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Epigenetic aging of Māui and Hector's dolphins

Hernandez, Keith1; Baker, Scott1; Horvath, Steve2; Constantine, Rochelle3

Published Jan 26, 2024 on Dryad. https://doi.org/10.5061/dryad.hx3ffbgm3

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Jan 26, 2024 version files 18.96 KB

Abstract

The age of an individual is an essential demographic parameter but is difficult to estimate without long-term monitoring or invasive sampling. Epigenetic approaches are increasingly used to age organisms, including non-model organisms such as cetaceans. Māui dolphins (Cephalorhynchus hectori maui) are a critically endangered subspecies endemic to Aotearoa New Zealand, and the age structure of this population is important for informing conservation. Here we present an epigenetic clock for aging Māui and Hector's dolphins (C. h. hectori) developed from methylation data using DNA from tooth aged individuals (n = 48). Based on this training dataset, the optimal model required only eight methylation sites, provided an age correlation of 0.95, and had a median absolute age error of 1.54 years. A leave-one-out cross-validation analysis with the same parameters resulted in an age correlation of 0.87 and median absolute age error of 2.09 years. To improve age estimate, we included previously published beluga whale (Delphinapterus leucas) data to develop a joint beluga/dolphin clock, resulting in a clock with comparable performance and improved estimation of older individuals. Application of the models to DNA from skin biopsy samples of living Māui dolphins revealed a shift in the median age of 8–9 years to a younger population aged 7–8 years 10 years later. These models could be applied to other dolphin species and demonstrate the ability to construct a clock even when the number of known age samples is limited, removing this impediment to estimating demographic parameters vital to the conservation of critically endangered species.