Divergence-time estimation

Divergence-time estimates are based on molecular dating techniques, which in turn depend on reliable fossil calibrations, i.e. reliably dated and correctly placed fossils. 

This interdisciplinary field of science is of paramount importance, being fundamental for downstream inferences of CLASSification and delimitation of chronospecies. It incorporates the following steps: 

1.) Branch-length estimation (quantifying the presumed amount of mutations accumulating within lineages): 

  • based on nDNA and/or mtDNA
  • genetic divergence (uncorrected pairwise distance, e.g. in the mitochondrial gene ND2)
  • calculated by software programs

2.) Fossil analysis (call for a paleontological online database to fascilitate access of latest data): 

  • age of fossils
  • phylogenetic placement of fossils

3.) Calibration process (transforming branch lengths into absolute ages; using relaxed clocks that take into account mutation rate heterogeneity among lineages; resolving conflict when branch lengths differ among sister taxa):  

  • fossil calibration (using fossils to set minimum ages; evaluate reliability of fossils; set calibration points with well-defined confidence intervals)
  • biogeographic calibration (using formation of land connections or emergence of islands as sources of age information)

References/Literature

Allio R, Donega S, Galtier N, and Nabholz B  (2017), Large variation in the ratio of mitochondrial to nuclear mutation rate across animals: implications for genetic diversity and the use of mitochondrial DNA as a molecular marker, Mol. Biol. Evol. 34(11), 2762-2772. (pdf)

 

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

 

Barba-Montoya J, Tao Q, and Kumar S (2021), Molecular and morphological clocks for estimating evolutionary divergence times, BMC Ecol. Evol. 21, e:83. (pdf) 

 

Binet M, Gascuel O, Scornavacca, C, Douzery EJP, and Pardi F (2016) Fast and accurate branch lengths estimation for phylogenomic trees, BMC Bioinformatics 17, e:23. (pdf)

 

Bromham L, Duchêne S, Hua X, Ritchie AM, Duchêne DA, and Ho SYW (2018), Bayesian molecular dating: opening up the black box, BiolRev. 93, 1165-1192. (abstract)

 

Brown JW, and Smith SA (2017), The past sure is tense: on interpreting phylogenetic divergence time estimates, Syst. Biol. 67(2), 340-353. (pdf)

 

Cadena CD, Cuervo AM, Céspedes LN, Bravo GA, Krabbe N, Schulenberg  TS, Derryberry GE, Silveira LF, Derryberry EP, Brumfield RT, and Fjeldså J (2021), Systematics, biogeography and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds, Auk 138(2), ukz077. (pdf)

 

Carruthers T, and Scotland RW (2020), Uncertainty in divergence time estimates, SystBiol. 70(4), 855-861. (abstract) 

 

Černy D, and Natale R (2021), Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes), bioRxiv (pdf)

 

Dickens JK, Bitton PP, Bravo GA, and Silveira LF (2021), Species limits, patterns of secondary contact and a new species in the Trogon rufus complex (Aves: Trogonidae), Zool. J. Linn. Soc. 20, 1-42. (abstract)

 

Didier G, Fau M, and Laurin M (2017), Likelihood of tree topologies with fossils and diversification rates estimation, Syst. Biol. 66(6), 964-987. (pdf)

 

Donoghue PCJ, and Yang Z (2016), The evolution of methods for establishing evolutionary timescales, Phil. Trans. R. Soc. B 371, e:20160020. (pdf) 

 

dos Reis M, Donoghue PC, and Yang Z (2016), Bayesian molecular clock dating of species divergences in the genomics era, Nat. Rev. Genet. 17, 71-80. (pdf)

 

dos Reis M, Gunnel GF, Barba-Montoya J, Wilkins A, Yang Z, and 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, SystBiol. 67(4), 594-615. (pdf)


Douglas J, Zhang R, and Bouckaert R (2021), Adaptive dating and fast proposals: revisiting the phylogenetic relaxed clock model, PLoS Comput. Biol. 17(2), e:1008322. (pdf)


Duchêne S, Lanfear S, and Ho SYW (2014), The impact of calibration and clock-model choice on molecular estimates of divergence times, Mol. Phylogenet. Evol. 78, 277-289.  (abstract)

 

Field DJ, Berv JS, Hsiang AY, Lanfear R, Landis MJ, and Dornburg A (2019), Timing the extant avian radiation: the rise of modern birds, and the importance of modeling rate variation, Bull. Am. Mus. Nat. Hist. 440. (pdf)

 

Heads M (2005), Dating nodes on molecular phylogenies: a critique of molecular biogeography, Cladistics 21, 62-78. (pdf)

 

Heath TA, Huelsenbeck JP, and Stadler T (2013), The fossilized birth-death process: a coherent model of fossil calibration for divergence time estimation, PNAS 111(29), E2957-E2966.  (pdf) 

 

Hipsley CA, and Müller J (2014), Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology, FrontGenet. 5, e:138. (pdf) 

 

Ho SYW, ed. (2020) The Molecular Evolutionary Clock, Springer, Cham. (link)

 

Ho SYW, and Duchêne S (2014), Molecular-clock methods for estimating evolutionary rates and timescales, Mol. Ecol. 23, 5947-65. (pdf)

 

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

 

Kan XZ, Li XF, Lei ZP, Chen L, Gao H, Yang ZY, Yang JK, Guo ZC, Yu L, Zhang LQ, and Qian CJ (2010), Estimation of divergence times for major lineages of galliform birds: evidence from complete mitochondrial genome sequences, Afr. J. Biotech. 9(21), 3073-78. (pdf)

 

Kinsella CM, Ruiz-Ruano FJ, Dion-Côté AM, Charles AJ, Gossmann TI, Cabrero J, Kappei D, Hemmings N, Simons MJP, Camacho JPM, Forstmeier W, and Suh A (2019), Programmed DNA elimination of germline development genes in songbirds, Nat. Commun. 10, e:5468. (pdf)

 

Ksepka DT, Benton MJ, Carrano MT, Gandolfo MA, Head JJ, Hermsen EJ, Joyce WG, Lamm KS, Patané JSL, Phillips MJ, Polly PD, van Tuinen M, Ware JL, Warnock CM, and Parham JF (2010) Synthesizing and databasing fossil calibrations: divergence dating and beyond, Biol. Lett. 7(6), 801-803. (pdf)

 

Lukoscheck V, Keogh S, and Avise JC (2012), Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches, Syst. Biol. 61, 22-43. (pdf)

 

Marjanović D (2021), The making of calibration sausage exemplified by recalibrating the transcriptomic timetree of jawed vertebrates, FrontGenet. 12, e:521693. (pdf) 

 

Mitchell JS, Etienne RS, and Rabosky DL (2019), Inferring diversification rate variation from phylogenies with fossils, Syst. Biol. 68(1), 1-18. (pdf)

 

Norris RW, Strope CL, McCandlish DM, and Stoltzfus A (2015), Bayesian priors for tree calibration: evaluating two new approaches based on fossil intervals, bioRxiv (pdf)

 

Nowak MD, Smith AB, Simpson C, and Zwickl DJ (2013), A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses, PLOS ONE 8(6), e:66245. (pdf)

 

O’Reilly JE, dos Reis M, and Donoghue PCJ (2015), Dating tips for divergence-time estimation, Trends Genet. 31(11), 636-65. (abstract)

 

O’Reilly JE, and Donoghue PCJ (2016), Tips and nodes are complementary not competing approaches to the calibration of molecular clocks, BiolLett. 12, e:20150975. (pdf)

 

Parham JF, Donoghue PCJ, Bell CJ, Calway TD, Head JJ, Holroyd PA, Inoue JG, Irmis RB, Joyce WG, Ksepka DT, Patané JSL, Smith ND, Tarver JE, van Tuinen M, Yang Z, Angielczyk KD, Greenwood JM, Hipsley CA, Jacobs L, Makovicky PJ, MüllerJ, Smith KT, Theodor JM, Warnock RCM, and Benton MJ (2012), Best practices for justifying fossil calibrations, Syst. Biol. 61(2), 346-359. (pdf)

 

Pyron RA, and Laurin M (2017), Editorial: dating the Tree of Life, FrontEcol. Evol. 5, e:42. (pdf)

 

Rannala B (2017), Conceptual issues in Bayesian divergence time estimation, Phil. TransRSocB 371, e:20150134. (pdf) 

 

Schwartz RS, and Müller RL (2010), Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks, BMC Evol. Biol. 10, e:5. (pdf)

 

Smith SA, Brown JW, and Walker JF (2018), So many genes, so little time: a practical approach to divergence-time estimation in the genomic era, PLOS ONE 13(5), e:0197433. (pdf)

 

Tamura K, Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, and Kumar S (2012), Estimating divergence times in large molecular phylogenies, PNAS 109(47), 19333-38. (pdf)

 

Tao Q, Barba-Montoya J, Huuki LA, Durnan MK, and Kumar S(2020), Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics, Mol. Biol. Evol. 37(6), 1819-1831. (pdf)

 

van Tuinen, M, and Torres CR (2015), Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families, Front. Genet. 6, e:203. (pdf)

 

Weir JT, and Schluter D (2009), Calibrating the avian molecular clock, Mol. Ecol. 17, 2321-2328. (pdf)

 

Yang Z, and Rannala B (2005), Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds, Mol. Biol. Evol. 23(1), 212-226. 

 

Yoder AD (2013) Fossils versus clocks, Science 339, 656-658.  (pdf)