Data from: A clockwork fish. Age-prediction using DNA methylation-based biomarkers in the European seabass

Age-related changes in DNA methylation do occur. Taking advantage of this,
mammalian and avian epigenetic clocks have been constructed to predict
age. In fish, studies on age-related DNA methylation changes are scarce
and no epigenetic clocks are available. However, in fisheries and
population studies there is a need for accurate estimation of age,
something that is often impossible for some economically important species
with the currently available methods. Here, we used the European sea bass,
a marine fish where age can be known with accuracy, to construct a piscine
epigenetic clock, the first one in a cold-blooded vertebrate. We used
targeted bisulfite sequencing to amplify 48 CpGs from four genes in muscle
samples and applied penalized regressions to predict age. We, thus,
developed an age predictor in fish that is highly accurate (0.824) and
precise (2.149 years of error). In juvenile fish, accelerated growth due
to elevated temperatures had no effect in age prediction, indicating that
the clock is able to predict the chronological age independently of
environmentally-driven perturbations. An epigenetic clock developed using
muscle samples accurately predicted age in samples of testis but not
ovaries, possibly reflecting the reproductive biology of fish. In
conclusion, we report the development of the first piscine epigenetic
clock, paving the way for similar studies in other species. Piscine
epigenetic clocks should be of great utility for fisheries management and
conservation purposes, where age determination is of crucial importance.