Assuming that molecular evolution is relatively clock-like, this implies that the frequency of hybridization is related to the time since divergence.
Because comparisons of these same taxa with G. max are clock-like, this suggests that the divergence date estimates from the nuclear genome are inappropriately high for estimating substitution rates of chloroplast genomes within this group of taxa.
More specifically, if rate variation for empirical data falls within the rate variation erroneously estimated for comparable clock-like data, this would suggest that the empirical rate variation is due to error in rate estimation rather than true differences among lineages in the underlying biological substitution process.
The CV was taken as an indication of how clock-like the evolution was: the lower the coefficient, the more clock-like the evolution.
This setting is recommended because it additionally gives an indication of how clock-like the data are [ 46].
But with clocks like this, conversely, we can understand that time passes at different speeds, depending on the time and place a clock is at".
On one hand, the low CV value of 0.10 and a highly significant LRT test did not indicate a clock-like evolution of this subset.
The presence of a clock-like signal in this dataset was investigated using Path-O-Gen [ 21], which roots the maximum-likelihood tree at the position that is most compatible with the assumption of the presence of a molecular clock.
Simulations were conducted using a clock-like substitution process; therefore, this observed rate variation must be due to error in rate estimation, both as a result of the stochastic substitution process producing different numbers of substitutions than expected along lineages, and misestimation of rates due to uncounted substitutions.
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