Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, 78412, USA.
Ripley's Aquariums, Orlando, FL, 32819, USA.
Sci Rep. 2024 Nov 1;14(1):26261. doi: 10.1038/s41598-024-78004-2.
Age data are essential for estimating life history parameters and are thus critical for population assessment, management, and conservation. Traditional vertebrae-based age estimation in elasmobranchs can be costly, time intensive, of low accuracy, and is by necessity lethal. Herein, epigenetic clocks were developed for an elasmobranch, the cownose ray (Rhinoptera bonasus), using aquarium-born individuals (n = 42) with known dates of birth (age range: 7-7,878 days or 0-21 years) and two tissue types (fin clips and whole blood) that can be sampled in a relatively non-invasive manner. Enzymatically-converted restriction site-associated DNA sequencing (ECrad-seq) was used to identify CpG sites that exhibited age-correlated DNA methylation. The epigenetic clocks developed were highly accurate (mean absolute error, MAE, < 0.75 years) and precise (R > 0.98). Age-associated CpG sites were identified across tissues, and a multi-tissue clock was also highly accurate (MAE < 1 year) and precise (R = 0.97). Using the developed fin clip clock, three wild-caught individuals of unknown age but managed in aquariums for > 22 years were predicted to be 22.10-23.49 years old. Overall, the results have important implications for future epigenetic clock development and noninvasive age estimation in elasmobranchs.
年龄数据对于估计生命史参数至关重要，因此对于种群评估、管理和保护至关重要。传统的基于脊椎的鲨鱼年龄估计既昂贵又费时，准确性低，而且是必要的致命性。在此，使用具有已知出生日期（年龄范围：7-7878 天或 0-21 岁）的水族馆出生个体（n=42）和两种组织类型（鳍夹和全血）开发了一种鲨鱼的表观遗传钟，这些组织类型可以以相对非侵入性的方式进行采样。酶转化的限制位点相关 DNA 测序（ECrad-seq）用于鉴定表现出年龄相关 DNA 甲基化的 CpG 位点。开发的表观遗传钟非常准确（平均绝对误差，MAE，<0.75 岁）和精确（R>0.98）。在组织中鉴定出与年龄相关的 CpG 位点，并且多组织时钟也非常准确（MAE<1 岁）和精确（R=0.97）。使用开发的鳍夹时钟，对三个未知年龄但在水族馆中饲养了>22 年的野生个体进行了预测，其年龄分别为 22.10-23.49 岁。总的来说，这些结果对未来鲨鱼的表观遗传钟开发和非侵入性年龄估计具有重要意义。
