Epigenetic clocks and nonlinear aging in Odocoileus deer

Abstract

Population age structure has important consequences for population dynamics and is a key parameter for wildlife demography and management. Epigenetic clocks have emerged as accurate molecular tools for estimating chronological age. Ungulates are among the most intensively managed wildlife worldwide, yet epigenetic clocks have been developed for only two cervid species. Here, we develop a novel epigenetic clock for mule deer (Odocoileus hemionus) and a multi-species clock for the Odocoileus genus, and use them to investigate variation in age-associated DNA methylation across the mule deer lifespan. The mule deer clock achieved accuracy comparable to recently developed mammalian epigenetic clocks (r {approx} 0.9; MAE {approx} 5% of species lifespan). The multi-species Odocoileus clock showed lower predictive performance (r = 0.72; MAE = 0.782 years), but its broader taxonomic applicability may be particularly valuable where Odocoileus species occur sympatrically and hybridize. Cross-sectional epigenetic age estimates supported nonlinear age-associated methylation dynamics across the mule deer lifespan, whereas longitudinal changes in epigenetic age indicated that clocks optimized for cross-sectional age estimation may lack sufficient resolution to quantify short-term within-individual changes. Overall, our results highlight the value of integrating clock-level, CpG-level, and longitudinal analyses to investigate aging in wild populations. We also identify strongly age-associated loci that provide candidates for developing targeted, scalable, and lower-cost assays.