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

PIRE：海洋生物多样性中心的百年遗传和物种转变

• 批准号: 1743711
• 负责人: Kent Carpenter
• 金额: $ 460.69万
• 依托单位: Old Dominion University Research Foundation
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-10-01 至 2023-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1743711&HistoricalAwards=false
• 关键词: PIRE; Centennial; Genetic; Species; Transformations

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.

Kent Carpenter(Pi)，Daniel Barshis(Old Dominion University)，Christopher Bird(德克萨斯农工大学-Corpus Christi)，Malin Pinsky(罗格斯大学)，Beth Polidoro(亚利桑那州立大学)今天人类面临的最大挑战之一是我们理解人类对我们赖以生存的自然资源的影响的能力。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，以供未来使用。选择成功的资源管理战略可确保今世后代资源的可持续性。在过去的一个世纪里，人类人口呈指数级增长，伴随而来的是对地球资源，特别是海洋渔业资源的前所未有的需求。幸运的是，史密森国家自然历史博物馆有大量的鱼类收藏，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，我国政府派遣了一支探险队前往那里，对他们的自然资源进行评估。这是在自然历史收藏品仅在酒精中保存的时代，酒精可以长期保存DNA(与大多数博物馆收藏品在福尔马林中保存的改变DNA的保存相比)。进行了广泛的收集，使我们能够审查在人类人口极端增长和对这些资源的开发期间人口动态的变化。我们将使用最初为人类医学开发的尖端先进基因组学方法，通过比较历史和当代收集来做到这一点。在高度开发的渔业上，从来没有完成过这种规模的工作，它不仅将给我们提供对菲律宾资源管理有价值的见解，而且还将帮助我们了解世界其他地区的影响。结果将通过广泛的外联活动提供给有关机构和公众。该项目将把实地和实验室研究目标与菲律宾每年为期一学期的学术活动结合起来。这些活动将培训相当数量的美国和菲律宾本科生和研究生以及早期职业生涯中的高级基因组方法论和海洋生态学专业人员。它还将促进我们两国之间的长期合作关系和善意。通过1907年至1909年在史密森国家自然历史博物馆保存的美国研究船信天翁号上从菲律宾收集的独特而广泛的藏品，有可能大幅增加过去一个世纪人类强烈影响下海洋鱼类基因组规模进化的知识。这项研究的首要研究问题是：在菲律宾海洋生物多样性的全球震中，在过去的一个世纪里，激烈的渔业开发和栖息地退化发生了哪些遗传和物种水平的变化？该项目利用菲律宾独有的大量历史收藏和与菲律宾科学家的重要合作来解决以下新的科学问题：1.菲律宾海洋物种的遗传多样性丧失了多大程度？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.在一个世纪的人类影响下，遗传多样性和物种多样性在多大程度上揭示了类似的变化？这将通过使用先进的基因组方法比较同一地区历史和当代种群的遗传构成，来衡量至少20种海洋鱼类进化潜力的百年尺度变化。基因组的影响将与利用1970年S收集的菲律宾海洋鱼类进行的更大规模的生物多样性变化进行比较，这些收集将被复制，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洞察力。

项目成果

Microplastics in marine sediments and rabbitfish (Siganus fuscescens) from selected coastal areas of Negros Oriental, Philippines

• DOI: 10.1016/j.marpolbul.2019.110685
• 发表时间: 2020-01-01
• 期刊: MARINE POLLUTION BULLETIN
• 影响因子: 5.8
• 作者: Bucol, Lilibeth A.;Romano, Edwin F.;Polidoro, Beth
• 通讯作者: Polidoro, Beth

Development of reproductive potential in protogynous coral reef fishes within Philippine no‐take marine reserves

菲律宾诺塔克海洋保护区内原生珊瑚礁鱼类繁殖潜力的开发

• DOI: 10.1111/jfb.14861
• 发表时间: 2021
• 期刊: Journal of Fish Biology
• 影响因子: 2
• 作者: Bucol, Abner A.;Abesamis, Rene A.;Stockwell, Brian L.;Lowe, Jake R.;Russ, Garry R.
• 通讯作者: Russ, Garry R.

Coral Reef Population Genomics in an Age of Global Change

全球变化时代的珊瑚礁种群基因组学

• DOI: 10.1146/annurev-genet-022123-102748
• 发表时间: 2023
• 期刊: Annual Review of Genetics
• 影响因子: 11.1
• 作者: Pinsky, Malin L.;Clark, René D.;Bos, Jaelyn T.
• 通讯作者: Bos, Jaelyn T.

Genetic and phenotypic variation exhibit both predictable and stochastic patterns across an intertidal fish metapopulation

潮间带鱼类集合种群的遗传和表型变异表现出可预测和随机模式

• DOI: 10.1111/mec.15829
• 发表时间: 2021
• 期刊: Molecular Ecology
• 影响因子: 4.9
• 作者: Thia, Joshua A.;McGuigan, Katrina;Liggins, Libby;Figueira, Will F.;Bird, Christopher E.;Mather, Andrew;Evans, Jennifer L.;Riginos, Cynthia
• 通讯作者: Riginos, Cynthia

The practice and promise of temporal genomics for measuring evolutionary responses to global change

• DOI: 10.1111/1755-0998.13789
• 发表时间: 2023-04-02
• 期刊: MOLECULAR ECOLOGY RESOURCES
• 影响因子: 7.7
• 作者: Clark，Rene D.;Catalano，Katrina A.;Pinsky，Malin L.
• 通讯作者: Pinsky，Malin L.