New Study Compares Epigenetic Clock of Different Organisms To Understand Evolutionary Dynamics

Epigenetics is the study of how environmental factors and life experiences can alter the expression of genes without changing the DNA sequence.

Epigenetic changes can affect traits such as metabolism, stress response, and aging.

In humans and other mammals, epigenetic changes accumulate over time and can be used to estimate an individual's chronological age.

These estimates are based on epigenetic clocks, which are mathematical models that measure the level of DNA methylation, a chemical modification that affects gene activity, at specific sites in the genome.

Epigenetic clocks have been widely used as biomarkers of aging and health in humans and other animals, but their existence and utility in plants have been largely unknown.

An international team of researchers has discovered that epigenetic clocks not only exist in plants but also keep ticking accurately over many generations.

In a new study published in the journal Science, the team describes how this clock can tell time with a resolution from decades to centuries, an accuracy that cannot be achieved with traditional DNA mutation-based clocks.

The research sheds new light on microevolutionary questions that have been challenging to resolve, such as the timing of the introduction of invasive species and the consequences of human activities since the emergence of modern industrialization.

How epigenetic clocks work in plants

(Photo : ZINYANGE AUNTONY/AFP via Getty Images)

The researchers first found evidence for an epigenetic clock in plants when they studied a 300-year-old poplar tree.

They analyzed the DNA methylation patterns across different branches of the tree and found that they correlated with the branch age, which was determined by counting tree rings.

They were able to estimate the age of one branch that could not be cured by using only DNA methylation data.

The team then tested whether epigenetic clocks could also work in other plant species with different modes of reproduction.

They focused on two model organisms: Arabidopsis thaliana, a self-fertilizing plant in the mustard family, and Zostera marina, a clonal seagrass that reproduces by producing genetically identical copies of itself.

They collected samples from natural populations of these species and measured their DNA methylation levels.

It is found that epigenetic clocks could accurately estimate the divergence times of intra-species phylogenetic or evolutionary trees, which reflect the historical relationships among different lineages within a species.

The researchers used experimental evolution populations of A. thaliana with known pedigrees to further validate their findings.

These plants were grown by single-seed descent for up to 32 generations from wild type exposed to different environments or from natural strains from distinct geographical origins.

The researchers identified a subset of epimutations, which are changes in DNA methylation that occur randomly and independently of DNA mutations, that were "clock-like" and could be used to estimate the time of the pedigree.

Also Read: This Clock Can Figure Out an Animals' True Biological Age

Why epigenetic clocks matter for plant evolution

The discovery of epigenetic clocks in plants has important implications for understanding plant evolution and ecology.

Epigenetic clocks can provide a new tool for dating evolutionary events that are difficult to infer from DNA mutations alone, such as speciation, hybridization, colonization, and adaptation.

It can also reveal how human activities have influenced plant diversity and distribution over time, such as through agriculture, urbanization, and climate change.

It may also have functional consequences for plant fitness and adaptation.

Epigenetic changes can affect gene expression and phenotypic variation, which can influence traits such as growth rate, stress tolerance, flowering time, and disease resistance.

It can also be inherited across generations or transmitted horizontally among individuals through grafting or horizontal gene transfer.

Therefore, epigenetic clocks may reflect not only the chronological age of plants but also their evolutionary potential and history.

The researchers hoped that their study will stimulate further research on epigenetic clocks in plants and other organisms.

They also suggested that epigenetic clocks could be integrated with other molecular markers and methods to provide a more comprehensive picture of evolutionary history and dynamics.

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