Epigenetic Clocks Can Predict Age in the Largemouth Bass-Complex Despite Spatial and Sexual Variation

Sustainable fisheries rely on balancing harvests with ecological impacts. Despite the importance of species' demographic profiles, many assessments forgo age due to methodological complexities. Developing non-lethal methods for age determination can improve stock assessments to ensure future sustainability. Epigenetic signals, specifically DNA methylation, are dynamic and considered to be associated with decreasing genomic stability with age. Subsequently, the modelling of methylation percentages at CpG loci has been utilized to accurately predict chronological age in many organisms, including several fish species. We examined the influence of age (1-14 years), location (Texas versus Tennessee), and sex on DNA methylation patterns of members of the largemouth bass-complex (LBc), consisting of largemouth bass (Micropterus nigricans), Florida bass (Micropterus salmoides), and their resulting hybrids, all recreational and commercially important species. As DNA methylation patterns are influenced by sex and environmental signals, we accounted for this when evaluating aging patterns in the LBc. Our results indicate global methylation patterns decrease with age, indicating potential genomic instability, and vary with sex and location. Non-random changes also occur involving physiological pathways of diverse function. Accounting for this variability, aging clocks using single or regions of CpG loci were derived from 124 LBc samples and validated using sets of naïve (n = 32) individuals, providing improved estimates over other non-lethal aging methods. Our results reveal insights into dynamic methylome patterns in the LBc, and when accounting for variability, informative and accurate age estimations can be determined with non-lethal molecular methods.