Non-invasive age estimation based on fecal DNA using
methylation-sensitive high-resolution melting for Indo-Pacific
bottlenose dolphins
Abstract
Age is necessary information for the study of life history of wild
animals. A general method to estimate the age of odontocetes is counting
dental growth layer groups (GLGs). However, this method is highly
invasive as it requires the capture and handling of individuals to
collect their teeth. Recently, the development of DNA-based age
estimation methods has been actively studied as an alternative to such
invasive methods, of which many have used biopsy samples. However, if
DNA-based age estimation can be developed from fecal samples, age
estimation can be performed without touching or disrupting individuals,
thus establishing an entirely non-invasive method. We developed an age
estimation model using the methylation rate of two gene regions,
GRIA2 and CDKN2A, measured through methylation-sensitive
high-resolution melting (MS-HRM) from fecal samples of wild Indo-Pacific
bottlenose dolphins (Tursiops aduncus). The age of individuals
was known through conducting longitudinal individual identification
surveys underwater. Methylation rates were quantified from 36 samples.
Both gene regions showed a significant correlation between age and
methylation rate. The age estimation model was constructed based on the
methylation rates of both genes which achieved sufficient accuracy
(after LOOCV: MAE = 5.08, R2 = 0.34) for the ecological studies
of the Indo-Pacific bottlenose dolphins, with a lifespan of 40-50 years.
This is the first study to report the use of non-invasive fecal samples
to estimate the age of marine mammals.