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，有独特的幼虫和成虫阶段。 这些物种的幼虫在浮游生物中发育数周，是微观的，游泳能力弱，容易被洋流驱散，通常死亡率很高，导致不稳定的成年种群补充。 决定招募成功和迁移或成年种群之间的连接的因素是海洋渔业管理，生态和保护的主要问题。 该研究项目结合生理基因组学和种群建模的工具来研究影响海洋补充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。 三个假设驱动的研究活动-基因作图，基因表达分析，和数学人口建模-预计将推进海洋招聘的内源性和外源性变异来源的知识。 虽然外源性因素，如洋流，温度和食物的可用性，长期以来一直在研究，并在这个项目中通过计算机模拟解决，内源性因素，如遗传和生理成分的幼虫健身，迄今为止很少受到关注。 这个项目的主题，太平洋牡蛎，是准备应用基因组方法来识别，量化和建模的内源性机制控制的生物复杂性的核心海洋招聘问题。 在关键的生理过程，如幼虫生长和耐饥饿的遗传变异，已被确定，并负责这种变化的基因将通过全面的基因表达谱揭示。 调节生理过程的基因也将被定位，利用现有的遗传图谱和适当的实验种群。 最后，实验数据的幼虫适应度的变化的内源性来源，可以合成到一个生化明确的，基于个人的幼虫种群动态模型，它允许逼真的计算机模拟招聘成功和人口丰富的短期和长期的环境变化。 开发基因组工具对于了解海洋动物至关重要，海洋动物巨大的繁殖力使它们与更熟悉和更好研究的陆地动物有着根本的不同。 该项目的首要科学意义是将海洋环境科学与基因组学、达尔文主义关于个体差异、适应和进化的观点融合在一起。该项目更广泛的科学影响有几个。 首先，该项目是交叉培训研究生和博士后研究人员的领域，其综合是至关重要的环境科学的未来-遗传学，基因组学，生理学，计算生物学和人口的数学模拟。 其次，通过NSF西海岸海洋科学教育卓越中心（COSEE-West）提供的基础设施，研究人员正在利用海洋科学来提高整个大洛杉矶地区多达200万K-12儿童的一般科学和数学教育。 第三，该项目通过向公共数据库（基因库）提供具有生态和经济重要性的海洋生物群体的基因图谱、基因表达谱和数万个DNA序列，加强科学基础设施。 最后，该项目通过识别影响幼虫存活或预测孵化场“种子”牡蛎产量的基因或基因表达模式，使大型牡蛎养殖业受益。 在全球范围内，滤食性双壳贝类在沿海沃茨生态中发挥着重要作用，是人类珍贵的食物。 事实上，自1998年以来，太平洋牡蛎已被引入除南极洲以外的所有大陆，其产量是世界上任何淡水或海洋养殖物种中最高的，每年约400万公吨（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).