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

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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) 

 

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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)

 

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

 

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

 

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