Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

Proceedings of the Royal Society B: Biological Sciences

Volumn 284, Issue 1857, 2017, Pages

  Warnock, Rachel C M ^a,b,c   Yang, Ziheng ^d   Donoghue, Philip C J ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b DEPARTMENT OF PALEOBIOLOGY   (United States)

^c ETH ZURICH   (Switzerland)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Bayesian phylogenetics; Fossil record; MCMCTREE; Molecular clock; Sampling bias

Indexed keywords

BAYESIAN ANALYSIS; CIRCADIAN RHYTHM; DATING METHOD; EVOLUTIONARY BIOLOGY; FOSSIL RECORD; MODEL TEST; MOLECULAR ECOLOGY; PHYLOGENETICS; PRESERVATION; SAMPLING BIAS; TESTING METHOD; TIMESCALE;

BAYES THEOREM; BIOLOGICAL MODEL; FOSSIL; MOLECULAR EVOLUTION; PHYLOGENY;

BAYES THEOREM; EVOLUTION, MOLECULAR; FOSSILS; MODELS, GENETIC; PHYLOGENY;

EID: 85021167836     PISSN: 09628452     EISSN: 14712954     Source Type: Journal    
DOI: 10.1098/rspb.2017.0227     Document Type: Article

References (42)

1. Holland SM. 2016 The non-uniformity of fossil preservation. Phil. Trans. R. Soc. B 371, 20150130. (doi:10.1098/rstb.2015.0130)
2. dos Reis M, Donoghue PC, Yang Z. 2016 Bayesian molecular clock dating of species divergences in the genomics era. Nat. Rev. Genet. 17, 71-80. (doi:10. 1038/nrg.2015.8)
3. dos Reis M, Yang Z. 2013 The unbearable uncertainty of Bayesian divergence time estimation. J. Syst. Evol. 51, 30-43. (doi:10.1111/j.1759-6831. 2012.00236.x)
4. Rannala B, Yang Z. 2007 Inferring speciation times under an episodic molecular clock. Syst. Biol. 56, 453-466. (doi:10.1080/10635150701420643)
5. Yang Z, 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. (doi:10.1093/molbev/ msj024)
6. dos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PCJ, Yang Z. 2015 Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Curr. Biol. 25, 2939-2950. (doi:10.1016/j.cub.2015.09.066)
7. Clarke JT, Warnock RCM, Donoghue PCJ. 2011 Establishing a time-scale for plant evolution. New Phytol. 192, 266-301. (doi:10.1111/j.1469-8137.2011.03794.x)
8. Heath TA, Huelsenbeck JP, Stadler T. 2014 The fossilized birth-death process for coherent calibration of divergence-time estimates. Proc. Natl Acad. Sci. USA 111, E2957-E2966. (doi:10.1073/ pnas.1319091111).
9. Ho SYW, Phillips MJ. 2009 Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst. Biol. 58, 367-380. (doi:10.1093/sysbio/syp035)
10. Inoue J, Donoghue P.CJ, Yang Z. 2010 The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst. Biol. 59, 74-89. (doi:10.1093/sysbio/syp096)
11. Warnock RCM, Parham JF, Joyce WG, Lyson TR, Donoghue PCJ. 2015 Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors. Proc. R. Soc. B 282, 20141013. (doi:10.1098/rspb.2014.1013)
12. Warnock RCM, Yang Z, Donoghue PCJ. 2012 Exploring uncertainty in the calibration of the molecular clock. Biol. Lett. 8, 156-159. (doi:10. 1098/rsbl.2011.0710)
13. Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S. 2015 A protocol for diagnosing the effect of calibration priors on posterior time estimates: a case study for the Cambrian explosion of animal phyla. Mol. Biol. Evol. 32, 1907-1912. (doi:10.1093/molbev/msv075)
14. Benton MJ, Donoghue PCJ. 2007 Paleontological evidence to date the tree of life. Mol. Biol. Evol. 24, 26-53. (doi:10.1093/molbev/msl150)
15. Muller J, Reisz RR. 2005 Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates. Bioessays 27, 1069-1075. (doi:10.1002/bies.20286)
16. Parham JF et al. 2012 Best practices for justifying fossil calibrations. Syst. Biol. 61, 346-359. (doi:10. 1093/sysbio/syr107)
17. dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PCJ, Yang Z. 2012 Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. R. Soc. B 279, 3491-3500. (doi:10.1098/rspb. 2012.0683)
18. Jarvis ED et al. 2014 Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320-1331. (doi:10.1126/science.1253451)
19. Meredith RW et al. 2011 Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification. Science 334, 521-524. (doi:10.1126/science.1211028)
20. Misof B et al. 2014 Phylogenomics resolves the timing and pattern of insect evolution. Science 346, 763-767. (doi:10.1126/science.1257570)
21. Wheat CW, Wahlberg N. 2013 Critiquing blind dating: the dangers of over-confident date estimates in comparative genomics. Trends Ecol. Evol. 28, 636-642. (doi:10.1016/j.tree.2013.07.007)
22. Holland SM. 1995 The stratigraphic distribution of fossils. Paleobiology 21, 92-109. (doi:10.1017/ S0094837300013099)
23. Holland SM. 2000 The quality of the fossil record: a sequence stratigraphic perspective. Paleobiology 26, 148-168. (doi:10.1666/0094-8373(2000)26 [148:Tqotfr]2.0.Co;2)
24. Foote M, Sepkoski JJ. 1999 Absolute measures of the completeness of the fossil record. Nature 398, 415-417. (doi:10.1038/18872)
25. Wagner PJ, Marcot JD. 2013 Modelling distributions of fossil sampling rates over time, space and taxa: assessment and implications for macroevolutionary studies. Methods Ecol. Evol. 4, 703-713. (doi:10. 1111/2041-210x.12088)
26. Yang Z. 2007 PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591. (doi:10.1093/molbev/msm088)
27. Marshall CR. 2008 A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. Am. Nat. 171, 726-742. (doi:10.1086/587523)
28. dos Reis M, Yang Z. 2011 Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol. Biol. Evol. 28, 2161-2172. (doi:10.1093/molbev/msr045)
29. dos Reis M, Zhu TQ, Yang Z. 2014 The impact of the rate prior on Bayesian estimation of divergence times with multiple loci. Syst. Biol. 63, 555-565. (doi:10.1093/sysbio/syu020)
30. Warnock RCM, Yang Z, Donoghue PCJ. 2017 Data from: Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution. Dryad Digital Repository. (http://dx.doi. org/10.5061/dryad.5706p)
31. Duchene D, Duchene S, Ho SYW. 2015 Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences. Mol. Ecol. Resour. 15, 785-794. (doi:10. 1111/1755-0998.12352)
32. Heath TA, Zwickl DJ, Kim J, Hillis DM. 2008 Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst. Biol. 57, 160-166. (doi:10.1080/10635150701884640)
33. Heled J, Drummond AJ. 2010 Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27, 570-580. (doi:10.1093/molbev/msp274)
34. Morrison DA. 2008 How to summarize estimates of ancestral divergence times. Evol. Bioinform. 4, 75-95.
35. Rodriguez-Trelles F, Tarrio R, Ayala FJ. 2002 A methodological bias toward overestimation of molecular evolutionary time scales. Proc. Natl Acad. Sci. USA 99, 8112-8115. (doi:10.1073/pnas. 122231299)
36. Hedges SB, Dudley J, Kumar S. 2006 TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22, 2971-2972. (doi:10. 1093/bioinformatics/btl505)
37. Sauquet H. 2013 A practical guide to molecular dating. C. R. Palevol. 12, 355-367. (doi:10.1016/j. crpv.2013.07.003)
38. Matschiner M, Musilova Z, Barth JM, Starostova Z, Salzburger W, Steel M, Bouckaert R. 2016 Bayesian phylogenetic estimation of clade ages supports trans-Atlantic dispersal of cichlid fishes. Syst. Biol. 66, 3-22. (doi:10.1093/ sysbio/syw076)
39. Nowak MD, Smith AB, Simpson C, Zwickl DJ. 2013 A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses. PLoS ONE 8, e0066245. (doi:10.1371/journal.pone.0066245)
40. Wilkinson RD, Steiper ME, Soligo C, Martin RD, Yang Z, Tavare S. 2011 Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst. Biol. 60, 16-31. (doi:10. 1093/sysbio/syq054)
41. Gavryushkina A, Welch D, Stadler T, Drummond AJ. 2014 Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput. Biol. 10, e1003919. (doi:10.1371/journal. pcbi.1003919)
42. Zhang C, Stadler T, Klopfstein S, Heath TA, Ronquist F. 2016 Total-evidence dating under the fossilized birth-death process. Syst. Biol. 65, 228-249. (doi:10.1093/sysbio/syv080)