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We propose a simple model for compositional evolution based on the temporal per base pair rate of mutations (the variable model).
Many compositional evolution studies, explicitly or implicitly, have used this model: that is, the per base pair rate of mutations is assumed to be temporally constant.
We basically followed Webster et al. (2003) to estimate the per base pair rate of mutations for various GC content classes.
Figure 7 shows the per base pair rate of GC→AT (u) and AT→GC (v) mutations corresponding to GC content in human chromosome 3 (HSA3).
To estimate accurate per base pair rate of GC→AT (u) and AT→GC (v) mutations (Sueoka 1988 , 1993, we need to reconstruct nucleotide compositions of the ancestral genome of the human population.
We call this model "the variable model": unlike the constant model, the per base pair rate of GC→AT (u) and AT→GC (v) mutations vary depending on time.
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This equates to a per base pair mutation rate of 2.95 (± 0.21 SE) × 10−8 mutations/site/generation and a genomic mutation rate of 0.18 (± 0.01 SE) mutations/genome/generation.
Scarcity of DNA precluded a third PCR, but these two mismatches translate into an per base pair error rate of about 0.014%, a measure in the range of known Taq error rates.
Thus, when calculating the per base pair (bp) rate of NCO, the numerator and denominator are identically ascertained (see below and 'Materials and methods' 'Determination of informative sites' for details).
(B ) The base pair unwinding rates of the combined enzymes at 5 µM dVTPs plotted against dTTP concentrations and fit to Equation 4 (solid lines) to obtain the maximal rate of unwinding (k cat) and K m for dTTP.
A MA study in Paramecium tetraurelia gave a base pair substitution rate estimate of ~1.9 × 10−11 per cell division (Sung et al. 2012), which is similar to D. discoideum.
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