Collaborative Proposal: Selection and Genetic Succession in the Intertidal -- Population Genomics of Pisaster ochraceus During a Wasting Disease Outbreak and its Aftermath

该项目旨在通过探索最近在2013年北太平洋东部造成90%赭色海星（Pisaster ochraceus）死亡的流行病，了解捕食者-疾病动态的结果。该研究小组将探索海洋物种的迁移和自然选择的相互作用等通常难以看到的过程是如何影响恢复的。虽然由于几年来异常高的招募，海星的数量目前正在反弹，但海星消瘦病继续维持在低水平。该项目旨在确定大流行的遗传后果和随后的恢复。该团队将确定大多数易感海星是否已经死亡，并确定易感海星幸存的可能避难所。他们将检查对这种疾病的抗性遗传变异的可能性，以评估新招募的人是否对消瘦具有耐受性或易感性。解决这些问题将有助于预测它们的恢复轨迹以及对未来大规模疾病暴发的潜在应对措施。将在一个合作讲习班上与资源管理人员和科学家分享研究成果，该讲习班将重点讨论推动海洋疾病研究的最先进方法。通过与UCSC西摩海洋探索中心的合作，公众将有机会了解更多关于海星消瘦病的信息，并可以使用www.seastarwasting.org上的在线互动地图跟踪疾病的发病率。结果将被纳入CalTeach教师的专业发展，并改编为符合大学水平的教材。该项目将培养不同的早期职业科学家-本科生，研究生和博士后学者-整合生态和基因组方法。在地理异质性和海洋pH值和温度的长期变化的更广泛背景下，了解大规模流行病的后果是一个新出现的当代问题。该项目采用海星消瘦病（SSWD）爆发的种群动态和遗传后果的长期特征来估计该物种的潜在长期后果，该疾病导致东北太平洋的Pisaster ochraceus种群中有90%的死亡率。虽然有记录的最大新兵涌入发生在2014-2016年，但尚不清楚他们来自哪里，新兵和幸存的成年人是否仍然容易感染这种持续低水平的疾病，以及这种动态可能持续多长时间。这一长期数据集为探索此类大规模疾病暴发的短期和长期影响及其引发的人口动态提供了独特的机会。该项目建立在对野生种群进行长期实地研究的基础上，以描述宿主种群动态、疾病和基因组多样性。目标是发现与SSWD相关的遗传变异，并将这种变异与归因于非生物环境变异的群体基因组效应分离开来。目标是：(1)在其分布范围内的24个站点进行普查，描述种群动态、SSWD流行情况，并测量非生物变量。(2)进行实验室实验，结合RNAseq分析，确定暴露于SSWD、温度、盐度和pCO2异常时的差异调控位点。(3)将ddRAD、RNAseq和候选位点定位到P. ochraceus基因组中。(4)进行为期3年的大范围种群基因组分析，以评估在非生物变异的地理马赛克上，野生捕获的有或没有SSWD的标本之间的遗传（SNP）变异。(5)探索SSWD与候选基因座（如EF1A）之间的联系。这些分析将描述疾病暴发的直接基因组后果，暴发引发的种群动态，以及影响这些变化的因素和机制（如疾病、温度、迁移、选择）的相互作用。研究结果将促进对沿海生态系统中形成种群基因组结构的一般过程和相互作用的理解，为未来的研究和沿海生物资源管理策略的设计提供资源。

This project seeks to understand the outcomes of predator-disease dynamics by exploring a recent pandemic that decimated 90% of ochre sea stars (Pisaster ochraceus) in the eastern North Pacific in 2013. The research team will explore how recovery may depend upon often difficult-to-see processes such as the interplay of migration and natural selection in marine species. While the population of sea stars is currently rebounding due to several years of unusually high recruitment, the sea star wasting disease continues to persist at low levels. This project aims to determine the genetic consequences of the pandemic and subsequent recovery. The team will determine whether the majority of susceptible sea stars have died and identify possible refuges where susceptible sea stars survived. They will examine the potential for heritable variation in resistance to this disease in order to assess whether the new recruits are tolerant or susceptible to wasting. Resolving these issues will enable predictions about the trajectory of their recovery and the potential responses to future large scale disease outbreaks. Research findings will be shared with resource managers and scientists at a collaborative workshop that will focus on state-of-the-art methods to advance research on marine diseases. The public will have the opportunity to learn more about sea star wasting disease through a partnership with the UCSC Seymour Marine Discovery Center and can track the incidence of disease using an online interactive map available at www.seastarwasting.org. Results will be incorporated into professional development for teachers with CalTeach and adapted for teaching materials up to college-level. This project will train diverse early career scientists - undergraduates, graduates, and a postdoctoral scholar - in integration of ecological and genomic methods.Understanding the consequences of large-scale pandemics in the broader contexts of geographic heterogeneity and chronic changes in ocean pH and temperature is an emerging contemporary issue. This project employs long-term characterization of population dynamics and genetic consequences of a sea star wasting disease (SSWD) outbreak, which caused median 90% mortality in Pisaster ochraceus populations in the northeastern Pacific, to estimate potential long-term consequences for the species. While the largest recorded influx of new recruits occurred in 2014-2016, it is unknown where they originated from, whether recruits and surviving adults remained susceptible to the disease, which persisted at low levels, and for how long these dynamics might continue. This long-term dataset provides a unique opportunity for exploring the short and long term repercussions of such large-scale disease outbreaks and the population dynamics that they precipitate. This project builds on long-term field studies of wild populations to describe host population dynamics, the disease, and genomic diversity. The goal is to discover genetic variation associated with SSWD and to dissociate that variation from population genomic effects attributable to abiotic environmental variation. Objectives are: (1) Census P. ochraceus at 24 sites throughout its range to describe population dynamics, the prevalence of SSWD, and measure abiotic variables. (2) Conduct laboratory experiments coupled with RNAseq analyses to determine loci differentially regulated during exposure to SSWD, temperature, salinity, and pCO2 anomalies. (3) Map ddRAD, RNAseq, and candidate loci under selection to a P. ochraceus genome. (4) Conduct range-wide population genomic analyses for 3 years to assess genetic (SNP) variation among wild-caught specimens with, versus without, SSWD across a geographic mosaic of abiotic variation. (5) Explore links between SSWD and candidate loci, such as EF1A. These analyses will describe the immediate genomic consequences of the disease outbreak, the population dynamics that the outbreak set in motion, and the interplay of factors and mechanisms - such as disease, temperature, migration, selection - that affected these changes. The results will advance understanding of general processes and interactions that shape population genomic structure in coastal ecosystems, providing resources to inform future research and applications in design of management strategies for coastal living resources.