Abstract
The fixation of phenotypes and underlying alleles is a typical
evolutionary process in speciation. As the primary molecular basis of
phenotypic plasticity, epigenetic mechanisms also play an essential role
in maintaining phenotypes. However, whether and how DNA evolution was
shaped by epigenetic alteration remains unknown, especially accompanied
DNA fixation in speciation. We used sperm methylomes of three rat
subspecies as epigenetic markers and screened out genomic regions that
experienced distinct differential methylation. To obtain independent
results, they were further filtrated according to genomic locations to
guarantee that their evolutionary features were not interactively
affected by nearby DMRs (differentially methylated regions) of other
datasets. By analyzing intraspecies and interspecies phylogenetic
relationships, we showed that, in the same genomic regions, the
significantly accelerated DNA evolution only occurred in individuals or
lineages that experienced differential methylation. Across the same
genomes, differential methylation led to a significant increase of
FST only in lineage-specific DMRs and a
significant increase of π in both individual-specific and
lineage-specific DMRs. Correlations among methylation, π and
FST showed that it was methylation consistency
rather than the absolute methylation difference that significantly
influenced both π and FST. The change of both π
and DNA fixation depended on the degree of intraspecies methylation
consistency. While the breakdown of methylation consistency facilitated
the promotion of π, the maintenance of methylation consistency
facilitated the acceleration of DNA fixation.