An epigenetic clock for accurate age prediction in Atlantic cod populations for improved fisheries management

Fisheries management relies on accurate stock assessments, which in turn depend on precise age information. Recent molecular tools called “epigenetic clocks” harness age-related DNA methylation changes to build accurate and precise age-prediction models. However, the influences of intrinsic and extrinsic factors on clock performance remain uncertain. In this study, we examined Atlantic cod aged 0 to 7 years, sampled from various locations across the North Sea, and developed an epigenetic clock using bisulfite restriction-site associated DNA sequencing (bis-RAD-seq) DNA methylation data from 73 CpG sites obtained from fin clips. This clock predicted age with 97.5 % accuracy and a precision of 2.8 months and generalized well in unseen data. Further, we addressed critical variables such as sex and maturity status, which are often overlooked, and we showed that clock performance was unaffected by sex-specific differences in growth, and it was lower in advanced sexually mature individuals, reflecting a slight bias towards younger fish. A key finding of our study is the discovery of a latitudinal cline in global DNA methylation patterns. We found that DNA methylation varied with latitude, despite the absence of genetic differences, while our clock maintained consistent performance across geographic locations. This resolves a major question regarding how generalizable epigenetic clocks are within the distribution of a species. Our clock demonstrates extensive applicability and enhanced practicality for real-world fisheries management. It provides accurate and precise age prediction for Atlantic cod irrespective of intrinsic differences or environmental influences associated with geographic locations.