First epigenetic DNA clock can reveal a zebra shark’s age from a blood sample

A shark’s age can be surprisingly hard to pin down, even when the animal is swimming in plain sight. For zebra sharks, researchers have now found a clue in blood: chemical marks on DNA that shift as the animals grow older.

A University of Georgia team built what it describes as the first epigenetic clock tested in sharks. The method estimates age by reading DNA methylation, chemical tags that change across the genome over time.

Published in Molecular Ecology, the work could give conservation biologists a less harmful way to estimate shark ages. Age structure can reveal whether a population is growing, stable or declining.

“Age structure is one of the most important things conservation biologists can measure,” said Benjamin Parrott, corresponding author of the study and an associate professor at UGA’s Savannah River Ecology Laboratory and Odum School of Ecology. “If we could figure out how old wild sharks are, we could finally understand the age structure of their populations. That’s incredibly important for conservation of marine populations.”

The researchers analyzed blood from more than 50 zebra sharks at southeastern aquariums, including the Georgia Aquarium. Many had known birth dates, allowing predicted ages to be checked against actual ages.

Across the genome, average DNA methylation declined slightly but significantly with age. The team found 158,015 CpG sites, locations where methylation can occur, with a significant relationship to age.

Most of the strongest age-linked sites lost methylation as sharks grew older. Among sites with an absolute Spearman correlation above 0.5, 95,736 showed declining methylation, while 16,796 showed increasing methylation.

The two groups appeared in different genomic regions. Sites that gained methylation were enriched near promoters and CpG-rich regions. Sites that lost methylation were more common in introns and CpG-poor regions.

Methylation also shifted more strongly between young and middle-aged sharks than between middle-aged and older animals, suggesting especially rapid epigenetic change early in life.

“The epigenome is a lot like an old barn. It starts out well built, but over time things slowly fall apart,” Parrott said. “Our bodies age the same way. Our skin changes, our hair turns gray and DNA patterns drift too. The clocks pick up on that process.”

The most complex models used fewer than 100 CpG sites and predicted age with high accuracy. In leave-one-out cross-validation, the models selected between 56 and 90 sites.

Predicted and actual age were highly correlated, with a Pearson correlation of 0.97. The median absolute error was 1.03 years.

Accuracy dropped in the oldest animals. For sharks younger than 20, the median error was 0.72 years. For those older than 20, it rose to 3.32 years.

Simpler models also performed well. A clock using just 10 CpGs predicted age with a median absolute error of 1.62 years. A 20-site model produced an error of 1.99 years.

The researchers also tested wild-caught sharks whose exact ages were unknown. For 10 animals with body-length measurements, they estimated minimum ages from a growth curve and compared them with DNA-based ages.

The median absolute difference was 3.34 years. For wild-caught sharks without length information, the difference between predicted age and minimum known age was 4.19 years.

Those comparisons remain uncertain because the animals’ true birth dates were unavailable.

Methylation did not move in a single direction across the lifespan.

Researchers identified 31,032 CpG sites that differed significantly among young, middle-aged and older groups. The most common pattern involved methylation falling early and rising later. It appeared at 13,939 sites, or 44.9%.

Another 12,198 sites, or 39.3%, declined consistently with age. Smaller groups showed the reverse patterns.

This nonlinear behavior may help explain why predictions became less accurate in older sharks. Many age-linked sites change most strongly early in life, which can cause models to underestimate older animals.

The patterns resemble those seen in mammals and some other vertebrates, raising the possibility that parts of epigenetic aging are shared across vertebrates.

“We knew that this process occurred in lots of mammals and some non-mammalian species, but we didn’t know how widespread this phenomenon was,” said Samantha Bock, corresponding author of the study and a doctoral graduate of the Odum School. “This finding means we can potentially unlock key insights into the foundation of long life.”

Traditional shark aging methods can require killing an animal and counting growth rings on its spine. Visual estimates can also be unreliable.

A blood-based epigenetic clock offers a nonlethal alternative.

“Determining the age of an animal is often very difficult,” Bock said. “But if we can use epigenetic patterns to measure the ages of sharks, we can use it as a tool to see these trends in vulnerable populations.”

The clock was trained mainly on aquarium-bred sharks, and conditions such as diet or stress may differ in the wild.

Prediction errors in wild-caught animals are also difficult to interpret. A mismatch could reflect model error, a true difference in epigenetic aging, or uncertainty about chronological age.

The clock may not transfer directly to other tissues or species. Future versions may need broader training samples, health measurements or DNA sites conserved across species.

Reliable age estimates could make shark population assessments more informative without requiring lethal sampling.

Knowing whether a population contains mostly young, middle-aged or older animals can help scientists interpret survival, reproduction and population trends. A population dominated by older sharks, for example, could signal decline.

The method may also help researchers test whether environmental pressures, disease or stress are associated with faster molecular aging.

Zebra sharks are listed as Endangered by the IUCN Red List of Threatened Species, making nonlethal tools especially valuable.

“Sharks play really important roles in maintaining balance in ecosystems,” Parrott said. “If you remove a predator from an ecosystem, things can get out of balance. The goal is to give conservation biologists another tool to make better management decisions.”

These resources explore how epigenetic clocks are being developed for wildlife, what they can reveal about animal aging, and the challenges of applying DNA-based age estimates to conservation.

Methods for analysing wildlife DNA methylation data
This 2026 review examines methods for using DNA methylation to estimate wildlife age and health, including a bottlenose dolphin case study, while highlighting why one epigenetic model may not accurately measure both chronological age and biological condition. (Conservation Physiology, 2026)

Designing Epigenetic Clocks for Wildlife Research
Researchers outline best practices for building and validating wildlife epigenetic clocks, including problems caused by uncertain ages, small sample sizes and limited tissue availability. The work uses polar bear data to show how reliable clocks can still be developed under common conservation constraints. (Molecular Ecology Resources, 2025)

An epigenetic clock for Xenopus tropicalis
This study developed a DNA methylation clock for an aquatic frog using samples from 192 animals, extending epigenetic age research beyond mammals and helping researchers examine how broadly molecular aging signals occur across vertebrates. (npj Aging, 2025)

Noninvasive, epigenetic age estimation in an elasmobranch, the cownose ray (Rhinoptera bonasus)
Scientists developed highly accurate epigenetic clocks from blood and fin samples in cownose rays, close relatives of sharks, with mean age errors below one year in several models. The work demonstrates the conservation potential of nonlethal DNA-based aging methods in elasmobranchs. (Scientific Reports, 2024)

Biological clocks as age estimation markers in animals: a systematic review and meta-analysis
This systematic review and meta-analysis evaluates DNA methylation and telomere-based biological clocks across animal species, assessing their usefulness as less-invasive tools for determining age and monitoring wildlife populations. (Biological Reviews, 2023)

Research findings are available online in the journal Molecular Ecology.

The original story "First epigenetic DNA clock can reveal a zebra shark’s age from a blood sample" is published in The Brighter Side of News.

Like these kind of feel good stories? Get The Brighter Side of News' newsletter.