BE/GEN-EN Genomic Approaches to Understanding Variation in Marine Larval Recruitment

大多数海洋动物都有复杂的生活史，有不同的幼体和成体阶段。这类物种的幼虫在浮游生物中发育数周，微小，游泳能力弱，容易被洋流驱散，通常死亡率高，导致不稳定的成年种群招募。决定捕捞成功和成年种群之间迁徙或连接的因素是海洋渔业管理、生态和养护方面的主要关切。本研究结合生理基因组学和种群模拟的工具，探讨影响海洋补给的生物因素的复杂性，以及这些因素之间的非线性相互作用。三项假设驱动的研究活动--基因作图、基因表达分析和数学种群建模--预计都将促进对海洋招募中内源和外源变异来源的了解。虽然外源因素，如洋流、温度和食物可获得性，早已被研究，并在该项目中通过计算机模拟来解决，但内源因素，如幼虫适合度的遗传和生理成分，迄今很少受到关注。这个项目的主题是太平洋牡蛎，准备应用基因组学方法来识别、量化和模拟控制海洋招募问题核心生物复杂性的内生机制。已经确定了关键生理过程中的遗传变异，如幼虫的生长和对饥饿的抗性，并将通过全面的基因表达谱揭示导致这种变异的基因。还将利用现有的遗传图谱和适当的实验种群来定位调节生理过程的基因。最后，关于幼虫适合度的内源变异来源的实验数据可以合成一个生物化学上明确的、基于个体的幼虫种群动态模型，该模型允许对短期和长期环境变化的招募成功率和种群丰度进行现实的计算机模拟。开发基因组工具对于理解海洋动物至关重要，海洋动物的巨大繁殖力使它们从根本上不同于更熟悉、研究更好的陆地动物。该项目的最重要的科学意义是将海洋环境科学与达尔文关于个体差异、适应和进化的基因组学观点结合起来。该项目的更广泛的科学影响有几个。首先，该项目正在交叉培训研究生和博士后研究人员，这些领域的综合对环境科学的未来至关重要-遗传学、基因组学、生理学、计算生物学和种群的数学模拟。其次，通过美国国家科学基金会西海岸海洋科学教育卓越中心(COSEE-West)提供的基础设施，调查人员正在利用海洋科学来加强整个大洛杉矶地区多达200万名K-12儿童的普通科学和数学教育。第三，该项目通过向公共数据库(GenBank)提供具有生态和经济重要性的海洋生物群体的遗传图谱、基因表达图谱和数万个DNA序列来加强科学基础设施。最后，该项目通过识别影响幼体存活的基因或基因表达模式，或预测孵化的“种子”牡蛎的产量，使大型牡蛎养殖业受益。在全球范围内，滤食性双壳类在沿海水域生态中发挥着重要作用，是一种珍贵的人类食物。事实上，太平洋牡蛎被引入除南极洲以外的所有大陆，是自1998年以来世界上淡水或海洋养殖物种产量最高的，每年约为400万吨(价值34亿美元)。

Most marine animals have complex life histories, with distinctive larval and adult phases. Larvae of such species develop for weeks in the plankton, are microscopic, weakly swimming, easily dispersed by ocean currents, and typically subject to high mortality, resulting in erratic recruitment to adult populations. Factors dictating recruitment success and migration or connectivity among adult populations are major concerns in marine fisheries management, ecology, and conservation. This research project combines the tools of physiological genomics and population modeling to investigate the complexity of biological factors affecting marine recruitment and the non-linear interactions among these factors. Three hypothesis-driven research activities - gene mapping, gene-expression analysis, and mathematical population modeling - are each expected to advance knowledge of the endogenous and exogenous sources of variation in marine recruitment. Although exogenous factors, such as ocean currents, temperature, and food availability, have long been studied and are addressed in this project through computer simulations, endogenous factors, such as genetic and physiological components of larval fitness, have received little attention to date. The subject for this project, the Pacific oyster, is poised for the application of genomic methods for identifying, quantifying, and modeling endogenous mechanisms controlling the biocomplexity at the heart of the marine recruitment problem. Genetic variation in key physiological processes, such as larval growth and resistance to starvation, has been identified, and genes responsible for this variation will be revealed through comprehensive gene-expression profiling. Genes regulating physiological processes will also be located, using available genetic maps and appropriate experimental populations. Finally, experimental data on endogenous sources of variation in larval fitness can be synthesized into a biochemically explicit, individual-based model of larval population dynamics, which permits realistic computer simulations of recruitment success and population abundance in response to both short-term and long-term environmental change. Developing genomic tools is vital to understanding marine animals, whose enormous fecundities make them fundamentally different from the more familiar and better-studied terrestrial animals. The overarching scientific significance of the project is the infusion of marine environmental science with a genomically enabled, Darwinian perspective on individual differences, adaptation, and evolution. The broader scientific impacts of the project are several. First, the project is cross training graduate students and postdoctoral researchers in fields whose synthesis is critical to the future of environmental science -genetics, genomics, physiology, computational biology, and mathematical simulations of populations. Second, through infrastructure provided by the NSF's West Coast Center for Ocean Science Education Excellence (COSEE-West), investigators are using ocean science to enhance the general science and math education of as many as 2 million K-12 children throughout the greater Los Angeles area. Third, the project enhances science infrastructure by contributing genetic maps, gene-expression profiles, and tens of thousands of DNA sequences to public databases (GenBank), for an ecologically and economically important group of marine organisms. Finally, the project benefits a large oyster aquaculture industry by identifying genes or patterns of gene expression that affect larval survival or predict yield of hatchery 'seed' oysters. Globally, filter-feeding bivalves play an important role in the ecology of coastal waters and are a prized human food. Indeed, the Pacific oyster, which has been introduced to all continents but Antarctica, has had the highest worldwide production of any cultured freshwater or marine species, since 1998, at about 4 million metric tons per year (worth $3.4 billion).