Age-based demography is fundamental to management of wild fish populations. Age estimates for individuals can determine rates of change in key life-history parameters such as length, maturity, mortality and fecundity. These age-based characteristics are critical for population viability analysis in endangered species and for developing sustainable harvest strategies. For teleost fish, age has traditionally been determined by counting increments formed in calcified structures such as otoliths. However, the collection of otoliths is lethal and therefore undesirable for threatened species. At a molecular level, age can be predicted by measuring DNA methylation. Here, we use previously identified age-associated sites of DNA methylation in zebrafish (Danio rerio) to develop two epigenetic clocks for three threatened freshwater fish species. One epigenetic clock was developed for the Australian lungfish (Neoceratodus forsteri) and the second for the Murray cod (Maccullochella peelii) and Mary River cod (Maccullochella mariensis). Age estimation models were calibrated using either known-age individuals, ages derived from otoliths or bomb radiocarbon dating of scales. We demonstrate a high Pearson's correlation between the chronological and predicted age in both the Lungfish clock (cor = .98) and Maccullochella clock (cor = .92). The median absolute error rate for both epigenetic clocks was also low (Lungfish = 0.86 years; Maccullochella = 0.34 years). This study demonstrates the transferability of DNA methylation sites for age prediction between highly phylogenetically divergent fish species. Given the method is nonlethal and suited to automation, age prediction by DNA methylation has the potential to improve fisheries and other wildlife management settings.

中文翻译：

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使用 DNA 甲基化对三种受威胁鱼类进行非致死年龄估计：澳大利亚肺鱼、墨累鳕鱼和玛丽河鳕鱼

基于年龄的人口统计学是野生鱼类种群管理的基础。对个人的年龄估计可以确定关键生活史参数的变化率，例如长度、成熟度、死亡率和繁殖力。这些基于年龄的特征对于濒危物种的种群生存能力分析和制定可持续收获策略至关重要。对于硬骨鱼，年龄传统上是通过计算耳石等钙化结构中形成的增量来确定的。然而，耳石的收集是致命的，因此对受威胁的物种是不可取的。在分子水平上，可以通过测量 DNA 甲基化来预测年龄。在这里，我们使用先前确定的斑马鱼 DNA 甲基化的年龄相关位点 ( Danio rerio) 为三种受威胁的淡水鱼类开发两个表观遗传时钟。一个表观遗传时钟是为澳大利亚肺鱼 ( Neoceratodus forsteri ) 开发的，第二个是为墨累鳕鱼 ( Maccullochella purgeii ) 和玛丽河鳕鱼 ( Maccullochella mariensis ) 开发的。年龄估计模型使用已知年龄的个体、来自耳石的年龄或规模的炸弹放射性碳测年进行校准。我们证明了肺鱼钟 (cor = .98) 和Maccullochella钟 (cor = .92)的年代顺序和预测年龄之间的高 Pearson 相关性。两个表观遗传时钟的中位绝对误差率也很低（肺鱼 = 0.86 年；Maccullochella = 0.34 年）。这项研究证明了 DNA 甲基化位点在高度系统发育差异的鱼类之间用于年龄预测的可转移性。鉴于该方法是非致命的并且适合自动化，通过 DNA 甲基化进行年龄预测有可能改善渔业和其他野生动物管理环境。