DISSERTATION RESEARCH: A coalescent analysis of the diversity of standing genetic variation and adaptive evolution in the threespine stickleback

自然选择的进化通常被认为需要数千年或数百万年。然而，物种生存的环境可以在短得多的时间尺度上发生巨大变化，物种必须迅速适应，否则就有灭绝的危险。在美国和加拿大的西海岸，有一种叫做三刺鱼的小鱼，可以在几十年内适应完全不同的环境。这项研究将通过关注物种基因库对其快速应对不断变化的环境的能力的影响，来研究刺鱼是如何实现这一壮举的。具体来说，拟议的研究将检查(1)适应性进化在多大程度上是由刺鱼基因库中已经存在的遗传变异所辅助的，以及(2)刺鱼的适应历史如何影响其整个基因组中遗传变异的组织。这种对适应潜力的理解对于我们预测物种和生态系统如何应对未来环境变化的能力至关重要，因此对保护和野生动物管理工作、减缓气候变化和农业具有重要意义。常备遗传变异是种群中可用于进化变化的可用遗传变异的集合。在新一代DNA测序技术和新的分析技术的推动下，最近的研究使关于遗传变异与新突变对适应性进化和物种形成的相对影响的争论重新活跃起来。由该基金资助的研究将使用基于聚结理论的方法，这是一种在系统遗传学和种群遗传学界面上的数学严格方法，以了解三刺棘鱼自然种群中站立变异的普遍性和影响。通过将限制性内切位点相关DNA测序（一种强大的全基因组推断方法）与新的长读测序能力相结合，拟议的研究将产生数万个位点的数据丰富的家谱，并为自然种群的适应提供前所未有的细节。

Evolution by natural selection is thought to often take thousands or millions of years. The environments in which species live can change drastically on much shorter timescales, however, and species must adapt quickly or risk extinction. Along the west coast of the US and Canada, a small fish species, the threespine stickleback, is known to adapt within decades to wildly different environments. This study will examine how stickleback achieve this feat by focusing on the influence a species' gene pool has on its ability to respond rapidly to a changing environment. Specifically, the proposed research will examine (1) how much of adaptive evolution is aided by genetic variation already existing in the stickleback gene pool, and (2) how the stickleback's history of adaptation has influenced the organization of genetic variation in its entire genome. This understanding of adaptive potential is crucial to our ability to predict how species and ecosystems will respond to future environmental shifts, and thus has implications for conservation and game management efforts, climate change mitigation, and agriculture. Standing genetic variation is the pool of available genetic variants in a population available for evolutionary change. Recent research, facilitated by next-generation DNA sequencing technologies and new analytical techniques, has revitalized the debate over the relative influence of standing genetic variation versus new mutation on adaptive evolution and speciation. The research funded by this grant will use approaches based in coalescent theory, a mathematically-rigorous approach at the interface of phylogenetics and population genetics, to understand the prevalence and influence of standing variation in natural populations of threespine stickleback fish. By combining restriction site-associated DNA sequencing, a powerful method for genome-wide inference, with new long-read sequencing capabilities, the proposed research will generate data-rich genealogies at tens of thousands of loci and provide unprecedented detail into adaptation of natural populations.