Scott Haag

A Multi-scale Segmentation Approach to Mapping Seagrass Habitats Using Airborne Digital Camera Imagery

The purpose of this study was to map the areal extent and density of submerged aquatic vegetation, principally the seagrasses, Zostera marina and Ruppia maritima, as part of ongoing monitoring for the Barnegat Bay, New Jersey National Estuary Program. We examine the utility of multiscale image segmentation/object-oriented image classification using the eCognition software to map seagrass across our 36,000 ha study area. The multi-scale image segmentation/ object oriented classification approach closely mirrored our conceptual model of the spatial structure of the seagrass habitats and successfully extracted the features of ecological interest. The agreement between the mapped results and the original field reference was 68 percent (Kappa � 56.5 percent) for the four category map and 83 percent (Kappa � 63.1 percent) for the presence/absence map; the agreement between the mapped results and the independent reference data was 71 percent (Kappa � 43.0 percent) for a simple presence/absence map. While the aerial digital camera imagery employed in this study had the advantage of flexible acquisition, suitable image scale, fast processing return time, and comparatively low cost, it had inconsistent radiometric response from image to image. This inconsistency made it difficult to develop a rule-based classification that was universally applicable across the 14 individual image mosaics. However, within the individual scene mosaics, using the eCognition software in a “manual classification” mode provided a flexible and time effective approach to mapping seagrass habitats.

Andean Speciation and Vicariance in Neotropical Macrocarpaea (Gentianaceae-Helieae)

Abstract The genus Macrocarpaea (Griseb.) Gilg (Gentianaceae, Helieae) is among the largest woody genera of tropical gentians, with most of its species occurring in the wet mountainous forests of the Andes. Phylogenetic and dispersal-vicariance analyses (DIVA) of 57 of the 105 currently recognized species in the genus, using two data sets from nuclear DNA (ITS and 5S-NTS sequences) and morphology, show a single origin of the Andean species from an ancestral distribution that includes southeastern Brazil. Within the Andes, species divide into two major clades: (1) northern species from the cordilleras of northern Ecuador, Colombia, and Venezuela; and (2) southern species of the Andean Amotape–Huancabamba Zone in Ecuador and Peru, as well as the Andes of central and southern Peru and Bolivia. The Amotape–Huancabamba Zone is supported as the ancestral area for Macrocarpaea within the Andes. There are repeated speciation patterns within the Andes, and three Mesoamerican species derive from the northern clade, as is the single sampled species from the Guayana Shield. The position of the subclade of the three Caribbean species is less certain, but it currently nests among Andean species. An Atlantic coastal Brazilian clade is placed as sister group to all other Macrocarpaea, providing further support for an ancestral refuge in southeastern Brazil for the Helieae. The biogeographic analysis showed that local speciation is more common than long-distance dispersal, and allopatric speciation is more common than sympatric speciation. Using detailed, georeferenced herbarium collection data, patterns in environmental characteristics between clades and sister species were analyzed with Spatial Evolutionary and Ecological Vicariance Analysis (SEEVA), utilizing geographic information system (GIS) and statistical methods. Sister clades and taxa were evaluated for statistical significance in variables such as annual rainfall and temperature, elevation, temperature and rainfall seasonality, geological bedrock age, and soil type to evaluate ecological vicariance between sister groups. The results indicate that there are no general patterns for each variable, but that there are many significant divergences in ecological niches between both larger sister groups and sister species, and ecological niche conservation was also observed when subsequent nodes in the phylogeny were compared.

Benthic Macrofaunal Community Structure along a Well-Defined Salinity Gradient in the Mullica River–Great Bay Estuary**

Abstract The benthic macrofaunal community of the Mullica River–Great Bay estuary in the Jacques Cousteau National Estuarine Research Reserve is characterized by both small-scale and large-scale distribution patterns that can be correlated to gradients in physicochemical parameters. Sediment composition is a major factor regulating the local distribution of benthic assemblages in the estuary, with the amount of silt-clay being particularly important. For example, one suite of benthic fauna (i.e., Ampelisca verrilli, Ensis directus, Haustorius arenarius, Pygospio elegans, and Oxyurostylis smithi) reported in the estuary has been found only in sediments with less than 20% silt-clay, whereas another (i.e., Acteocina canaliculata, Lumbrineris tenuis, Maldinopsis elongata, Tellina agilis, Turbonilla sp., and Unciola irrorata) has been observed only in sediments with more than 38% silt-clay. Other physicochemical factors (e.g., organic carbon content of the sediments, dissolved oxygen levels, bottom currents, and turbidity) might also influence the local distribution patterns of the fauna. On the estuary scale, environmental gradients from upriver to down-bay regions strongly affect the distribution of the benthos over broader spatial areas. Hence, four distinct regional assemblages of benthic invertebrates have been identified in the Mullica River–Great Bay estuary, including river-, bay-, lower bay–, and estuary-wide forms. The dominant assemblage—the estuary-wide forms distributed along the length of the estuary—consists of the most abundant populations with the widest salinity tolerances. Examples are Ampelisca abdita, Corophium cylindricum, Cyathura polita, Notomastus latericeus, Polydora ligni, Scoloplos robustus, and Turbonilla sp. Because Great Bay exhibits marked changes in sediment type from predominantly sands in the eastern perimeter to generally finer deposits along the western margin, the abundance, species richness, and species composition of benthic invertebrates vary considerably over relatively small spatial scales.

Seagrass Demographic and Spatial Habitat Characterization in Little Egg Harbor, New Jersey, Using Fixed Transects

Abstract A detailed submerged aquatic vegetation (SAV) study was conducted in Little Egg Harbor (39°35′N, 74°14′W), New Jersey, a lagoonal estuary located within the boundaries of the Jacques Cousteau National Estuarine Reserve, to assess the demographic characteristics and spatial habitat changes of Zostera marina beds over an annual growing period and to determine the species composition, relative abundance, and potential impacts of benthic macroalgae on seagrass habitat in the system. Two disjunct seagrass beds in Little Egg Harbor, covering an area of ∼1700 ha, were sampled at 10 equally spaced points along six, east–west-trending transects in spring, summer, and fall (June–November) of 2004. During this period, 180 seagrass samples were collected at 60 transect sites, together with an array of water quality measurements. Results of this investigation indicate that both aboveground and belowground biomass of seagrass peaked during June–July and declined significantly into the fall months. Mean aboveground biomass ranged from 18.22 to 106.05 g dry wt m−2, and mean belowground biomass from 50.48 to 107.64 g dry wt m−2. Biomass values were higher along the northernmost sampling transects than along those farther to the south. They were also higher at interior sampling sites within the seagrass beds than along the bed margins for two of the three sampling periods. Mean seagrass blade length was consistent throughout the study period, averaging 31.83–34.02 cm. The percentage of cover by seagrass, which ranged from 21% to 45%, peaked in June–July at the time of maximum seagrass biomass. The percentage of cover by macroalgae was lower than that of seagrass, averaging 13%–21%, with maximum cover occurring in August–September. Most of the macroalgal species collected in the seagrass beds were red algae, although the dominant species was typically the green seaweed, Ulva lactuca. During the 6-month study period, no brown tide (Aureococcus anophagefferens) blooms were recorded, and phytoplankton abundance did not appear to cause shading problems for seagrass in the system. However, benthic macroalgal blooms were observed in the seagrass beds, most notably U. lactuca. These blooms blanketed parts of the seagrass beds and appeared to degrade them over extensive areas. Nutrient enrichment, elevated turbidity levels, and prop scarring are anthropogenic factors that may significantly influence seagrass beds in Little Egg Harbor during the growing season.

Side-Scan Sonar Imaging of Subtidal Benthic Habitats in the Mullica River–Great Bay Estuarine System**

Abstract Side-scan sonar imaging conducted in Great Bay, New Jersey, during August 2003 reveals local variations in acoustic backscatter from the seabed that can be related to small-, medium-, and large-scale bedforms. Analysis of 600-kilohertz side-scan sonar data collected at a System-Wide Monitoring Program (SWMP) survey site of the Jacques Cousteau National Estuarine Research Reserve shows a relationship between backscatter intensity, bathymetry, and changing seabed morphology. Side-scan sonar records obtained at the survey site in Great Bay via deployment of an autonomous underwater vehicle (Remote Environmental Monitoring UnitS) provide in-depth characterization of an array of complex and multiscaled bedforms and associated benthic habitats. Bedforms documented within the swath map region by side-scan sonar imaging include constructive transverse forms, notably ripples, dunes, and sand waves. These bedforms are valuable for assessing potentially important habitats for benthic invertebrate and demersal finfish populations.

Comparison of remotely-sensed surveys vs. in situ plot-based assessments of sea grass condition in Barnegat Bay-Little Egg Harbor, New Jersey USA

With the increasing appreciation that sea grass habitats are in global decline, there is a great need to be able to efficiently and effectively assess and characterize the status and trends of sea grass in our coastal ecosystems. This paper examines the utility of remotely sensed vs. in situ plot-based monitoring using the Barnegat Bay-Little Egg Harbor (BB-LEH), New Jersey, USA estuarine system as a case study. Eelgrass (Zostera marina) is the dominant species, while widgeon grass (Ruppia maritima) is also common in lower salinity regions of the BB-LEH. Aerial imagery collected during the months of July and August 2009 was interpreted and mapped using object based image analysis techniques, similar to techniques used in the 2003 mapping survey of this system. Boat-based in situ monitoring data were collected concurrently with the aerial photography to assist the image interpretation and for an independent accuracy assessment. We compared the remotely-sensed mapping of sea grass cover change (in 2003 vs. 2009) vs. in situ plot-based monitoring conducted from 2004 through 2009. Comparison of the remotely-sensed vs. the in situ plot-change analysis suggests that the two methodologies had broadly similarly results, with the percent area showing declines in sea grass cover greater than those that exhibited increases. In conclusion, the two studies provide corroborating evidence that sea grass has declined in percent cover in the BB-LEH system during the decade of the 2000’s. While remotely-sensed surveys provide synoptic information for a “big picture” view on sea grass distribution, site specific in situ sampling is required to determine other aspects of sea grass status, e.g. above vs. below-ground biomass, blade length, shoot density, epiphytic loading, etc. Either method alone gives an incomplete picture. As demonstrated in this study, to fully characterize the spatial extent, health, and density of sea grass meadows across the entire estuary, combining remote sensing surveys concomitantly with comprehensive in situ assessment provides the most robust approach.

Seagrass Habitat Characterization in Estuarine Waters of the Jacques Cousteau National Estuarine Research Reserve Using Underwater Videographic Imaging Techniques

Abstract A benthic habitat assessment study conducted in the Barnegat Bay-Little Egg Harbor Estuary from June to November 2006 reveals that boat-based videographic imaging is comparable to in situ diver observations for determining the occurrence and percent cover of seagrasses in actively growing beds. A Seaviewer Sea Drop camera and recorder unit deployed along 12 transects in the estuary generated 331 images of seagrass habitat during the study period. A comparison of video still images with data derived from diver observations indicates consistent results in terms of the presence/absence and percent cover of seagrass on the estuarine floor throughout the seagrass growing season. Plots of the percent cover of seagrass recorded by the camera system vs. in situ diver observations reveal a high correlation for the June–July, August–September, and October–November sampling periods (R2 = 0.936, 0823, and 0.894, respectively) as well as for the entire June–November sampling period (R2 = 0.888). A kappa statistic calculated for the presence/absence of seagrass in the estuary (0.83) reflects a nearly perfect level of agreement between the two methods (camera and diver) of data collection. In addition to generating rapid databases, digital underwater video imaging requires less field time than the use of divers and other traditional field monitoring methods. Digital videographic files can also be post-processed, geolocated using a global positioning system, analyzed by multiple investigators, and stored for later analysis, thereby offering several other advantages over traditional in situ monitoring techniques in shallow estuarine systems.

Structure-level fuel load assessment in the wildland-urban interface: a fusion of airborne laser scanning and spectral remote-sensing methodologies

Large-scale fuel assessments are useful for developing policy aimed at mitigating wildfires in the wildland–urban interface (WUI), while finer-scale characterisation is necessary for maximising the effectiveness of fuel reduction treatments and directing suppression activities. We developed and tested an objective, consistent approach for characterising hazardous fuels in the WUI at the scale of individual structures by integrating aerial photography, airborne laser scanning and cadastral datasets into a hazard assessment framework. This methodology is appropriate for informing zoning policy questions, targeting presuppression planning and fuel reduction treatments, and assisting in prioritising structure defence during suppression operations. Our results show increased variability in fuel loads with decreasing analysis unit area, indicating that fine-scale differences exist that may be omitted owing to spatial averaging when using a coarser, grid-based approach. Analyses using a local parcel database indicate that approximately 75% of the structures in this study have ownership of less than 50% of the 30 m buffer around their building, illustrating the complexity of multiple ownerships when attempting to manage fuels in the WUI. Our results suggest that our remote-sensing approach could augment, and potentially improve, ground-based survey approaches in the WUI.

Assessment of eutrophication in the Barnegat Bay-Little Egg Harbor system: use of sav biotic indicators of estuarine condition

EXECUTIVE SUMMARY Results of a comprehensive investigation of the seagrass demographics in the Barnegat Bay-Little Egg Harbor Estuary during 2008 indicate ongoing degradation of seagrass habitat associated with increasing eutrophic conditions. Surveys of seagrass beds in Barnegat Bay and Little Egg Harbor from spring to fall in 2008 show that the seagrass beds have not yet recovered from the marked reduction of plant biomass (g dry wt m), density (shoots m), blade length, and percent cover recorded in 2006. Quadrat, core, and hand sampling, as well as digital camera imaging at 120 transect sites in 4 disjunct seagrass beds of the estuary during the June-November period in 2008, as in