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.