Skip to main content
SpringerLink
Log in

Efficient Methods for Dating Evolutionary Divergences

  • Chapter
  • First Online:
The Molecular Evolutionary Clock

Abstract

Reliable estimates of divergence times are crucial for biological studies to decipher temporal patterns of macro- and microevolution of genes and organisms. Molecular sequences have become the primary source of data for estimating divergence times. The sizes of molecular data sets have grown quickly due to the development of inexpensive sequencing technology. To deal with the increasing volumes of molecular data, many efficient dating methods are being developed. These methods not only relax the molecular clock and offer flexibility to use multiple clock calibrations, but also complete calculations much more quickly than Bayesian approaches. Here, we discuss the theoretical and practical aspects of these non-Bayesian approaches and present a guide to using these methods effectively. We suggest that the computational speed and reliability of non-Bayesian relaxed-clock methods offer opportunities for enhancing scientific rigour and reproducibility in biological research for large and small data sets.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 129.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Åkerborg Ö, Sennblad B, Lagergren J (2008) Birth-death prior on phylogeny and speed dating. BMC Evol Biol 8:77

    Article  PubMed  PubMed Central  Google Scholar 

  • Andújar C, Soria-Carrasco V, Serrano J, Gómez-Zurita J (2014) Congruence test of molecular clock calibration hypotheses based on Bayes factor comparisons. Methods Ecol Evol 5:226–242

    Article  Google Scholar 

  • Barba-Montoya J, dos Reis M, Yang Z (2017) Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating. Mol Phylogenet Evol 114:386–400

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barba-Montoya J, dos Reis M, Schneider H, Donoghue PCJ, Yang Z (2018) Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution. New Phytol 218:819–834

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Battistuzzi FU, Tao Q, Jones L, Tamura K, Kumar S (2018) RelTime relaxes the strict molecular clock throughout the phylogeny. Genome Biol Evol 10:1631–1636

    Article  PubMed  PubMed Central  Google Scholar 

  • Bhatnagar N, Bogdanov A, Mossel E (2011) The computational complexity of estimating MCMC convergence time. In: Goldberg LA, Jansen K, Ravi R, Rolim JDP (eds) Approximation, randomization, and combinatorial optimization. Algorithms and techniques. Springer, Heidelberg, pp 424–435

    Chapter  Google Scholar 

  • Biek R, Pybus OG, Lloyd-Smith JO, Didelot X (2015) Measurably evolving pathogens in the genomic era. Trends Ecol Evol 30:306–313

    Article  PubMed  PubMed Central  Google Scholar 

  • Bollyky PL, Holmes EC (1999) Reconstructing the complex evolutionary history of hepatitis B virus. J Mol Evol 49:130–141

    Article  CAS  PubMed  Google Scholar 

  • Britton T, Oxelman B, Vinnersten A, Bremer K (2002) Phylogenetic dating with confidence intervals using mean path lengths. Mol Phylogenet Evol 24:58–65

    Article  CAS  PubMed  Google Scholar 

  • Britton T, Anderson CL, Jacquet D, Lundqvist S, Bremer K (2007) Estimating divergence times in large phylogenetic trees. Syst Biol 56:741–752

    Article  PubMed  Google Scholar 

  • Bromham L, Duchêne S, Hua X, Ritchie AM, Duchêne DA, Ho SYW (2018) Bayesian molecular dating: opening up the black box. Biol Rev 93:1165–1191

    PubMed  Google Scholar 

  • Chernikova D, Motamedi S, Csürös M, Koonin EV, Rogozin IB (2011) A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes. Biol Direct 6:26

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chikina M, Robinson JD, Clark NL (2016) Hundreds of genes experienced convergent shifts in selective pressure in marine mammals. Mol Biol Evol 33:2182–2192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chriki-Adeeb R, Chriki A (2016) Estimating divergence times and substitution rates in Rhizobia. Evol Bioinform 12:87–97

    Article  Google Scholar 

  • Crosby RW, Williams TL (2017) Fast algorithms for computing phylogenetic divergence time. BMC Bioinform 18:514

    Article  Google Scholar 

  • Doolittle RF, Feng DF, Tsang S, Cho G, Little E (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470–477

    Article  CAS  PubMed  Google Scholar 

  • dos Reis M, Inoue J, Hasegawa M, Asher RJ, Donoghue PC, 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

    Article  PubMed  PubMed Central  Google Scholar 

  • dos Reis M, Donoghue PC, Yang Z (2014) Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biol Lett 10:20131003

    Article  PubMed  PubMed Central  Google Scholar 

  • dos Reis M, Thawornwattana Y, Angelis K, Telford MJ, Donoghue PC, Yang Z (2015) Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Curr Biol 25:1–12

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • dos Reis M, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z, Yoder AD (2018) Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case. Syst Biol 67:594–615

    Article  PubMed  PubMed Central  Google Scholar 

  • Douzery EJP, Snell EA, Bapteste E, Delsuc F, Philippe H (2004) The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci USA 101:15386–15391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Drummond A, Rodrigo AG (2000) Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA. Mol Biol Evol 17:1807–1815

    Article  CAS  PubMed  Google Scholar 

  • Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLOS Biol 4:e88

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Eizirik E, Murphy W, O’Brien S (2001) Molecular dating and biogeography of the early placental mammal radiation. J Hered 92:212–219

    Article  CAS  PubMed  Google Scholar 

  • Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P (2014) The early spread and epidemic ignition of HIV-1 in human populations. Science 346:56–61

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Feng DF, Cho G, Doolittle RF (1997) Determining divergence times with a protein clock: update and reevaluation. Proc Natl Acad Sci USA 94:13028–13033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Filipski A, Murillo O, Freydenzon A, Tamura K, Kumar S (2014) Prospects for building large timetrees using molecular data with incomplete gene coverage among species. Mol Biol Evol 31:2542–2550

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fitch WM (1976) Molecular evolutionary clocks. In: Ayala FJ (ed) Molecular evolution. Sinauer, Sunderland, MA, pp 160–178

    Google Scholar 

  • Fourment M, Holmes EC (2014) Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evol Biol 14:163

    Article  PubMed  PubMed Central  Google Scholar 

  • Gillespie JH (1984) The molecular clock may be an episodic clock. Proc Natl Acad Sci USA 81:8009–8013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Graur D, Martin W (2004) Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet 20:80–86

    Article  CAS  PubMed  Google Scholar 

  • Gunter NL, Weir TA, Slipinksi A, Bocak L, Cameron SL (2016) If dung beetles (Scarabaeidae: Scarabaeinae) arose in association with dinosaurs, did they also suffer a mass co-extinction at the K-Pg boundary? PLOS ONE 11:e0153570

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hasegawa M, Kishino H, Yano T (1989) Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in Hominoidea. J Hum Evol 18:461–476

    Article  Google Scholar 

  • Heath TA (2012) A hierarchical Bayesian model for calibrating estimates of species divergence times. Syst Biol 61:793–809

    Article  PubMed  PubMed Central  Google Scholar 

  • Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB (2001) Molecular evidence for the early colonization of land by fungi and plants. Science 293:1129–1133

    Article  CAS  PubMed  Google Scholar 

  • Hedges SB, Kumar S (2003) Genomic clocks and evolutionary timescales. Trends Genet 19:200–206

    Article  CAS  Google Scholar 

  • Hedges SB, Kumar S (2004) Precision of molecular time estimates. Trends Genet 20:242–247

    Article  CAS  PubMed  Google Scholar 

  • Hedges SB, Kumar S (2009) The timetree of life. Oxford University Press, Oxford, UK

    Google Scholar 

  • Hedges SB, Shah P (2003) Comparison of mode estimation methods and application in molecular clock analysis. BMC Bioinform 4:31

    Article  Google Scholar 

  • Hedges SB, Parker PH, Sibley CG, Kumar S (1996) Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226–229

    Article  CAS  PubMed  Google Scholar 

  • Hedges SB, Marin J, Suleski M, Paymer M, Kumar S (2015) Tree of life reveals clock-like speciation and diversification. Mol Biol Evol 32:835–845

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hedges SB, Tao Q, Walker M, Kumar S (2018) Accurate timetrees require accurate calibrations. Proc Natl Acad Sci USA 115:E9510–E9511

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hipsley CA, Müller J (2014) Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology. Front Genet 5:138

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ho SYW (2009) An examination of phylogenetic models of substitution rate variation among lineages. Biol Lett 5:421–424

    Article  PubMed  PubMed Central  Google Scholar 

  • Ho SYW (2014) The changing face of the molecular evolutionary clock. Trends Ecol Evol 29:496–503

    Article  PubMed  Google Scholar 

  • Ho SYW, Duchêne S (2014) Molecular-clock methods for estimating evolutionary rates and timescales. Mol Ecol 23:5947–5965

    Article  PubMed  Google Scholar 

  • Ho SYW, Phillips MJ (2009) Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol 58:367–380

    Article  PubMed  Google Scholar 

  • Ho SYW, Duchêne S, Duchêne D (2015a) Simulating and detecting autocorrelation of molecular evolutionary rates among lineages. Mol Ecol Resour 15:688–696

    Article  CAS  PubMed  Google Scholar 

  • Ho SYW, Tong KJ, Foster CS, Ritchie AM, Lo N, Crisp MD (2015b) Biogeographic calibrations for the molecular clock. Biol Lett 11:20150194

    Article  PubMed  PubMed Central  Google Scholar 

  • Huerta-Cepas J, Gabaldón T (2011) Assigning duplication events to relative temporal scales in genome-wide studies. Bioinformatics 27:38–45

    Article  CAS  PubMed  Google Scholar 

  • Hughes LC, Ortí G, Huang Y, Sun Y, Baldwin CC, Thompson AW, Arcila D, Betancur-R R, Li C, Becker L, Bellora N, Zhao X, Li X, Wang M, Fang C, Xie B, Zhou Z, Huang H, Chen S, Venkatesh B, Shi Q (2018) Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc Natl Acad Sci USA 115:6249–6254

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jaynes ET, Kempthorne O (1976) Confidence intervals vs Bayesian intervals. In: Harper WL, Hooker CA (eds) Foundations of probability theory, statistical inference, and statistical theories of science. Springer, Dordrecht, pp 175–257

    Chapter  Google Scholar 

  • Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473:97–100

    Article  CAS  PubMed  Google Scholar 

  • Kishino H, Thorne JL, Bruno WJ (2001) Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol 18:352–361

    Article  CAS  PubMed  Google Scholar 

  • Kodandaramaiah U (2011) Tectonic calibrations in molecular dating. Curr Zool 57:116–124

    Article  Google Scholar 

  • Kooistra WH, Medlin LK (1996) Evolution of the diatoms (Bacillariophyta): IV. A reconstruction of their age from small subunit rRNA coding regions and the fossil record. Mol Phylogenet Evol 6:391–407

    Article  CAS  PubMed  Google Scholar 

  • Ksepka DT, Parham JF, Allman JF, Benton MJ, Carrano MT, Cranston KA, Donoghue PC, Head JJ, Hermsen EJ, Irmis RB, Joyce WG, Kohli M, Lamm KD, Leehr D, Patané JL, Polly D, Phillips MJ, Smith NA, Smith ND, Van Tuinen M, Ware JL, Warnock RCM (2015) The Fossil Calibration Database, a new resource for divergence dating. Syst Biol 64:853–859

    Article  CAS  PubMed  Google Scholar 

  • Kumar S (2005) Molecular clocks: four decades of evolution. Nat Rev Genet 6:654–662

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392:917–920

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Hedges SB (2016) Advances in time estimation methods for molecular data. Mol Biol Evol 33:863–869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langley CH, Fitch WM (1974) An examination of the constancy of the rate of molecular evolution. J Mol Evol 3:161–177

    Article  CAS  PubMed  Google Scholar 

  • Lartillot N, Rodrigue N, Stubbs D, Richer J (2013) PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst Biol 62:611–615

    Article  CAS  PubMed  Google Scholar 

  • Li WLS, Drummond AJ (2012) Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics. Mol Biol Evol 29:751–761

    Article  CAS  PubMed  Google Scholar 

  • Li WH, Tanimura M, Sharp PM (1988) Rates and dates of divergence between AIDS virus nucleotide sequences. Mol Biol Evol 5:313–330

    CAS  PubMed  Google Scholar 

  • Li H-T, Yi T-S, Gao L-M, Ma P-F, Zhang T, Yang J-B, Gitzendanner MA, Fritsch PW, Cai J, Luo Y, Wang H, van der Bank M, Zhang S-D, Wang Q-F, Wang J, Zhang Z-R, Fu C-N, Yang J, Hollingsworth PMN, Chase MW, Soltis DE, Soltis PS, Li D-Z (2019) Origin of angiosperms and the puzzle of the Jurassic gap. Nat Plants 5:461–470

    Article  PubMed  Google Scholar 

  • Louca S, Shih PM, Pennell MW, Fischer WW, Parfrey LW, Doebeli M (2018) Bacterial diversification through geological time. Nat Ecol Evol 2:1458–1467

    Article  PubMed  Google Scholar 

  • Lu L-M, Mao L-F, Yang T, Ye J-F, Liu B, Li H-L, Sun M, Miller JT, Mathews S, Hu H-H, Niu Y-T, Peng D-X, Chen Y-H, Smith SA, Chen M, Xiang K-L, Le C-T, Dang V-C, Soltis PS, Soltis DE, Li J-H, Chen Z-D (2018) Evolutionary history of the angiosperm flora of China. Nature 554:234–238

    Article  CAS  PubMed  Google Scholar 

  • Marin J, Hedges SB (2018) Undersampling genomes has biased time and rate estimates throughout the tree of life. Mol Biol Evol 35:2077–2084

    Article  CAS  PubMed  Google Scholar 

  • Marin J, Battistuzzi FU, Brown AC, Hedges SB (2017) The timetree of prokaryotes: new insights into their evolution and speciation. Mol Biol Evol 34:437–446

    CAS  PubMed  Google Scholar 

  • Marshall CR (2008) A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. Am Nat 171:726–742

    Article  PubMed  Google Scholar 

  • Mello B (2018) Estimating timetrees with MEGA and the TimeTree resource. Mol Biol Evol 35:2334–2342

    Article  CAS  PubMed  Google Scholar 

  • Mello B, Tao Q, Tamura K, Kumar S (2017) Fast and accurate estimates of divergence times from big data. Mol Biol Evol 34:45–50

    Article  CAS  PubMed  Google Scholar 

  • Mello B, Tao Q, Kumar S (2021) Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches. Mol Ecol Resour (in press)

    Google Scholar 

  • Meredith RW, Janečka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simão TL, Stadler T, Rabosky DL, Honeycutt RL, Flynn JJ, Ingram CM, Steiner C, Williams TL, Robinson TJ, Burk-Herrick A, Westerman M, Ayoub NA, Springer MS, Murphy WJ (2011) Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334:521–524

    Article  CAS  PubMed  Google Scholar 

  • Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC (2017) Zika virus evolution and spread in the Americas. Nature 546:411–415

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O, Petersen M, Izquierdo-Carrasco F, Wappler T, Rust J, Aberer AJ, Aspöck U, Aspöck H, Bartel D, Blanke A, Berger S, Böhm A, Buckley TR, Calcott B, Chen J, Friedrich F, Fukui M, Fujita M, Greve C, Grobe P, Gu S, Huang Y, Jermiin LS, Kawahara AY, Krogmann L, Kubiak M, Lanfear R, Letsch H, Li Y, Li Z, Li J, Lu H, Machida R, Mashimo Y, Kapli P, McKenna DD, Meng G, Nakagaki Y, Navarrete-Heredia JL, Ott M, Ou Y, Pass G, Podsiadlowski L, Pohl H, von Reumont BM, Schütte K, Sekiya K, Shimizu S, Slipinski A, Stamatakis A, Song W, Su X, Szucsich NU, Tan M, Tan X, Tang M, Tang J, Timelthaler G, Tomizuka S, Trautwein M, Tong X, Uchifune T, Walzl MG, Wiegmann BM, Wilbrandt J, Wipfler B, Wong TK, Wu Q, Wu G, Xie Y, Yang S, Yang Q, Yeates DK, Yoshizawa K, Zhang Q, Zhang R, Zhang W, Zhang Y, Zhao J, Zhou C, Zhou L, Ziesmann T, Zou S, Li Y, Xu X, Zhang Y, Yang H, Wang J, Wang J, Kjer KM, Zhou X (2014) Phylogenomics resolves the timing and pattern of insect evolution. Science 346:763–767

    Article  CAS  PubMed  Google Scholar 

  • Miura S, Tamura K, Tao Q, Huuki LA, Pond SLK, Priest J, Deng J, Kumar S (2020) A new method for inferring timetrees from temporally sampled molecular sequences. PLOS Comput Biol 16:e1007046

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Morris JL, Puttick MN, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PC (2018) The timescale of early land plant evolution. Proc Natl Acad Sci USA 115:E2274–E2283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morrison DA (2008) How to summarize estimates of ancestral divergence times. Evol Bioinform 4:75–95

    Article  Google Scholar 

  • Muse SV, Weir BS (1992) Testing for equality of evolutionary rates. Genetics 132:269–276

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nascimento FF, dos Reis M, Yang Z (2017) A biologist’s guide to Bayesian phylogenetic analysis. Nat Ecol Evol 1:1446–1454

    Article  PubMed  PubMed Central  Google Scholar 

  • Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, Oxford, UK

    Google Scholar 

  • Oliveros CH, Field DJ, Ksepka DT, Barker FK, Aleixo A, Andersen MJ, Alström P, Benz BW, Braun EL, Braun MJ, Bravo GA, Brumfield RT, Chesser RT, Claramunt S, Cracraft J, Cuervo AM, Derryberry EP, Glenn TC, Harvey MG, Hosner PA, Joseph L, Kimball RT, Mack AL, Miskelly CM, Peterson AT, Robbins MB, Sheldon FH, Silveira LF, Smith BT, White ND, Moyle RG, Faircloth BC (2019) Earth history and the passerine superradiation. Proc Natl Acad Sci USA 116:7916–7925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Paradis E (2013) Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion. Mol Phylogenet Evol 67:436–444

    Article  PubMed  Google Scholar 

  • Phillips MJ (2015) Geomolecular dating and the origin of placental mammals. Syst Biol 65:546–557

    Article  PubMed  Google Scholar 

  • Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, Lemmon AR (2015) A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526:569–578

    Article  CAS  PubMed  Google Scholar 

  • Rambaut A (2000) Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16:395–399

    Article  CAS  PubMed  Google Scholar 

  • Russo C, Takezaki N, Nei M (1995) Molecular phylogeny and divergence times of drosophilid species. Mol Biol Evol 12:391–404

    CAS  PubMed  Google Scholar 

  • Sagulenko P, Puller V, Neher RA (2018) TreeTime: maximum-likelihood phylodynamic analysis. Virus Evol 4:vex042

    Article  PubMed  PubMed Central  Google Scholar 

  • Sanderson MJ (1997) A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol 14:1218–1231

    Article  CAS  Google Scholar 

  • Sanderson MJ (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol 19:101–109

    Article  CAS  PubMed  Google Scholar 

  • Sanderson MJ (2003) r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301–302

    Article  CAS  PubMed  Google Scholar 

  • Sarich VM, Wilson AC (1967) Immunological time scale for hominid evolution. Science 158:1200–1203

    Article  CAS  PubMed  Google Scholar 

  • Sarich VM, Wilson AC (1973) Generation time and genomic evolution in primates. Science 179:1144–1147

    Article  CAS  PubMed  Google Scholar 

  • Sauquet H, Ho SYW, Gandolfo MA, Jordan GJ, Wilf P, Cantrill DJ, Bayly MJ, Bromham L, Brown GK, Carpenter RJ, Lee DM, Murphy DJ, Sniderman JM, Udovicic F (2012) Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Syst Biol 61:289–313

    Article  PubMed  Google Scholar 

  • Schenk JJ (2016) Consequences of secondary calibrations on divergence time estimates. PLOS ONE 11:e0148228

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Smith SA, O’Meara BC (2012) treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28:2689–2690

    Article  CAS  PubMed  Google Scholar 

  • Smith SA, Brown JW, Walker JF (2018) So many genes, so little time: a practical approach to divergence-time estimation in the genomic era. PLOS ONE 13:e0197433

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Stadler T, Yang Z (2013) Dating phylogenies with sequentially sampled tips. Syst Biol 62:674–688

    Article  PubMed  Google Scholar 

  • Tajima F (1993) Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599–607

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takezaki N, Rzhetsky A, Nei M (1995) Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol 12:823–833

    CAS  PubMed  Google Scholar 

  • Tamura K, Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S (2012) Estimating divergence times in large molecular phylogenies. Proc Natl Acad Sci USA 109:19333–19338

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Tao Q, Kumar S (2018) Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates. Mol Biol Evol 35:1170–1182

    Article  CAS  Google Scholar 

  • Tao Q, Tamura K, Battistuzzi FU, Kumar S (2019) A machine learning method for detecting autocorrelation of evolutionary rates in large phylogenies. Mol Biol Evol 36:811–824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tao Q, Tamura K, Mello B, Kumar S (2020) Reliable confidence intervals for RelTime estimates of evolutionary divergence times. Mol Biol Evol 37:280–290

    Article  CAS  PubMed  Google Scholar 

  • Testo W, Sundue M (2016) A 4000-species dataset provides new insight into the evolution of ferns. Mol Phylogenet Evol 105:200–211

    Article  PubMed  Google Scholar 

  • Thorne JL, Kishino H, Painter IS (1998) Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 15:1647–1657

    Article  CAS  PubMed  Google Scholar 

  • To T-H, Jung M, Lycett S, Gascuel O (2016) Fast dating using least-squares criteria and algorithms. Syst Biol 65:82–97

    Article  CAS  PubMed  Google Scholar 

  • Tong KJ, Duchêne DA, Duchêne S, Geoghegan JL, Ho SYW (2018) A comparison of methods for estimating substitution rates from ancient DNA sequence data. BMC Evol Biol 18:70

    Article  PubMed  PubMed Central  Google Scholar 

  • Volz E, Frost S (2017) Scalable relaxed clock phylogenetic dating. Virus Evol 3:vex025

    Google Scholar 

  • Warnock RCM, Yang Z, Donoghue PCJ (2017) Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution. Proc R Soc B 284:20170227

    Article  PubMed  PubMed Central  Google Scholar 

  • Wiens JJ, Moen DS (2008) Missing data and the accuracy of Bayesian phylogenetics. J Syst Evol 46:307–314

    Google Scholar 

  • Wiens JJ, Morrill MC (2011) Missing data in phylogenetic analysis: reconciling results from simulations and empirical data. Syst Biol 60:719–731

    Article  PubMed  Google Scholar 

  • Wilke T, Schultheiß R, Albrecht C (2009) As time goes by: a simple fool’s guide to molecular clock approaches in invertebrates. Am Malacol Bull 27:25–45

    Article  Google Scholar 

  • Worobey M, Han G-Z, Rambaut A (2014) A synchronized global sweep of the internal genes of modern avian influenza virus. Nature 508:254–257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wray GA, Levinton JS, Shapiro LH (1996) Molecular evidence for deep Precambrian divergences among metazoan phyla. Science 274:568–573

    Article  CAS  Google Scholar 

  • Wu C-I, Li W-H (1985) Evidence for higher rates of nucleotide substitution in rodents than in man. Proc Natl Acad Sci USA 82:1741–1745

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia X (2018a) DAMBE7: New and improved tools for data analysis in molecular biology and evolution. Mol Biol Evol 35:1550–1552

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia X (2018b) Bioinformatics and the cell: modern computational approaches in genomics, proteomics and transcriptomics. Springer International, New York

    Google Scholar 

  • Xia X, Yang Q (2011) A distance-based least-square method for dating speciation events. Mol Phylogenet Evol 59:342–353

    Article  PubMed  Google Scholar 

  • Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Yang Z, O’Brien JD, Zheng X, Zhu H-Q, She Z-S (2007) Tree and rate estimation by local evaluation of heterochronous nucleotide data. Bioinformatics 23:169–176

    Article  PubMed  CAS  Google Scholar 

  • Yoder AD, Yang Z (2000) Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol 17:1081–1090

    Article  CAS  PubMed  Google Scholar 

  • Yu Y, Xiang Q, Manos PS, Soltis DE, Soltis PS, Song B-H, Cheng S, Liu X, Wong G (2017) Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) – Insights from transcriptome sequences. PLOS ONE 12:e0171361

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zeng L, Zhang Q, Sun R, Kong H, Zhang N, Ma H (2014) Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat Commun 5:4956

    Article  CAS  PubMed  Google Scholar 

  • Zheng Y, Wiens JJ (2015) Do missing data influence the accuracy of divergence-time estimation with BEAST? Mol Phylogenet Evol 85:41–49

    Article  PubMed  Google Scholar 

  • Zheng Y, Wiens JJ (2016) Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Mol Phylogenet Evol 94:537–547

    Article  PubMed  Google Scholar 

  • Zhu T, dos Reis M, Yang Z (2015) Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci. Syst Biol 64:267–280

    Article  CAS  PubMed  Google Scholar 

  • Zuckerkandl E, Pauling L (1962) Molecular disease, evolution, and genic heterogeneity. In: Kasha M, Pullman B (eds) Horizons in biochemistry. Academic, New York, pp 189–225

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA

    Qiqing Tao & Sudhir Kumar

  2. Department of Biology, Temple University, Philadelphia, PA, USA

    Qiqing Tao & Sudhir Kumar

  3. Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan

    Koichiro Tamura

  4. Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan

    Koichiro Tamura

  5. Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia

    Sudhir Kumar

Authors
  1. Qiqing Tao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Koichiro Tamura
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sudhir Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sudhir Kumar .

Editor information

Editors and Affiliations

  1. School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia

    Simon Y. W. Ho

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Tao, Q., Tamura, K., Kumar, S. (2020). Efficient Methods for Dating Evolutionary Divergences. In: Ho, S.Y.W. (eds) The Molecular Evolutionary Clock. Springer, Cham. https://doi.org/10.1007/978-3-030-60181-2_12

Download citation

Publish with us

Policies and ethics

Search

Navigation