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.