NSFDEB-NERC: Ecological Genomics of Adaptive Polymorphism

个体具有巨大的基因多样性，即使这些个体在相同的环境中生活得很近。这种高度多样性对可持续农业和生物多样性的保护具有重要意义，因为遗传多样性使作物和野生动植物能够在面对疾病和其他环境挑战时持续存在。了解遗传多样性在医学上也很重要，因为个体对疾病的易感性不同，对相同治疗的反应也不同；这就是最近强调“个性化医疗”的基础。然而，高遗传多样性是令人惊讶的，因为我们期望拥有共同基因库和经历相似环境的当地人群应该具有相对的遗传同质性。这个项目解决了关于为什么种群（包括人类）中的个体具有如此大的基因多样性的争论。具体来说，研究小组将测试一个重要的假设：高度多样性得以维持，是因为罕见的基因变异给携带它们的个体带来了优势（即，它们受到自然选择的青睐）。该项目还将确定作为这种选择直接目标的基因。由于需要在人类或农业物种中进行实验来回答这些问题是不可能的，因此该项目将使用一种脊椎动物，这种动物具有众所周知的自然历史、生态和行为，并且最近可以获得其基因组序列（特立尼达孔雀鱼）。这些小鱼在身体颜色上有很高的遗传多样性，这项研究将检验关于为什么：(1)具有罕见图案的鱼存活得更好，或者(2)具有罕见图案的鱼繁殖得更成功的相互竞争的观点。该项目还将为在校儿童制作教育材料和活动。这个材料将通过使用许多学生已经熟悉的动物来增强学生对遗传学，生态学和进化生物学的理解，因为孔雀鱼在家庭水族馆中很受欢迎。解释具有重要生态意义的性状的高度遗传多样性的持久性是群体遗传学的一个基本问题，并且对农业、医学和保护生物学具有根本性的影响。关于维持变异的过程的争论导致了重要的种群遗传学原理和假说的发展，但更大的问题仍然没有答案。这个项目将测试这样一个假设，即在空间或时间上变化的选择（“平衡选择”）保持了自然种群的遗传多样性，并将这些选择过程直接与它们所针对的遗传变异联系起来。研究人员将把基因组学和生态学方法结合起来，研究一个物种，它展示了最著名的适应性多态性案例之一，即特立尼达孔雀鱼（Poecilia reticulata）的颜色模式。对捕食者密度、繁殖行为和颜色模式变化的实地和实验室研究将决定哪些生态过程促进了遗传变异。对13个自然种群的孔雀鱼进行全基因组测序，将鉴定出富含中频等位基因的基因组区域；使用来自许多种群的数据将使我们能够区分平衡选择下的位点和那些由于随机遗传漂变和迁移等非选择过程而多态性的位点。这种多管齐下的方法将使维持变异的进化过程直接与它们所针对的遗传变异（多态性）联系起来。

Individuals are enormously genetically diverse, even when those individuals live close together in the same environments. This high diversity has important implications for sustainable agriculture and for the conservation of biodiversity because genetic diversity allows crops and wild plants and animals to persist in the face of disease and other environmental challenges. Understanding genetic diversity is also important in medicine because individuals have different susceptibility to disease and they can respond differently to the same treatment; this is the foundation of the recent emphasis on "personalized medicine". However, high genetic diversity is surprising because we expect that local populations that share a common gene pool and experience similar environments should be relatively genetically homogenous. This project addresses the debate about why individuals within populations (including humans) are so genetically diverse. Specifically, the research team will test a prominent hypothesis: that high diversity is maintained because rare gene variants confer an advantage to individuals who bear them (i.e., they are favored by natural selection). The project will also identify the genes that are the direct targets of this kind of selection. Because experiments required to answer these questions would be impossible in humans or agricultural species, the project will use a vertebrate animal that has well-known natural history, ecology, and behavior, and for which the genome sequence has recently become available (the Trinidad guppy). These small fish have high genetic diversity for body color, and this research will examine competing ideas about why: (1) fish with rare patterns survive better, or (2) fish with rare patterns reproduce more successfully. This project will also produce educational material and activities for school children. This material will enhance students' understanding of genetics, ecology, and evolutionary biology by using an animal with which many students are already familiar since guppies are popular in home aquariums.Accounting for the persistence of high genetic diversity in ecologically-important traits is a fundamental problem in population genetics, and one that has fundamental implications for agriculture, medicine, and conservation biology. Debate about what processes maintain variation has led to the development of important population-genetic principles and hypotheses, but the larger question remains unanswered. This project will test the hypothesis that selection that varies in space or time ("balancing selection") maintains genetic diversity in natural populations and will link these selective processes directly to the genetic variants they target. Researchers will combine genomic and ecological approaches in a species exhibiting one of the best-known cases of adaptive polymorphism, the colour patterns in the Trinidadian guppy (Poecilia reticulata). Field and laboratory studies of predator density, reproductive behavior, and color-pattern variation will determine which ecological processes promote genetic variation. Whole-genome sequencing of guppies from 13 natural populations will identify regions of the genome enriched for intermediate-frequency alleles; using data from many populations will allow us to differentiate between loci under balancing selection and those that are polymorphic because of non-selective processes such as random genetic drift and migration. This multipronged approach will enable linking evolutionary processes that maintain variation directly to the genetic variants (polymorphisms) they target.