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If base composition is close to equilibrium, this is an indicator of selection or BGC in favour of GC base pairs (see §1).
Equilibrium for base composition implies an equal number of GC→AT and AT→GC substitutions along a lineage, regardless of the action of selection or BGC.
According to the role that these two forces play in CGI maintenance, CGIs can be classified as hypo-deaminated CGIs or BGC CGIs.
If these differences are not assumed to reflect varying mutational biases over time, selective forces (i.e., either natural selection or BGC) need to be causing biases in fixation probabilities that partly compensate for the mutational biases.
Interestingly, the total substitution rate is higher in both tCGI and dCGI than in their flanking regions, suggesting that these regions have undergone a period of positive selection for high GC content or BGC (supplementary fig. 7, Supplementary Material online).
We found evidence that selection on synonymous codons is significantly weaker in the selfers compared with the outcrossers and that this difference cannot be fully accounted for by mutational biases or BGC.
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One million BGC-823/MTA2 BGC-823/MTA2 orells in 100 μl PBS were injected through tail vein, respectively.
As before, the HKY85:π model uses the true neutral substitution biases, π, without BGC or selection in both test and reference region.
If BGC or selection are the underlying causes for the observed discrepancies between mutational biases and genomic nucleotide contents, then these processes would likely be acting throughout the genome, making it very difficult to find truly neutrally evolving regions.
Consequently, these results indicate that many genomic regions that have arisen by non-methylation related processes (BGC or chance) and have been co-opted as current CGIs, exhibiting highly variable DNA methylation across different tissues.
A relationship between levels of recombination and GC-content was recently demonstrated for many bacteria, suggesting that BGC, or a mechanism similar to BGC, may affect nucleotide content in bacteria in a similar manner (Touchon et al. 2009; Lassalle et al. 2015).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com