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Equations (1) and (2) share the same unknowns except the constant clock offset (a0 resp. b0) which is assumed to be different for each band due to ionosphere delays.
In this test, deviations from a linear growth of clock time differences, i.e., deviations from constant clock drift, were small; these residual errors were less than 0.10 ms over all 1 week intervals for all clock pairs.
For the TMRCA of the Upland and Lowland clades, the constant clock TMRCA estimates 15.19 mya (mid-Miocene) or 9.11 mya (late Miocene), respectively.
With respect to SMO, for the TUX clade the constant clock TMRCA estimated divergence times of 614,000 (0.12-1.55 Mya) and 202,000 (0.05-0.47 Mya) years ago for 2 and 5% substitution/My, respectively.
For all MEGA and BEAST analyses, a constant clock with a mutation rate of 1.665 × 10-8 basubstitutionion per nucleotide per year [ 4] for the complete mitochondrial genome was applied.
Furthermore, these three genomes showed evidence of deviation in the molecular clock rate which could have confused the analyses presented here since the models in ClonalFrame [ 19] and ClonalOrigin [ 21] assume a constant clock rate (Additional file 1: Figure S1).
Similar(6)
Application of the procedure described above for cyt b resulted in adoption of HKY+I as the model for each codon position, with a constant clock-like mutation rate.
Thus, we found that there was not a good fit to a "constant clock-like" rate in the Plasmodium mitochondrial genome and that it exhibits rate heterogeneity among genes.
Two independent runs of 120 million generations were performed, under constant-clock conditions with a constant coalescent model of species evolution.
The ultrametric tree (UT) is a commonly used model for evolutionary trees assuming that the rate of evolution is constant (molecular clock hypothesis).
Assuming a mutation rate of 15% (range 10 20%) per site Myr−1 for the control region [13], [21] [24], a constant molecular clock and a generation time of 2 years [18], we obtain a divergence time for the two clades of 87 (65–141) and 65 (49 98) kyr BP for DXY and DA, respectively.
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