-J., Macaulay V., and Richards M. (Eds). Human Mitochondrial DNA and the Evolution of Homo sapiens (2006), Springer, Berlin 47-90
10. Burridge C.P., Craw D., Fletcher D., and Waters J.M. Geological dates and molecular rates: Fish DNA sheds light on time dependency. Mol. Biol. Evol. 25 (2008) 624-633
11. Ho S.Y.W., Phillips M.J., Cooper A., and Drummond A.J. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol. Biol. Evol. 22 (2005) 1561-1568
12. Ho S.Y.W., Shapiro B., Phillips M., Cooper A., and Drummond A.J. Evidence for time dependency of molecular rate estimates. Syst. Biol. 56 (2007) 515-522
13. Ho S.Y.W., and Larson G. Molecular clocks: When times are a-changin'. Trends Genet. 22 (2006) 79-83
14. Atkinson Q.D., Gray R.D., and Drummond A.J. mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory. Mol. Biol. Evol. 25 (2008) 468-474
15. Endicott P., and Ho S.Y.W. A Bayesian evaluation of human mitochondrial substitution rates. Am. J. Hum. Genet. 82 (2008) 895-902
16. Kemp B.M., Malhi R.S., McDonough J., Bolnick D.A., Eshleman J.A., Rickards O., Martinez-Labarga C., Johnson J.R., Lorenz J.G., Dixon E.J., et al. Genetic analysis of early holocene skeletal remains from Alaska and its implications for the settlement of the Americas. Am. J. Phys. Anthropol. 132 (2007) 605-621
17. Stoneking M., Sherry S.T., Redd A.J., and Vigilant L. New approaches to dating suggest a recent age for human mtDNA ancestor. Philos. Trans. R. Soc. Lond. B Biol. Sci. 337 (1992) 167-175
18. Anderson S., Bankier A.T., Barrell B.G., de Bruijn M.H., Coulson A.R., Drouin J., Eperon I.C., Nierlich D.P., Roe B.A., Sanger F., et al. Sequence and organisation of the human mitochondrial genome. Nature 290 (1981) 457-465
19. Drummond A.J., Rambaut A., Shapiro B., and Pybus O.G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22 (2005) 1185-1192
20. Achilli A., Rengo C., Magri C., Battaglia V., Olivieri A., Scozzari R., Cruciani F., Zeviani M., Briem E., Carelli V., et al. The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am. J. Hum. Genet. 75 (2004) 910-918
21. Gamble C., Davies W., Pettitt P., and Richards M. Climate change and evolving human diversity in Europe during the last glacial. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359 (2004) 243-253
22. Tamm E., Kivisild T., Reidla M., Metspalu M., Smith D.G., Mulligan C.J., Bravi C.M., Rickards O., Martinez-Labarga C., Khusnutdinova E.K., et al. Beringian standstill and spread of Native American founders. PLoS ONE 2 (2007) e829
23. Kitchen A., Miyamoto M.M., and Mulligan C.J. A three-stage colonization model for the peopling of the Americas. PLoS ONE 3 (2008) e1596
24. Ingman M., Kaessmann H., Paabo S., and Gyllensten U. Mitochondrial genome variation and the origin of modern humans. Nature 408 (2000) 708-713
25. Hudjashov G., Kivisild T., Underhill P.A., Endicott P., Sanchez J.J., Lin A.A., Shen P., Oefner P., Renfrew C., Villems R., et al. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc. Natl. Acad. Sci. USA 104 (2007) 8726-8730