Introduced species present one of the greatest threats to biodiversity of native species, and knowledge of introduced species ecology is imperative for the development of management plans to ensure conservation of native species populations. We sought to determine the distribution and nesting behavior of an introduced population of red-bellied squirrels (Sciurus aureogaster) on islands of the Florida Keys currently managed as part of Biscayne National Park, and document potential for the species to impact native flora and fauna. Squirrels were difficult to observe in the dense vegetation of the subtropical forest, so we relied on their leaf nests, which were highly visible in the canopy of trees, to determine current presence and distribution on the Park's islands. We found nests throughout the mixed-hardwood forests of Elliott Key and Sands Key, and also documented a single, old nest on Old Rhodes Key, the first ever documentation of the species that far south in the Upper Keys. Nests were located in tall trees with more canopy linkages than random focal trees, and nests were placed in the upper canopy on the north side of the nest tree more often than expected by chance. Squirrels selected West Indies mahogany (Swietenia mahagoni) to place nests more often than available in the forest. Squirrels used areas with greater tree density and canopy cover, but lower recent hurricane damage and fewer woody shrub stems, than areas available at random in the forest. Squirrels built nests only in mixed-hardwood forest. Overall, this introduced species exhibited nest site selection behavior similar to other tree squirrels, and appears capable of continued spread despite the initial site of introduction on an oceanic island. Knowledge obtained from this research is being used by managers and applied to an eradication program to remove this invasive species from Biscayne National Park.

Two experiments were performed to determine the effect of ocean acidification on Montastraea faveolata vertical skeletal growth and lesion healing. The first experiment used three different CO2 concentrations: present day atmospheric pCO2, 380 microatm, and the atmospheric pCO2 expected by the years 2050, 560 microatm, and 2100, 800 microatm. The second experiment used 380 and 560 microatm. In the second experiment where the influence of parent colony was analyzed, M. faveolata fragments from one coral colony had significantly slower skeletal growth rates and less healed lesion area than other colonies. Corals that calcify and regenerate tissue slower may have less resilience to ocean acidification. The experiments demonstrated that the corals in 800 microatm grew significantly slower than corals in 380 or 560 microatm. Increased CO2 concentrations increased M. faveolata skeletal growth rates and healed lesion area until a threshold was reached, 560 microatm, then growth rates and healed lesion area decreased. Less than 1% of the variability in healing rates could be explained by CO2. The Nature Conservancy Resilience Model was used as a framework to identify current management strategies of wider Caribbean MPAs that may increase coral reef resilience to climate change. Seven out of the 8 MPAs had representation, critical areas, connectivity, and effective management as determined by each MPA's management plan. Three management plans had specific climate management strategies. Each management plan had actions to build coral reef resilience, but institutional incapacities and other barriers can decrease the ability to increase reef resilience. Because of the weaknesses of the Resilience Model, revised resilience guidelines were developed with the Florida Keys National Marine Sanctuary (FKNMS) as a case study. The coral lesion experiment results and interviews with FKNMS managers and the FKNMS's Sanctuary Advisory Council helped design the revised resilience guidelines. The revised climate-based coral reef resilience guidelines are to 1) incorporate more no-take zones and hedge the risks against ocean acidification, 2) identify resilient coral reefs and perform more climate change research, 3) reduce local stressors, 4) enhance coral reef recovery, and 5) increase public awareness and education on climate change impacts to coral reefs.

The Along-Track Reef-Imaging System (ATRIS) is a vessel-mounted, digital camera, depth sounder and Global Positioning System (GPS) package that facilitates the rapid capture of underwater images in shallow-water benthic environments. This technology has the potential to collect ecologically significant data, particularly in benthic habitats less than 10 m in depth, with better location referencing and in less time than is required for surveys carried out by Scuba divers. In October 2004, ATRIS was tested coincidently with SCUBA-assisted video along transects on five patch reefs in Biscayne National Park. Images from both data sets were subsampled, viewed, and benthic cover under random points were identified and counted. Digital-still images of reef benthos collected by ATRIS were of higher quality than SCUBA-acquired video imagery, allowing more reliable classification of benthos. “Substrate”, which included areas of hard-ground, sand or rubble, was the most frequently identified benthic category (43%), followed by octocoral (21%), unidentifiable (19%), and macroalgae (12%). Total stony coral cover averaged less than 5%. ATRIS-acquired benthic-cover data were compared with rugosity data derived from the Experimental Advanced Airborne Research Lidar (EAARL), revealing no strong correlations, probably because much of the hard substrate patch reef topography was created by corals that have died in the past few decades. ATRIS, diver-acquired data, and EAARL provide different scales of information, all of which can be valuable tools for assessing and managing coral reefs.

Shallow seagrass ecosystems frequently experience physical disturbance from vessel groundings. Specific restoration methods that modify physical, chemical, and biological aspects of disturbances are used to accelerate recovery. This study evaluated loss and recovery of ecosystem structure in disturbed seagrass meadows through plant and soil properties used as proxies for primary and secondary production, habitat quality, benthic metabolism, remineralization, and nutrient storage and exchange. The efficacy of common seagrass restoration techniques in accelerating recovery was also assessed. Beyond removal of macrophyte biomass, disturbance to seagrass sediments resulted in loss of organic matter and stored nutrients, and altered microbial and infaunal communities. Evidence of the effectiveness of restoration actions was variable. Fill placement prevented additional erosion, but the resulting sediment matrix had different physical properties, low organic matter content and nutrient pools, reduced benthic metabolism, and less primary and secondary production relative to the undisturbed ecosystem. Fertilization was effective in increasing nitrogen and phosphorus availability in the sediments, but concurrent enhancement of seagrass production was not detected. Seagrass herbivores removed substantial seagrass biomass via direct grazing, suggesting that leaf loss to seagrass herbivores is a spatially variable but critically important determinant of seagrass transplanting success. Convergence of plant and sediment response variables with levels in undisturbed seagrass meadows was not detected via natural recovery of disturbed sites, or through filling and fertilizing restoration sites. However, several indicators of ecosystem development related to primary production and nutrient accumulation suggest that early stages of ecosystem development have begun at these sites. This research suggests that vessel grounding disturbances in seagrass ecosystems create more complex and persistent resource losses than previously understood by resource managers. While the mechanics of implementing common seagrass restoration actions have been successfully developed by the restoration community, expectations of consistent or rapid recovery trajectories following restoration remain elusive.