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Molecular dating analysis including several time constraints revealed a divergence time of ∼120 Ma for A. lucayanum and B. floridae.
Molecular dating analysis of the refractory clade revealed that it originated, i.e. had a most recent common ancestor (MRCA), about 12.4 – 13.8 MYA.
Although HRV-C is a newly described HRV species, molecular dating analysis using sequences of the VP4/2 coding regions indicated that these viruses have been circulating for at least 250 years, with an estimated evolutionary rate of 6.6×10−4 substitutions per site per year.
The tree presented in Figure 3 was used as the reference topology for molecular dating analysis.
Markov chain Monte Carlo Tree (MCMCTree) requires a safe upper bound for the root age in its molecular dating analysis.
Moreover, two new orchid fossils described in 2009 have not yet been incorporated in a molecular dating analysis.
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In addition, the general incongruence between the (exogenous) virus and host phylogenies precluded any reliable molecular clock dating analysis.
We used a relaxed molecular-clock method for dating analysis developed by Thorne and Kishino [ 63] to estimate divergence times.
Total evidence analysis, where fossils are placed as terminal taxa in the dating analysis using both molecular and morphological data matrix, could help in exploring the robustness of fossil placement [ 85], but as pointed above, the lack of characters in the Solanaceae seed fossils does not currently permit such analyses.
TLPC carried out the molecular genetic studies, the sequence alignment, phylogenetic and dating analysis, and drafted the manuscript.
A dating analysis is run using an uncorrelated relaxed molecular clock model within a Bayesian framework with direct fossil calibrations.
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