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In contrast, it appears that methylation divergence between paralogous CpG sites is largely unlinked to the time since the corresponding duplication event.
Despite the observed links with DNA sequence motifs, one of the strongest correlates to DNA methylation divergence between paralogous CpG sites was found to be discordance in the distance to the nearest Alu element.
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In other words, divergent recombination hotspots between humans and chimpanzees do not coincide with DNA methylation divergence hotspots between these species.
In addition, considering the multiple data filtering steps using different methods, the number of identified DMRs in this study was likely an underestimation of the between-species methylation divergence in the brain.
We further examined the relationship between genetic and methylation divergence among samples using sliding windows across the whole genome.
The above results, i.e., the CHH methylation tree's inconsistency with the genomic tree and the low correlation between non-CG methylation divergence and genetic divergence, imply that high-level methylation in CG context might be more conserved than low-level methylation in CHG and CHH contexts among species.
To examine the relationship between genetic and methylation divergence, the average number of nucleotide differences per site among samples for different genomic regions was calculated using SNPs obtained from the above step with 50 kb sliding window and a step of 25 kb through the whole genome, which was used to measure genetic divergence.
Moreover, in light of emerging data on comparative DNA methylation maps of humans and chimpanzees, we can directly test whether the observed rapid divergence of recombination hotspots between humans and chimpanzees is caused by interspecific DNA methylation divergence, as expected if DNA methylation is the underlying driver of recombination hotspot evolution.
This radiation presents the opportunity to investigate DNA methylation divergence at both shallow and deeper timescales (0.380-1.4 My).
However, as shown in table 1, particular motifs were observed to be linked to methylation divergence.
The difference in DNA methylation, according to methylation status (hyper- or hypo-) and the average methylation difference between MS and controls, was validated by an independent sample.
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