The precision of the hominid timescale estimated by relaxed clock methods

Journal of Evolutionary Biology

Volumn 26, Issue 4, 2013, Pages 746-755

  Schrago, C G ^a   Voloch, C M ^a  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

Hominidae; Hominoidea; Infinite sites theory; Relaxed molecular clock; Speciation

Indexed keywords

CHRONOLOGY; DATA SET; DIVERGENCE; EVOLUTION; EVOLUTIONARY BIOLOGY; HOMINID; PRECISION; TIMESCALE;

ANIMAL; ARTICLE; BAYES THEOREM; CLASSIFICATION; GENETIC VARIABILITY; GENETICS; GENOME; HOMINID; METHODOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETICS; REPRODUCIBILITY; SEQUENCE ALIGNMENT; TIME;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; GENETIC VARIATION; GENETICS, POPULATION; GENOME; HOMINIDAE; PHYLOGENY; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; TIME FACTORS;

HOMINIDAE; HOMINOIDEA; PRIMATES; SIMIIFORMES;

EID: 84876130548     PISSN: 1010061X     EISSN: 14209101     Source Type: Journal    
DOI: 10.1111/jeb.12076     Document Type: Article

References (45)

1. Benton, M.J. & Donoghue, P.C. 2007. Paleontological evidence to date the tree of life. Mol. Biol. Evol. 24: 26-53.
2. Burgess, R. & Yang, Z. 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol. Biol. Evol. 25: 1979-1994.
3. Chaimanee, Y., Jolly, D., Benammi, M., Tafforeau, P., Duzer, D., Moussa, I. et al. 2003. A Middle Miocene hominoid from Thailand and orangutan origins. Nature 422: 61-65.
4. Chaimanee, Y., Suteethorn, V., Jintasakul, P., Vidthayanon, C., Marandat, B. & Jaeger, J.J. 2004. A new orang-utan relative from the Late Miocene of Thailand. Nature 427: 439-441.
5. Chatterjee, H.J., Ho, S.Y., Barnes, I. & Groves, C. 2009. Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evol. Biol. 9: 259.
6. Degnan, J.H. & Rosenberg, N.A. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24: 332-340.
7. Drummond, A.J. & Rambaut, A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214.
8. Drummond, A.J., Ho, S.Y.W., Phillips, M.J. & Rambaut, A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4: 699-710.
9. Edwards, S.V. 2009. Is a new and general theory of molecular systematics emerging? Evolution 63: 1-19.
10. Felsenstein, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22: 521-565.
11. Gibbs, R.A., Rogers, J., Katze, M.G., Bumgarner, R., Weinstock, G.M., Mardis, E.R. et al. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234.
12. Goodman, M., Braunitzer, G., Stangl, A. & Schrank, B. 1983. Evidence on Human Origins from Hemoglobins of African Apes. Nature 303: 546-548.
13. Guindon, S. & Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52: 696-704.
14. Hartwig, W.C. 2002 The Primate Fossil Record, 1st edn. Cambridge University Press.
15. Hasegawa, M., Kishino, H. & Yano, T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174.
16. Hobolth, A., Christensen, O.F., Mailund, T. & Schierup, M.H. 2007. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 3: 294-304.
17. Knowles, L.L. & Carstens, B.C. 2007. Delimiting species without monophyletic gene trees. Syst. Biol. 56: 887-895.
18. Kumar, S. & Hedges, S.B. 1998. A molecular timescale for vertebrate evolution. Nature 392: 917-920.
19. Kumar, S., Filipski, A., Swarna, V., Walker, A. & Hedges, S.B. 2005. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proc. Natl Acad. Sci. USA 102: 18842-18847.
20. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J. et al. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
21. Laurin, M. 2012. Recent progress in paleontological methods for dating the Tree of Life. Front. Genet. 3: 130.
22. Liu, L., Yu, L.L., Pearl, D.K. & Edwards, S.V. 2009. Estimating Species Phylogenies Using Coalescence Times among Sequences. Syst. Biol. 58: 468-477.
23. Locke, D.P., Hillier, L.W., Warren, W.C., Worley, K.C., Nazareth, L.V., Muzny, D.M. et al. 2011. Comparative and demographic analysis of orang-utan genomes. Nature 469: 529-533.
24. Marshall, C.R. 2008. A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. Am. Nat. 171: 726-742.
25. Mikkelsen, T.S., Hillier, L.W., Eichler, E.E., Zody, M.C., Jaffe, D.B., Yang, S.-P. et al. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
26. Pamilo, P. & Nei, M. 1988. Relationship between gene trees and species trees. Mol. Biol. Evol. 5: 568-583.
27. Perelman, P., Johnson, W.E., Roos, C., Seuanez, H.N., Horvath, J.E., Moreira, M.A. et al. 2011. A molecular phylogeny of living primates. PLoS Genet. 7: e1001342.
28. Plummer, M., Nicky, B., Cowles, K. & Vines, K. 2006. CODA: Convergence Diagnosis and Output Analysis for MCMC. R News 6: 7-11.
29. Pond, S.L.K., Frost, S.D.W. & Muse, S.V. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
30. Rannala, B. & Yang, Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.
31. Rannala, B. & Yang, Z.H. 2007. Inferring speciation times under an episodic molecular clock. Syst. Biol. 56: 453-466.
32. Ranwez, V., Delsuc, F., Ranwez, S., Belkhir, K., Tilak, M.K. & Douzery, E.J. 2007. OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics. BMC Evol. Biol. 7: 241.
33. dos Reis, M., Inoue, J., Hasegawa, M., Asher, R.J., Donoghue, P.C. & Yang, Z. 2012. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. Biol. Sci. 279: 3491-3500.
34. Sarich, V.M. & Wilson, A.C. 1967. Immunological Time Scale for Hominid Evolution. Science 158: 1200-1203.
35. Scally, A., Dutheil, J.Y., Hillier, L.W., Jordan, G.E., Goodhead, I., Herrero, J. et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483: 169-175.
36. Schrago, C.G. & Russo, C.A. 2003. Timing the origin of New World monkeys. Mol. Biol. Evol. 20: 1620-1625.
37. Steiper, M.E., Young, N.M. & Sukarna, T.Y. 2004. Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence. Proc. Natl Acad. Sci. USA 101: 17021-17026.
38. Takai, M. & Anaya, F. 1996. New specimens of the oldest fossil platyrrhine, Branisella boliviana, from Salla, Bolivia. Am. J. Phys. Anthropol. 99: 301-317.
39. Templeton, A.R. 1983. Phylogenetic Inference from Restriction Endonuclease Cleavage Site Maps with Particular Reference to the Evolution of Humans and the Apes. Evolution 37: 221-244.
40. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G. et al. 2001. The sequence of the human genome. Science 291: 1304-1351.
41. Wilkinson, R.D. & Tavare, S. 2009. Estimating primate divergence times by using conditioned birth-and-death processes. Theor. Popul. Biol. 75: 278-285.
42. Wilkinson, R.D., Steiper, M.E., Soligo, C., Martin, R.D., Yang, Z.H. & Tavare, S. 2011. Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data. Syst. Biol. 60: 16-31.
43. Yang, Z.H. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586-1591.
44. Yang, Z.H. & Rannala, B. 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23: 212-226.
45. Yoder, A.D. & Yang, Z. 2000. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17: 1081-1090.