A Model Framework for Predicting Reef Fish Distributions Across the Seascape Using GIS Topographic Metrics and Benthic Habitat Associations

Increased topographic complexity has been linked to increased species diversity and/or abundance in many ecological communities, including coral reefs. Several topographic metrics can be measured remotely in GIS using high resolution bathymetry, including elevation, surface rugosity, and seafloor volume within specified areas. Statistical relationships between these data and organismal distributions within mapped habitats can be used to make predictions across the entire bathymetric dataset. In this study a model framework is presented which utilizes statistically significant relationships between reef fish abundance and species richness and GIS topographic complexity measurements for samples within similar benthic habitats to create GIS-based prediction maps of abundance and species richness for the entire seascape. Reef fish associations with GIS topographic metrics were significant and varied between habitats. Model evaluation showed that patterns in the measured data emerged in the prediction data. The results allow for viewing of data trends throughout the seascape, quantification of assemblages in non-sampled areas, and statistical comparisons of areas within the region to support and guide management related decisions. This model framework can be adapted to other communities (e.g. benthic organisms) and/or parameters (e.g. diversity) that relate to topographic complexity

Characterize the Condition of Previously Known and Newly Identified Large Dense Acropora cervicornis Patches in Southeast Florida

Historically, Acropora spp. are the major reef building corals seen throughout the Caribbean and parts of the Western Atlantic that can grow relatively rapidly in dominant mono-specific stands. Their rapid growth and fragmentation allows them to out compete other benthic organisms and form the major framework for entire reef zones. They are the most abundant and important species for reef accretion. Their branching morphologies provide important habitat for many other reef species and no other Caribbean coral species fills these ecosystem functions. Acroporids were once the dominant reef builder in the Caribbean and provided the majority of live coral cover, but have had extensive population declines. Despite the recent declines, dense patches of Acropora have been reported in several areas throughout the Caribbean. Perhaps the most surprising of these locations is southeast Florida (SE). SE Florida reefs are a higher latitude system that transitions from a subtropical to temperate climate and is in close proximity to about 6 million people. These are some of, if not, the largest dense patches of A. cervicornis in the continental United States and offer a unique opportunity to evaluate population demographic structure and condition in a growth form (dense patches) which was once dominant but now rare. In the 1990’s seven large high-cover Acropora patches were identified and characterized at 6 meters depth or less in Broward County. In 2014, an additional twenty-eight new patches were found covering an area of approximately 110,000 m². The patch delineations were not ideal due to mapping resolution and that they need to be mapped with higher precision. The threatened ESA status requires a plan to facilitate the recovery of the species back to historical levels. Thus, understanding the current population extents and condition is necessary to establish a reference baseline condition. These data were needed to determine if management strategies are necessary, which to employ, and reasonable success criteria for management actions. Hence, this study was conducted to provide these data. Mean total cover between all patches was 56.5% ± 14.9. Live and dead cover were similar. Mean rubble was 12.5% (± 9.2). Mean disease cover was low (0.8% ± 0.7). Mean fireworm predation density was 1.4 m-² ± 1.09. On average, there was one damselfish garden every 5.9 square meters (0.17 m-² ± 0.14). And the mean density of disease occurrences was 0.91 m-² ± 0.84. Multivariate analyses of percent live, dead, rubble, and disease Acropora cervicornis at the densest portion of each patch indicated three main categories: Good (2 sites) – high amounts of live tissue; Moderate (20 sites) – similar amounts of live tissue and standing dead framework; Poor (13 sites) – high amounts of dead framework and rubble. The Poor group had an average of 26% cover of dead framework, 21% rubble, and 10% live cover. The Moderate group had an average of 20% cover of dead framework, 8% rubble, and 26% live cover. The Good group had an average of 13% cover of dead framework, 4% rubble, and 62% live cover. Twenty-three perimeters were mapped around 35 dense patches. The imagery indicated that the dense patches are still distinctly different, however, the in situ surveys indicate that several dense patches are spread out and connected to adjacent patches. The diver GPS perimeter mapping yielded a total patch area of approximately 826,609 m² (204 acres). This study found that six percent of the dense patches are in Good condition, fifty-seven percent in Moderate condition, and thirty-seven percent in Poor condition. Without having previous data on most of the patches, not much can be said about their condition trajectories or what caused their declines into the Moderate and Poor states. Little disease was recorded during this study indicating that disease was not a big factor of present patch condition. However, the large amounts of dead framework measured in our study indicate a relatively recent decline in condition. Due to the lack of frequent monitoring, it is unknown how much past disease events contributed to the amount of the present dead framework and rubble cover. Although not significant, Gillliam and Larson (2014) previously found that Rapid Tissue Loss (RTL) disease coincided with decreases in live cover, especially after hurricane Sandy and tropical storm Isaac. Presumably, this could have affected the condition of many of the SE FL dense patches. The cause of increased RTL after these storms is unknown and should be established to mitigate for future impacts to A. cervicornis live cover. Glimpses at patch condition trajectories were possible for a few sites based on historical data from a few longer-term studies. Vargas-Angel et al. (2003) patch categorization contained three groups: A, B, and C. Group A, their mostly-dead site (Coral Ridge), which has since disappeared, was not evident in recent aerial photographs. The exact timing of its disappearance is unknown, but it was before 2007 and is thought to have been due to a strong storm event; perhaps Hurricane Wilma. Group B, defined by relatively high coral cover and greatest A. cervicornis density (Commercial I, Commercial II, and Dave), have persisted through time. The Dave patch was renamed as FTL6 in the Broward County annual reef monitoring and BCA in the Southeast Coral Reef Evaluation and Monitoring Program. This patch has been studied extensively. Group C patches (Oakland I, Cervicornis II, and Oakland II) have increased in A. cervicornis. The Oakland I patch was renamed Scooter and has been monitored at least semi-annually since 2007. SE FL is presently in a hurricane drought. The last strong storm to hit the direct area was hurricane Wilma in 2005. Hurricanes Sandy and Matthew came close along the eastern seaboard but they were mostly rain events for south Florida. Increases in live cover have been measured over periods in between storms that may be related to low storm activity (Gilliam and Larson 2014). This needs more investigation as the correlation is not obvious and it is unknown if this is due to lower RTL prevalence or reduced physical impacts. Events like hurricane Sandy and tropical storm Isaac may have catalyzed RTL outbreaks (Gilliam and Larson, 2014), but were not strong enough to move large amounts of framework. A direct hit from a hurricane could spread the patches of mostly dead framework off the reefs leaving little to no live fragments behind to maintain dense patch status similar to the Coral Ridge patch. This scenario could drastically affect the number of dense patches, their condition, and extents. The patch mapping efforts, funded by NSU, show that spreading continues at both BCA and Scooter however, the densest areas in the patches still exist in the original locations. These patches are in Poor condition. In terms of the percent live cover to total Acropora measured in each patch, Scooter ranked 26 out of 35 sites and BCA ranked 34 out of 35. We estimated live cover at 9.7% which is similar to other recent results. After revisiting BCA and mapping the perimeter during this study, it is clear that live cover has decreased and not just moved away. Scooter was a similar story to BCA in that live cover had decreased through time at the densest areas in the patch to about 15% and did not significantly change from 2011 to 2013 (Gilliam and Larson, 2014). Changes in live cover occurred between 2008 and 2011 where the majority of live cover shifted away from the densest framework areas. After visiting Scooter it was obvious the densest portions were degraded, however because the site is so large, shifting of live cover to a new area was not obvious or investigated. A visual comparison of 2013 aerial photography and 2017 ESRI satellite imagery do not show obvious differences, but the ESRI imagery cannot be statistically analyzed. The perimeter surveys showed that most of the patches are much larger than originally visualized in the 2013 aerial imagery. It appears they have also spread across the reef-scape through time. The densest areas are still the areas with the most concentrated colonies, but many of the perimeters span between these areas. This study elucidated new data on the extent and condition of the dense patches of Acropora cervicornis in SE FL. Approximately 20% of the dense patches were previously known before Walker and Klug (2014) and only two were previously mapped. This study statistically analyzed dense patch conditions and binned them into three groups based on the amount of live, dead, disease, and rubble cover. The GPS diver mapping identified the spreading of dense patches and increased total area of dense A. cervicornis to 826,609 m² (204 acres), an increase of over 500% from previous estimates. This new information highlights more critical gaps in our knowledge of regional A. cervicornis distributions and population distribution, demographics, and status. Below are a series of recommendations to help fill those knowledge gaps: Conduct A. cervicornis mapping and condition assessments more frequently to determine cause of live tissue declines. Establish a cause of increased RTL after storm events to mitigate for future impacts to live cover. Analyze historical imagery to determine the timing of dense A. cervicornis patch inception and persistence over time. Collect regular, periodic regional standardized imagery to elucidate the dynamics of dense patches and document the current extent of nearshore resources. Investigate the genetic diversity of the dense A. cervicornis patches to determine if they are genetically similar to each other and other local populations. Monitor fecundity and reproduction to identify if environmental factors and patch conditions are related to reproductive success

Southeast Florida Reef-Wide Post-Irma Coral Disease Surveys

Florida’s coral reefs are currently experiencing a multi-year outbreak of coral disease that have resulted in the mortality of millions of corals across southeast Florida, Biscayne National Park, and the Upper and Middle Florida Keys. In early September 2017, Hurricane Irma impacted the entire FRT. The purpose of this project was to conduct field surveys to identify the current state of the coral reefs in southeast Florida and coordinate with other concomitant reef tract efforts to improve the regional understanding of the extent of the disease outbreak and identify recent hurricane injury to direct future restoration. Through a broader partner network, 62 sites from Key Biscayne to St. Lucie Reef were targeted for survey. Twenty-nine sites were chosen based on previous data that indicated high coral values of richness, density, and/or cover at those locations. Thirty-three sites were chosen with FDEP reef managers where there were previous data gaps. A new protocol was developed, which was a modification of the Florida Reef Resilience Program (FRRP) Disturbance Response Monitoring (DRM) methodology. This included collecting additional disease and injury metrics in transects and by rover diver to prioritize sites for triage and restoration activities. The analyses showed that hurricane impacts on corals were quite low where 82.3% (51/62) of the sites were listed as Tier 3 (minimal impact/triage not needed). There were nine sites listed with at least some Tier 2 damage (moderate impact/secondary priority if resources allow). Site 33 was listed as 100% Tier 2 and Site 30 was 100% Tier 1 (triage recommended). Site 30 had some impressive impacts including large (2 - 5 m) slabs of fractured hardbottom lifted and thrown several meters eastward atop other hardbottom affecting a ~ 2 m Orbicella faveolata colony that was mostly covered leaving only the very top exposed. One day of triage was conducted at a dense Acropora cervicornis patch to stabilize many coral fragments and collect loose debris (mostly gorgonians). Lack of capacity and weather deterred further triage attempts for several months. It was eventually decided that triage efforts were not a priority for SE Florida because of the ongoing disease. Coral disease prevalence was high. The rover diver surveys found 11.4% total disease prevalence across all sites (243/2130) infecting 43.3% of the species found, and prevalence at the southern sites was higher. Mean density and richness at sites with previous relatively high values were considerably lower than their historic values with a 57.2% and 42.2% decrease respectively, indicating profound changes in the coral populations. Perhaps the most striking result was the low density of Eusmilia fastigiata, Meandrina meandrites, Dichocoenia stokesi, Colpophyllia natans, Pseudodiploria strigosa, Diploria labyrinthiformis, and Orbicella annularis. We found 36 individuals of all these species combined out of 1,165 colonies (3.1%). A comparison of the percentages of each species to the total in the southern sites to those of the 2004 annual monitoring data in Broward County showed drastic differences in the populations that likely go beyond any bias in survey differences. These data support the idea that the Florida Reef Tract is becoming more homogenous and dominated by eurytopic, generalist species that can tolerate a wider range of environmental conditions. However, this disease event contradicts the notion that the present assemblages are stable because they have “withstood a number of recent perturbations, including thermal stress and disease”. After moving through the more vulnerable species, the disease is now affecting hardier species thought to be more resistant to stress like Montastrea cavernosa and Siderastrea siderea. It is important that actions are taken to curtail this disease quickly so that the remaining population can stabilize and recovery and restoration efforts can begin. There should be continued focus on the remaining corals because they are apparently resistant to the disease and perhaps better acclimated to the stressful conditions over the past several years

Accuracy Assessment and Monitoring for NOAA Florida Keys Mapping AA ROI-1 (Hawk Channel Near American Shoal)

This report describes the methodologies, analyses, and results for an independent accuracy assessment of a thematic benthic habitat map produced by NOAA for the Florida Keys. It is an analysis of four regional accuracy assessments. Over the course of the Florida Keys mapping project, NOAA amended part of the classification scheme. The original scheme for mapping benthic cover was a tiered approach where certain benthic cover categories were given priority over others (e.g. coral was most important). Recently, this was modified to a dominant benthic cover scheme where the habitat is characterized by the single most dominant cover type and all habitats are characterized for percent cover of coral. The data and data analyses from Walker and Foster (2009 and 2010) were used to evaluate the accuracy of the reclassified map for Regions Of Interest (ROI) 1 and 2. New data were collected for ROIs 3 and 4 as part of this report. All four regions were combined and analyzed to determine total map accuracy. Data were collected in January 2009 at ROI 1 (eastern Lower Keys), in June 2009 at ROI 2 (western Lower Keys), in September 2012 and February, March, and May 2013 at ROI 3 (back country), and in May 2013 at ROI 4 (Key Largo) (Figure 1). A total of 2029 sampling stations were visited, of which 1969 were used in the accuracy assessment. The sites were selected using a stratified random sampling protocol that equally distributed sampling points amongst the detailed structure categories. Most sites were sampled by deploying a weighted drop camera with the vessel drifting in idle and recording 30-120 seconds of dGPS-referenced video. The shallowest sites were sampled by snorkel, waverunner, or kayak, using a hand-held dGPS for navigation and a housed camera to record video. Each sampling station was given a Detailed Structure, Biological, and Coral Cover assignment in the field. These field classifications were reevaluated post-survey during a systematic review of video and photographic data, designed to ensure consistency within classifications. The efficacy of the benthic habitat map was assessed by a number of classification metrics derived from error matrices of the Major and Detailed levels of Geomorphological Structure and Biological Cover. The overall, producer’s, and user’s accuracies were computed directly from the error matrices. The analyses of the combined ROIs 1 – 4 gave an overall accuracy of the benthic habitat map of 90.4% and 84.6% at the Major and Detailed levels of Structure respectively, and 85.1% and 76.5% at the Major and Detailed levels of cover. The known map proportions, i.e. relative areas of mapped classes, were used to remove the bias introduced to the producer’s and user’s accuracies by differential sampling intensity (points per unit area). The overall accuracy at the Major and Detailed levels of Structure changed to 92.3% and 85.9%. The overall accuracy at the Major and Detailed levels of cover changed to 84.3% and 79%. The overall accuracies were also adjusted to the number of map categories using the Tau coefficient. Tau is a measure of the improvement of the classification scheme over a random assignment of polygons to categories, bounded between -1 (0% overall accuracy for 2 map categories) and 1 (100% accuracy for any number of categories). The Tau coefficients were 0.807 ± 0.026 and 0.829 ± 0.018 at the Major and Detailed levels of Structure, and 0.814 ± 0.020 and 0.745 ± 0.020 at the Major and Detailed levels of cover. Percent coral cover was classified for every polygon, thus coral cover was evaluated separately. Total accuracy for Coral in all habitats for all ROIs was 89.6% and 93.4% after adjusting for map marginal proportions. This calculation, however, was not realistic because it evaluated coral cover in non-coral habitat which inflated the number of correct sites. To account for this, coral cover was also evaluated at only those sites found to be Coral Reef and Hardbottom habitats. Total map accuracy for mapping coral cover on Coral Reef and Hardbottom habitats was 79.8%, and 82.7% after adjusting for habitat proportions. The accuracy varied greatly between the two coral categories present. User’s and Producer’s accuracies for Coral 0% - \u3c10% were near or equal to 90%. Conversely, Coral 10% - \u3c50% user’s and producer’s accuracies were 54.3% and 66.5% respectively. Adjusted producer’s accuracy was reduced to 55.2%. The adjustment for map proportions was very relevant here due to the large disparity of area between the two classes. The map contained 658.5 km² of Coral 0% - \u3c10% and 39.8 km² of Coral 10% -\u3c50%. Further 583 of AA points on Coral Reef and Hardbottom habitat were in Coral 0% - \u3c10% and 219 were in Coral 10% - \u3c50%. Interestingly, there were no mapped polygons of Coral 50% - \u3c90% and 90% - 100%. There was confusion between coral classes where 88 locations mapped as Coral 10% - \u3c50% were actually Coral 0% - \u3c10% and 60 locations mapped as Coral 0% - \u3c10% were found to be Coral 10% - \u3c50%. Confusion between 11 locations that were mapped as Coral 10% - \u3c50% were actually Coral 50% - \u3c90% and 1 location mapped as Coral 10% - \u3c50% was found to be Coral 90% - 100%. These sites were all located in the patch reefs of Hawk Channel. It is unknown if these sites met the minimum mapping unit criteria, but the field data indicated high coral cover at these locations. The relatively low adjusted producer’s accuracy for Coral 10% - \u3c50% (55.2%) suggests that not all higher coral cover areas were captured in the map. Furthermore the relatively low user’s accuracy (54.3%) indicates that the areas of Coral 10% - \u3c50% portrayed in the map are highly variable. Combining all the results into a total map accuracy assessment gave a sense of how the overall map portrays the seascape. However, it should be noted that large gaps in map coverage exist, especially between Marathon and Key Largo, a 137 km stretch. The results given in the appendices are more representative of their specific regions. ROIs 1 and 2 covered most of the lower Keys and their results are a good representation of map accuracy for that region. ROI 3 covered the Backcountry which had higher accuracies, presumably due to a reduced diversity of habitats and lack of coral cover. ROI 4 is a good representation of the upper Keys map accuracy. It is difficult to know which assessment best represents the middle Keys. The landscape is more similar to the upper Keys, but Hawk Channel becomes deeper and more turbid

Southeast Florida Shallow-Water Habitat Mapping & Coral Reef Community Characterization

Baseline mapping and quantitative assessment data are required prior to future permitted or un-permitted impacts in order to determine the pre-existing state of the benthic resources; therefore, it is imperative that these data be collected on the ecologically sensitive and economically valuable shallow-water coral reef habitats in southeast Florida. In southeast Florida, the nearshore reef habitats are most vulnerable to coastal construction activities and other anthropogenic impacts, therefore these habitats were the focus for this study. The study goals were to provide a spatially appropriate map of increased resolution and a regional quantitative characterization of nearshore benthic resources to evaluate differences in benthic communities between habitats and with latitude for the southeast Florida region of the Florida Reef Tract. This study is a snapshot habitat characterization providing the current status of shallow-water coral reef community composition. Additionally, these data can be used to reduce un-permitted impacts by informing marine zoning efforts and aid in the creation of new no-anchor zones. Detailed 1ft resolution overlapping aerial photographs were collected for the Nearshore Ridge Complex (NRC) and Inner Reef from Key Biscayne to Hillsboro Inlet, 68.5km of coastline by PhotoScience, Inc. on March 8, 2013. The imagery and recent bathymetry were visually interpreted into benthic habitat maps. Quantitative groundtruthing of 265 targeted and randomized sites was conducted between April and June 2014. Five 1km wide cross-shelf corridors were placed as evenly as possible across the mapped space while maintaining consistent habitat types and amounts between corridors and avoiding any major anthropogenic influences like shipping channels and proximity to inlets and outfalls. Survey site locations were stratified across three main habitats within each corridor: Colonized Pavement-Shallow, Ridge-Shallow, and Linear Reef-Inner. Percent cover data at each site was collected. Additionally, species, colony size (length, width, height), percent mortality, condition (pale or bleached), and presence of disease was recorded for stony corals. Gorgonians were categorized by morphology (rod, plume, fan) and counted in four size classes (4-10, 11-25, 26-50, and \u3e50cm). Xestospongia muta and Cliona spp. were also counted. Then an accuracy assessment was performed where drop camera video with GPS data were collected at 494 locations randomly stratified across all habitat types. The overall accuracy was 97.9% at the Major Habitat level. Of the 172.73km² seafloor mapped, the polygon totals indicated 41.34% was Sand, 47.07% was Coral Reef and Colonized Pavement, 9.35% was Seagrass, and 2.25% was Other Delineations. These totals are estimates due to some habitats having a large mix of sand within. Three habitat types dominated the mapped hardbottom area. The largest was Colonized Pavement (38.36km²), followed by Ridge-Shallow (25.52km²), and Linear Reef-Inner (14.99km²). These comprised 97% of the hardbottom habitats. Seagrass accounted for 9.35% of the map and was solely contained south of Government Cut. Sand comprised 41.34% of the map and Other Delineations accounted for 2.25%. The clear, high-resolution images enabled the delineation of thirty-five dense Acropora cervicornis patches. Some of these corresponded to known locations of dense patches. These are the largest dense patches in the continental United States. Using aerial photography delineations area estimates, the seven patches near the known existing locations totaled approximately 46,000m² whereas the 28 newly confirmed areas exceed 110,000m². Dense Acropora cervicornis comprised 1% of the mapped hardbottom habitats. Significant differences in percent benthic cover between habitats occurred in all corridors, however some comparisons were stronger than others. Corridor 1 exhibited clear differences between the colonized pavement and inner reef sites due to the high percentages of seagrass on the colonized pavement that did not occur on the Inner Reef sites (nor any other habitat in the region). Corridor 2 showed much weaker differences between habitat types, however the colonized pavement sites were significantly distinct from the inner reef and ridge sites due to the comparatively high percentage of sand on the colonized pavement versus the inner reef and ridge. Corridor 3 ridge was significantly distinct from the colonized pavement and inner reef sites mostly due to lower percentage of Palythoa spp. on the ridge. Corridor 4 inner reef sites were significantly different from the others driven by much higher percentage of macroalgae and higher Palythoa spp. Corridor 5 exhibited significant differences between all habitat types. Inner reef sites had higher percentages of Palythoa spp., gorgonians, and sponges than any other habitat. Colonized pavement sites had the lowest percentages of gorgonians and Palythoa spp. while having the highest percentages of sand. Comparisons of benthic cover percentages between all sites in a given habitat type were conducted to evaluate latitudinal community differences. Among colonized pavement sites, Corridor 1 was significantly different from all other corridors due to the presence of seagrass which only occurred in Corridor 1 colonized pavement. Corridor 5 was also significantly distinct from all other corridors due to a low percentage of gorgonians, stony corals, and Palythoa spp. with a high percentage of turf algae. The ridge sites comparisons showed distinct clustering of corridors 2, 3, and 5 in the MDS indicating that there are latitudinal differences in benthic cover in the ridge habitat. The main dissimilarity contributors in corridor 2 were lower percentages of palythoa spp. and macroalgae than corridors 3 and 5 and higher percentages of gorgonians and stony corals than corridor 5. Corridor 3 had higher percentages of macroalgae, stony corals, and gorgonians than corridor 5. The inner reef sites also exhibited latitudinal differences in benthic cover. Corridors 1 and 5 separated out from the other corridors and each other. The main cover classes driving the clustering of corridor 1 sites were high percentages of gorgonians and Palythoa spp, while the main contributor to the corridor 4 cluster was high macroalgae percentages in that corridor. A total of 4,568 stony coral colonies were identified, counted, and measured. Twenty-two species were found, but Porites astreoides (29.7%), Siderastrea siderea (17.5%), and Acropora cervicornis (10.3%) comprised 57.5% of the total number of stony corals measured in this study. The largest coral measured in the study was a Siderastrea siderea located in corridor 4 which measured 225 cm long, 200 cm wide, 140 cm tall and an estimated 4.1 m² of live tissue. Stony coral density pooled for the entire surveyed area of 4,200m² was 1.09 corals/m². Mean coral density was lowest in the colonized pavement sites and highest in the inner reef sites, however this also varied by corridor. The colonized pavement coral density in Corridors 1 and 5 was lowest and highest in Corridors 3 and 4. Coral density on ridge habitat had a similar pattern to colonized pavement with corridor 3 having the highest density. Conversely coral density on the inner reef was highest in corridor 1 and corridor 4. Acropora cervicornis was found in higher densities than S. siderea on the colonized pavement but it only occurred in corridors 3 and 4. It was also found in higher density on ridge habitat except for corridor 5. Of the 471 A. cervicornis colonies counted, only 5.3% occurred on the inner reef. Two hundred and thirty-five (49.9%) were found in the colonized pavement and 211 (44.8%) at the ridge sites. The mean number of coral species (richness) varied by corridor and habitat. Colonized pavement sites had the lowest richness and it was highest on inner reef. Mean richness also varied by corridor within habitats. Among the colonized pavement sites, corridor 3 and corridor 4 had the highest mean richness and corridor 5 the lowest. Similarly, among the ridge site, mean coral richness was highest in corridor 3 and lowest in corridor 5. Mean richness among inner reef sites were not very different however corridor 1 was significantly higher than corridor 3. A total of 30,076 gorgonians were counted, classified by morpho-type (Fan, Plume, Rod), and binned into size classes. Rods were the most abundant comprising almost 72% of the total number counted and plumes were second-most comprising 24% of the total. This varied by corridor and habitat. With all size classes combined, fans were lowest on the colonized pavement and highest on the ridge. Plumes were higher on the inner reef than the colonized pavement and ridge. Conversely rods were lower on the inner reef than the colonized pavement and ridge. Gorgonians also varied within habitat types by corridor. In colonized pavement, fans were highest in corridors 3 and 4 whereas plumes were more abundant in the southern corridors. Rods were dominantly abundant throughout the colonized pavement except for corridor 5 where they were conspicuously absent. In the ridge habitat, fans varied among corridors without a clear latitudinal pattern. Plumes were more abundant in the southern corridors, while rods were dominantly abundant throughout. The inner reef habitats generally had a higher abundance of plumes and a more even ratio of rod and plume abundance throughout all corridors. Plumes were the most abundant type in corridor 1, but were also high in corridors 3 and 5. Xestospongia muta colonies were predominantly found at the inner reef sites. Of the 262 total colonies counted, 87.7% were at inner reef sites. Densities were lower than gorgonians and stony corals throughout the study. Mean X. muta abundance varied between corridors. In colonized pavement and ridge habitats, X. muta predominantly occurred on corridor 4 however mean abundance was very low. At the inner reef sites, X. muta was much lower in corridor 1 than all other corridors, which did not significantly vary. This study elucidated new data on the extent of the Endangered Species Act threatened coral species, Acropora cervicornis. Only approximately 30% of the discovered dense patches were identified as previously known and the total regional area of A. cervicornisdense patches is now estimated at 156,000 m². The condition of the coral in these patches cannot be surmised from the images. Additionally, the polygons depicted in the habitat map are likely under-representative of the shape and sizes of these patches due to their fuzzy boundaries. A detailed study to map their boundaries and characterize their condition is needed to properly inventory these patches and their condition. Furthermore, the only way to fully understand if the net amount is increasing is to investigate it on a regional level. Previous imagery must be identified and used to determine the timing of when these patches came into existence. Unfortunately no consistent data sets have been identified that can be used for this purpose at this time. A compilation of local imagery has been helpful in some cases. It is recommended that a regional set of imagery be repeatedly collected in the future to elucidate the dynamics of dense patches of A. cervicornis and document the current extent of nearshore resources. This is especially important after large storm events. This study has expanded the present knowledge on the amount, location, and species type of ecologically important large coral colonies. Although smaller than the minimum mapping unit for this study (and thus not in this study’s scope and funded separately), 187 blips in the LIDAR associated with dark specs in the imagery were identified and a portion investigated. Of the 53 that were visited, 47 were stony corals estimated between 2 and 5 m in diameter. Twenty-three (43%) were alive in various conditions. These were predominantly Orbicella faveolata (20), but 2 were Siderastrea siderea and one was a Montastrea cavernosa. Corals of this size are likely to be hundreds of years old, meaning they have persisted through the multitude of anthropogenic impacts that have occurred in the region. Large coral colonies are more fecund, giving an exponentially increased amount of reproductive output making these colonies particularly important in the restoration of the reef system. It is recommended that a host of important studies be conducted to understand the full extent, size, condition of these large, resilient corals and to monitor them through time, investigate their reproduction and genetic diversity, and perhaps use them to help propagate naturally resilient corals in restoration efforts

Southeast Florida Large Coral Assessment 2015

The 2013 nearshore mapping project conducted by Walker and Klug expanded the previous knowledge on the amount, location, and species type of ecologically important large (\u3e2 m) coral colonies in southeast Florida. They discovered over 110 previously undocumented large corals of which 60 were dead and 50 were still alive; 40 of the living corals were larger than 2 m wide and up to 5 m in diameter. Because these corals are the largest and oldest organisms on our reefs, they deserve special attention. Currently there is unprecedented disease and bleaching in the northern portion of the Florida Reef Tract. It is imperative that the large coral baseline condition is documented to understand the present condition of the large corals in southeast Florida. Understanding how the coral populations are affected by this outbreak and identifying which individuals were resilient enough to recover is critical to the management of the SE FL coral reef ecosystem therefore the objective of this project was to achieve recommendation four from Walker and Klug (2014): conduct a full inventory study to understand the extent, size, condition of the large (\u3e 2 m diameter) corals. Live corals greater than 2 m diameter identified during reconnaissance were assessed by SCUBA divers. High resolution photographs and video were collected of the coral as a permanent record of its condition. Photographs were taken systematically at each of the four main compass headings (north, east, south, and west) and from overhead. In cases where the coral was too large or the visibility was poor, multiple pictures of the coral were taken at a closer distance. Divers then estimated the percent live tissue cover and percent recent and old dead skeleton remaining, percentage of bleached tissue, percentage of diseased tissue, and the number of tissue isolates. Each coral was then measured using a rigid meter stick was used to measure height, the linear distance along the longest axis, and the widest axis perpendicular to the first axis and a measuring tape to measure the distance over the surface of the coral. In areas with multiple large corals, a Garmin 76csx GPS in an underwater housing with a floating antenna was used to collect the coordinate of each coral. Surveys were conducted over eleven days between September and November 2015. Additional reconnaissance surveys were conducted to assess sixty-two new targets that were not previously visited due to poor visibility during Government Cut channel dredging. A total of 115 corals were inventoried and measured. See Appendix 1 for images and data collected on each coral. The majority of corals were Orbicella faveolata (78.2%), followed by Montastrea cavernosa, Siderastrea siderea, Colpophyllia natans, Orbicella annularis, and Pseudodiploria strigosa. Corals were found between 4.6 m and 8.8 m depth predominantly in the nearshore colonized pavement and shallow ridge habitats at an average depth of 6.4 m. Colonies were evenly distributed between Miami-Broward and Biscayne Coral Reef Ecosystem Regions. A few corals were spread out but most were clustered into smaller areas. There was no apparent pattern of size with latitude. Eight corals, all O. faveolata, were measured larger than 4 m and spanned from Key Biscayne to Hollywood. The two largest corals, which measured 5.6 m long, were located off Key Biscayne and contained 50% and 70% live tissue. One other coral measured 5.1 m long located near Bal Harbor and had 30% live tissue. Almost half of all large corals did not show signs of stress from bleaching or disease, however all of the M. cavernosa, O. annularis, and C. natans had either or both conditions. Thirty-seven percent of all corals had some recent mortality, including all four O. annularis and C. natans colonies and about half of the M. cavernosa, S. siderea, and P. strigosa colonies. Twenty-three percent of all corals had some bleaching, but M. cavernosa appeared to be affected more than other species. There were many smaller M. cavernosa colonies not captured in this study with extensive bleaching, especially in the Biscayne region. Eight percent of all colonies had both bleaching and disease. The diseases visually observed in this study were white plague, black band, dark spot and possibly Caribbean yellow band. Coral diseases are very difficult to identify precisely in the field and require histological and genetic analyses to be conducted. Changes in condition were noted between the reconnaissance and the surveys. In 2015, bleaching recovery was noted within 41 days on recently surveyed corals near Key Biscayne. This coincided with a period of noticeable cooler water temperatures and is likely indicative that the 2015 bleaching event was subsiding accordingly. Conversely, the halting of disease progression was not noted in our surveys. For example white plague disease on a C. natans had killed significant tissue over 27 days. The condition and fate of that colony is presently unknown. Changes in coral condition and live tissue cover were noted between 2014 and 2015. In 2015 corals were found completely bleached that were not bleached in 2014. Colonies were also found fully and partially bleached in 2014 and 2015 where portions of the partially bleached areas were bleached in both years and portions were not. The timing of these changes is worth noting because in south Florida corals usually bleach from heat stress later in the summer around August and September. Corals originally surveyed in June 2014 may have still bleached in 2014, recovered, and bleached again in 2015. Without regular monitoring this cannot be determined. Disease was not noted to occur in corals between years through our initial photo and video documentation evaluations but it was observed in 2015 when not present in 2014. Percent mortality was high in all corals combined. When including all of the dead corals found in the reconnaissance, 100% mortality was the highest (34%). However the partial mortality percentages were also high with 43% of corals between 25% and 99% partial mortality and 31% at least half dead. Twenty-three percent were less than one quarter dead including 5% that were more than 90% living. This study documented baseline conditions of the largest and oldest corals of the southeast Florida reefs which are analogous to the “redwoods” of our nearshore community. In southeast FL, corals grow about 1 cm per year. Corals greater than 2 meters in diameter can be hundreds of years old. The largest corals in a population are the oldest and have exponentially more reproductive capacity than smaller ones, making them the most important demographic of their respective species. Their age indicates that they have persisted through the multitude of anthropogenic impacts and stressors that have occurred in the region since the western colonization of Florida. Their size also provides habitat for a diverse and abundant assemblage of fish. A large proportion of the large corals are in the relatively flat, nearshore habitats, and thus provide an oasis for many fish species. High partial mortality is an indicator of more stressed systems. We found 65% of large corals were either dead or had less than half of their live tissue remaining. The dead ones are difficult to assess as one must collect samples to identify the species and we do not know when they died. This would be valuable information because it would allow us to determine if the frequency of mortality in these corals is increasing through time. In other words conditions are more stressful today causing more frequent mortality. This can be determined by drilling the corals and determining their ages by comparing them to a reference coral. Assessing these corals through time is important. We can identify which events reduce their tissues, whether they recover from bleaching, the frequency of bleaching and disease for each coral and the total population, and how resilient they are to stress events. The overwhelming majority of these corals were O. faveolata, a reef-building species listed as threatened under the Endangered Species Act. These resilient corals might give clues to the ability of certain corals to recover from adversity and help in the restoration of the species across the reef tract. Further, large coral colonies are more fecund, giving an exponentially increased amount of reproductive output also making these colonies particularly important in the species’ recovery. A list of recommendations of work critical to the understanding and management of the Southeast Florida coral populations, especially for O. faveolata, which is threatened under the Endangered Species Act includes: (1) Spatial analysis of large coral distribution, (2) Regular assessments of the large live corals, (3) Identifying the dead coral species and timing of death, (4) Histology and reproductive study, (5) Genetic studies, and (6) Restoration

Gross Brain Morphology in the Yellow Stingray, Urobatis jamaicensis

The yellow stingray, Urobatis jamaicensis (family Urolophidae), a short-lived, relatively small elasmobranch species (35--40 cm total length), is a common inhabitant of hard bottom and coral reef communities in southeastern Florida and many parts of the Caribbean. A paucity of published studies deal with the yellow stingray, none however on the gross morphology of its nervous system. The gross brain structure of the yellow stingray is compared with previously published studies on other batoid elasmobranchs. The external brain structure of Urobatis jamaicensis was similar to that reported for other Dasyatids, including presence of an asymmetric cerebellum. The bilaterally symmetric brain is well developed and quite large in proportion to body size (≈1--2% bw). Stingrays generally possess a brain three to 10 times the size of their sister groups, the electric rays, guitarfish, and skates (Northcutt, 1989), the yellow stingray is no exception