Despite the potential violation of the molecular clock, divergence of synonymous substitutions was used for dating estimation because it permitted us to use a different set of assumptions (rates of divergence, biogeographic milestones and models of nucleotide substitutions) than two relaxed molecular clock methods: penalized likelihood and Bayesian dating estimation.
Molecular dating did not allow estimation of divergence times between minor gene pools.
A regression analysis between the ages obtained for all nodes was highly significantly positive (R = 0.88; t test: P < 0.001) indicating that missing data in our dataset are likely to have little influence on age estimations in molecular dating.
It is worth noting that due to the ongoing debate regarding the true mutation rate [ 36, 57], and the limitations of the rho statistic method of molecular dating [ 34], the conversion of age estimates in mutations into ages in years and the estimation of associated error values are to be considered approximations only.
Moreover, molecular date estimates can come with substantial uncertainty, so that it can be difficult to draw strong conclusions from molecular date estimates if the associated estimation error is taken into account.
ESWW carried out molecular dating.
In spite of this somewhat low precision of time estimation, the molecular dating results (Fig. 4; [ 42]) consistently suggest that Agamidae and Chamaeleonidae were separated after the Middle-Late Jurassic break-up of Pangea into Laurasia and Gondwanaland (Fig. 6.2) and when the latter two supercontinents were further fragmented by plate tectonics [ 63].
Some of these can be directly compared to genera of the extant family Sargassaceae, as Cystoseirites (similar to Cystoseira) or Paleohalidrys (which has modern representatives) that are in the order Fucales, and provide a valuable framework for evolutionary parameter estimation and molecular dating of Fucaceae [ 37].
Chapter 2 contains two additional sections after the summary Appendix 2.1: Molecular Dating Methods and Appendix 2.2: Phylogeny Estimation.
Molecular dating may nevertheless result in contrasting estimations, as illustrated by some examples given below (see also Fig. 2): According to Yao et al. (2002a), most mtDNA lineages are very ancient in East Asia, with an age greater than 50,000 years, the oldest ones being most frequent in the south (81,000 and 75,000 years for R9 and B, respectively).
