Epigenetic aging of Māui and Hector's dolphins

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.