Current Supported Projects
Environmental Epigenetics
##### Alleviating Regulatory Impediments to Native Shellfish Aquaculture
_Summary_:The overarching goal of this project is to increase our knowledge of local adaptation in Olympia oysters to address concerns that interbreeding between potentially maladapted cultured and wild stocks could negatively impact wild populations. Our approach is to simultaneously address local adaptation in three genetically differentiated populations of Olympia oysters by evaluating genotype-by-environment interactions. We will reciprocally transplant seed produced from wild parents collected from contrasting environments into all environments. This extensive reciprocal transplant experiment can test for local population advantages in survival, maturation and growth in Olympia oysters. In order to attain our goal, the specific objectives of this proposal are to 1) Evaluate fitness components and performance of seed from different origins in a reciprocal transplant experiment, and 2) Characterize genetic and epigenetic markers associated with oysters from different origins in a reciprocal transplant experiment
##### Developing genomic resources to support restoration and protection of the Olympia Oyster in Puget Sound
_Summary_: There is a significant gap in our fundamental understanding of this species’ resilience in the face of environmental change, ecological interactions, and population structure. This information is critical to local restoration efforts and to predicting how molluscs will adapt to long-term environmental change. There is recent evidence that oysters have the capacity to respond to environmental change at a rate beyond what would be predicted by genetic variation alone. The overall objective of this research is to produce genomic resources and capacity to understand the response of Olympia oysters to environmental change. Specifically, a draft genome assembly for the Olympia oyster will be produced and used to understand how responses of the Olympia oyster to environmental changes are inherited (i.e., genetic or epigenetic) using restriction site associated DNA sequencing (RAD-Seq) and bisulfite sequencing (BS-Seq). A web-based platform will be developed based on these resources that will be used for discovery and further collaboration.
##### Assessing the Capacity for Evolutionary Adaptation to Ocean Acidification in Geoduck
_Summary_: We will investigate the roles of standing genetic (DNA sequence) and epigenetic (DNA methylation) variation in the response to ocean acidification and elevated temperature in geoduck at the vulnerable larval stage. The specific research objectives are to (1) characterize changes in allele frequencies under ocean acidification and temperature stress at single nucleotide polymorphisms (SNPs) throughout the genome, and (2) determine the change in frequency of methylation states (epialleles) under ocean acidification and temperature stress throughout the epigenome. To meet our objectives, we will employ a within-generation selection experiment on larvae subjected to ambient and high pCO2 and ambient and high temperature in a factorial cross. This experimental design allows us to uncover changes in standing genetic and epigenetic variation in response to ocean acidification and elevated temperature, and will provide essential information on how marine invertebrate populations can respond to, and persist in, an acidifying ocean.
Reproductive Biology and Ecology
##### Using satellite pop-up tags to track movements of sablefish during spawning and changes in vertical position in the water column
_Summary_: The Sablefish (_Anoplopoma fimbria_) is a deep-water groundfish species widely distributed throughout the northern Pacific Ocean. While some broadscale movements of sablefish have been addressed with tagging studies, two fundamental questions related to sablefish movements are 1) Where do sablefish go during spawning and; 2) Are sablefish adults exclusively benthic inhabitants? To address these questions we will use “pop-up” satellite tag (PSAT) technology. Pop-up satellite tags are composed of a data-logger and battery, and a float with attached antenna. The tag is tethered to the fish and the data logger is programmed to continually collect depth, temperature, and location for a specified duration (weeks to months). At the end of the programmed time, a detachment mechanism is automatically activated that releases the data logger/float and antenna from the tether. The float carries the data logger to the surface where the antenna transmits the data to an orbiting satellite of the ARGOS System that then transmits data back to the researcher. Time series analysis will be employed to determine periodicity in depth profiles and relationships with other environmental parameters such as temperature. Data from this study will allow us to discern daily/weekly and monthly patterns in vertical positioning in the water column and will provide information on possible spawning locations.
##### Maturation processes in the marine mollusc, _Panopea generosa_
Maturation processes in marine molluscs are not well-characterized and large gaps in our understanding remain. Many studies have concluded that steroids are involved in mollusc reproduction, but the majority of these studies were targeted at vertebrate steroids that may not play a role given the apparent lack of functional receptors for androgens and estrogens. The topdown approaches used in the past focused on reproduction molecules from divergent phyla may be missing the mark for the phylum mollusca. An entirely different mechanism for reproductive maturation processing may be at play. While the existing evidence does not definitively rule out a role for steroids, the validity of a different, bottom-up approach is evident. Combining highthroughput proteomic data acquisition with comprehensive bioinformatic data analysis as proposed here, will lead to the discovery of factors controlling maturation processes in this diverse phylum.
[more info](http://eagle.fish.washington.edu/trilobite/Proposal_Database/RRF_Geoduck2013.pdf)
##### Eelgrass as refuge: exploring diurnal distribution of bivalve larvae across habitats
To evaluate the distribution of Pacific oyster (_Crassostrea gigas_) and geoduck (_Panopea generosa_) larvae across eelgrass (Zostera marina) and unstructured habitats, and to quantify temporal and spatial variation in larval supply across sites in Puget Sound and the Washington coast through the collection of field data in targeted experiments. Results will assist scientists in developing stewardship recommendations to adaptively manage leased activities and wildstock geoduck harvest on State Owned Aquatic Lands.
Aquaculture Resource Development
##### Engaging Students and Public in Marine Conservation through Sustainable Shellfish Aquaculture
_Summary_: The UW Shellfish Farm is a project conceived by several graduate students, faculty and staff at the School of Aquatic & Fishery Sciences (SAFS), in collaboration with the School of Marine & Environmental Affairs (SMEA) and the College of the Environment. We seek to establish a student-run shellfish farm at the Big Beef Creek Research Station, a SAFS field site on Hood Canal. The overarching goals of the project are:
1) Provide students and with a hands-on opportunity to experience sustainable seafood production.
2) Conduct outreach and education on estuarine health and climate change impacts on the marine environment.
3) Conduct monitoring to quantify environmental impacts of shellfish aquaculture on estuarine health.
4) Serve as a field site for ongoing shellfish research at UW.
5) Become self-sustaining by selling cultivated shellfish (e.g. clams, oysters) through wholesalers, UW dining establishments, a subscription service, and other outlets.
[more info](https://csf.uw.edu/project/531)
##### Resource coordination workshops focused on oysters and other shellfish
_Summary_: This proposal sets out to build on results of our group’s prior effort to develop an open platform for querying disparate oyster datasets using SQLShare and other freely available resources (see <http://oystergen.es/query>). In collaboration with the eScience Institute at the University of Washington we have deployed this platform and successfully used it in many efforts. At this point we realize there are biological questions that are beyond the scope of our program and feel that bringing the community together for in person discussion will allow us to work together effectively to address questions, and importantly reveal new questions that likely would not surface without direct person-person interactions. For instance our group primarily focuses on organismal physiology and we have limited experience with population genetics or breeding design.
##### Crossbreeding and Selection for Resistance to Ocean Acidification in Pacific Oysters
_Summary_: We propose to utilize the large number of genetically distinct, pair-mated Pacific oyster lines produced through Taylor Shellfish Company’s breeding program to initiate large-scale and high throughput testing for evaluating differential response in Pacific oysters during two critical and sensitive larval life history phases to increased levels of pCO2 under experimental conditions. Information on relative resilience (measured as survivorship, growth and lipid energy reserves) to OA conditions in genetically distinct oyster lines will inform and guide the production of genetically improved broodstocks and provide the shellfish industry with better surviving/performing intraspecific hybrid oysters. This research will also enable us to greatly expand upon ongoing WA Sea Grant supported work that is investigating the critical importance of OA exposure during the sexual development phase (e.g. conditioning) in adults on subsequent larval and seed survivorship and growth (e.g. intergenerational effects).