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If reliable correlates of rate variation can be identified, this information could be exploited to improve molecular dating methods [ 15, 16, 19, 20].
This makes intuitive sense when considering that ancestor and descendant lineages are likely similar in body size, generation time, DNA repair efficiency, population size and other traits influencing rates of sequence evolution, and the most popular molecular dating methods available indeed implicitly assume that rates are autocorrelated across a tree [ 66, 67].
Chapter 2 contains two additional sections after the summary Appendix 2.1: Molecular Dating Methods and Appendix 2.2: Phylogeny Estimation.
This makes very difficult to date the formation and the diversification of the CD complex by molecular dating methods.
We investigate the effect of such assumptions using different molecular dating methods.
Recent progress in molecular dating methods nevertheless would allow for establishment of uncertainties in fossil calibrations [ 18, 76].
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It may seem straightforward to use a molecular dating method to either accept or reject the possibility of a recent human influence in the origin of the allopolyploid CD genome.
Secondary calibration points generated by these previous Annonaceae studies were avoided as a different molecular dating method and calibration points were employed in this study.
Although the methodology and assumptions implemented in each molecular dating method can be readily compared, our knowledge of how time estimates are influenced by the choice of method is still poor.
The large amount of combinations of parameters influencing age estimates limits straightforward explanations of these differences with previous studies (e.g., topology used [ 46]; fossil species and priors used to define and model age constraints [ 47]; molecular dating method [ 13]).
The molecular dating method gave the divergence between the two main subgenera of Alnus at the Eocene (around 48,6 My ago), and the original split between A. cordata and the A. glutinosa- incana complex at the Oligocene (around 22,9 My ago; Figure 1).
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