Code for: Environmental fluctuations dampen the effects of clonal reproduction on evolutionary rescue

Evolutionary rescue occurs when genetic change allows a population to persist in response to an environmental change that would otherwise have led to extinction. Most studies of evolutionary rescue assume that species have either fully clonal or fully sexual reproduction; however, many species have partially clonal reproductive strategies in which they reproduce both clonally and sexually. Furthermore, the few evolutionary rescue studies that have evaluated partially clonal reproduction did not consider fluctuations in the environment, which are nearly ubiquitous in nature. Here, we use individual-based simulations to investigate how environmental fluctuations (either uncorrelated or positively autocorrelated) influence the effect of clonality on evolutionary rescue. We show that, for moderate magnitudes of environmental fluctuations, as was found in the absence of fluctuations, increasing the degree of clonality increases the probability of population persistence in response to an abrupt environmental change, but decreases the persistence in response to a continuous, directional environmental change. However, with large magnitudes of fluctuations, both the benefits of clonality following a step change and the detrimental effects of clonality following a continuous, directional change are generally reduced; in fact, in the latter scenario, increasing clonality can even become beneficial if environmental fluctuations are autocorrelated. We also show that increased generational overlap dampens the effects of environmental fluctuations. Overall, we demonstrate that understanding the evolutionary rescue of partially clonal organisms requires not only knowledge of the species life history and the type of environmental change, but also an understanding of the magnitude and autocorrelation of environmental fluctuations.

Methods
A full description of the methods can be found in the appendix of the associated manuscript.

进化拯救（evolutionary rescue）指当种群借助遗传变化得以存续，从而应对原本会导致其灭绝的环境变化时的现象。现有绝大多数进化拯救研究均假设物种仅采用专性无性繁殖（fully clonal reproduction）或专性有性繁殖（fully sexual reproduction）策略，但诸多物种实际采用兼性无性生殖策略，即可同时进行无性生殖与有性生殖。此外，现有少数针对兼性无性生殖的进化拯救研究，未考虑自然界中几乎无处不在的环境波动。本研究采用基于个体的模拟（individual-based simulations），探究无关联或正自相关的环境波动如何影响无性生殖程度对进化拯救的作用。
研究结果显示，在环境波动幅度中等的情况下（与无波动时的结论一致），提升无性生殖程度会提升种群应对突发环境变化的存续概率，但会降低其应对持续方向性环境变化的存续概率。然而，当环境波动幅度较大时，阶跃变化下无性生殖的优势以及持续方向性变化下无性生殖的不利影响通常都会被削弱；事实上，在后一种情景中，若环境波动存在自相关性，提升无性生殖程度甚至可能变为有利因素。我们还发现，世代重叠（generational overlap）程度的提升会减弱环境波动的影响。综上，我们证明，要理解兼性无性生殖生物的进化拯救，不仅需要了解该物种的生活史以及环境变化的类型，还需要掌握环境波动的幅度与自相关性。

研究方法
研究方法的完整说明可参见相关论文的附录。