The goal of this project was to determine the effects of oyster reef restoration on oyster coverage, wave height dissipation and seagrass recruitment. First, to assess the current versus historical coverage of natural, dead and restored oyster reefs within Mosquito Lagoon, aerial photographs from 2009, provided by Saint Johns River Water Management District, were digitized using ArcGIS software. Live reefs, restored reefs and dead reefs were screen digitized using a reef ‘signature’ in order to estimate the area of each type of reef. The 2009 maps were used as a guide to digitizing the historical aerial photographs (1943, 1951, 1967, 1971, 1984, 1995, 2006). Dead reefs increased both in number and aerial extent during the study period (1943 – 2009), with 2009 having over 10 acres of dead reef coverage. Dead reefs were more likely to be found along major boating channels. Several dead reefs exhibited migration into the mangrove islands located landward of the 1943 footprint, with some dead reefs completely washing up into the shoreline. Restoration of dead reefs added 0.5 acres of live oysters to the Mosquito Lagoon area as of January 2009. Second, I examined how different oyster reef types (natural reef, restored reef, dead reef) reduced wave height. To determine wave height attenuation on each reef type, experiments were conducted in a 9 meter long wave tank using sensors that measured changes in wave height. For each reef type, replicate reefs were created in the wave tank. Shoreline sediment without oysters was used as a control. Using the wave generator, wave heights similar to Mosquito Lagoon boat wakes were created. Restored reefs reduced the incoming wave height by 25% compared to sediment without oysters. iii Lastly, I examined the potential link between oyster reef restoration and recruitment of seagrass fragments. Monthly surveys were performed to quantify the number of seagrass fragments encountering the three oyster reef types: dead reefs, natural reefs and restored reefs. The quantity of seagrass fragments was found to be similar on the three different reef types, but did show a significant trend of seasonality, which corresponds with the growing season of Halodule wrightii. Next, I tested retention of experimentally manipulated seagrass fragments on five natural and five restored reefs. Restored reefs retained seagrass fragments for significantly longer than natural reefs. I also measured seagrass fragment entanglement on each reef type inside the wave tank. I found that seagrass fragments were significantly more likely to become entangled and retained on restored reefs compared to dead and natural reefs. Overall, these metrics are important for determining the success of long-term oyster restoration project in Mosquito Lagoon, Florida. This project has found that oyster restoration is increasing the area of oyster habitat as well as providing important ecosystem services.

The United States Pacific Northwest is well known for its shellfish farming. Historically, commercial harvests were dominated by the native Olympia oyster, Ostrea lurida, but over-exploitation, habitat degradation, and competition and predation by non-native species has drastically depleted their densities and extirpated many local populations. As a result, shellfish aquaculture production has shifted to the introduced Pacific oyster, Crassostrea gigas. An underlying objective of this dissertation is the use of molecular genetics to improve our ability to accurately identifying optimal oyster broodstock for either restoration of Olympia oysters or farming of Pacific oysters. The ecological benefits provided by oysters as well as the Olympia oyster's historical significance, has motivated numerous restoration/supplementation efforts but these efforts are proceeding without a clear understanding of the genetic structure among extant populations, which could be substantial as a consequence of limited dispersal, local adaptation and/or anthropogenic impacts. To facilitate this understanding, we isolated and characterized 19 polymorphic microsatellites and used 8 of these to study the genetic structure of 2,712 individuals collected from 25 remnant Olympia oyster populations between the northern tip of Vancouver Island BC and Elkhorn Slough CA. Gene flow among geographically separated extant Olympia oyster populations is surprisingly limited for a marine invertebrate species whose free-swimming larvae are capable of planktonic dispersal as long as favorable water conditions exist. We found a significant correlation between geographic and genetic distances supporting the premise that coastal populations are isolated by distance. Genetic structure among remnant populations was not limited to broad geographic regions but was also present at sub-regional scales in both Puget Sound WA and San Francisco Bay CA. Until it can be determined whether genetically differentiated O. lurida populations are locally adapted, restoration projects and resource managers should be cautious of random mixing or transplantation of stocks where gene flow is restricted. As we transition from our Olympia oyster population analysis to our Pacific oyster quantitative analysis, we recognize that traditional quantitative trait locus (QTL) mapping strategies use crosses among inbred lines to create segregating populations. Unfortunately, even low levels of inbreeding in the Pacific oyster (Crassostrea gigas) can substantially depress economically important quantitative traits such as yield and survival, potentially complicating subsequent QTL analyses. To circumvent this problem, we constructed an integrated linkage map for Pacific oysters, consisting of 65 microsatellite (18 of which were previously unmapped) and 212 AFLP markers using a full-sib cross between phenotypically differentiated outbred families. We identified 10 linkage groups (LG1-LG10) spanning 710.48 cM, with an average genomic coverage of 91.39% and an average distance between markers of 2.62 cM. Average marker saturation was 27.7 per linkage group, ranging between 19 (LG9) and 36 markers (LG3). Using this map we identified 12 quantitative trait loci (QTLs) and 5 potential QTLs in the F1 outcross population of 236 full-sib Pacific oysters for four growth-related morphometric measures, including individual wet live weight, shell length, shell width and shell depth measured at four post-fertilization time points: plant-out (average age of 140 days), first year interim (average age of 358 days), second year interim (average age of 644 days) and harvest (average age of 950 days). Mapped QTLs and potential QTLs accounted for an average of 11.2% of the total phenotypic variation and ranged between 2.1 and 33.1%. Although QTL or potential QTL were mapped to all Pacific oyster linkage groups with the exception of LG2, LG8 and LG9, three groups (LG4, LG10 and LG5) were associated with three or more QTL or potential QTL. We conclude that alleles accounting for a significant proportion of the total phenotypic variation for morphometric measures that influence harvest yield remain segregating within the broodstock of West Coast Pacific oyster selective breeding programs. / Graduation date: 2012