Dental Ageing Offers New Insights Into the First Epigenetic Clock for Common Dolphins (Delphinus delphis)

Abstract

Determining exact age in wild odontocetes is essential for understanding population dynamics, survival, and reproduction, yet remains logistically challenging. Although epigenetic ageing is emerging as a valuable approach, only nine species-specific clocks currently exist. Most have been calibrated using known-age animals in human care or well-studied wild populations. Only three previous studies have used dental ages from stranded or bycaught individuals. This is due to concerns that dental age inaccuracies, especially in older animals, may affect epigenetic clock performance. To explore this, we developed the first species-specific epigenetic clock for common dolphins (Delphinus delphis), analysing DNA methylation at 37,492 cytosine-phosphate-guanine sites in skin samples from stranded and bycaught dolphins with estimated dental ages. Elastic net models with Leave-One-Out Cross-Validation were applied to three subsets: the ‘relaxed’ subset (all individuals; n = 75, median absolute error (MAE) = 2.02, r = 0.81, R² = 0.66), the ‘strict’ subset (excluding individuals with minimum dental age estimates only; n = 73, MAE = 2.29, r = 0.81, R² = 0.66), and the ‘restricted’ subset (excluding outliers with prediction errors > 6 years; n = 63, MAE = 1.80, r = 0.91, R² = 0.82) to compare performance. Our models consistently underestimated the age of dolphins > 16 years, even when minimum dental ages were applied, suggesting that absolute errors between dental and epigenetic estimates are unlikely to reflect the dental ageing error. Additionally, post-mortem decomposition condition code (DCC 1 to 3) did not affect age prediction, signalling promise for future epigenetic clocks calibrated with strandings and bycaught individuals.