Abstract
Accurate identification of individual ages within wild bottlenose dolphins (Tursiops truncatus) is critical for determining population health and the development of population management strategies. As such, we analyzed DNA methylation (DNAm) patterns by applying a custom methylation array (HorvathMammalMethyl40) to both blood (n= 140) and skin samples (n= 87) from known age or approximate age (0–57 years) bottlenose dolphins. We present three bottlenose dolphin specific age estimation clocks using combined blood and skin [48 CpGs,R= 0.93, median absolute error (MAE) = 2.13 years], blood only (64 CpGs, R = 0.97, error = 1.46 years) and skin only (39 CpGs,R= 0.95, error = 2.53). We characterized individual cytosines that correlate with sex and age in dolphins and developed a sex estimator based on 71 CpGs that predicts the sex of any odontocete species with 99.5% accuracy. The presented epigenetic clocks are expected to be useful for conservation efforts and for determining if anthropogenic events affect aging rates in wild populations.
Highlights
Accurate age estimation of wild cetaceans is an important component of any population health assessment and is critical for the development of management plans designed to help wild populations in need (Robeck et al, 2021b)
The objectives of our research were (1) to apply the mammalian methylation array technology to develop highly accurate bottlenose dolphin clocks based on blood and/or skin samples; (2) to characterize significant aging associated CpGs identified via epigenome-wide association studies (EWAS); (3) to characterize sex linked CpGs, and (4) to develop sex estimators for odontocetes based on DNA methylation (DNAm) data
This study describes the development of three highly accurate bottlenose dolphin DNAm epigenetic aging clocks using combined blood and skin, blood only or skin only that were developed with samples collected from known (88%) or approximately known age animals
Summary
Accurate age estimation of wild cetaceans is an important component of any population health assessment and is critical for the development of management plans designed to help wild populations in need (Robeck et al, 2021b). Long term photo identification studies have produced the most robust and accurate data concerning life history of a few populations of bottlenose dolphins, these studies face limitations, e.g., the inability to accurately define animals that had already reached physical maturity at the start of the surveys (Würsig and Jefferson, 1990; Wells, 2014). Another challenge faced by long-term photo identification programs. These limitations render them less efficient for rapid and time-sensitive evaluations of critically endangered or threatened populations
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