Epigenetic age estimation in a long-lived, deepwater scorpionfish: insights into epigenetic clock development

Abstract

Age estimates are essential for fisheries assessment and management, but deepwater (>200 m) fishes are often difficult to age using traditional techniques. Therefore, age-predictive epigenetic clocks were developed for a model deepwater reef fish, blackbelly rosefish Helicolenus dactylopterus, using two tissue types (fin clips and muscle; n = 61 individuals; 9−60 years) and Δ14C-validated consensus age estimates. The influence of biological information (length and sex) on epigenetic clock accuracy, and the potential for developing a multi-tissue clock, were also assessed. Bisulfite-converted restriction site-associated DNA sequencing (bsRADseq) was used to identify CpG sites (cytosines followed by guanines) exhibiting age-correlated DNA methylation, and epigenetic clocks showed strong agreement (R2 > 0.98) between predicted and consensus ages. Including length and sex data enhanced accuracy and precision (R2 > 0.99; MAE < 1 year). Age-associated CpG sites were identified across tissues, but a multi-tissue clock performed poorly relative to single-tissue clocks. Overall, results demonstrate that accurate and precise epigenetic clocks can be developed for deepwater fishes, and the inclusion of biological information may enhance clock accuracy and precision.