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Project Work Plan

U.S. Geological Survey Greater Everglades Science Initiative (Place-Based Studies)

Fiscal Year 2004 Project Work Plan


Project Title: Quantitative Sampling of Freshwater Fish Species within the Big Cypress National Preserve: A Long-Term Research Program to Evaluate the Ecological Effects of CERP. (Continuation of FY02 project entitled: Inventory of Freshwater Fish Species within the Big Cypress National Preserve, with emphasis on methods testing to design a long-term, aquatic-biota sampling program).
Project Start Date: 10/2002 Project End Date: 09/2006
Funding Source: USGS Place-Based Studies Initiative (PBS), NPS Inventory and Monitoring Program, National Audubon Society (NAS)
Principal Investigator(s): William F. Loftus (USGS)
Email address: bill_loftus@usgs.gov
Phone: (305) 242-7835 Fax: 305-242-7836
Mail address: FISC-CWRS, Everglades National Park Field Station, 40001 State Route 9336, Homestead FL 33034
Other Investigator(s): Jerome J. Lorenz
Email address: jlorenz@audubon.org
Phone: (305) 852-5092 Fax: (305) 852-8012
Mail address: Audubon of Florida, 115 Indian Mound Trail, Tavernier FL 33070

Project Summary: Although a major ecosystem of the South Florida area, the Big Cypress National Preserve (BICY), is poorly understood in biological terms. To detect changes in natural and artificial habitats resulting from CERP restoration programs, baseline data on constituent aquatic communities and their ecology are needed before and after restoration actions. Fishes and aquatic invertebrates serve as indicators of the health of these wetlands. These organisms are also important because they are major prey for many of the characteristic South Florida predatory species, especially alligators and wading birds. This project will establish a long-term, quantitative monitoring program for prey-base aquatic organisms and is intended to detect changes in aquatic-animal populations resulting from CERP hydrologic alterations.

Project Objectives and Strategy: This project has several objectives, the foremost of which is to continue a program of aquatic study in BICY begun in 2002. Work will be performed in partnership with National Audubon Society (NAS) and the National Park Service to design and implement a spatially and temporally explicit, quantitative sampling program for aquatic animals in BICY. This program will 1) provide baseline data which may be used to track changes in hydrology as a result of CERP projects 2) document the distribution, composition, and habitat use by native and introduced aquatic animals to evaluate the effects of CERP on BICY aquatic habitats, 3) provide ecological data for use in the ATLSS fish simulation model used to plan and evaluate restoration actions during CERP (presently, inappropriate data from the Everglades are being used in the model for cells that lie in BICY). The strategy used to accomplish these goals will be to employ techniques used by the co-principal investigators in establishing monitoring programs in the Everglades (since 1977) and the mangrove zone of Florida Bay (since 1989).

Potential Impacts and Major Products: Clients from Big Cypress NP are partnering in this effort to obtain the first detailed, quantitative data about aquatic communities in that system by providing office space, logistical support in helicopter/fixed-wing flights, airboat and swamp buggy transport for sampling, etc. This input indicates the level of interest in this project. The data gathered and interpreted from this study will be publishable as the first extensive data set from this large ecosystem. Those data are providing information not only on the native fauna but also on the exotic fauna, and has produced first records for several introduced species in the Preserve already. These baseline data will allow comparison of conditions throughout aquatic habitats in the Swamp prior to CERP projects, and if funding permits, during and after CERP implementation. We anticipate a monograph on the fishes of the Big Cypress NP, papers on community dynamics and effects of water management changes on those communities, and extensive data for refining the ATLSS fish model for this ecosystem.

Collaborators: National Audubon Society

Clients: BICY


Title of Task 1: Long-term aquatic community research within the Big Cypress National Preserve
Task Funding: USGS’s Greater Everglades Science Program (PBS Initiative), NPS Inventory and Monitoring Program, National Audubon Society (NAS)
Task Leaders: William F. Loftus
Phone: (305) 242-7835
FAX: 305-242-7836
Task Status (proposed or active): Active
Task priority: (Medium)
Task Personnel: Jerome J. Lorenz (NAS), Greg Ellis (NAS) Marcus Zokan (NAS)

Task Summary and Objectives: The Big Cypress Swamp ecosystem covers a large area of southwestern Florida, yet has been poorly studied compared with the Everglades. The Department of Interior is responsible for management of the Big Cypress National Preserve (BICY), which comprises much of this ecosystem, and several smaller National Wildlife Refuges. Human-induced changes have affected the natural variability of environmental conditions through the construction of canals and levees that can either act to drain or flood wetlands (Gunderson and Loftus 1993). Levees act as barriers to animal movement among habitats, probably preventing mixing of populations and access to refuges. Canals are conduits for movements by animals, serve as artificial refuges for native and introduced large-bodied fishes, and may be sinks for small fishes and invertebrates produced by adjacent wetlands. The Big Cypress Swamp landscape has been affected by all of these anthropogenic activities, yet their effects are unclear because of the lack of study. However there can be little doubt that the standing stocks of aquatic animals and their population sizes have been affected negatively by those activities.

The goal of this project in FY04 is to develop and implement sampling methods for a long-term aquatic biota research program for the Big Cypress National Preserve. We propose to describe large and small fish and macro-invertebrate ecology in representative habitats of the Swamp from FY04 to FY06 to provide basic inventory information on Swamp communities and ecological data for use in the ATLSS fish simulation model. The model is used to plan and evaluate restoration actions during CERP. Presently, inappropriate data from the Everglades are used in the model for cells representing the Swamp.

Fishes are essential to the successful functioning of wetlands in southern Florida through their roles as prey and predators. Any changes that reduce the population sizes, community composition, or availability of aquatic animals will affect all facets of the ecology of these wetlands. Communities of small-bodied fishes have been studied in EVER since 1977 by using throw traps in spikerush marshes at many Everglades sites (Loftus and Eklund 1994, Trexler et al. 2002). The data analyses allow evaluation of seasonal and long-term dynamics, shifts in relative abundance and size-structure, and produce correlations of fish abundance to water depth, hydroperiod, and plant community structure.

Several programs (ModWaters, CERP) to restore lost structure and function to the South Florida landscape are now being planned. To have the ability to detect changes in natural and artificial habitats resulting from these restoration programs, baseline data on the constituent aquatic communities and their ecology are needed before, during, and after restoration actions. Baseline data collections are also needed to document animal community composition, ecology, and dynamics, because those animals support many of the predatory species, especially alligators and wading birds. Fishes and aquatic invertebrates can serve as indicators of the health of these wetlands. The data collected here will provide important inventory information about the aquatic animals that inhabit the system, and will also examine the relationships of the animals with the hydrological regimes.

This project has several objectives, the foremost of which is to begin a program of aquatic study in a large and relatively neglected ecosystem. Future studies should investigate the differences between aquatic animal communities in the Big Cypress and Everglades systems as a construct around which to test ideas. In this project, the main objectives are:

  • Work with partners from National Audubon Society (NAS) and clients from the National Park Service to establish a sampling program for freshwater fishes and invertebrates in the Big Cypress National Preserve (BICY) that will address the needs of a long-term research and monitoring program. Program should complement sampling program in the Everglades system that has been running for nearly 30 years (Loftus and Eklund 1994; Trexler et al. 2002).
  • Document the distribution, composition, community dynamics, and habitat use by native and introduced fishes and invertebrates with relation to hydrology to provide a baseline of data for CERP.
  • Work with ATLSS modelers to provide data and model rules to refine existing model.

In 2002, NPS funded NAS as a CESU-partner to perform the inventory of freshwater fishes of BICY. However, the funding level was inadequate. The USGS PI was able to obtain PBS funds to match the NPS funds, thereby partnering with NAS to support a more rigorously scientific inventory of BICY that has served as the basis for a long-term program of research. BICY will be affected by CERP activities and will need baseline data on fish fauna as will as long-term study of community structure and function. Those data will provide the necessary to understand the effects of CERP on the fauna. The NAS and USGS project leaders plan and direct the project. USGS is also providing sampling gear, such as electrofishing equipment, to enable successful completion of the project.

Work to be undertaken during the proposal year and a description of the methods and procedures:

Specific sampling locations will be selected based on consultations with BICY hydrology staff and will be identified in the FY03 annual report (due September 30). Accessibility, and potential accuracy and precision of sampling gear, will be taken into account when selecting study sites. In general, locations for monitoring will be selected based on the potential to gather data for CERP projects that will affect hydrology. We anticipate that the most conspicuous effects will occur along the boarders of the Preserve. In particular, the Decompartmentalization of WCA3 Project will alter freshwater flows along the eastern and southern peripheries. The proximal impact of the project will be along the eastern boundary of the Preserve, but the effects will also be transmitted downstream to the ecotonal areas between the freshwater and estuarine areas of the Preserve. Those regions will receive the most sampling attention. However, the western and northern boundaries may also be affected by CERP projects. In particular, the western Preserve may be affected by restoration efforts in the Southern Golden Glades Estates region and the northern boundary by replumbing activities in the Seminole and Miccosukee reservation abutting the Preserve. Although these effects may not be as pronounced as the eastern and southern areas, there is a possibility for hydrologic changes. Furthermore, it is important to have "reference" sites as part of a long-term sampling program. Low-impact areas of the Preserve will serve as "control" sites within our natural experiment so that the magnitude of changes in the high-impact areas may be measured using a BACI design (Before-After-Control-Impact comparisons). Sampling locations in the interior and along the western periphery should be ideal candidates for low-impact sampling sites.

Similar suites of aquatic habitats within these sectors will be routinely sampled. Our preliminary results suggest that cypress sloughs, freshwater prairies and marshes, and ecotonal swamps and marshes may be ideal for monitoring sites. Sampling within these habitat types will be stratified between ephemeral wetlands and deep-water, dry season refugia for aquatic organisms. For example, alligator holes or ditches adjacent to wetlands will be routinely sampled to quantify the seasonal movements of fishes along a depth gradient. The concentration of prey species into these refugia is particularly important to understanding wading-bird foraging patterns within the Big Cypress region.

The habitat being sampled will determine the sampling protocols. We will use the sampling protocol established in the cooperative program for the Everglades, to the extent possible to allow comparability of data (Trexler et al. 2002). This will allow for linkages between the data collection in the Big Cypress Swamp to adjacent regions within the Greater Everglades. The goal would be to produce a system-wide tracking of aquatic animal communities, and will utilize the different habitat conditions in the regional compartments to assess animal responses. However, it must be recognized that habitats within the Preserve are more diverse than in the Everglades and will require that other methods be used in unique habitats. The findings of the first-year pilot study allow us to suggest the following sampling designs for target habitats. However, until monitoring sites are established it must be recognized that our approach must be somewhat plastic so as to adapt to unforeseen inherent idiosyncrasies associated with any sampling site.

In shallow marsh habitats, the throw trap and drift-fence/minnow-trap arrays (Loftus et al. 2002) used in EVER will be used to collect fishes and invertebrates. In forested areas, complex root and stem systems preclude the use of throw traps, so a modified drop trap method will be substituted for throw trapping, however, the drift-fence arrays will still be useful in these areas. In deep strands, alligator holes, and ditches, we plan to use a boat-mounted electrofisher to sample larger species (Nelson and Loftus 1996). Specimens will be preserved and returned to the laboratory for identification and enumeration. The specimens will be saved as vouchers and for processing for life-history data. Large-bodied species will mainly be field-processed and returned alive, except for voucher and life-history samples. Correlative hydrological data will be gathered as discontinuous data from local staff gauges, and as continuous daily data from recording stations. Ancillary habitat data on vegetation cover and local water depths will be taken. We will purchase data-logging water-quality units to record seasonal physico-chemical characteristics of the habitats, such as dissolved oxygen, pH, specific conductance, and temperature. During the dry season, it will be necessary to reach sample sites by hiring or borrowing a swamp buggy and/or helicopter, or by ATV’s. In wet periods, the USGS airboat and a van will be used for transport.

We anticipate sampling five times per year in February (winter), April (dry season), July (summer), October (wet season), and December (transition between wet and dry). This schedule uses the successful elements from the Everglades program-sampling regime to this study to reduce the amount of method development. The number of monitoring sites established will be ambitious and will cover all suitable habitat types along the Preserve periphery as described above. However, the actual number of sites will depend on the effort needed to sampling them and the resources available. The collection effort should be supported for a minimum of three years to sample across a range of climatic conditions.

Planned Outreach:

We plan to make presentations at the Big Cypress National Preserve and at regional scientific meetings, particularly GEER, to discuss our results. The Everglades database is being used to develop the fish simulation model used in evaluating restoration scenarios and reconstructing historical communities. There are no such quantitative data for the Big Cypress Swamp ecosystem. That lack of baseline data limits the assessment of future restoration actions in that ecosystem. This study will address that need. The lack of information also affects the ability to judge whether restoration actions meet Performance Measure Success criteria, in part because there are no baseline data for aquatic communities in this region. The data will improve the ATLSS fish model, which now inappropriately applies Everglades information to the Big Cypress landscape model. Data specific to this federally managed ecosystem will provide confidence and credibility in the tools used in restoring this region.


This study provides quantification of the ecological responses of the fish community to CERP- induced changes in the hydrology of BICY (thereby linking this project to the agency mission of assisting in the management of DOI property). The project will provide baseline data that then may be used to track changes in hydrology as a result of CERP projects. The baseline data also will provide ecological inputs for use in ATLSS fish-simulation model used to plan and evaluate restoration actions. The data will also provide valuable information on the role of aquatic refugia for aquatic fauna and the degree of incursion by non-indigenous fish species in natural habitats of this system. CERP projects that will influence BICY hydrology include Decompartmentalization of WCA3 and the SW Florida Feasibility Projects.

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