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

这一行动为2017财年NSF生物学博士后研究奖学金-使用生物收藏进行研究-提供资金。该奖学金支持将以创新方式利用生物收藏的研究员的研究和培训。在此过程中，拟议的研究将突出自然历史收集的重要性，以扩大我们对生物多样性是如何产生的理解，相对于栖息地等生态变量，以及与所有动物赖以生存的微生物的共生关系。具体地说，这项研究调查了栖息地的利用和与发光细菌的共生对一组生物发光珊瑚礁鱼类的多样性的影响。将开发的从博物馆标本中提取宿主和共生体DNA的方法将创造新的机会，以了解宿主动物及其细菌共生体随着时间的推移而相对于彼此及其环境发生变化的方式。这种信息在这个快速变化的环境威胁着与重要的共生联系脱钩的关键时刻特别有价值。物种对特定生境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，可以用来预测它们未来对即将到来的环境变化的反应。这个项目研究了共生发光的珊瑚鱼Siphamia属(Perciformes：Apogonidae)，作为一个模型，用来研究栖息地的利用及其与发光细菌作为宿主物种形成驱动力的共生。通过将下一代测序方法应用于博物馆存档标本，具体的研究目标是(I)推断西帕米亚鱼类之间的系统发育关系，(Ii)比较西帕米亚相对于物种栖息地用途和生物地理分布的确定的分化模式，(Iii)鉴定不同西帕米亚宿主物种的发光共生体，以及(Iv)比较共生体的基因类型和与宿主差异模式和环境特征(如深度和温度)的系统发育关系。为了实现这些目标，该研究员将从博物馆收藏品中代表其地理范围的所有23个所描述的西帕米亚物种的组织中提取DNA，并将应用限制性内切酶相关测序(RAD-Seq)方法来解决宿主鱼类的系统发育问题。该研究员还将从西帕米亚发光器官中提取发光共生体的DNA，包括从该项目期间收集的现代标本中提取的DNA，并将对已知在弧菌科发光细菌之间存在差异的基因进行排序，以推断发光器官共生体的系统发育。然后将宿主鱼类的分化模式与它们的栖息地使用、分布和共生体多样化模式进行比较，以测试这些因素驱动的生态物种形成的特征，揭示可能塑造这种珊瑚礁鱼类多样性及其生物发光共生的潜在生态过程。这项研究将设在加州科学院(CAS)，并将通过旨在强调珊瑚礁生态系统中生物多样性的重要性及其当前威胁的推广计划和展览，促进公众参与微生物共生和物种适应环境等基本主题。该项目的其他重要方面包括在中科院的鱼类学、微生物学和冰冻DNA收集中纳入新的标本，以用于未来的研究，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.