PIRE: Centennial Genetic and Species Transformations in the Epicenter of Marine Biodiversity

Kent Carpenter (PI), Daniel Barshis （Old Dominion大学），Christopher Bird (Texas a&m University - Corpus Christi), Malin Pinsky （Rutgers大学），Beth Polidoro （Arizona州立大学）当今人类面临的最大挑战之一是我们是否有能力理解人类对我们赖以生存的自然资源的影响。了解迄今为止的影响将使我们能够更好地保存和保护重要资源，以供将来使用。选择一个成功的资源管理策略可以确保今世后代资源的可持续性。过去一个世纪以来，人口呈指数级增长，同时对地球资源，特别是海洋渔业资源提出了前所未有的需求。幸运的是，史密森国家自然历史博物馆收藏了大量鱼类，这为了解过去一个世纪人类对海洋鱼类的影响提供了一个独特的窗口。1907-1909年，在美国殖民菲律宾后不久，我国政府派了一支考察队去评估那里的自然资源。当时的自然历史藏品都是单独保存在酒精中，这样可以长时间保存DNA（相比之下，大多数博物馆藏品都保存在福尔马林中，这会改变DNA）。我们收集了大量的资料，这将使我们能够研究在人口急剧增长和对这些资源的开发期间人口动态的变化。我们将通过使用最初为人类医学开发的尖端先进基因组学方法来比较历史和当代收藏品来做到这一点。这种规模的工作从来没有在严重开发的渔业中完成过，它不仅会给我们提供对菲律宾资源管理有价值的见解，而且还会帮助我们了解对世界其他地区的影响。结果将通过广泛的外联活动向有关机构和公众提供。该项目将把实地和实验室研究目标与在菲律宾的年度学期学术活动结合起来。这些活动将在先进的基因组方法学和海洋生态学方面培训大量美国和菲律宾的本科生和研究生以及早期职业专业人员。它还将促进我们两国之间的长期合作关系和善意。美国研究船信天翁号（Albatross）于1907年至1909年期间在菲律宾收集了大量独特的海洋鱼类基因组，这使我们有机会大大增加对过去一个世纪人类强烈影响下海洋鱼类基因组进化的了解。该船目前保存在史密森国家自然历史博物馆。本研究的首要研究问题是：在过去的一个世纪里，在菲律宾这个全球海洋生物多样性中心，激烈的渔业开发和栖息地退化发生了什么遗传和物种水平的变化？该项目利用菲律宾独特的广泛历史收藏和与菲律宾科学家的重要合作来解决以下新颖的科学问题：菲律宾海洋物种的遗传多样性丧失到何种程度？2. 过度捕捞和栖息地丧失是否减少了海洋种群之间的基因流动？3. 基因多样性和物种多样性在多大程度上揭示了一个世纪以来人类影响的类似变化？这将通过使用先进的基因组方法，通过比较来自同一地区的历史种群和当代种群的基因组成，来测量至少20种海洋鱼类进化潜力的百年尺度变化来实现。基因组影响将与更大规模的生物多样性变化进行比较，使用1970年菲律宾海洋鱼类的收集，将复制以直接测量物种和群落规模的变化。总之，这些调查将为人类对海洋生物多样性和进化的影响提供前所未有的见解。

Kent Carpenter (PI), Daniel Barshis (Old Dominion University), Christopher Bird (Texas A&M University - Corpus Christi), Malin Pinsky (Rutgers University), Beth Polidoro (Arizona State University)One of the greatest challenges facing humanity today is our ability to understand the impacts humans have on the natural resources we rely on for our existence. Understanding the impacts to date will allow us to better conserve and protect vital resources for future use. Choosing a successful resource management strategy ensures sustainability of resources for present and future generations. Exponential human population growth over the past century has been accompanied by unprecedented demands on the earth's resources, particularly marine fisheries resources. Fortunately, there exists a large collection of fishes at the Smithsonian National Museum of Natural History that offers a unique window into the human impacts on marine fishes over the past century. In 1907-1909, not long after the U.S. colonized the Philippines, our government sent an expedition there to take stock of their natural resources. This was at a time when natural history collections were stored solely in alcohol which preserves DNA over long periods (compared to most museum collections preserved in formalin that alters DNA). Extensive collections were made that will allow us to examine the changes in the dynamics of populations over a period of extreme human population growth and exploitation of these resources. We will do this by comparing historical and contemporary collections using cutting-edge advanced genomics methods initially developed for human medicine. No work of this scale has ever been accomplished on heavily exploited fisheries and not only will it give us insights valuable for Philippine resource management, but it will also help us understand impacts in other parts of the world. Results will be made available to relevant institutions and the public through extensive outreach activities. This project will integrate field and laboratory research objectives with annual semester-long academic activities in the Philippines. These activities will train a significant number of American and Filipino undergraduate and graduate students and early career professionals in advanced genomic methodology and marine ecology. It will also foster long term collaborative ties and good will between our countries. An opportunity to dramatically increase the knowledge of genome-scale evolution in marine fishes over the past century of intense human impacts is possible through a unique and extensive collection from the Philippines that took place from 1907 to 1909 on board the US Research Vessel Albatross, maintained at the Smithsonian National Museum of Natural History. The overarching research question in this study is: what genetic and species-level changes have taken place over the past century of intense fisheries exploitation and habitat degradation in the Philippine global epicenter of marine biodiversity? This project takes advantage of the extensive historical collections unique to the Philippines and essential collaborations with Philippine scientists to address the following novel scientific questions: 1. To what extent has genetic diversity been lost from marine species in the Philippines? 2. Have overfishing and habitat loss reduced gene flow between marine populations? 3. To what extent do genetic diversity and species diversity reveal similar changes over a century of human impacts? This will be accomplished by measuring the centennial scale changes in the evolutionary potential of at least 20 species of marine fishes by comparing the genetic makeup of historical and contemporary populations from the same localities using advanced genomic methodologies. The genomic impacts will be compared to larger scale biodiversity changes using 1970's collections of Philippine marine fishes that will be replicated to directly measure species and community scale changes. Together, these investigations will give unprecedented insight into anthropogenic impacts on marine biodiversity and evolution.