There is a range of molecular clock calculations available, depending on whether one uses more modern relaxed clock methods or fairly simplistic distance estimates, which will vary based on whether one uses model-corrected or uncorrected distances for either COI or 16S sequences.
Alternatively, a tree like that in c can be scaled to time (e.g., in millions of years before the present), for example if fossil or "molecular clock" data are available for calibrating the specific timing of branching events (Benton and Ayala 2003; see also Fig. 9).
We acknowledge that there is no available calibrated molecular clock with fossils for closely-related passerines in this geographical region, and we do not mean to imply that this rate is strictly accurate.
Because the fossil record of freshwater planarians is non-existent, no molecular clock for the Tricladida is available.
Therefore, the rich fossil history of cetaceans (see [ 32]), the development of relaxed molecular clocks, and newly available computer programs to implement this advancement in phyogenetic modeling (e.g., BEAST; [ 33]) may provide powerful new tools to examine the phylogenetic history of cetaceans.
The only molecular clock data on Heterobranchia [ 14] available prior to the present study suffers from unreliable calibration, which is considered as the most sensible and critical part of divergence time estimations [ 76].
We have taken care to address criticisms of past molecular clock studies and have used all available timing methods applicable to protein sequence data, including global (constant rate) and local (variable rate) methods.
By allowing to reciprocally estimate the posterior age of different nodes for which paleontological constraint are available, the Bayesian molecular clock method might help to identify unreliable calibration points and groups for which older fossils are likely to be found.
To further investigate the time of colonization of land by animals, we sequenced two nuclear genes, glyceraldehyde-3-phosphate dehydrogenase and enolase, in representative arthropods and conducted phylogenetic and molecular clock analyses of those and other available DNA and protein sequence data.
Moreover, a relaxed molecular clock and Bayesian MCMC search optima are available within it [ 44, 45].
