The species tree has an average height of 1.6 ∑ i = 2 5 1 / 0. 8 i, which equals 8e-3 mutations when height is interpreted as millions of years and using a substitution rate of 0.005 per million years.
Using a substitution rate of 1 % per million years [ 9, 41], the time of demographic expansion for northern group and southern group was estimated as ~440 ka (90 % CI: 313.9-682.4 ka) BP and ~190 ka (90 % CI: 104.4-259.3 ka) BP, respectively (Table 6).
The mean number of substitutions per site compared to the most common ancestor of each clade was calculated [62] and converted into time using a substitution rates of 1.26 × 10-8 [63].
The calculated KS values of the 2-member gene clusters were converted to divergence time, using a substitution rate of 6.5 × 10−9 mutations per site per year34.
The observed divergence was translated into an insertion date using a substitution rate of 1,3 × 10-8 mutation/site/year [ 18].
Using a substitution rate of 1.3 × 10− substitutions per site per year (Ma and Bennetzen 2004), the insertion date can be computed for each LTR-RT.
The observed divergence was translated into an insertion date using a substitution rate of 1.3 × 10−8 mutation/site/year (Ma and Bennetzen 2004).
Using a substitution rate of 1,3 × 10-8 mutation/site/year [ 18], we estimated that Route66 has been active in rice in the last 230,000 years.
Numbers of substitutions were calculated for each pair and translated into divergence time using a substitution rate of 1.05 × 10-9 nucleotides per site per year, as previously determined for fungi [ 71, 72].
By using a substitution rate of 1,3 × 10-8 mutation/site/year [ 18], we estimate that this corresponds to a 1,5 My old radiation whereas both species diverged more than 50 Mya.
The mean number of mutations per site to the most recent common ancestor was estimated and converted to real time using a substitution rate of 1.26 × 10-8 per site per year [ 40].
