Age estimation in fishes using epigenetic clocks: Applications to fisheries management and conservation biology

Abstract

The distribution of age classes is a key demographic parameter of populations and thus proper age estimation is crucial for fisheries management and for conservation biology. Age estimation in fishes has traditionally relied on the analysis of growth marks in hard structures such as otoliths. However, besides being lethal this method is time-consuming, can have low accuracy in some species and cannot be applied in others. Thus, there is a need for the development of new methods. DNA methylation is an epigenetic modification consisting in the addition of a methyl group in cytosine-guanine loci. Aging is associated with changes in DNA methylation. Among a background of global and weak genome hypomethylation, there are some loci in which age-associated DNA methylation changes are of a “clock-like” nature and thus predictable. Chronological age estimators built from DNA methylation are termed ‘epigenetic clocks’. Epigenetic clocks have been developed in the last ten years for many species, notably vertebrates, including already several fish species. Here, we review the piscine epigenetic clocks built so far and outline the major considerations to be taken into account for the development of new epigenetic clocks for additional species, which include the number of samples to be collected and tissues to be targeted. The steps on how to develop such a clock and the techniques available to do so are also discussed. Next, we focus on the features of epigenetic clocks as measuring devices, considering aspects such as accuracy, precision and reproducibility. Finally, we discuss the possibility of developing a multi-species piscine epigenetic clock and how processing automation can greatly reduce the cost per sample. One important knowledge gap is to determine how environmental changes, especially temperature and food availability, may affect the tick rate of piscine epigenetic clocks. Improved age prediction through the use of piscine epigenetic clocks can contribute to better fisheries management practices in a context of overexploited fish stocks worldwide, and in the estimation of age classes in endangered species.