Data from: Non-invasive age estimation based on fecal DNA using methylation-sensitive high-resolution melting for Indo-Pacific bottlenose dolphins

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.

年龄是野生动物生活史研究的核心必要信息。齿鲸类（odontocetes）年龄估算的通用方法为计数牙齿生长层组（dental growth layer groups，GLGs），但该方法具有极强侵入性，需捕获、接触个体以采集其牙齿样本。近年来，作为此类侵入性方法的替代方案，基于DNA的年龄估算方法得到了广泛研究，其中诸多方案均采用活检样本。但若可通过粪便样本开发基于DNA的年龄估算方法，则无需接触或干扰个体即可完成年龄检测，从而建立一套完全非侵入性的年龄估算体系。本研究以野生印太瓶鼻海豚（Tursiops aduncus）的粪便样本为材料，通过甲基化敏感高分辨率熔解（methylation-sensitive high-resolution melting，MS-HRM）技术检测两个基因区域（GRIA2与CDKN2A）的甲基化率，构建了年龄估算模型。研究通过水下长期个体识别调查获取了已知年龄的个体样本，共对36份样本的甲基化率进行了定量检测。两个基因区域的甲基化率均与年龄呈现显著相关性。基于双基因甲基化率构建的年龄估算模型，经留一交叉验证（leave-one-out cross validation，LOOCV）后达到了足够的预测精度（平均绝对误差（mean absolute error，MAE）=5.08，决定系数（coefficient of determination，R²）=0.34），可满足寿命为40~50年的印太瓶鼻海豚的生态研究需求。本研究首次报道了利用非侵入性粪便样本估算海洋哺乳动物年龄的研究成果。