Epigenetic clocks decode DNA in dolphin faeces to estimate its age
Studies in humans have provided deep insight into what regulates ageing-related genetic activity. DNA methylation—a process that does not alter gene sequences but can affect the activity of a DNA segment—helps estimate age since its abundance in the body is age-dependent. However, our understanding of age-related metrics in wildlife remains limited, primarily due to the inherent challenges in obtaining samples from our animal counterparts.
A recent study conducted by a team of researchers from Mie University, Kyoto University, Tokai University and Mikurashima Tourism Association began applying DNA methylation to some animals, but with a caveat. Direct and exceedingly long-term observation is necessary for age estimation of migratory wildlife or animals that are challenging to monitor closely. In particular, wild dolphins—and even captive ones—live relatively long lives. Obtaining dolphin genes can be a tricky hoop to jump through, practically and ethically.
An idea dropped in the pot, the team realised that epigenetic clocks—a biochemical technique to measure age—could facilitate analysing marine animals’ DNA from their faeces. Epigenetic clocks take advantage of the fact that DNA methylation levels in the body fluctuate, depending on age-related factors, to act as biomarkers.
However, considering faeces contain much less DNA than blood and skin, sample collection risks becoming rather messy and inefficient due to the weak faecal consistency in an aquatic environment. Nevertheless, the undeterred researchers entered the vast, open water closet with only a plastic tube and camera to collect the precious fresh dolphin deposits from 30 individuals.
Underwater longitudinal individual identification surveys revealed the age of 30 Indo-Pacific bottlenose dolphins (Tursiops aduncus), who matter-of-factly contributed 36 faecal samples. The researchers used methylation-sensitive high-resolution melting to obtain the methylation rates of two gene regions, GRIA2 and CDKN2A.
Using a single linear regression analysis, the researchers could correlate age with methylation rate for the Indo-Pacific bottlenose, which has an average lifespan of 40 years in non-captivity and can live up to 50 years. The statistical error in the estimation model was roughly 5%.
The study’s results, which employed three different test models, showed that the overall methylation rate of both genes increased with age, was not gender-related, and was significantly lower among nursing females.
Notably, this non-invasive method of approximating age preserves dolphins’ environment and ecology. Moreover, age-related metrics are essential data for predicting population dynamic parameters. The method can also be applied to other elusive marine or land animals.
Despite the dirty labour involved, the team hopes its epigenetic clock analysis, which repurposes bodily waste, will advance our understanding of animal life history and ecology and improve wildlife management.
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The paper “Non-invasive age estimation based on faecal DNA using methylation-sensitive high-resolution melting for Indo-Pacific bottlenose dolphins” appeared on 2 December 2023 in Current Biology, with doi: 10.1111/1755-0998.13906