Genome-wide DNA methylation patterns harbor signatures of hatchling sex and past incubation temperature in a species with environmental sex determination (embryonic DNA methylation)

Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic datasets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulfite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligator (Alligator mississippiensis), a TSD species lacking reliable markers of sexual dimorphism in early life-stages. We show that DNAm patterns in blood cells may serve as non-lethal markers of hatchling sex and past incubation conditions in conservation applications. DNAm patterns are further compared between hatchling blood cells and embryonic gonads undergoing TSD.

热敏感物种的保护工作，有赖于实时监测生物体及种群对环境变化的响应。表观遗传过程正日益被视为将环境条件整合进发育可塑性响应的关键机制，而与之相关的表观基因组数据集，有望揭示与保护工作相关的隐秘表型。本研究针对一类尤其脆弱的物种——即具有温度依赖型性别决定（temperature-dependent sex determination, TSD）的物种，展示了全基因组DNA甲基化（DNA methylation, 缩写为DNAm）模式在应对气候变化时的应用价值。由于这类物种在发育过程中依赖温度信号决定性别命运，当前的温度变化预计会扭曲后代性别比例，最终破坏脆弱种群的稳定性。本研究采用简化代表性亚硫酸氢盐测序（reduced-representation bisulfite sequencing）技术，对早期发育阶段缺乏可靠性别二态性标记的TSD物种美洲短吻鳄（Alligator mississippiensis）幼体的血细胞DNA甲基化组进行了解析。研究结果显示，血细胞中的DNAm模式可作为保护应用中幼体性别及既往孵化条件的非致死性标记物。本研究还对幼体血细胞与经历TSD的胚胎性腺中的DNAm模式进行了对比分析。