Dynamic changes in DNA methylation during postnatal development in zebra finches (Taeniopygia guttata) exposed to different temperatures

Epigenetic changes associated with early life conditions are known to play a significant role in shaping the adult phenotype. Studies of DNA methylation in wild animals are lacking, yet are important for understanding the fitness consequences of environmentally induced epigenetic change. In our study, we quantified variation in DNA methylation in wild, post-hatch zebra finches Taeniopygia guttata developing at seasonally variable temperatures in the Australian desert. We also compared variation in DNA methylation among captive zebra finch siblings raised in temperature controlled ‘hot’ or ‘cool’ rooms. We detected an increase in genome-wide levels of DNA methylation between day 3 and day 11 of post hatch development in wild zebra finches. In the wild, ambient temperatures were also found to affect genome-wide levels of DNA methylation and plasticity in the methylation state of individual loci. Family effects had a significant influence on DNA methylation throughout our study, and while we did not detect an effect of temperature on DNA methylation levels in non-related captive birds, our sibling pair analyses revealed that within families, elevated temperatures were associated with higher levels of DNA methylation. Our findings suggest a wide window in early development during which climatically induced variation in DNA methylation could occur. Further work is necessary to understand the potential for such variation to promote ecologically relevant variation in wild birds.

Methods
See Methods section of paper for more details. 

Blood samples were collected from zebra finch nestlings at day 3 and day 11 of development. DNA was then extracted and screened for variation in DNA methylation using MS-AFLP. We used peakscanner and rawgeno to analyse the data. We  calculated percent DNA methylation and the extent of DNA-methylation state change across developemnt. We assessed variation in DNA methylation using R 3.6.1.

已知，与早期生命条件相关的表观遗传学变化在塑造成年表型方面发挥着重要作用。野生动物DNA甲基化的研究尚显不足，然而，这对于理解由环境诱导的表观遗传学变化所引发的适应性后果至关重要。在我们的研究中，我们量化了在澳大利亚沙漠季节性温度可变条件下，野生、孵化后斑马雀（Taeniopygia guttata）DNA甲基化的变异。我们还比较了在受控温度的“高温”或“低温”房间中饲养的笼养斑马雀兄弟姐妹之间DNA甲基化的变异。我们发现在野生斑马雀孵化后发育的第3天至第11天，全基因组DNA甲基化水平有所上升。在野外，环境温度也被发现会影响全基因组DNA甲基化水平以及个体位点甲基化状态的可塑性。在整个研究过程中，家族效应对DNA甲基化产生了显著影响，尽管我们没有检测到温度对非相关笼养鸟类DNA甲基化水平的影响，但我们的兄弟姐妹对分析揭示，在家族内部，较高的温度与更高的DNA甲基化水平相关联。我们的研究结果表明，在早期发育过程中存在一个广泛的窗口，在此期间，气候诱导的DNA甲基化变异可能发生。为进一步理解此类变异在野生鸟类中促进生态相关变异的潜力，需要进行进一步的研究。