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的时间。然而，物种生存的环境可能会在短得多的时间尺度上发生巨大变化，物种必须迅速适应，否则就有灭绝的风险。在美国和加拿大的西海岸，已知一种名为三刺鱼的小型鱼类在几十年内就能适应截然不同的环境。这项研究将考察刺鱼如何通过关注一个物种的基因库对其快速应对环境变化的能力的影响来实现这一壮举。具体地说，这项拟议的研究将考察(1)刺鱼基因库中已存在的遗传变异在多大程度上有助于适应进化，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将如何应对未来的环境变化至关重要，因此对保护和狩猎管理努力、气候变化缓解和农业具有影响。常备遗传变异是种群中可用于进化变化的可用遗传变异库。在新一代DNA测序技术和新的分析技术的推动下，最近的研究重新点燃了关于长期遗传变异和新突变对适应性进化和物种形成的相对影响的辩论。这项由这笔赠款资助的研究将使用基于联合理论的方法，这是一种在系统发育学和种群遗传学的交界处的数学严格方法，以了解三刺鱼自然种群中立地变异的流行率和影响。通过将限制位点相关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，拟议的研究将在数万个基因座生成丰富的数据家谱，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.