Epigenetics: challenging Genetic Phylogenetics


The field of genetic phylogenetics, which aims to reconstruct evolutionary relationships between organisms, has historically focused almost exclusively on changes in DNA sequences. However, a growing body of evidence indicates that epigenetic modifications, which alter gene expression without changing the underlying DNA sequence, can also play a significant role in evolution. This realization has led to a recent surge in interest in incorporating epigenetics into phylogenetic analyses.

Here's a breakdown of how and why this shift is occurring:

Traditional Phylogenetics and its Limitations:

  • DNA-centric view:

  • Traditional phylogenetics relies heavily on comparing DNA sequences to infer evolutionary relationships. The assumption is that changes in these sequences, through mutations, are the primary drivers of evolutionary divergence.

  • This approach has been successful in reconstructing evolutionary trees for many groups of organisms.

  • Neglecting Epigenetics:

  • For a long time, epigenetic modifications, such as DNA methylation and histone modifications, were considered to be transient and limited to regulating gene expression within an individual.

  • Therefore, they were largely ignored in phylogenetic studies.

The Rise of Epigenetics:

  • Transgenerational Epigenetic Inheritance:

  • Research has shown that epigenetic modifications can be inherited across generations, a phenomenon known as transgenerational epigenetic inheritance.

  • This finding shows that epigenetic changes can contribute to heritable phenotypic variation and potentially influence evolutionary trajectories.

  • Environmental Influence:

  • Epigenetic modifications are often influenced by environmental factors, providing a mechanism for organisms to rapidly adapt to changing conditions.


  • This adaptability can have evolutionary consequences, as environmentally induced epigenetic changes may become fixed in populations over time.

  • Phyloepigenetics:

  • The term Phyloepigenetics is emerging, to define the combination of phylogenetic analysis, with epigenetic data. This is a very new area of research.

  • Technological Advancements:

  • Advances in sequencing technologies and bioinformatics have made it possible to study epigenetic modifications on a large scale.

  • This has facilitated the integration of epigenetic data into phylogenetic analyses.

Why Integrating Epigenetics Matters:

  • Improved Accuracy:

  • Incorporating epigenetic data can improve the accuracy of phylogenetic reconstructions, especially for closely related species where DNA sequence differences may be subtle.

  • Epigenetics can provide additional data points to resolve evolutionary relationships.

  • Understanding Adaptation:

  • Epigenetics can shed light on the mechanisms by which organisms adapt to environmental changes.

  • By studying the evolution of epigenetic modifications, researchers can gain insights into the role of environmental factors in shaping evolutionary trajectories.

  • Expanding Evolutionary Theory:

  • The inclusion of epigenetics challenges the traditional DNA-centric view of evolution and expands our understanding of the factors that contribute to evolutionary change.

In conclusion, the recognition of the role of epigenetics in evolution is a relatively recent development. As technology improves, the integration of epigenetic data into phylogenetic studies is likely to become increasingly common, leading to a more comprehensive and accurate understanding of evolutionary relationships.


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