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Modifying the crossover rate or the mutation rate does not improve the results.
Although HCV has a high mutation rate, a high mutation rate does not necessarily imply that certain traits will be easily acquired (as reviewed in detail by Smith and Simmonds [75]).
Furthermore we repeated the analyses under the BSP tree prior for 20 datasets with randomly shuffled sample ages to test if the estimated mutation rate does not solely depend on the age of the sample points.
We observe that the mutation rate does not influence f significantly.
However, the overall mutation rate does not change significantly in any of the cases.
The within-patient estimate of mutation rate does not have the same measurement problems and gave a consistent result.
Similar(42)
They state that minisatellite mutation rate measurements show 'significant repeatability' among populations of the same species and for probes applied to the same population, and that mutation rate did not vary between different probes or enzymes.
They found that whilst an elevated mutation rate was not required for carcinogenesis to occur in a reasonable time, an increased mutation rate did reduce the waiting time to cancer (Beerenwinkel et al. 2007).
Meanwhile, in the third patient, TpC* mutation rate did not show a comparable elevation (Additional file 9: Figure S4) indicating that this mutation pattern is not ubiquitous for bladder cancer.
The mutation rate did not differ according to the primary tumor site if the tumor location was classified as either ascending, hepatic flexure, transverse, splenic flexure, descending, sigmoid, or rectum.
Together, these results imply that variation in selective constraint or mutation rate do not explain elevated divergence between X. birchmanni and X. malinche at loci in conspecific LD. 10.7554/eLife.02535.021 Figure 6.
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