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牙齿老化为普通海豚的首个表观遗传时钟提供了新的见解。

Dental aging offers new insights to the first epigenetic clock for common dolphins ().

作者信息

Hanninger Eva-Maria F, Peters Katharina J, Gerber Livia, Barratclough Ashley, Betty Emma L, Palmer Emily I, Horvath Steve, Stockin Karen A

机构信息

Cetacean Ecology Research Group, School of Natural Sciences, Massey University, Auckland, New Zealand.

Marine Vertebrate Ecology Lab, Environmental Futures, School of Science, University of Wollongong, Wollongong, Australia.

出版信息

bioRxiv. 2025 Jul 23:2025.07.20.665818. doi: 10.1101/2025.07.20.665818.

Abstract

Determining exact age in wild odontocetes is essential for understanding population dynamics, survival, and reproduction, yet remains logistically challenging. While epigenetic aging is emerging as a valuable approach, only nine species-specific clocks currently exist. Most have been calibrated using captive known-age animals or well-studied wild populations. Only two previous studies have used dental ages from stranded or bycaught individuals. This is due to concerns that dental age inaccuracies, especially in older animals, may affect epigenetic clock performance. To explore this, we developed the first species-specific epigenetic clock for common dolphins (), analysing DNA methylation at 37,492 cytosine-phosphate-guanine sites in skin samples from stranded and bycaught dolphins with estimated dental ages. Elastic net models with Leave-One-Out Cross-Validation were applied to three subsets: the '' subset (all individuals; = 75, MAE = 1.94, = 0.82, R² = 0.64), the '' subset (excluding individuals with minimum dental age estimates only; = 70, MAE = 1.91, = 0.85, R² = 0.68), and the '' subset (excluding outliers with prediction errors > 6 years; = 64, MAE = 1.75, = 0.91, R² = 0.80) to compare performance. Our models consistently underestimated the age of dolphins >16 years, even when minimum dental ages were applied, suggesting discrepancies between dental and epigenetic estimates unlikely reflect dental aging error. Additionally, post-mortem decomposition change (DCC 1 to 3) did not affect age prediction, signalling promise for future epigenetic clocks calibrated with strandings and bycaught individuals.

摘要

确定野生齿鲸的确切年龄对于理解种群动态、生存和繁殖至关重要,但在实际操作中仍具有挑战性。虽然表观遗传衰老正成为一种有价值的方法,但目前仅存在9种特定物种的时钟。大多数已使用圈养的已知年龄动物或经过充分研究的野生种群进行校准。之前仅有两项研究使用了搁浅或误捕个体的牙齿年龄。这是因为担心牙齿年龄的不准确,尤其是在年龄较大的动物中,可能会影响表观遗传时钟的性能。为了探究这一点,我们开发了首个针对普通海豚的特定物种表观遗传时钟,分析了来自搁浅和误捕海豚皮肤样本中37492个胞嘧啶-磷酸-鸟嘌呤位点的DNA甲基化情况,并给出了估计的牙齿年龄。采用留一法交叉验证的弹性网络模型应用于三个子集:“全部”子集(所有个体;n = 75,平均绝对误差 = 1.94,皮尔逊相关系数 = 0.82,决定系数R² = 0.64),“排除仅具有最小牙齿年龄估计值的个体”子集(n = 70,平均绝对误差 = 1.91,皮尔逊相关系数 = 0.85,决定系数R² = 0.68),以及“排除预测误差>6年的异常值”子集(n = 64,平均绝对误差 = 1.75,皮尔逊相关系数 = 0.91,决定系数R² = 0.80)以比较性能。我们的模型始终低估了年龄大于16岁的海豚的年龄,即使应用了最小牙齿年龄,这表明牙齿和表观遗传估计之间的差异不太可能反映牙齿衰老误差。此外,死后分解变化(DCC 1至3)并未影响年龄预测,这为未来使用搁浅和误捕个体校准的表观遗传时钟带来了希望。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23eb/12330489/9c3bdc16ccd4/nihpp-2025.07.20.665818v1-f0001.jpg

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