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

• 批准号: 1756751
• 负责人: Hannes Baumann
• 金额: $ 32.53万
• 依托单位: University of Connecticut
• 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 2023-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1756751&HistoricalAwards=false
• 关键词: Collaborative; research; genomic; underpinnings; local

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.

海洋是较大的开放式栖息地，以前认为它们缺乏明显的分散障碍会导致广泛的混合，从而阻止生物体在遗传上适应特定的栖息地。然而，最近已经很清楚，许多海洋物种被细分为多个种群，这些人群在对比的当地环境条件下发展为最佳成长。然而，我们仍然对面对持续混合的基因组机制知之甚少。该项目的重点是大西洋银层（Menidia menidia），这是一种小型河口鱼，在生长速率上表现出显着的局部适应性，并且在跨纬度的气候梯度紧密相关的其他特征方面表现出了很大的适应性。数十年来的先前实验室和现场研究使大西洋银色成为海洋物种之一，我们对此对进化的特征和选择驱动因素的进化折衷有最好的理解，从而导致适应性差异。然而，迄今为止的基因组基础是完全未知的。研究人员将将来自整个分布范围的野生鱼类的整个基因组测序数据与实验室中的繁殖实验相结合，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，从而产生了迫切需要的见解，以更好地预测物种如何应对快速环境变化。该项目将为博士后以及两名来自代表性不足的少数民族的研究生和几名本科生提供跨学科培训。这些发现还将被利用，以开发引人入胜的教学和外展材料（例如，视频纪录片和流行的科学文章），以更好地了解科学专业学生和公众对生态，进化和当地适应的理解。该项目的目的是表征梅尼迪亚植物中局部适应的基因组基础和建筑，并检查自适应差异如何通过不同水平的基因流量来塑造并在生态时尺度上保持。该项目分为四个相互连接的组件。第1部分检查沿自适应层的基因组分化的细尺度空间模式a）表征连通性景观，b）识别在不同选择下的基因组区域，c）通过研究等位基因频率在与环境因素和生物地理学特征之间的关系中如何变化来推断潜在的驱动因素和选择目标。第2部分将密钥局部适应的特征映射到基因组，以剖析其潜在的基因组基础。第3部分整合了野生（第1部分）的变化模式以及在受控条件下的特征（第2部分）与a）研究局部适应基础适应性的基因组体系结构在基因流动方案中如何变化以及b）阐明染色体重排的潜在作用，并在适应性等位置上进行适应性分子之间的其他紧密链接。最后，第4部分检查了分散 - 在季节性时间尺度上的选择动力学到a）推断出对移民的选择及其后代如何保持局部适应性，尽管连通性均匀，并且b）验证候选基因座以进行局部适应。整个物种范围内的基因流量的不同水平创建了一个自然实验，用于测试有关基因流动时能够自适应差异的基因组机制的一般预测。因此，这些发现将具有广泛的影响，并会大大提高我们对基因组建筑在修改基因流的作用 - 沿海环境内的选择平衡所扮演的作用。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子和广泛影响的评估来通过评估来支持的。

项目成果

Otolith-based growth reconstructions in young-of-year Atlantic silversides Menidia menidia and their implications for sex-selective survival

基于耳石的大西洋银鳅幼鱼的生长重建及其对性别选择性生存的影响

• DOI: 10.3354/meps13174
• 发表时间: 2019
• 期刊: Marine Ecology Progress Series
• 影响因子: 2.5
• 作者: Pringle, JW;Baumann, H
• 通讯作者: Baumann, H

Temperature-dependent effects on fecundity in a serial broadcast spawning fish after whole-life high CO2 exposure

终生高二氧化碳暴露后温度对连续广播产卵鱼繁殖力的影响

• DOI: 10.1093/icesjms/fsab217
• 发表时间: 2021
• 期刊: ICES Journal of Marine Science
• 影响因子: 3.3
• 作者: Concannon, Callie A;Cross, Emma L;Jones, Lucas F;Murray, Christopher S;Matassa, Catherine M;McBride, Richard S;Baumann, Hannes
• 通讯作者: Baumann, Hannes