Bisulfite sequencing (RRBS-seq): CpG methylation reports for Australian invasive cane toads

In response to novel environments, invasive populations often evolve rapidly. Standing genetic variation is an important predictor of evolutionary response but epigenetic variation may also play a role. Here we use an iconic invader, the cane toad (Rhinella marina), to investigate how manipulating epigenetic status affects phenotypic traits. We collected wild toads from across Australia, bred them, and experimentally manipulated DNA methylation of the subsequent two generations (G1, G2) through exposure to the DNA methylation inhibitor zebularine and/or conspecific tadpole alarm cues. Direct exposure to alarm cues (an indicator of predation risk) increased the potency of G2 tadpole chemical cues, but this was accompanied by reductions in survival. Exposure to alarm cues during G1 also increased the potency of G2 tadpole cues, indicating intergenerational plasticity in this inducible defence. In addition, the negative effects of alarm cues on tadpole viability (i.e., the costs of producing the inducible defence) were minimised in the second generation. Exposure to zebularine during G1 induced similar intergenerational effects, suggesting a role for alteration in DNA methylation. Accordingly, we identified intergenerational shifts in DNA methylation at some loci in response to alarm cue exposure. Substantial demethylation occurred within the Sodium Channel Epithelial 1 Subunit Gamma gene (SCNN1G) in alarm cue-exposed individuals and their offspring. This gene is a key to regulation of sodium in epithelial cells and may help to maintain the protective epidermal barrier. These data suggest that early-life experiences of tadpoles induce intergenerational effects through epigenetic mechanism, which enhance larval fitness.

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面对新颖的环境，入侵物种往往能够迅速演化。静止的遗传变异是进化响应的重要预测因子，但表观遗传变异也可能扮演一定的角色。在本研究中，我们选取了著名的入侵物种——箭毒蛙（Rhinella marina）作为研究对象，旨在探讨操控表观遗传状态如何影响表型特征。我们收集了来自澳大利亚各地的野生箭毒蛙，进行了繁殖，并通过暴露于DNA甲基化抑制剂zebularine以及同种蝌蚪的警报信号来实验性地操控其后代两代（G1，G2）的DNA甲基化。直接暴露于警报信号（捕食风险指标）增强了G2蝌蚪的化学信号的有效性，但这也伴随着生存率的降低。G1阶段暴露于警报信号同样增强了G2蝌蚪信号的有效性，这表明了在此可诱导防御中的跨代可塑性。此外，警报信号对蝌蚪存活能力（即产生可诱导防御的成本）的负面影响在第二代中得到了最小化。G1阶段暴露于zebularine也引起了类似的跨代效应，这表明DNA甲基化改变可能发挥了作用。因此，我们确定了在暴露于警报信号后，某些基因位点上的DNA甲基化发生了跨代变化。暴露于警报信号的个体及其后代中，钠通道上皮1亚基Gamma基因（SCNN1G）内部发生了显著的脱甲基化。该基因是调节上皮细胞中钠的重要基因，可能有助于维持保护性表皮屏障。这些数据表明，蝌蚪在幼年时期的经历通过表观遗传机制诱导了跨代效应，从而增强了幼虫的适应性。使用说明
查阅README文件。