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Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline

合作研究：尽管基因沿着沿海环境线流动，但局部适应的基因组基础

基本信息

批准号：
1756316
负责人：
Nina Therkildsen
金额：
$ 86.1万
依托单位：
Cornell University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2018
资助国家：
美国
起止时间：
2018-03-01 至 2023-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1756316&HistoricalAwards=false
关键词：
Collaborative research genomic underpinnings local

项目摘要

Oceans are large, open habitats, and it was previously believed that their lack of obvious barriers to dispersal would result in extensive mixing, preventing organisms from adapting genetically to particular habitats. It has recently become clear, however, that many marine species are subdivided into multiple populations that have evolved to thrive best under contrasting local environmental conditions. Nevertheless, we still know very little about the genomic mechanisms that enable divergent adaptations in the face of ongoing intermixing. This project focuses on the Atlantic silverside (Menidia menidia), a small estuarine fish that exhibits a remarkable degree of local adaptation in growth rates and a suite of other traits tightly associated with a climatic gradient across latitudes. Decades of prior lab and field studies have made Atlantic silverside one of the marine species for which we have the best understanding of evolutionary tradeoffs among traits and drivers of selection causing adaptive divergence. Yet, the underlying genomic basis is so far completely unknown. The investigators will integrate whole genome sequencing data from wild fish sampled across the distribution range with breeding experiments in the laboratory to decipher these genomic underpinnings. This will provide one of the most comprehensive assessments of the genomic basis for local adaptation in the oceans to date, thereby generating insights that are urgently needed for better predictions about how species can respond to rapid environmental change. The project will provide interdisciplinary training for a postdoc as well as two graduate and several undergraduate students from underrepresented minorities. The findings will also be leveraged to develop engaging teaching and outreach materials (e.g. a video documentary and popular science articles) to promote a better understanding of ecology, evolution, and local adaptation among science students and the general public. The goal of the project is to characterize the genomic basis and architecture underlying local adaptation in M. menidia and examine how the adaptive divergence is shaped by varying levels of gene flow and maintained over ecological time scales. The project is organized into four interconnected components. Part 1 examines fine-scale spatial patterns of genomic differentiation along the adaptive cline to a) characterize the connectivity landscape, b) identify genomic regions under divergent selection, and c) deduce potential drivers and targets of selection by examining how allele frequencies vary in relation to environmental factors and biogeographic features. Part 2 maps key locally adapted traits to the genome to dissect their underlying genomic basis. Part 3 integrates patterns of variation in the wild (part 1) and the mapping of traits under controlled conditions (part 2) to a) examine how genomic architectures underlying local adaptation vary across gene flow regimes and b) elucidating the potential role of chromosomal rearrangements and other tight linkage among adaptive alleles in facilitating adaptation. Finally, part 4 examines dispersal - selection dynamics over seasonal time scales to a) infer how selection against migrants and their offspring maintains local adaptation despite homogenizing connectivity and b) validate candidate loci for local adaptation. Varying levels of gene flow across the species range create a natural experiment for testing general predictions about the genomic mechanisms that enable adaptive divergence in the face of gene flow. The findings will therefore have broad implications and will significantly advance our understanding of the role genomic architecture plays in modifying the gene flow - selection balance within coastal environments.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

海洋是大型、开放的栖息地，以前人们认为，海洋缺乏明显的扩散障碍，会导致广泛的混合，从而阻止生物体在基因上适应特定的栖息地。然而，最近已经清楚的是，许多海洋物种被细分为多个种群，这些种群已经进化到在对比鲜明的当地环境条件下能够最好地繁衍生息。尽管如此，我们对面对持续的混合而实现不同适应的基因组机制仍然知之甚少。该项目的重点是大西洋银鱼（Menidia menidia），这是一种小型河口鱼类，在生长速度方面表现出显着的局部适应能力，并且具有一系列与跨纬度气候梯度密切相关的其他特征。数十年的实验室和实地研究使大西洋银鳀成为我们最了解导致适应性分歧的性状和选择驱动因素之间的进化权衡的海洋物种之一。然而，潜在的基因组基础迄今为止完全未知。研究人员将把从分布范围内采集的野生鱼类的全基因组测序数据与实验室的育种实验结合起来，以破译这些基因组基础。这将为迄今为止海洋局部适应的基因组基础提供最全面的评估之一，从而产生迫切需要的见解，以便更好地预测物种如何应对快速的环境变化。该项目将为一名博士后以及两名研究生和几名来自少数族裔的本科生提供跨学科培训。研究结果还将用于开发引人入胜的教学和推广材料（例如视频纪录片和科普文章），以促进理科学生和公众更好地了解生态学、进化论和当地适应。该项目的目标是表征 M. menidia 局部适应的基因组基础和结构，并研究适应性分歧是如何通过不同水平的基因流形成并在生态时间尺度上维持的。该项目分为四个相互关联的部分。第 1 部分沿着适应性谱线研究基因组分化的精细空间模式，以 a) 表征连通性景观，b) 识别发散选择下的基因组区域，c) 通过检查等位基因频率如何随环境因素和生物地理特征变化来推断潜在的驱动因素和选择目标。第 2 部分将关键的本地适应性特征映射到基因组，以剖析其潜在的基因组基础。第 3 部分整合了野生环境中的变异模式（第 1 部分）和受控条件下的性状图谱（第 2 部分），以 a) 检查局部适应的基因组结构如何在基因流模式中变化，b) 阐明染色体重排和适应性等位基因之间的其他紧密联系在促进适应方面的潜在作用。最后，第 4 部分研究了季节时间尺度上的扩散-选择动态，以 a) 推断针对移民及其后代的选择如何在连接均质化的情况下保持局部适应，b) 验证局部适应的候选基因座。跨物种范围内不同水平的基因流创造了一个自然实验，用于测试基因组机制的一般预测，这些机制在面对基因流时能够实现适应性分歧。因此，这些发现将具有广泛的影响，并将显着增进我们对基因组结构在改变沿海环境中基因流选择平衡中所起的作用的理解。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。