Techniques for spatial analysis and visualization of benthic mapping data: final report

The mapping and geospatial analysis of benthic environments are multidisciplinary tasks that have become more accessible in recent years because of advances in technology and cost reductions in survey systems. The complex relationships that exist among physical, biological, and chemical seafloor components require advanced, integrated analysis techniques to enable scientists and others to visualize patterns and, in so doing, allow inferences to be made about benthic processes. Effective mapping, analysis, and visualization of marine habitats are particularly important because the subtidal seafloor environment is not readily viewed directly by eye. Research in benthic environments relies heavily, therefore, on remote sensing techniques to collect effective data. Because many benthic scientists are not mapping professionals, they may not adequately consider the links between data collection, data analysis, and data visualization. Projects often start with clear goals, but may be hampered by the technical details and skills required for maintaining data quality through the entire process from collection through analysis and presentation. The lack of technical understanding of the entire data handling process can represent a significant impediment to success. While many benthic mapping efforts have detailed their methodology as it relates to the overall scientific goals of a project, only a few published papers and reports focus on the analysis and visualization components (Paton et al. 1997, Weihe et al. 1999, Basu and Saxena 1999, Bruce et al. 1997). In particular, the benthic mapping literature often briefly describes data collection and analysis methods, but fails to provide sufficiently detailed explanation of particular analysis techniques or display methodologies so that others can employ them. In general, such techniques are in large part guided by the data acquisition methods, which can include both aerial and water-based remote sensing methods to map the seafloor without physical disturbance, as well as physical sampling methodologies (e.g., grab or core sampling). The terms benthic mapping and benthic habitat mapping are often used synonymously to describe seafloor mapping conducted for the purpose of benthic habitat identification. There is a subtle yet important difference, however, between general benthic mapping and benthic habitat mapping. The distinction is important because it dictates the sequential analysis and visualization techniques that are employed following data collection. In this paper general seafloor mapping for identification of regional geologic features and morphology is defined as benthic mapping. Benthic habitat mapping incorporates the regional scale geologic information but also includes higher resolution surveys and analysis of biological communities to identify the biological habitats. In addition, this paper adopts the definition of habitats established by Kostylev et al. (2001) as a “spatially defined area where the physical, chemical, and biological environment is distinctly different from the surrounding environment.” (PDF contains 31 pages)

Survey report of NOAA Ship McArthur II cruises AR-04-04, AR-05-05 and AR-06-03: Habitat classification of side scan sonar imagery in support of deep-sea coral/sponge explorations at the Olympic Coast National Marine Sanctuary

Habitat mapping and characterization has been defined as a high-priority management issue for the Olympic Coast National Marine Sanctuary (OCNMS), especially for poorly known deep-sea habitats that may be sensitive to anthropogenic disturbance. As a result, a team of scientists from OCNMS, National Centers for Coastal Ocean Science (NCCOS), and other partnering institutions initiated a series of surveys to assess the distribution of deep-sea coral/sponge assemblages within the sanctuary and to look for evidence of potential anthropogenic impacts in these critical habitats. Initial results indicated that remotely delineating areas of hard bottom substrate through acoustic sensing could be a useful tool to increase the efficiency and success of subsequent ROV-based surveys of the associated deep-sea fauna. Accordingly, side scan sonar surveys were conducted in May 2004, June 2005, and April 2006 aboard the NOAA Ship McArthur II to: (1) obtain additional imagery of the seafloor for broader habitat-mapping coverage of sanctuary waters, and (2) help delineate suitable deep-sea coral/sponge habitat, in areas of both high and low commercial-fishing activities, to serve as sites for surveying-in more detail using an ROV on subsequent cruises. Several regions of the sea floor throughout the OCNMS were surveyed and mosaicked at 1-meter pixel resolution. Imagery from the side scan sonar mapping efforts was integrated with other complementary data from a towed camera sled, ROVs, sedimentary samples, and bathymetry records to describe geological and biological (where possible) aspects of habitat. Using a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999), we created a preliminary map of various habitat polygon features for use in a geographical information system (GIS). This report provides a description of the mapping and groundtruthing efforts as well as results of the image classification procedure for each of the areas surveyed. (PDF contains 60 pages.)

Olympic Coast National Marine Sanctuary Habitat Mapping: Survey report and classification of side scan sonar data from surveys HMPR-114-2004-02 and HMPR-116-2005-01.

The Olympic Coast National Marine Sanctuary (OCNMS) continues to invest significant resources into seafloor mapping activities along Washington’s outer coast (Intelmann and Cochrane 2006; Intelmann et al. 2006; Intelmann 2006). Results from these annual mapping efforts offer a snapshot of current ground conditions, help to guide research and management activities, and provide a baseline for assessing the impacts of various threats to important habitat. During the months of August 2004 and May and July 2005, we used side scan sonar to image several regions of the sea floor in the northern OCNMS, and the data were mosaicked at 1-meter pixel resolution. Video from a towed camera sled, bathymetry data, sedimentary samples and side scan sonar mapping were integrated to describe geological and biological aspects of habitat. Polygon features were created and attributed with a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999). For three small areas that were mapped with both side scan sonar and multibeam echosounder, we made a comparison of output from the classified images indicating little difference in results between the two methods. With these considerations, backscatter derived from multibeam bathymetry is currently a costefficient and safe method for seabed imaging in the shallow (<30 meters) rocky waters of OCNMS. The image quality is sufficient for classification purposes, the associated depths provide further descriptive value and risks to gear are minimized. In shallow waters (<30 meters) which do not have a high incidence of dangerous rock pinnacles, a towed multi-beam side scan sonar could provide a better option for obtaining seafloor imagery due to the high rate of acquisition speed and high image quality, however the high probability of losing or damaging such a costly system when deployed as a towed configuration in the extremely rugose nearshore zones within OCNMS is a financially risky proposition. The development of newer technologies such as intereferometric multibeam systems and bathymetric side scan systems could also provide great potential for mapping these nearshore rocky areas as they allow for high speed data acquisition, produce precisely geo-referenced side scan imagery to bathymetry, and do not experience the angular depth dependency associated with multibeam echosounders allowing larger range scales to be used in shallower water. As such, further investigation of these systems is needed to assess their efficiency and utility in these environments compared to traditional side scan sonar and multibeam bathymetry. (PDF contains 43 pages.)

A pilot study of hogfish (Lachnolaimus maximus Walbaum 1792) movement in the Conch Reef Research Only Area (northern Florida Keys)

The largely sedentary behavior of many fishes on coral reefs is well established. Information on the movement behavior of individual fish, over fine temporal and spatial scales, however, continues to be limited. It is precisely this type of information that is critical for evaluating the success of marine reserves designed for the conservation and/or management of vagile fishes. In this pilot study we surgically-tagged eight hogfish (Lachnolaimus maximus Walbaum 1792) with coded-acoustic transmitters inside the Conch Reef Research Only Area (a no-take marine reserve) in the northern Florida Keys National Marine Sanctuary. Our primary objective was to characterize the movement of L. maximus across Conch Reef in the vicinity of the reserve. All fish were captured, surgically-tagged and released in situ during a saturation mission to the Aquarius Undersea Laboratory, which is located in the center of the reserve. Movement of tagged L. maximus was recorded for up to 95 days by three acoustic receivers deployed on the seafloor. Results showed clear diel patterns in L. maximus activity and regular movement among the receivers was recorded for seven of the eight tagged fish. Fidelity of tagged fish to the area of release was high when calculated at the scale of days, while within-day fidelity was comparatively low when calculated at the scale of hours. While the number of fish departures from the array also varied, the majority of departures for seven of the eight fish did not exceed 1-hr (with the exception of one 47-day departure), suggesting that when departures occurred, the fish did not travel far. Future efforts will significantly expand the number of receivers at Conch Reef such that fish movement behavior relative to the reserve boundaries can be quantified with increased temporal and spatial resolution. (PDF contains 22 pages.)

Movement of yellowtail snapper (Ocyurus chrysurus Block 1790) and black grouper (Mycteroperca bonaci Poey 1860) in the northern Florida Keys National Marine Sanctuary as determined by acoustic telemetry

We tagged a total of 14 yellowtail snapper (Ocyurus chrysurus Bloch 1790) and black grouper (Mycteroperca bonaci Poey 1860) inside the Conch Reef Research Only Area (a no-take marine reserve) in the northern Florida Keys National Marine Sanctuary in November 2001. Both species are heavily exploited in the region. Our objective was to characterize site fidelity and movement behavior along the reef tract to the north and south of the release point. Fishes were collected by baited hook and line from the surface, surgically-tagged with coded-acoustic transmitters, and returned to the reef by snorkelers. Tracking of fish movement behavior was conducted by five acoustic receivers deployed on the seafloor from Davis Reef in the south to Pickles Reef in the north. Fishes were tracked for up to eight months. Results indicated that the majority of signal detections for individual fish from both species were recorded at the two Conch Reef receivers. Limited movement from Conch Reef to Davis Reef was recorded, but no signal detections were recorded at the two sites to the north of Conch Reef. These results suggest that both species show site fidelity to Conch Reef. Future studies will seek to characterize this site fidelity with increased temporal and spatial resolution at Conch Reef. (PDF contains 25 pages.)

Biogeographic analysis of the Tortugas Ecological Reserve: Examining the refuge effect following reserve establishment

Almost 120 days at sea aboard three NOAA research vessels and one fishing vessel over the past three years have supported biogeographic characterization of Tortugas Ecological Reserve (TER). This work initiated measurement of post-implementation effects of TER as a refuge for exploited species. In Tortugas South, seafloor transect surveys were conducted using divers, towed operated vehicles (TOV), remotely operated vehicles (ROV), various sonar platforms, and the Deepworker manned submersible. ARGOS drifter releases, satellite imagery, ichthyoplankton surveys, sea surface temperature, and diver census were combined to elucidate potential dispersal of fish spawning in this environment. Surveys are being compiled into a GIS to allow resource managers to gauge benthic resource status and distribution. Drifter studies have determined that within the ~ 30 days of larval life stage for fishes spawning at Tortugas South, larvae could reach as far downstream as Tampa Bay on the west Florida coast and Cape Canaveral on the east coast. Together with actual fish surveys and water mass delineation, this work demonstrates that the refuge status of this area endows it with tremendous downstream spillover and larval export potential for Florida reef habitats and promotes the maintenance of their fish communities. In Tortugas North, 30 randomly selected, permanent stations were established. Five stations were assigned to each of the following six areas: within Dry Tortugas National Park, falling north of the prevailing currents (Park North); within Dry Tortugas National Park, falling south of the prevailing currents (Park South); within the Ecological Reserve falling north of the prevailing currents (Reserve North); within the Ecological Reserve falling south of the prevailing currents (Reserve South); within areas immediately adjacent to these two strata, falling north of the prevailing currents (Out North); and within areas immediately adjacent to these two strata, falling south of the prevailing currents (Out South). Intensive characterization of these sites was conducted using multiple sonar techniques, TOV, ROV, diver-based digital video collection, diver-based fish census, towed fish capture, sediment particle-size, benthic chlorophyll analyses, and stable isotope analyses of primary producers, fish, and, shellfish. In order to complement and extend information from studies focused on the coral reef, we have targeted the ecotone between the reef and adjacent, non-reef habitats as these areas are well-known in ecology for indicating changes in trophic relationships at the ecosystem scale. Such trophic changes are hypothesized to occur as top-down control of the system grows with protection of piscivorous fishes. Preliminary isotope data, in conjunction with our prior results from the west Florida shelf, suggest that the shallow water benthic habitats surrounding the coral reefs of TER will prove to be the source of a significant amount of the primary production ultimately fueling fish production throughout TER and downstream throughout the range of larval fish dispersal. Therefore, the status and influence of the previously neglected, non-reef habitat within the refuge (comprising ~70% of TER) appears to be intimately tied to the health of the coral reef community proper. These data, collected in a biogeographic context, employing an integrated Before-After Control Impact design at multiple spatial scales, leave us poised to document and quantify the postimplementation effects of TER. Combined with the work at Tortugas South, this project represents a multi-disciplinary effort of sometimes disparate disciplines (fishery oceanography, benthic ecology, food web analysis, remote sensing/geography/landscape ecology, and resource management) and approaches (physical, biological, ecological). We expect the continuation of this effort to yield critical information for the management of TER and the evaluation of protected areas as a refuge for exploited species. (PDF contains 32 pages.)

Spawning, egg development, and early life history dynamics of arrowtooth flounder (Atheresthes stomias) in the Gulf of Alaska

Arrowtooth flounder (Atheresthes stomias) has the highest biomass of any groundfish species in the Gulf of Alaska, is a voracious predator of age 1 walleye pollock (Theragra chalcogramma), and is a major component in the diet of Steller sea lions (Eumetopias jubatus). Owing to its ecological importance in the Gulf of Alaska and the limited information available on its reproduction, interest has intensified in describing its spawning and early life history. A study was undertaken in late January–February 2001–2003 in the Gulf of Alaska to obtain information on adult spawning location, depth distribution, and sexual maturity, and to obtain fertilized eggs for laboratory studies. Adults were found 200–600 m deep east of Kodiak Island over the outer continental shelf and upper slope, and southwest along the shelf break to the Shumagin Islands. Most ripe females (oocytes extruded with light pressure) were found at 400 m and most ripe males (milt extruded with light pressure) were found at depths ≥450 m. Eggs were fertilized and incubated in the laboratory at 3.0°, 4.5°, and 6.0°C. Eggs were reared to hatching, but larvae did not survive long enough to complete yolk absorption and develop pigment. Eggs were staged according to morphological hallmarks and incubation data were used to produce a stage duration table and a regression model to estimate egg age based on water temperature and developmental stage. Arrowtooth flounder eggs (1.58–1.98 mm in diameter) were collected in ichthyoplankton surveys along the continental shelf edge, primarily at depths ≥400 m. Early-stage eggs were found in tows that sampled to depths of ≥450 m. Larvae, which hatch between 3.9 and 4.8 mm standard length, increased in abundance with depth. Observations on arrowtooth flounder eggs and early-stage larvae were used to complete the description of the published partial developmental series.(PDF file contains 34 pages.)

Nassau grouper (Epinephelus striatus) spawning aggregations: hydroacoustic surveys and geostatistical analysis

With the near extinction of many spawning aggregations of large grouper and snapper throughout the Caribbean, Gulf of Mexico, and tropical Atlantic, we need to provide baselines for their conservation. Thus, there is a critical need to develop techniques for rapidly assessing the remaining known (and unknown) aggregations. To this end we used mobile hydroacoustic surveys to estimate the density, spatial extent, and total abundance of a Nassau grouper spawning aggregation at Little Cayman Island, Cayman Islands, BWI. Hydroacoustic estimates of abundance, density, and spatial extent were similar on two sampling occasions. The location and approximate spatial extent of the Nassau grouper spawning aggregation near the shelf-break was corroborated by diver visual observations. Hydroacoustic density estimates were, overall, three-times higher than the average density observed by divers; however, we note that in some instances diver-estimated densities in localized areas were similar to hydroacoustic density estimates. The resolution of the hydroacoustic transects and geostatistical interpolation may have resulted in over-estimates in fish abundance, but still provided reasonable estimates of total spatial extent of the aggregation. Limitations in bottom time for scuba and visibility resulted in poor coverage of the entire Nassau grouper aggregation and low estimates of abundance when compared to hydroacoustic estimates. Although the majority of fish in the aggregation were well off bottom, fish that were sometimes in close proximity to the seafloor were not detected by the hydroacoustic survey. We conclude that diver observations of fish spawning aggregations are critical to interpretations of hydroacoustic surveys, and that hydroacoustic surveys provide a more accurate estimate of overall fish abundance and spatial extent than diver observations. Thus, hydroacoustics is an emerging technology that, when coupled with diver observations, provides a comprehensive survey method for monitoring spawning aggregations of fish.

Marine flora and fauna of the Eastern United States Anthozoa: Acitniaria, Corallimorpharia, Ceriantharia, and Zoanthidea

This key includes 60 species of sea anemones and their relatives in the orders Actiniaria, Corallimorpharia, Ceriantharia, and Zoanthidea. Species from the intertidal zone, continental slope, and deep sea are included over a geographic range from Atlantic Canada to approximately South Carolina. In addition to the illustrated key itself, characteristics of each species are summarized in tabular form, including morphology, distribution, and types and sizes of cnidae. Ecological and taxonomic information on each species are also included in an annotated species list. (PDF file contains 76 pages.)

Water Temperatures and Climatological Conditions South of New England, 1974-83

From 1974 through 1983, we conducted monitoring to provide the first long-term, year-round record of sea water temperatures south of New England from surface to bottom, and from nearshore to the continental slope. Expendable bathythermograph transects were made approximately monthly during the ten years by scientists and technicians from numerous institutions, working on research vessels that traversed the continental shelf off southern New England. Ten-year (1974-83) means and variability are presented for coastal and bottom water temperatures, for mid-shelf water column temperatures, and for some atmospheric and oceanographic conditions that may influence shelf and upper-slope water temperatures. Possible applications of ocean temperature monitoring to fishery ecology are noted. Some large departures from mean conditions are discussed; particularly notable during the decade were the response of water temperatures to the passage of Gulf Stream warm-core rings, and the magnitude and persistence of shelf-water cooling associated with air temperatures in three successive very cold winters (1976-77, 1977-78, and 1978-79). (PDF file contains 51 pages.)

Abundance and Distribution of Ichthyoplankton along an Inshore-Offshore Transect in Onslow Bay, North Carolina

The distribution and abundance of ichthyoplankton was investigated from November 1979 to March 1980 along a transect from coastal to continental slope waters in Onslow Bay, North Carolina. Representatives of 66 families were collected; 24 of which were tropical families, a category that also includes families of typically oceanic and deep-sea fishes. Larvae of tropical species were collected in coastal and shelf waters, demonstrating the intrusion of Gulf Stream waters onto the continental shelf. From December through March, frontal waters that separated cold open-shelf surface waters from warm Gulf Stream surface waters were observed. Higher abundances of fish larvae were sometimes, but not consistently, associated with frontal waters. A great diversity of taxa was collected in offshore waters, and densities of larvae were low in coastal waters; low densities were attributed to gear selectivity rather than low larval abundance. Larvae of commercially and recreationally important estuarine-dependent species, especially Leiostomus xanthus and Micropogonias undulatus, were dominant components of the ichthyoplankton. Representatives of the families Bothidae, Clupeidae, Gadidae, Gonostomatidae, Myctophidae, Ophidiidae, and Sparidae were also important components of the ichthyoplankton. Larvae of species representing two strikingly different life history types-mesopelagic and estuarine-dependent frequently cooccurred.(PDF file contains 32 pages.)

三维离散元可变形、断裂模型及其在边坡工程中的应用

该文主要是在三维面-面接触离散刚体单元模型基础上，提出考虑可变形、断裂三维离散单元模型，并推导其相应的物理方程及运动方程.在已有划分块体单元计算算法基础上，对单元的自动划分算法作了相应改进.针对具有倾斜表面边坡坡体，可以利用堆积法自动划分块体单元，更加贴近工程实际应用，使三维离散单元法程序应用更广.

Codend selection of winter flounder Pseudopleuronectes americanus

Codend selection of winter flounder (Pseudopleuronectes americanus) in 76-127 mm mesh codends was examined from experiments conducted in Long Island Sound during the spring of 1986-87. The results show a slightly larger size at selection than was found in earlier work as indicated by the selection factor, 2.31 in the present study compared with 2.2 and 2.24 from previous studies. Diamond mesh was found to have a length at 50% retention about 1 cm longer (Lso =22.6 cm), and a selection range (3.4 cm) about 1 cm narrower, than square mesh in 102-mm codends. Tow duration varied from 1 to 2 hours using 114-mm diamond mesh. As has been found in previous studies, tow duration and Lso are positively related, with I-hour tows averaging 24.6 cm and 2-hour tows averaging 26.6 cm. The importance of the slope of the selection curve was examined in yield-per-recruit analyses by comparing knife-edge and stepwise recruitment. In all mesh sizes, stepwise recruitment provides a more conservative estimate of yield in the presence of a minimum size limit. Differences in yield estimates between the two models were generally small (1-7%), except in the largest mesh size, 127 mm, where yield is overestimated by 10% when assuming knife-edge recruitment. (PDF file contains 16 pages.)

Greenland turbot Reinhardtius hippoglossoides of the eastern Bering Sea and Aleutian Islands region

Greenland turbot (Reinhardtius hippoglossoides) is a commercially important flounder in both the North Atlantic and North Pacific Oceans. In the latter, its center of abundance is in the eastern Bering Sea and along the Aleutian Islands chain where its population is managed as a single stock. Harvest levels in this region of the North Pacific during the period 1970-81 were comparable with those in the northwest and northeast Atlantic, with annual average catches of 53,000 metric tons (t). However, the catch in 1984 dropped sharply to 23,100 t, in part because of reduced quotas arising from concern over continued poor recruitment and declining catch-per-unit-effort. Recruitment failure was manifested in 1) the sharp decline in the catch rate of young flsh in annual research trawl surveys on the continental shelf of the eastern Bering Sea and 2) an increasing proportion of older and larger fish in the commercial catch from the continental slope of both the eastern Bering Sea and Aleutian Islands. The cause ofthe decline in recruitment could not be clearly identifled. Greenland turbot of the Bering Sea-Aleutian Islands share certain distributional features with the North Atlantic form. There is an apparent bathymetric change in the size and age of fish, with younger animals occupying continental shelf depths and the older individuals residing at depths of the continental slope. At shallow depths the young are exposed to temperature fluctuations, whereas older animals along the slope are exposed to relatively stable temperatures. A hypothesis is proposed for describing the temporal and spatial paths by which young animals reach the mature or spawning portion of the population. (PDF file contains 38 pages.)

Marine flora and fauna of the northeastern United States. Echinodermata: Echinoidea

The echinoid fauna from littoral to abyssal depths off the northeastern United States (Cape Hatteras, NC, to northern Nova Scotia) comprises 31 species, in 26 genera and 19 families. An introduction to the external morphology, distribution, and natural history is given along with an illustrated key to the species, an annotated systematic list, and an index. The fauna Includes 17 species with wide-ranging distributions on continental slopes or abyssal plains. The remaining 14 species occur in shallower waters on the continental shelf or upper slope. Of these, eight are tropical in distribution with their northern range extending to the northeastern United States and three are mainly boreal with the northeastern United States at the southern limit of their range. Two species occur only off the eastern United States and one species is cosmopolitan. (PDF file contains 33 pages.)