We estimated the date of integration using the substitution rate of the neutrally evolving Nicotiana ITS nrDNA sequences (29 sequences, 517 sites).
However, it is unclear whether it is appropriate to use mutation rates based on contemporary data to date this transition because comparative rates of substitution in bacteria have been shown to be lower than those based on mutation accumulation experiments (Ochman 2003).
As such, our study extends and strengthens this conclusion, providing the most comprehensive quantitative measure to date of the association between opiate substitution treatment and risk of incident HIV infection.
Models of substitution applied in the dating analysis (4 partitions, PartitionFinder).
While planarians have some of the lowest rates of substitution, this does not invalidate the dating results obtained.
There was a significant positive correlation between ML root-to-tip branch lengths and dates of isolation, suggesting substitution mutations have been occurring at a regular rate (fig. 1 D).
To date, only one study [ 2- 6] presented information about the efficiency of substitution in glaucoma care, and its consequences for both quality of care and cost-effectiveness.
For example, the combination of systematic error in the number of substitutions estimated on long branches with calibrations located on long branches can lead to the underestimation of substitution rates and, therefore, the overestimation of dates on shallower nodes [41].
The molecular clock was calibrated with sampling dates and a uniform prior distribution for the mean rate of substitution ranging from 10−3 to 10−8 substitutions per site per year (s/s/y) (Holmes 2009).
This approach has the advantage of simultaneous estimation of substitution model parameters, topology, branch lengths and fossil-based date calibration, using the Bayesian inference and MCMC method.
The molecular clock was also used to compute the date of duplication by calculating the number of substitutions per silent site (Ks).
