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Evolution rate estimates revealed that about 15%and6%6% sites– for branch D1a and branch D1b, respectively – evolved under positive selection.
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Values for T were calculated using an evolution rate estimated at 4.4% per Myr [ 21].
These values are in average twice as low as previous evolution rates estimated by Chevaldonné et al. [50] and Johnson et al. [51] for other hydrothermal invertebrates using the mtCO1 gene.
With short-term C difficile evolution rates estimated from serial sampling of 91 patients with samples taken between 1 and 561 days apart at 2.3 SNVs/genome/year (95% credibility interval 1.6 3.0).
Gene evolution rates were estimated here by the GC content of genes instead of by non-synonymous substitution rates (Ka), since both parameters are highly correlated in Buchnera.
This, together with the divergence time of the entire macro-haplogroup T, only 16.0 ky obtained by using a constant mtDNA sequence evolution rate and an estimated bifurcation between yak and bison versus cattle of 2 million years [9], agrees with a single B. taurus domestication event in the Fertile Crescent, followed by spread with the migrations of farmers and pastoralists.
The evolution rate K was estimated to be 0.16 base/day, which is similar to the reported evolution rate of HIV-1 virus [ 10].
Consistent with the raw number of difference estimates, the evolution rate of the 18S rDNA relative to the proteome is much lower in unicellular species (analysis of covariance unicellulars versus multicellulars p = 0.048) (Figure 2).
Similarly, we determined the best clock model for estimating the evolution rate of the gag gene.
We first evaluated the marginal likelihood of the three clock models employed in this study to determine the best clock model for estimating the evolution rate of the pol gene.
We propose a mathematical model to estimate the evolution rate of the SARS coronavirus genome and the time of the last common ancestor of the sequenced SARS strains.
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