Using Remote Sensing and Spatial Information Technologies to Detect and Map Two Aquatic Macrophytes

This paper describes the light reflectance characteristics ofwaterhyacinth [Eichhornia crassipes (Mort.) Solms] and hydrilla [Hydrilla verticillata (L.F.) Royle] and the application of airborned videography with global positioning system (GPS) and geographic information system (GIS) technologies for distinguishing and mapping the distribution of these two aquatic weeds in waterways of southern Texas. Field reflectance measurements made at several locations showed that waterhyacinth generally had higher near-infrared (NIR) reflectance than associated plant species and water. Hydrilla had lower NIR reflectance than associated plant species and higher NIR reflectance than water. Reflectance measurements made on hydrilla plants submerged below the water surface had similar spectral characteristics to water. Waterhyacinth and hydrilla could be distinguished in color-infrared (CIR) video imagery where they had bright orange-red and reddish-brown image responses, respectively. Computer analysis of the imagery showed that waterhyacinth and hydrilla infestaions could be quantified. An accuracy assessment performed on the classified image showed an overall accuracy of 87.7%. Integration of the GPS with the video imagery permitted latitude/longitude coordinates of waterhyacinth and hydrilla infestation to be recorded on each image. A portion of the Rio Grande River in extreme southern Texas was flown with the video system to detect waterhyacinth and hydrilla infestaions. The GPS coordinates on the CIR video scenes depicting waterhyacinth and hydrilla infestations were entered into a GIS to map the distribution of these two noxious weeds in the Rio Grande River.

MAP CAMP Project "Lebanon": final integrated project document

(287 page document)

Protected species aerial survey data collection and analysis in waters underlying the R-5306A airspace: final report submitted to US Marine Corps, MCAS Cherry Point

To be in compliance with the Endangered Species Act and the Marine Mammal Protection Act, the United States Department of the Navy is required to assess the potential environmental impacts of conducting at-sea training operations on sea turtles and marine mammals. Limited recent and area-specific density data of sea turtles and dolphins exist for many of the Navy’s operations areas (OPAREAs), including the Marine Corps Air Station (MCAS) Cherry Point OPAREA, which encompasses portions of Core and Pamlico Sounds, North Carolina. Aerial surveys were conducted to document the seasonal distribution and estimated density of sea turtles and dolphins within Core Sound and portions of Pamlico Sound, and coastal waters extending one mile offshore. Sea Surface Temperature (SST) data for each survey were extracted from 1.4 km/pixel resolution Advanced Very High Resolution Radiometer remote images. A total of 92 turtles and 1,625 dolphins were sighted during 41 aerial surveys, conducted from July 2004 to April 2006. In the spring (March – May; 7.9°C to 21.7°C mean SST), the majority of turtles sighted were along the coast, mainly from the northern Core Banks northward to Cape Hatteras. By the summer (June – Aug.; 25.2°C to 30.8°C mean SST), turtles were fairly evenly dispersed along the entire survey range of the coast and Pamlico Sound, with only a few sightings in Core Sound. In the autumn (Sept. – Nov.; 9.6°C to 29.6°C mean SST), the majority of turtles sighted were along the coast and in eastern Pamlico Sound; however, fewer turtles were observed along the coast than in the summer. No turtles were seen during the winter surveys (Dec. – Feb.; 7.6°C to 11.2°C mean SST). The estimated mean surface density of turtles was highest along the coast in the summer of 2005 (0.615 turtles/km², SE = 0.220). In Core and Pamlico Sounds the highest mean surface density occurred during the autumn of 2005 (0.016 turtles/km², SE = 0.009). The mean seasonal abundance estimates were always highest in the coastal region, except in the winter when turtles were not sighted in either region. For Pamlico Sound, surface densities were always greater in the eastern than western section. The range of mean temperatures at which turtles were sighted was 9.68°C to 30.82°C. The majority of turtles sighted were within water ≥ 11°C. Dolphins were observed within estuarine waters and along the coast year-round; however, there were some general seasonal movements. In particular, during the summer sightings decreased along the coast and dolphins were distributed throughout Core and Pamlico Sounds, while in the winter the majority of dolphins were located along the coast and in southeastern Pamlico Sound. Although relative numbers changed seasonally between these areas, the estimated mean surface density of dolphins was highest along the coast in the spring of 2006 (9.564 dolphins/km², SE = 5.571). In Core and Pamlico Sounds the highest mean surface density occurred during the autumn of 2004 (0.192 dolphins/km², SE = 0.066). The estimated mean surface density of dolphins was lowest along the coast in the summer of 2004 (0.461 dolphins/km², SE = 0.294). The estimated mean surface density of dolphins was lowest in Core and Pamlico Sounds in the summer of 2005 (0.024 dolphins/km², SE = 0.011). In Pamlico Sound, estimated surface densities were greater in the eastern section except in the autumn. Dolphins were sighted throughout the entire range of mean SST (7.60°C to 30.82°C), with a tendency towards fewer dolphins sighted as water temperatures increased. Based on the findings of this study, sea turtles are most likely to be encountered within the OPAREAs when SST is ≥ 11°C. Since sea turtle distributions are generally limited by water temperature, knowing the SST of a given area is a useful predictor of sea turtle presence. Since dolphins were observed within estuarine waters year-round and throughout the entire range of mean SST’s, they likely could be encountered in the OPAREAs any time of the year. Although our findings indicated the greatest number of dolphins to be present in the winter and the least in the summer, their movements also may be related to other factors such as the availability of prey. (PDF contains 28 pages)

User’s Guide to ADMB2R: A Set of AD Model Builder Output Routines Compatible with the R Statistics Language

ADMB2R is a collection of AD Model Builder routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 ADMB2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the ADMB2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer ADMB2R to others in the hope that they will find it useful. (PDF contains 30 pages)

User’s Guide to C2R: A Set of C Language Output Routines Compatible with the R Statistics Language

C2R is a collection of C routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 C2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the C2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer C2R to others in the hope that they will find it useful. (PDF contains 27 pages)

User’s Guide to For2R: A Module of Fortran 95 Output Routines Compatible with the R Statistics Language

For2R is a collection of Fortran routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 For2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the For2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer For2R to others in the hope that they will find it useful. (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.)

Developing alternatives for optimal representation of seafloor habitats and associated communities in Stellwagen Bank National Marine Sanctuary

The implementation of various types of marine protected areas is one of several management tools available for conserving representative examples of the biological diversity within marine ecosystems in general and National Marine Sanctuaries in particular. However, deciding where and how many sites to establish within a given area is frequently hampered by incomplete knowledge of the distribution of organisms and an understanding of the potential tradeoffs that would allow planners to address frequently competing interests in an objective manner. Fortunately, this is beginning to change. Recent studies on the continental shelf of the northeastern United States suggest that substrate and water mass characteristics are highly correlated with the composition of benthic communities and may therefore, serve as proxies for the distribution of biological biodiversity. A detailed geo-referenced interpretative map of major sediment types within Stellwagen Bank National Marine Sanctuary (SBNMS) has recently been developed, and computer-aided decision support tools have reached new levels of sophistication. We demonstrate the use of simulated annealing, a type of mathematical optimization, to identify suites of potential conservation sites within SBNMS that equally represent 1) all major sediment types and 2) derived habitat types based on both sediment and depth in the smallest amount of space. The Sanctuary was divided into 3610 0.5 min2 sampling units. Simulations incorporated constraints on the physical dispersion of sampling units to varying degrees such that solutions included between one and four site clusters. Target representation goals were set at 5, 10, 15, 20, and 25 percent of each sediment type, and 10 and 20 percent of each habitat type. Simulations consisted of 100 runs, from which we identified the best solution (i.e., smallest total area) and four nearoptimal alternates. We also plotted total instances in which each sampling unit occurred in solution sets of the 100 runs as a means of gauging the variety of spatial configurations available under each scenario. Results suggested that the total combined area needed to represent each of the sediment types in equal proportions was equal to the percent representation level sought. Slightly larger areas were required to represent all habitat types at the same representation levels. Total boundary length increased in direct proportion to the number of sites at all levels of representation for simulations involving sediment and habitat classes, but increased more rapidly with number of sites at higher representation levels. There were a large number of alternate spatial configurations at all representation levels, although generally fewer among one and two versus three- and four-site solutions. These differences were less pronounced among simulations targeting habitat representation, suggesting that a similar degree of flexibility is inherent in the spatial arrangement of potential protected area systems containing one versus several sites for similar levels of habitat representation. We attribute these results to the distribution of sediment and depth zones within the Sanctuary, and to the fact that even levels of representation were sought in each scenario. (PDF contains 33 pages.)

Benthic habitat mapping in the Olympic Coast National Marine Sanctuary: Classification of side scan sonar data from survey HMPR-108-2002-01: Version I

In September 2002, side scan sonar was used to image a portion of the sea floor in the northern OCNMS and was mosaiced at 1-meter pixel resolution using 100 kHz data collected at 300-meter range scale. Video from a remotely-operated vehicle (ROV), bathymetry data, sedimentary samples, and sonar mapping have been integrated to describe geological and biological aspects of habitat and polygon features have been created and attributed with a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999). The data can be used with geographic information system (GIS) software for display, query, and analysis. Textural analysis of the sonar images provided a relatively automated method for delineating substrate into three broad classes representing soft, mixed sediment, and hard bottom. Microhabitat and presence of certain biologic attributes were also populated into the polygon features, but strictly limited to areas where video groundtruthing occurred. Further groundtruthing work in specific areas would improve confidence in the classified habitat map. (PDF contains 22 pages.)

Oceanographic results during VERTEX particle interceptor trap experiment 17 August to 8 September 1980

This report presents oceanographic data supporting the detailed chemical studies in the VERTEX Particle Interceptor Trap (PIT) experiment off the central California coast. Prior to the deployment of the PITs, an oceanographic survey of the intended study area was made on R/V CAYUSE from 17 to 21 August 1980. During this cruise, twenty CTD stations (Fig. 1) were occupied in a grid centered about the PIT site selected earlier based on archival oceanographic data. During the second leg of the VERTEX experiment from 25 August to 3 September, CTO profiles were taken as time permitted. In addition, a short survey near the PITs was made on 2 September. The intent of the pre-deployment cruise was to obtain data characterizing the vertical and horizontal variability of physical and chemical properties and to map the geostrophic flow field. Toward this end, vertical profiles of salinity, temperature and dissolved oxygen were made using a Plessey 9040 CTOa profiler. Considerable effort was expended to make vertical beam attenuation profiles to

Oceanographic observations from the eastern Pacific Ocean collected by the R/V Shoyo Maru, October 1963 – March 1964

ENGLISH: The Nankai Regional Fisheries Research Laboratory of Kochi, Japan conducted a long-line fishery exploration and hydrographic survey in the eastern Pacific Ocean aboard the R/V Shoyo Maru during October 1963- March 1964. An invitation to the Inter-American Tropical Tuna Commission to participate in the cruise gave its investigators the opportunity to make surface biological observations and to preserve water samples for subsequent analyses of nutrients. The result of this survey is a comprehensive body of physical, chemical and biological data covering a large portion of the eastern half of the Pacific Ocean. SPANISH: El Nankai Regional Fisheries Research Laboratory de Rochi, Japón, llevó a cabo una exploración pesquera con palangre y un reconocimiento hidrográfico en el Océano Pacífico oriental, a bordo del barco de investigación Shoyo Maru, desde octubre de 1963 hasta marzo de 1964. Una invitación dirigida a la Comisión Interamericana del Atún Tropical para participar en el crucero, confirió a sus investigadores la oportunidad de hacer observaciones biológicas superficiales y conservar muestras de agua para el subsiguiente análisis de los nutrientes. El resultado de este reconocimiento es un conjunto de datos físicos, químicos y biológicos que abarcan una gran parte del sector medio oriental del Océano Pacífico. (PDF contains 153 pages.)

Toxicity of Gramoxone super(R) and detergent to nile tilapia (Oreochromis niloticus) L. fingerlings

Acute toxicity tests on the effects of Gramoxone and detergent (both applied as a single dose) to nile tilapia, Oreochromis niloticus, fingerlings (mean weight 2.7~c1 g) were conducted using static bioassay. The 96-h LC sub(50) of Gramoxone and detergent applied were 0.08ml/l and 0.004 g/l, respectively. The fingerlings showed increased hyperactivities exemplified by erratic movement, loss of reflex, and hyperventilation during the period of exposure. These effects increased with increasing concentrations of Gramoxone or detergent throughout the duration of exposure. Tilapia fingerlings of the same size showed different levels of tolerance to the same concentration of both pollutants

Fundamental aspects of the feeding of the amphipod Gammarus (R.) balcanicus (Crustacea, Amphipoda). [Translation from: Nauchn.Dokl.vyssh.Shkoly (Biol.Nauk) 1970(7) 12-16, 1970]

The amphipods are major food items for many commercial fishes, and they are used as protein food for agricultural animals. In the present paper are presented the results of four-year observations on the feeding of Gammarus balcanicus in nature and in an aquarium. Among the studied aspects were the dependence of daily food ration on sex and physiological state (with and without eggs) and feeding on different kinds of plant food. The study concludes that Gammarus balcanicus willingly feed on soft half-decayed plant residues; into their ration also enters food of animal origin. In contrast to other amphipods, G. balcanicus eats representatives of its own species very rarely, and only dead or immobile ones.