EcoGIS – GIS tools for ecosystem approaches to fisheries management

Executive Summary: The EcoGIS project was launched in September 2004 to investigate how Geographic Information Systems (GIS), marine data, and custom analysis tools can better enable fisheries scientists and managers to adopt Ecosystem Approaches to Fisheries Management (EAFM). EcoGIS is a collaborative effort between NOAA’s National Ocean Service (NOS) and National Marine Fisheries Service (NMFS), and four regional Fishery Management Councils. The project has focused on four priority areas: Fishing Catch and Effort Analysis, Area Characterization, Bycatch Analysis, and Habitat Interactions. Of these four functional areas, the project team first focused on developing a working prototype for catch and effort analysis: the Fishery Mapper Tool. This ArcGIS extension creates time-and-area summarized maps of fishing catch and effort from logbook, observer, or fishery-independent survey data sets. Source data may come from Oracle, Microsoft Access, or other file formats. Feedback from beta-testers of the Fishery Mapper was used to debug the prototype, enhance performance, and add features. This report describes the four priority functional areas, the development of the Fishery Mapper tool, and several themes that emerged through the parallel evolution of the EcoGIS project, the concept and implementation of the broader field of Ecosystem Approaches to Management (EAM), data management practices, and other EAM toolsets. In addition, a set of six succinct recommendations are proposed on page 29. One major conclusion from this work is that there is no single “super-tool” to enable Ecosystem Approaches to Management; as such, tools should be developed for specific purposes with attention given to interoperability and automation. Future work should be coordinated with other GIS development projects in order to provide “value added” and minimize duplication of efforts. In addition to custom tools, the development of cross-cutting Regional Ecosystem Spatial Databases will enable access to quality data to support the analyses required by EAM. GIS tools will be useful in developing Integrated Ecosystem Assessments (IEAs) and providing pre- and post-processing capabilities for spatially-explicit ecosystem models. Continued funding will enable the EcoGIS project to develop GIS tools that are immediately applicable to today’s needs. These tools will enable simplified and efficient data query, the ability to visualize data over time, and ways to synthesize multidimensional data from diverse sources. These capabilities will provide new information for analyzing issues from an ecosystem perspective, which will ultimately result in better understanding of fisheries and better support for decision-making. (PDF file contains 45 pages.)

Juvenile and small resident fishes of Florida Bay, a critical habitat in the Everglades National Park, Florida

This compendium presents information on the life history, diet, and abundance and distribution of 46 of the more abundant juvenile and small resident fish species, and data on three species of seagrasses in Florida Bay, Everglades National Park. Abundance and distribution of fish data were derived from three sampling schemes: (1) an otter trawl in basins (1984–1985, 1994–2001), (2) a surface trawl in basins (1984–1985), and (3) a surface trawl in channels (1984–1985). Results from surface trawling only included pelagic species. Collections made with an otter trawl in basins on a bi-monthly basis were emphasized. Nonparametric statistics were used to test spatial and temporal differences in the abundance of species and seagrasses. Fish species accounts were presented in four sections – Life history, Diet, Abundance and distribution, and Length-frequency distributions. Although Florida Bay is a subtropical estuary, the majority of fish species (76%) had warm-temperate affinities; i.e., only 24% were solely tropical species. The five most abundant species collected, in descending order, by (1) otter trawl in basins were: Eucinostomus gula, Lucania parva, Anchoa mitchilli, Lagodon rhomboides, and Syngnathus scovelli; (2) surface trawl in basins were: Hyporhamphus unifasciatus, Strongylura notata, Chriodorus atherinoides, Anchoa hepsetus, and Atherinomorus stipes; (3) surface trawl in channels were: Hypoatherina harringtonensis, A. stipes, A. mitchelli, H. unifasciatus, and C. atherinoides. (PDF file contains 219 pages.)

Deep reef fish surveys by submersible on Alderdice, McGrail, and Sonnier Banks in the Northwestern Gulf of Mexico

Submersible surveys at numerous reefs and banks in the northwestern Gulf of Mexico (NWGOM) were conducted as part of the Sustainable Seas Expedition (SSE) during July/August 2002 to identify reef fish communities, characterize benthic habitats, and identify deep coral reef ecosystems. To identify the spatial extent of hard bottom reef communities, the Flower Garden Banks National Marine Sanctuary (FGBNMS) and the U.S. Geological Survey (USGS) mapped approximately 2000 km2 of the Northwestern Gulf of Mexico (NWGOM) continental shelf during June 2002 with high-resolution multibeam bathymetry. Previous investigations conducted on the features of interest (with the exceptions of East and West Flower Garden and Sonnier Banks, accessible by SCUBA) had not been conducted since the 1970s and 1980s, and did not have the use of high-resolution maps to target survey sites. The base maps were instrumental in navigating submersibles to specific features at each study site during the Sustainable Seas Expedition (SSE)—a submersible effort culminating from a partnership between the National Atmospheric and Oceanic Administration (NOAA) and the National Geographic Society (NGS). We report the initial findings of our submersible surveys, including habitat and reef fish diversity at McGrail, Alderdice, and Sonnier Banks. A total of 120 species and 40,724 individuals were identified from video surveys at the three banks. Planktivorous fishes constituted over 87% by number for the three banks, ranging from 81.4% at Sonnier Banks to 94.3% at Alderdice Bank, indicating a direct link to pelagic prey communities, particularly in the deep reef zones. High numbers of groupers, snappers, jacks, and other fishery species were observed on all three features. These sites were nominated as Habitat Areas of Particular Concern (HAPC) by the Gulf of Mexico Fishery Council in March 2004. Data obtained during this project will contribute to benthic habitat characterization and assessment of the associated fish communities through future SCUBA, ROV, and submersible missions, and allow comparisons to other deep reef ecosystems found throughout the Gulf of Mexico and western Atlantic Ocean.

Acoustic signatures of the seafloor: Tools for predicting grouper habitat

Groupers are important components of commercial and recreational fisheries. Current methods of diver-based grouper census surveys could potentially benefit from development of remotely sensed methods of seabed classification. The goal of the present study was to determine if areas of high grouper abundance have characteristic acoustic signatures. A commercial acoustic seabed mapping system, QTC View Series V, was used to survey an area near Carysfort Reef, Florida Keys. Acoustic data were clustered using QTC IMPACT software, resulting in three main acoustic classes covering 94% of the area surveyed. Diver-based data indicate that one of the acoustic classes corresponded to hard substrate and the other two represented sediment. A new measurement of seabed heterogeneity, designated acoustic variability, was also computed from the acoustic survey data in order to more fully characterize the acoustic response (i.e., the signature) of the seafloor. When compared with diver-based grouper census data, both acoustic classification and acoustic variability were significantly different at sites with and without groupers. Sites with groupers were characterized by hard bottom substrate and high acoustic variability. Thus, the acoustic signature of a site, as measured by acoustic classification or acoustic variability, is a potentially useful tool for stratifying diver sampling effort for grouper census.

Detecting fish aggregations from reef habitats mapped with high resolution side scan sonar imagery

As part of a multibeam and side scan sonar (SSS) benthic survey of the Marine Conservation District (MCD) south of St. Thomas, USVI and the seasonal closed areas in St. Croix—Lang Bank (LB) for red hind (Epinephelus guttatus) and the Mutton Snapper (MS) (Lutjanus analis) area—we extracted signals from water column targets that represent individual and aggregated fish over various benthic habitats encountered in the SSS imagery. The survey covered a total of 18 km2 throughout the federal jurisdiction fishery management areas. The complementary set of 28 habitat classification digital maps covered a total of 5,462.3 ha; MCDW (West) accounted for 45% of that area, and MCDE (East) 26%, LB 17%, and MS the remaining 13%. With the exception of MS, corals and gorgonians on consolidated habitats were significantly more abundant than submerged aquatic vegetation (SAV) on unconsolidated sediments or unconsolidated sediments. Continuous coral habitat was the most abundant consolidated habitat for both MCDW and MCDE (41% and 43% respectively). Consolidated habitats in LB and MS predominantly consisted of gorgonian plain habitat with 95% and 83% respectively. Coral limestone habitat was more abundant than coral patch habitat; it was found near the shelf break in MS, MCDW, and MCDE. Coral limestone and coral patch habitats only covered LB minimally. The high spatial resolution (0.15 m) of the acquired imagery allowed the detection of differing fish aggregation (FA) types. The largest FA densities were located at MCDW and MCDE over coral communities that occupy up to 70% of the bottom cover. Counts of unidentified swimming objects (USOs), likely representing individual fish, were similar among locations and occurred primarily over sand and shelf edge areas. Fish aggregation school sizes were significantly smaller at MS than the other three locations (MCDW, MCDE, and LB). This study shows the advantages of utilizing SSS in determining fish distributions and density.

Integration of technologies for understanding the functional relationship between reef habitat and fish growth and production

Functional linkage between reef habitat quality and fish growth and production has remained elusive. Most current research is focused on correlative relationships between a general habitat type and presence/absence of a species, an index of species abundance, or species diversity. Such descriptive information largely ignores how reef attributes regulate reef fish abundance (density-dependent habitat selection), trophic interactions, and physiological performance (growth and condition). To determine the functional relationship between habitat quality, fish abundance, trophic interactions, and physiological performance, we are using an experimental reef system in the northeastern Gulf of Mexico where we apply advanced sensor and biochemical technologies. Our study site controls for reef attributes (size, cavity space, and reef mosaics) and focuses on the processes that regulate gag grouper (Mycteroperca microlepis) abundance, behavior and performance (growth and condition), and the availability of their pelagic prey. We combine mobile and fixed-active (fisheries) acoustics, passive acoustics, video cameras, and advanced biochemical techniques. Fisheries acoustics quantifies the abundance of pelagic prey fishes associated with the reefs and their behavior. Passive acoustics and video allow direct observation of gag and prey fish behavior and the acoustic environment, and provide a direct visual for the interpretation of fixed fisheries acoustics measurements. New application of biochemical techniques, such as Electron Transport System (ETS) assay, allow the in situ measurement of metabolic expenditure of gag and relates this back to reef attributes, gag behavior, and prey fish availability. Here, we provide an overview of our integrated technological approach for understanding and quantifying the functional relationship between reef habitat quality and one element of production – gag grouper growth on shallow coastal reefs.

The distribution and size composition of finfish, American lobster, and long-finned squid in Long Island Sound based on the Connecticut Fisheries Division Bottom Trawl Survey, 1984–1994

The distribution, abundance, and length composition of marine finfish, lobster, and squid in Long Island Sound were examined relative to season and physical features of the Sound, using Connecticut Department of Environmental Protection trawl survey data collected from 1984 to 1994. The following are presented: seasonal distribution maps for 59 species, abundance indices for 41 species, and length frequencies for 26 species. In addition, a broader view of habitat utilization in the Sound was examined by mapping aggregated catches (total catch per tow, demersal catch per tow, and pelagic catch per tow) and by comparing species richness and mean aggregate catch/tow by analysis of variance (ANOVA) among eight habitat types defined by depth interval and bottom type. For many individual species, seasonal migration patterns and preference for particular areas within Long Island Sound were evident. The aggregate distribution maps show that overall abundance was lower in the eastern Sound than the central and western portions. Demersal and pelagic temporal abundance show opposite trends—demersals were abundant in spring and declined through summer and fall, whereas pelagic abundance was low in spring and increased into fall. The analysis of habitat types revealed significant differences for both species richness and mean catch per tow. Generally, species richness was highest in habitats within the central area of the Sound and lowest in eastern habitats. The aggregate mean catch was highest in the western and central habitats, and declined eastward. (PDF file contains 199 pages.)

Southeastern U.S. Deepwater Reef Fish Assemblages, Habitat Characteristics, Catches, and Life History Summaries

There are 19 economically important reef fish species in the deepwater (l00-300 m) fishery of the southeastern United States. Five species make up the majority (over 97% by weight) of the catch. In descending order of total landings for 1995, they are: tilefish, Lopholatilus chamaeleonticeps, snowy grouper, Epinephelus niveatus, blueline tilefish, Caulolatilus microps, warsaw grouper, Epinephelus nigritus, and yellowedge grouper, E. flavolimbatus. Life history summaries and estimates of catches from 1972 through 1995 for 14 species are described. (PDF file contains 45 pages.)

NOAA Coastal Change Analysis Program (C-CAP): Guidance for Regional Implementation

EXECUTIVE SUMMARY: The Coastal Change Analysis Programl (C-CAP) is developing a nationally standardized database on landcover and habitat change in the coastal regions of the United States. C-CAP is part of the Estuarine Habitat Program (EHP) of NOAA's Coastal Ocean Program (COP). C-CAP inventories coastal submersed habitats, wetland habitats, and adjacent uplands and monitors changes in these habitats on a one- to five-year cycle. This type of information and frequency of detection are required to improve scientific understanding of the linkages of coastal and submersed wetland habitats with adjacent uplands and with the distribution, abundance, and health of living marine resources. The monitoring cycle will vary according to the rate and magnitude of change in each geographic region. Satellite imagery (primarily Landsat Thematic Mapper), aerial photography, and field data are interpreted, classified, analyzed, and integrated with other digital data in a geographic information system (GIS). The resulting landcover change databases are disseminated in digital form for use by anyone wishing to conduct geographic analysis in the completed regions. C-CAP spatial information on coastal change will be input to EHP conceptual and predictive models to support coastal resource policy planning and analysis. CCAP products will include 1) spatially registered digital databases and images, 2) tabular summaries by state, county, and hydrologic unit, and 3) documentation. Aggregations to larger areas (representing habitats, wildlife refuges, or management districts) will be provided on a case-by-case basis. Ongoing C-CAP research will continue to explore techniques for remote determination of biomass, productivity, and functional status of wetlands and will evaluate new technologies (e.g. remote sensor systems, global positioning systems, image processing algorithms) as they become available. Selected hardcopy land-cover change maps will be produced at local (1:24,000) to regional scales (1:500,000) for distribution. Digital land-cover change data will be provided to users for the cost of reproduction. Much of the guidance contained in this document was developed through a series of professional workshops and interagency meetings that focused on a) coastal wetlands and uplands; b) coastal submersed habitat including aquatic beds; c) user needs; d) regional issues; e) classification schemes; f) change detection techniques; and g) data quality. Invited participants included technical and regional experts and representatives of key State and Federal organizations. Coastal habitat managers and researchers were given an opportunity for review and comment. This document summarizes C-CAP protocols and procedures that are to be used by scientists throughout the United States to develop consistent and reliable coastal change information for input to the C-CAP nationwide database. It also provides useful guidelines for contributors working on related projects. It is considered a working document subject to periodic review and revision.(PDF file contains 104 pages.)

Benthic macrofauna and habitat monitoring on the Continental Shelf of the northeastern United States: I. Biomass

Information on long-term temporal variability of and trends in benthic community-structure variables, such as biomass, is needed to estimate the range of normal variability in comparison with the effects of environmental change or disturbance. Fishery resource distribution and population growth will be influenced by such variability. This study examines benthic macrofaunal biomass and related data collected annually between 1978 and 1985 at 27 sites on the continental shelf of the northwestern Atlantic, from North Carolina to the southern Gulf of Maine. The study was expanded at several sites with data from other studies collected at the same sites prior to 1978. Results indicate that although there was interannual and seasonal variability, as expected, biomass levels over the study period showed few clear trends. Sites exhibiting trends were either in pollution-stressed coastal areas or influenced by the population dynamics of one or a few species, especially echinoderms. (PDF file contains 34 pages.)

Species composition, distribution, and relative abundance of fishes in the coastal habitat off the southeastern United States

Ichthyofauna of the coastal «10 m depth) habitat of the South Atlantic Bight were investigated between Cape Fear, North Carolina, and the St. John's River, Florida. Trawl collections from four nonconsecutive seasons in the period July 1980 to December 1982 indicated that the fish community is dominated by the family Sciaenidae, particularly juvenile forms. Spot (Leiostomus xanthurus) and Atlantic croaker (Micropogonias undulatus) were the two most abundant species and dominated catches during all seasons. Atlantic menhaden (Brevoortin tyrannus) was also very abundant, but only seasonally (winter and spring) dominant in the catches. Elasmobranch fIShes, especially rajiforms and carcharinids, contributed to much of the biomass of fishes collected. Total fish abundance was greatest in winter and lowest in summer and was influenced by the seasonality of Atlantic menhaden and Atlantic croaker in the catches. Biomass was highest in spring and lowest in summer, and was influenced by biomass of spot. Fish density ranged from 321 individuals and 12.2 kg per hectare to 746 individuals and 25.2 kg per hectare. Most species ranged widely throughout the bight, and showed some evidence of seasonal migration. Species assemblages were dominated by ubiquitous year-round residents of the coastal waters of the bight. Diversity (H') was highest in summer, and appeared influenced by the evenness of distribution of individuals among species. (PDF file contains 56 pages.)

Evaluation of salmon and steelhead spawning habitat quality in the South Fork Trinity River Basin, 1997

Sediment sampling was used to evaluate chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) spawning habitat quality in the South Fork Trinity River (SFTR) basin. Sediment samples were collected using a McNeil-type sampler and wet sieved through a series of Tyler screens (25.00 mm, 12.50 mm, 6.30 mm, 3.35 mm, 1.00 mm, and 0.85 mm). Fines (particles < 0.85 mm) were determined after a l0-minute settling period in Imhoff cones. Thirteen stations were sampled in the SFTR basin: five stations were located in mainstem SFTR between rk 2.1 and 118.5, 2 stations each were located in EF of the SFTR, Grouse Creek, and Madden Creek, and one station each was located in Eltapom and Hayfork Creeks. Sample means for fines(particles < 0.85 mm) fer SFTR stations ranged between 14.4 and 19.4%; tributary station sample mean fines ranged between 3.4 and 19.4%. Decreased egg survival would be expected at 4 of 5 mainstem SFTR stations and at one station in EF of SFTR and Grouse Creek where fines content exceed 15%. Small gravel/sand content measured at all stations were high, and exceed levels associated with reduced sac fry emergence rates. Reduction of egg survival or sac fry emergence due to sedimentation in spawning gravels could lead to reduced juvenile production from the South Fork Trinity River. (PDF contains 18 pages.)

Limited resources? Let the habitat priority planner help!

In this time of scarce resources, coastal resource managers must find ways to prioritize conservation, land use, and restoration efforts. The Habitat Priority Planner (HPP) is a free geospatial tool created by the National Oceanic and Atmospheric Administration’s Coastal Services Center that has received wide praise for its ease of use and broad applicability to conservation strategic planning, restoration, climate change scenarios, and other natural resource management actions. Not a geographic information system (GIS) user? Don’t worry―this tool was designed to be used in a team setting. One intermediate-level GIS user can push the buttons to show quick results while a roomful of resource managers and stakeholders provide input criteria that determine the results. The Habitat Priority Planner is a toolbar for ESRI’s ArcGIS platform that is composed of three modules: Habitat Classification, Habitat Analysis, and Data Explorer. The tool calculates basic ecological statistics that are used to examine how habitats function within a landscape. The tool pre‐packages several common landscape metrics into a user‐friendly interface for intermediate GIS users. In addition, HPP allows the user to build queries interactively using a graphical interface for demonstrating criteria selections quickly in a visual manner that is useful in stakeholder interactions. Tool advocates and users include land trusts, conservation alliances, nonprofit organizations, and select National Estuarine Research Reserves and refuges of the U.S. Fish and Wildlife Service. Participants in this session will learn the basic requirements for HPP use and the multiple ways the HPP has been applied to geographies nationwide. (PDF contains 5 pages)

Habitat enhancing marine structures: Creating habitat in urban waters

Although maritime regions support a large portion of the world’s human population, their value as habitat for other species is overlooked. Urban structures that are built in the marine environment are not designed or managed for the habitat they provide, and are built without considering the communities of marine organisms that could colonize them (Clynick et al., 2008). However, the urban waterfront may be capable of supporting a significant proportion of regional aquatic biodiversity (Duffy-Anderson et al., 2003). While urban shorelines will never return to their original condition, some scientists think that the habitat quality of urban waterfronts could be significantly improved through further research and some design modifications, and that many opportunities exist to make these modifications (Russel et al., 1983, Goff, 2008). Habitat enhancing marine structures (or HEMS) are a potentially promising approach to address the impact of cities on marine organisms including habitat fragmentation and degradation. HEMS are a type of habitat improvement project that are ecologically engineered to improve the habitat quality of urban marine structures such as bulkheads and docks for marine organisms. More specifically, HEMS attempt to improve or enhance the physical habitat that organisms depend on for survival in the inter- and sub-tidal waterfronts of densely populated areas. HEMS projects are targeted at areas where human-made structures cannot be significantly altered or removed. While these techniques can be used in suburban or rural areas restoration or removal is preferred in these settings, and HEMS are resorted to only if removal of the human-made structure is not an option. Recent research supports the use of HEMS projects. Researchers have examined the communities found on urban structures including docks, bulkheads, and breakwaters. Complete community shifts have been observed where the natural shoreline was sandy, silty, or muddy. There is also evidence of declines in community composition, ecosystem functioning, and increases in non-native species abundances in assemblages on urban marine structures. Researchers have identified two key differences between these substrates including the slope (seawalls are vertical; rocky shores contain multiple slopes) and microhabitat availability (seawalls have very little; rocky shores contain many different types). In response, researchers have suggested designing and building seawalls with gentler slopes or a combination of horizontal and vertical surfaces. Researchers have also suggested incorporating microhabitat, including cavities designed to retain water during low tide, crevices, and other analogous features (Chapman, 2003; Moreira et al., 2006) (PDF contains 4 pages)

Predicting the effects of climate change on sea turtle nesting habitat in Florida

Rising global temperatures threaten the survival of many plant and animal species. Having already risen at an unprecedented rate in the past century, temperatures are predicted to rise between 0.3 and 7.5C in North America over the next 100 years (Hawkes et al. 2007). Studies have documented the effects of climate warming on phenology (timing of seasonal activities), with observations of early arrival at breeding grounds, earlier ends to the reproductive season, and delayed autumnal migrations (Pike et al. 2006). In addition, for species not suited to the physiological demands of cold winter temperatures, increasing temperatures could shift tolerable habitats to higher latitudes (Hawkes et al. 2007). More directly, climate warming will impact thermally sensitive species like sea turtles, who exhibit temperature-dependent sexual determination. Temperatures in the middle third of the incubation period determine the sex of sea turtle offspring, with higher temperatures resulting in a greater abundance of female offspring. Consequently, increasing temperatures from climate warming would drastically change the offspring sex ratio (Hawkes et al. 2007). Of the seven extant species of sea turtles, three (leatherback, Kemp’s ridley, and hawksbill) are critically endangered, two (olive ridley and green) are endangered, and one (loggerhead) is threatened. Considering the predicted scenarios of climate warming and the already tenuous status of sea turtle populations, it is essential that efforts are made to understand how increasing temperatures may affect sea turtle populations and how these species might adapt in the face of such changes. In this analysis, I seek to identify the impact of changing climate conditions over the next 50 years on the availability of sea turtle nesting habitat in Florida given predicted changes in temperature and precipitation. I predict that future conditions in Florida will be less suitable for sea turtle nesting during the historic nesting season. This may imply that sea turtles will nest at a different time of year, in more northern latitudes, to a lesser extent, or possibly not at all. It seems likely that changes in temperature and precipitation patterns will alter the distribution of sea turtle nesting locations worldwide, provided that beaches where the conditions are suitable for nesting still exist. Hijmans and Graham (2006) evaluate a range of climate envelope models in terms of their ability to predict species distributions under climate change scenarios. Their results suggested that the choice of species distribution model is dependent on the specifics of each individual study. Fuller et al. (2008) used a maximum entropy approach to model the potential distribution of 11 species in the Arctic Coastal Plain of Alaska under a series of projected climate scenarios. Recently, Pike (in press) developed Maxent models to investigate the impacts of climate change on green sea turtle nest distribution and timing. In each of these studies, a set of environmental predictor variables (including climate variables), for which ‘current’ conditions are available and ‘future’ conditions have been projected, is used in conjunction with species occurrence data to map potential species distribution under the projected conditions. In this study, I will take a similar approach in mapping the potential sea turtle nesting habitat in Florida by developing a Maxent model based on environmental and climate data and projecting the model for future climate data. (PDF contains 5 pages)