To dissect the relative contributions of replication and transcription on the extent of substitutional asymmetries, we used a set of 492 human genes where information for all three potentially explanatory variables the distance of the gene to its nearest ORI (variable β), germ line expression level (variable ε), and the relative mutation rate (variable τ)—is available.
Thus, there is evidence that the mutation rate is variable within some animal species.
The proposed solution - namely a variable mutation rate as an independent variable, at least in one case - is compared to other optimization techniques, such as random search / hill climbing / Nelder-Mead.
The action of AID is focused predominantly on the variable regions of the immunoglobulin genes and it is estimated that the AID leads to a mutation rate in the variable regions that is approximately 1 million times higher than would occur by spontaneous mutation alone [ 168].
In humans, heterozygosities generally exceed 0.5 and range as high as 0.9, with as many as 50 alleles per locus [ 24], and mutation rates, though variable among loci, exceed rates for non-microsatellite loci by up to four orders of magnitude [ 25, 26].
A phylogenetic analysis of cytochrome b third-codon position confirms that the mitochondrial DNA mutation rate is quite variable in birds, passerines being the fastest evolving order.
Melanoma metastases have been shown to have a high mutation rate [ 9], variable phenotype, a clinically diffuse dissemination pattern [ 10], and the unique ability to elicit spontaneous antigen-specific host immune responses [ 11].
If the apparent variation in τHC among loci is due to mutation rate variation, accounting for variable mutation rates among loci should lead to a reduction in the number of significant results.
In this paper, we show that the proposed variable mutation rate outperforms fixed mutation rates and other common search algorithms in the effectiveness of their solutions.
Differences in base composition, variable mutation rate and gene conversion are all mechanism by which the synonymous substitution rates could vary between genes.
