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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
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Related Experiment Video

Updated: Nov 1, 2025

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
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An Analysis of Methylome Evolution in Primates.

Arne Sahm1, Philipp Koch2, Steve Horvath3

  • 1Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany.

Molecular Biology and Evolution
|June 27, 2021
PubMed
Summary

Epigenetic marks like DNA methylation are evolutionarily conserved across species, allowing phylogenetic methods to reconstruct evolutionary history. However, enhancer regions show rapid evolution, impacting immune gene regulation.

Keywords:
epigenomicsgreat apeshumanmethylationphylogeneticspolycomb repressor 2

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Area of Science:

  • Evolutionary biology
  • Epigenetics
  • Genomics

Background:

  • Understanding the long-term evolution of epigenetic marks is crucial but challenging due to a lack of systematic investigation strategies.
  • DNA methylation patterns are increasingly recognized for their role in gene regulation and evolutionary processes.

Purpose of the Study:

  • To adapt and apply classic phylogenetic methods to interval-scaled epigenetic data for evolutionary analysis.
  • To investigate the evolutionary conservation and dynamics of DNA methylation in great apes.

Main Methods:

  • Systematic adaptation of phylogenetic methods (maximum likelihood, parsimony, distance-based) for epigenetic data.
  • Analysis of DNA methylation patterns in a great apes blood dataset, including CpGs in promoters, enhancers, and genic regions.
  • Correlation analysis between epigenomic conservation and transcription factor binding density.

Main Results:

  • DNA methylation is evolutionarily conserved at individual CpG sites across various genomic regions.
  • Epigenomic conservation correlates with transcription factor binding density, with accelerated evolution at specific binding sites (e.g., AP-1, BRCA1).
  • Phylogenetic tree reconstruction using methylation data is comparable to sequence-based methods for most regions, but ineffective for enhancers.

Conclusions:

  • Phylogenetic analysis of DNA methylation provides insights into evolutionary conservation and dynamics.
  • Enhancer regions exhibit rapid epigenomic evolution, particularly those controlling immune genes, posing challenges for phylogenetic reconstruction.
  • Specific transcription factor binding sites show distinct evolutionary rates in methylation patterns.