NSF Postdoctoral Fellowship in Biology FY 2017: Investigating drivers of ecological speciation in a symbiotically luminous coral reef fish

本行动资助美国国家科学基金会2017年度生物学博士后研究奖学金，利用生物馆藏进行研究。该奖学金支持研究和培训将以创新的方式利用生物收集的研究员。在这样做的过程中，拟议的研究将突出自然历史收藏的重要性，以扩大我们对生物多样性如何相对于生态变量（如栖息地）和与微生物的共生关系（所有动物都依赖于这些变量）产生的理解。具体而言，本研究探讨了生境利用和与发光细菌的共生关系对一组生物发光珊瑚礁鱼类多样化的作用。将开发从博物馆标本中提取宿主和共生体DNA的方法，将为了解宿主动物及其细菌共生体相对于彼此和环境随时间变化的方式提供新的机会。当快速变化的环境威胁到基本共生关系的分离时，这些信息在这个关键时刻尤其有价值。物种对特定栖息地的依赖及其适应新条件的能力的历史模式，以及它们的共生体，可以用来预测它们对即将到来的环境变化的未来反应。本项目研究了共生发光属的珊瑚鱼Siphamia (Perciformes: Apogonidae)，作为研究栖息地利用及其与发光细菌作为宿主物种形成驱动因素的共生模式。通过将下一代测序方法应用于博物馆标本，具体的研究目标是：(i)推断Siphamia鱼类之间的系统发育关系，（ii）比较相对于物种栖息地利用和生物地理分布的已定义的Siphamia分化模式，（iii）确定不同Siphamia宿主物种的发光共生体。（iv）比较共生体基因型和系统发育关系与宿主分化模式和环境特征，如深度和温度。为了实现这些目标，该研究员将从具有地理范围代表性的博物馆藏品中提取所有23种被描述的虹膜鱼的组织DNA，并将应用限制性内切位点相关测序（RAD-Seq）方法来解决宿主鱼的系统发育问题。该研究人员还将从Siphamia光器官中提取发光共生体的DNA，包括在该项目中收集的现代标本，并将对已知的弧菌科发光细菌之间的基因进行测序，以推断光器官共生体的系统发育。然后将宿主鱼的分化模式与它们的栖息地使用、分布和共生多样化模式进行比较，以测试由这些因素驱动的生态物种形成的特征，揭示可能形成这种珊瑚礁鱼类及其生物发光共生的多样性的潜在生态过程。这项研究将以加州科学院（CAS）为基础，通过外展计划和展览，旨在强调珊瑚礁生态系统生物多样性的重要性及其当前的威胁，促进公众对微生物共生和物种对环境的适应性反应的潜在主题的参与。该项目的其他重要方面包括将中国科学院的鱼类学、微生物学和冷冻DNA标本纳入未来研究，以及对本科生进行应用分子方法的培训。

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2017, Research Using Biological Collections. The fellowship supports research and training of the fellow that will utilize biological collections in innovative ways. In doing so, the proposed research will highlight the importance of natural history collections in broadening our understanding of how biodiversity arises relative to ecological variables such as habitat and to symbiotic associations with microbes, upon which all animals depend. Specifically, this study investigates the role of habitat use and a symbiosis with luminous bacteria on the diversification of a group of bioluminescent coral reef fish. The methods that will be developed to extract both host and symbiont DNA from museum specimens will establish new opportunities to understand the way in which host animals and their bacterial symbionts change over time relative to each other and to their environments. Such information is especially valuable at this critical time when rapidly changing environments threaten to de-couple essential symbiotic associations. The historical patterns of species' dependencies on particular habitats and their abilities to adapt to new conditions, along with their symbionts, can be used to predict their future responses to impending environmental changes.This project examines the symbiotically luminous genus of coral reef fish Siphamia (Perciformes: Apogonidae) as a model with which to investigate both habitat use and its symbiosis with luminous bacteria as drivers of speciation in the host. By applying next generation sequencing methods to archived museum specimens, the specific research objectives are (i) to infer the phylogenetic relationships among Siphamia fishes, (ii) to compare the defined divergence patterns in Siphamia relative to species-habitat use and biogeographic distributions, (iii) to identify the luminous symbionts of various Siphamia hosts species, and (iv) to compare symbiont genotypes and phylogenic relationships with both host divergence patterns and environmental characteristics such as depth and temperature. To carry out these objectives, the fellow will extract DNA from the tissue of all 23 described Siphamia species archived in museum collections from sites representative of their geographic ranges and will apply restriction site associated sequencing (RAD-Seq) methods to resolve the phylogeny of the host fish. The fellow will also extract the DNA of the luminous symbionts from Siphamia light organs, including those from modern specimens collected during this project, and will sequence genes known to vary between luminous bacteria in the Vibrionaceae family to infer a phylogeny of the light organ symbionts. The divergence patterns in the host fish will then be compared to their habitat use, distributions, and patterns of symbiont diversification to test for signatures of ecological speciation driven by these factors, revealing the underlying ecological processes that might have shaped the diversification of this coral reef fish and its bioluminescent symbiosis. This research will be based at the California Academy of Sciences (CAS) and will foster public engagement on the underlying themes of microbial symbioses and of species-adaptive responses to their environment through outreach programs and exhibits designed to highlight the importance of biodiversity in coral reef ecosystems and its current threats. Other important aspects of this project include the incorporation of new specimens in the ichthyology, microbiology, and frozen DNA collections at CAS for use in future research as well as the training of undergraduate students on the applied molecular methods.