Atlantic menhaden is an ecologically and economically important species along the U.S. east coast. As a filter-feeder and key prey fish, it provides a critical link between primary production, phytoplankton, and larger piscivorous predators, such as striped bass, bluefish, and weakfish. The species is also the target of one of the largest commercial fisheries in the country. Menhaden are assessed as a single, coastwide stock, and recent assessments indicate that it is not overfished. However, there is very limited population genetics data to support the assumption of a single stock. Additionally, the recent consolidation of the fishery and localization of harvests within and around Chesapeake Bay have raised concerns over the possibility of ‘localized depletion’ of the species in this area. This study used rapidly evolving molecular markers to examine Atlantic menhaden stock structure along the U.S. Atlantic coast, specifically to determine the potential for the loss of unique genetic variation resulting from concentrated fishing pressure in and around Chesapeake Bay. Samples were collected from up to three cohorts of Atlantic menhaden (2005, 2006, and 2007 year classes), at four geographic locations along the U.S. Atlantic coast (New England, mid-Atlantic, Chesapeake Bay, and U.S. south Atlantic) in 2006 and 2007. Two independent classes of molecular markers were surveyed: the mitochondrial cytochrome c oxidase subunit I (COI) gene region and seven nuclear microsatellite loci. All markers revealed considerable genetic variation. Hierarchical analyses of molecular variance (AMOVA) and examination of pairwise ΦST, FST, and RST estimates indicate a homogeneous distribution of genetic variation within Atlantic menhaden (all region AMOVAs: ΦST = -0.00873, FST = 0.00515 (FST method), FST = -0.00666 (RST method); p>0.05). The genetic connectivity between the regional collections suggests that concentrated fishing pressure in and around Chesapeake Bay will not result in a significant loss of unique genetic variation.

The maintenance of a population within the geographic range is influenced by the physical and environmental conditions under which breeding occurs. It is hypothesized that environmental conditions under which egg capsules are successfully hatched will influence the range of potential habitat of the invasive veined rapa whelk, Rapana venosa, and the native Atlantic oyster drill, Urosalpinx cinerea, in the Chesapeake Bay. This study examines the environmental conditions of temperature, salinity, and the time of deposition of egg capsules within the reproductive period (here quantified as cumulative number of day degrees at egg capsule deposition). The range of R. venosa and U. cinerea habitat in the Chesapeake Bay, in relation to environmental conditions, is important given the potential impact of both species on native shellfish stocks. Egg capsule hatching success and egg capsule incubation time for R. venosa and U. cinerea were examined at temperatures (18oC, 22oC, 26oC, 30oC, and ambient York River water temperature) and salinities (7 ppt, 14 ppt, 21 ppt, 28 ppt, and ambient York River salinity) reflective of the Chesapeake Bay during egg capsule deposition. Salinity is the greatest factor influencing R. venosa and U. cinerea egg capsule hatching success. Increasing salinities increase the percentage of R. venosa and U. cinerea egg capsules to hatch as well as the percentage of U. cinerea embryos alive at hatch. For R. venosa, the percentage of egg capsules to hatch is greatest at 21 ppt. For U. cinerea the percentage of egg capsules to hatch and the percentage of embryos alive at hatch are greatest at salinities of 21 ppt or 28 ppt. R. venosa and U. cinerea egg capsules do not hatch at 7 ppt in the temperature range examined. Temperature within the range examined was not found to be an important factor influencing egg capsule hatching success for either species. However, temperature was an important factor influencing the rate at which the egg capsule hatching process occurs. The percentage of R. venosa egg capsules to hatch increases and the percentage of U. cinerea alive at hatch decreases along the egg capsule deposition time series. For R. venosa, an increase in the percentage of egg capsules to hatch occurs if egg capsules are deposited later in the time series. For U. cinerea the percentage of egg capsules to hatch is not affected by position in the egg capsule deposition time series, but the percentage of embryos alive at hatch decreases along the time series examined. The temperatures and salinities for optimal R. venosa egg capsule hatching range from 18oC to 30oC and from 11 ppt to 28 ppt and vary based on the timing of egg capsule deposition. The temperatures and salinities for optimal U. cinerea egg capsule hatching range from 18oC to 30oC and from 20 ppt to 28 ppt and do not vary based on the timing of egg capsule deposition. Optimal egg capsule hatching for R. venosa and U. cinerea occur at different temperature-salinity combinations throughout the majority of the egg capsule deposition time series.

Natural coastal habitats throughout Chesapeake Bay are increasingly threatened with shoreline modification due to population growth and rising rates of development. The replacement of these natural coastlines with hardened structures such as seawalls (bulkheads) and stone revetments (riprap) not only compromises vegetation at the land-water interface, but also can influence several elements of local aquatic food webs. Effects of these alterations have been well-studied with respect to fish assemblages and intertidal communities, particularly in conjunction with larger-scale watershed development, and recently, interest has shifted toward investigation of the effects of shoreline development on subtidal benthic infaunal communities.This study evaluated the direct, local impacts of bulkhead and riprap compared to natural marsh shorelines, as well as the effects of sediment characteristics, predator abundance, and system-specific physical features on benthic infauna in the Patuxent River, Chesapeake Bay. Forty-five sites were divided among three shoreline types and distributed across three main river zones. At each site, a benthic infaunal suction sample (3-mm mesh), push-core sample (500-μm mesh), sediment samples, water-quality measurements, and trawls for predators were taken. Samples were sorted to determine density, diversity, and biomass of infaunal organisms. Data were assessed using an Information-Theoretic approach (AIC analysis) to determine the most influential variables, of those measured, on the infaunal community for two benthic data sets: 3-mm-suctions and 500-μm-cores. Results from these analyses on 3-mm samples suggested that shoreline type was the best predictor of diversity, while wave energy, sediment chlorophyll concentration, sediment type, and predator abundance best predicted density and biomass. Benthic responses within the 500-μm dataset were not strongly affected by shoreline type. Rather, responses were best predicted by sediment chlorophyll, wave energy, sediment type, predator abundance, and sediment organic carbon (TOC) content.Results indicate that, compared to other Bay tributaries, the Patuxent River is a relatively degraded system. The small range in long-term responses of Patuxent infauna from previous work provides a possible explanation as to why I was unable to see significant differences in infaunal response among shoreline types in the current study (i.e., there was little scope for change by shoreline in the system as a whole). However, I suggest that natural marsh habitats are healthier subsystems of the Patuxent River, due to the greater variety of infaunal feeding guilds and higher infaunal biomass observed at these compared to hardened sites. Higher predator abundance was associated with higher infaunal biomass at natural marsh sites in both size fractions, suggesting the bottom-up control of higher-trophic-level species in this system, as predators seek out suitable prey items. Given these observations, and the fact that influential variables such as wave energy, sediment nutrient and chlorophyll content, predator abundance, and sediment type may vary according to shoreline type, the replacement of natural shoreline with hardened structures will lead to complex changes in subtidal benthic communities in Chesapeake Bay tributaries and should be minimized to maintain qualities of the natural system.

With the recent growth of the hard clam aquaculture industry, sites of intensive aquaculture have emerged as large-scale agro-ecosystems where the success of aquaculture production is dynamically linked to ecosystem function. Large scale clam aquaculture operations are associated with a range of potential positive and negative feedbacks related to nutrient dynamics, water and sediment quality, proliferation of macroalgae, and carrying capacity. Quantitative modeling tools are needed to support system-level planning related to site selection, scale of operations, production capacity and ecosystem function. The purpose of this study was to develop a model for Cherrystone Inlet, VA, where one-third (1.9 km2) of the sub-tidal bottom area is held as 37 separate, private shellfish leases with an estimated 100-150 million cultured clams. A reduced complexity estuarine ecosystem model was coupled with a hard clam energetics and growth model and a watershed loading model. The linked models facilitate ecosystem-based management and enable regional spatial planning in a full ecosystem context, through coupled simulations of aquaculture activities, land use changes, nutrient loading, climate change, and estuarine response. Modeled output for hard clam growth and water column chlorophyll-o, dissolved oxygen, and dissolved inorganic nitrogen and phosphorous reproduced in situ data. Simulations with increasing clam numbers up to 500 million resulted in diminishing returns in terms of reduced growth rates, increased time to harvestable size, and reduced harvestable biomass, confirming observations by Cherrystone farmers of reduced clam growth rates above 200 million cultured clams. Modeled hard clam production capacity decreased in the absence of benthic microalgal resuspension (6%) and without the input of external production from the Chesapeake Bay (41%), and increased in simulations with increased water column chlorophyll-o (11%) and the removal of predator exclusion nets (13%). Simulations to optimize siting indicated that the highest hard clam growth rates occurred up-estuary. Model simulations with changes in land use and climate indicated that clam growth is most sensitive to increasing temperature, with rates decreasing by 37% when temperatures were increased by 5°C, while changes in land use, sea level rise and salinity did not result in large changes in hard clam production. At the system scale hard clam aquaculture was predicted to account for 14% of total nitrogen inputs to the water column between sediment recycling of clam feces (13%) and direct clam excretion (1%). The Cherrystone ecosystem model fills a critical gap on the Eastern Shore of Virginia and in similar coastal systems, providing resource managers with the most current available science in a decision-support framework to promote effective regional spatial planning and sustainability of hard clam operations and the surrounding coastal ecosystems.

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