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DNA evolution depends on differential methylation patterns in rat speciation
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  • Xiao-Hui Liu,
  • Ying Song,
  • Ning Li,
  • Dawei Wang,
  • Fei Ling,
  • Jin-Min Lian,
  • Qiye Li,
  • Yabin Jin,
  • Zhiyong Feng,
  • Lin Cong,
  • Dandan Yao,
  • Chan Luo,
  • Ming D. Li
Xiao-Hui Liu
Chinese Academy of Agricultural Sciences Institute of Plant Protection
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Ying Song
Chinese Academy of Agricultural Sciences Institute of Plant Protection
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Ning Li
Chinese Academy of Agricultural Sciences Institute of Plant Protection
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Dawei Wang
Chinese Academy of Agricultural Sciences Institute of Plant Protection
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Fei Ling
South China University of Technology School of Bioscience and Bioengineering
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Jin-Min Lian
China National GeneBank
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Qiye Li
China National GeneBank
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Yabin Jin
South China University of Technology School of Bioscience and Bioengineering
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Zhiyong Feng
Guangdong Academy of Agricultural Sciences
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Lin Cong
Plant Protection Institute, Heilongjiang Academy of Agricultural Sciences
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Dandan Yao
Guangdong Academy of Agricultural Sciences
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Chan Luo
Heilongjiang Academy of Agricultural Sciences
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Ming D. Li
Zhejiang University School of Medicine First Affiliated Hospital
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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.

Peer review status:UNDER REVIEW

12 May 2021Submitted to Molecular Ecology
17 May 2021Assigned to Editor
17 May 2021Submission Checks Completed
01 Jun 2021Reviewer(s) Assigned