Calibrating the tree of life: Fossils, molecules and evolutionary timescales

Annals of Botany

Volumn 104, Issue 5, 2009, Pages 789-794

  Forest, Félix ^a  

^a JODRELL LABORATORY   (United Kingdom)

Author keywords

Calibration; Fossil; Incompleteness; Molecular dating; Rate heterogeneity; Relaxed molecular clock; Uncertainty

Indexed keywords

CALIBRATION; DATING METHOD; DIVERGENCE; DNA; ERROR ANALYSIS; EVOLUTIONARY BIOLOGY; FOSSIL RECORD; MOLECULAR ANALYSIS; PHYLOGENETICS; PROTEIN;

ARTICLE; FOSSIL; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; PLANT; TIME;

EVOLUTION, MOLECULAR; FOSSILS; PHYLOGENY; PLANTS; TIME FACTORS;

EID: 70349599032     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mcp192     Document Type: Article

References (46)

1. Anderson CL, Bremer K, Friis EM. 2005. Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points. American Journal of Botany 92: 1737-1748.
2. Baldwin BG, Sanderson MJ. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences, USA 95: 9402-9406.
3. Benton MJ, Ayala FJ. 2003. Dating the tree of life. Science 300: 1698-1700.
4. Benton MJ, Donoghue PCJ. 2007. Paleontological evidence to date the tree of life. Molecular Biology and Evolution 24: 26-53.
5. Britten RJ. 1986. Rates of DNA-sequence evolution differ between taxo-nomic groups. Science 231: 1393-1398.
6. Christie DM, Duncan RA, McBirney AR, et al. 1992. Drowned islands downstream from the Galapagos hotspot imply extended speciation times. Nature 355: 246-248.
7. Conroy CJ, Van Tuinen M. 2003. Extracting time from phylogenies: positive interplay between fossil and genetic data. Journal of Mammalogy 84: 444-455.
8. Conti E, Rutschmann F, Eriksson T, Sytsma KJ, Baum DA. 2004. Calibration of molecular clocks and the biogeographic history of Crypteroniaceae: a reply to Moyle. Evolution 58: 1874-1876.
9. Doyle JA, Hotton CL. 1991. Diversification of early angiosperm pollen in a cladistic context. In: Blackmore S, Barnes SH. eds. Pollen and spores: patterns of diversification. Oxford: Clarendon, 169-195.
10. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
11. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006. Relaxed phylo-genetics and dating with confidence. PLoS Biology 4: 699-710.
12. Foote M. 1997. Estimating taxonomic durations and preservation probability. Paleobiology 23: 278-300.
13. Foote M, Hunter JP, Janis CM, Sepkoski JJ. 1999. Evolutionary and preser-vational constraints on origins of biologic groups: divergence times of eutherian mammals. Science 283: 1310-1314.
14. Forest F, Savolainen V, Chase MW, Lupia R, Bruneau A, Crane PR. 2005. Teasing apart molecular-versus fossil-based error estimates when dating phylogenetic trees: a case study in the birch family (Betulaceae). Systematic Botany 30: 118-133.
15. Garzione CN, Hoke GD, Libarkin JC, et al. 2008. Rise of the Andes. Science 320: 1304-1307.
16. Graur D, Martin W. 2004. Reading the entrails of chickens: molecular time-scales of evolution and the illusion of precision. Trends in Genetics 20: 80-86.
17. Heads M. 2005. Dating nodes on molecular phylogenies: a critique of molecular biogeography. Cladistics 21: 62-78.
18. Herendeen PS, Crane PR. 1995. The fossil history of the monocotyledons. In: Rudall PJ, Cribb PJ, Cutler DF, Humphries CJ. eds. Monocotyledons: systematics and evolution. Kew: Royal Botanic Gardens, Kew, 1-21.
19. Hickman CS, Lipps JH. 1985. Geologic youth of Galapagos islands confirmed by marine stratigraphy and paleontology. Science 227: 1578-1580.
20. Hugall AF, Foster R, Lee MSY. 2007. Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Systematic Biology 56: 543-563.
21. Lee MSY, Oliver PM, Hutchinson MN. 2009. Phylogenetic uncertainty and molecular clock calibrations: a case study of legless lizards (Pygopodidae, Gekkota). Molecular Phylogenetics and Evolution 50: 661-666.
22. Magallón SA. 2004. Dating lineages: molecular and paleontological approaches to the temporal framework of clades. International Journal of Plant Sciences 165: S7-S21.
23. Magallon S, Castillo A. 2009. Angiosperm diversification through time. American Journal of Botany 96: 349-365.
24. Magallón SA, Sanderson MJ. 2005. Angiosperm divergence times: the effect of genes, codon positions, and time constraints. Evolution 59: 1653-1670.
25. Marshall CR. 1990. Confidence-intervals on stratigraphic ranges. Paleobiology 16: 1-10.
26. Marshall CR. 1994. Confidence-intervals on stratigraphic ranges - partial relaxation of the assumption of randomly distributed fossil horizons. Paleobiology 20: 459-469.
27. Marshall CR. 1997. Confidence intervals on stratigraphic ranges with nonran-dom distributions of fossil horizons. Paleobiology 23: 165-173.
28. Marshall CR. 2008. A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. American Naturalist 171: 726-742.
29. Near TJ, Meylan PA, Shaffer HB. 2005. Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. American Naturalist 165: 137-146.
30. Parham JF, Irmis RB. 2008. Caveats on the use of fossil calibrations for molecular dating: a comment on Near et al. American Naturalist 171: 132-136.
31. Pulquério MJF, Nichols RA. 2007. Dates from the molecular clock: how wrong can we be? Trends in Ecology and Evolution 22: 180-184.
32. Rassmann K. 1997. Evolutionary age of the Galapagos iguanas predates the age of the present Galapagos Islands. Molecular Phylogenetics and Evolution 7: 158-172.
33. Ree RH, Smith SA. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57: 4-14.
34. Reisz RR, Müller J. 2004. Molecular timescales and the fossil record: a paleontological perspective. Trends in Genetics 20: 237-241.
35. Richardson JE, Pennington RT, Pennington TD, Hollingsworth PM. 2001. Rapid diversification of a species-rich genus of neotropical rain forest trees. Science 293: 2242-2245.
36. Rutschmann F. 2006. Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Diversity and Distributions 12: 35-48.
37. Rutschmann F, Eriksson T, Abu Salim K, Conti E. 2007. Assessing calibration uncertainty in molecular dating: the assignment of fossils to alternative calibration points. Systematic Biology 56: 591-608.
38. Sanderson MJ. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution 14: 1218-1231.
39. Sanderson MJ. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution 19: 101-109.
40. Sanderson MJ, Doyle JA. 2001. Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data. American Journal of Botany 88: 1499-1516.
41. Springer MS. 1995. Molecular clocks and the incompleteness of the fossil record. Journal of Molecular Evolution 41: 531-538.
42. Strauss D, Sadler PM. 1989. Classical confidence-intervals and Bayesian probability estimates for ends of local taxon ranges. Mathematical Geology 21: 411-421.
43. Tavaré S, Marshall CR, Will O, Soligo C, Martin RD. 2002. Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature 416: 726-729.
44. Thorne JL, Kishino H, Painter IS. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15: 1647-1657.
45. Whittle CA, Johnston MO. 2003. Broad-scale analysis contradicts the theory that generation time affects molecular evolutionary rates in plants. Journal of Molecular Evolution 56: 223-233.
46. Zuckerkandl E, Pauling L. 1965. Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ. eds. Evolving genes and proteins. New York: Academic Press, 97-166.