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Big Cypress National Preserve Fish Inventory & Monitoring Data

Fish Inventory Database Methodology | Fish Monitoring and Assessment Methodology

Methods for Big Cypress National Preserve Fish Inventory Database

Sampling was conducted according to a stratified design based on habitat type. The majority of sites were located within 250 meters of roads or trails passable by truck to simplify access. Sites were also reached by boat, all-terrain vehicle, helicopter, and airboat when these means of transportation were available. Habitat heterogeneity made random selection of sites difficult, particularly during the dry season, as no sufficiently detailed hydrology data existed to insure that randomly selected sites would be inundated. In those cases, sites were haphazardly selected to insure the presence of standing surface water.

Habitat Types

The habitat type classification scheme used was based on the seasonally inundated habitats identified by Duever et al (1986). Eight broad categories based on dominant vegetation and hydroperiod were used. Six of these are subject to seasonal drydown. They are ranked by hydroperiod as follows:

  • Cypress forest- The dominant trees of Big Cypress, the bald cypress Taxodium distichum and pond cypress T. ascendens, are characteristic of this habitat. It includes both cypress domes and cypress strands. Hydroperiods in these areas are in excess of 240 days per year, and may be over 290 (NPS 1991).
  • Mixed swamp forest- These are long hydroperiod forested wetlands which are dominated by hardwoods such as Acer rubrum, Fraxinus caroliniana, and Annona glabra. Taxodium is frequently present, but is not dominant, in these areas. Hydroperiods are in the range of 270 days per year (Duever et al 1986).
  • Freshwater marshes- This habitat has hydroperiods of 150-250 days per year and is dominated by Pontedaria spp., Sagitarria spp., Typha spp., and a variety of grasses and sedges (NPS 1991).
  • Coastal marshes- Southwestern sections of Big Cypress include herbaceous wetlands that seasonally vary between fresh and brackish salinity regimes. Hydroperiods are similar to freshwater marshes. Dominant forms of vegetation include Spartina spartinae, Distichilis spicata, and Eleocharis cellulosa (NPS 1991).
  • Cypress prairie- The community is characterized by an open overstory of sparsely distributed dwarf pond cypress. It often flanks and intergrades with cypress forests. Hydroperiods are approximately 120 days/year (NPS 1991).
  • Herbaceous prairie- A variety of grasses dominate these areas, including Muhlenbergia capillaris, Spartina bakerii, Cladium jamaicense, Panicum hemitomon, and Rhynchospora spp. (Duever et al 1986). This is the shortest-hydroperiod habitat, with a maximum of 70 days wetted per year (NPS 1991).

Two additional habitats hold water year-round:

  • Canals- Canals within or bordering on Big Cypress include Barron Collier canal, L28 Interceptor, L28, Loop Road Canal, and Tamiami Canal. They provide a refuge for large fishes during the dry season and allow for rapid movement across the Preserve, assisting in the spread of exotic species.
  • Sloughs/ponds/rivers- This category includes all naturally occurring persistent water bodies in the preserve. Ponds and rivers cover only a small geographic extent of the Preserve, but include such features as Deep Lake, Mud Lake, and Turner River.

Sampling Techniques

The diversity of habitat types in Big Cypress presents considerable challenges to the development of a comprehensive sampling regime, as the effectiveness of any given methodology varies between habitats. To compensate for this, numerous techniques have been employed during this study. A variety of fish traps have been used extensively, as well as electrofishing gear, gill nets, cast nets, dip nets, and angling.

Traps: Traps provide a means of sampling with a standardized unit of effort and are suitable for use in virtually any habitat. They are also relatively portable, and therefore suitable for work in remote locations. They have the disadvantage of having inherent selection biases, based both on trap construction, and size and behavior of targeted species. To attempt to minimize these, we deployed a variety of small-fish traps simultaneously. These included Gee-type minnow traps, box traps, collapsible mesh traps, and Breder traps. Soak times were generally 24 hours, although one-hour sets were also performed. Small-fish traps were consistently fished unbaited and relied on passive encounters to generate captures.

Hoop nets were used to sample larger fishes in deeper water. They were fished unbaited with or without leads, and were also baited with cheese to selectively target catfish species that had proved difficult to obtain otherwise. The hoop nets used here were 1.4 meters in overall length and were constructed from four 50-cm diameter fiberglass hoops and tar-coated twine with a 2.5 cm mesh size. The nets had two throats and an approximately 15 cm diameter aperture. Typically, hoop nets were deployed for 24-hour intervals.

Electrofishing: Electrofishing was conducted in locations where habitat composition allowed. Two electrofishing setups were used. The first utilized a boat-mounted Smith-Root type 6A electrofisher with a maximum current output of 1008 volts DC at 120 pulses per second or 720 volts AC at 60 hertz. It was used extensively for sampling in canals but was too large to penetrate into other habitats. Effort was generally standardized by conducting 100-meter transects, although opportunistic sampling around structures such as bridge pilings was conducted as well.

Forested habitats and marshes were sampled using a small barge carrying a Smith-Root model 2.5 GPP electrofisher with a maximum current of 1000 volts at either 120 pulses per second DC or 60 hertz AC. The barge drew only several centimeters of water and was only a meter wide, but still could not penetrate into heavily vegetated habitats. Samples were standardized to 300 seconds of total shock time.

Nets: Experimental gill nets were used to sample canal fishes. Two nets each composed of 4 242 cm deep x 180 wide cm panels were fished in tandem. The first had mesh sizes of 1.2, 2.5, 3.7, and 5 cm while the second was composed of panels with mesh of 6.2, 7.6, 8.8, and 11 cm. Nets were typically set from 1 to 4 hours. Reptile entanglements were problematic when using these nets. Encounters with alligators were particularly damaging, precluding longer sets.

While unsuitable for providing quantitative data, cast nets were used extensively in an opportunistic fashion to capture species sighted in canals. The cast nets had a radius of 180 cm and a 1.2 cm mesh size. Dip nets were used for sampling in dense vegetation. These nets had fine mesh (<1mm) and were the most effective method for collecting small species, such as least killifish (Heterandria formosa) and Everglades pygmy sunfish (Elassoma evergladei).

Other: Opportunistic sampling was conducted using light-tackle, hook-and-line fishing with a variety of lures and live or dead baits. Lines of baited hooks were also occasionally deployed in canals in attempts to catch catfish, although hoop nets proved substantially more effective. Finally, sight records were kept for any species observed in the field that could be positively identified without being captured.


We recorded the location of each sampling site as universal transverse mercator (UTM) coordinates using a Garmin Etrex Vista GPS. For each sample, all specimens were identified to species, and total catch per species recorded. We measured total lengths for the first 20 randomly selected individuals of each species to obtain a representative size distribution. Water temperature, pH, salinity, and dissolved oxygen were measured for each site when possible, however, instrumentation problems precluded this for much of the year. Recently, we borrowed a Hydrolab 4a minisonde and datalogger from the BICY hydrology department to resolve these problems. For electrofishing expeditions, water conductivity was determined using a YSI-33 conductivity meter.

Voucher Specimens

We collected and curated representative vouchers for all captured species whenever practical. Specimens too large to effectively preserve have been documented photographically. Vouchers have been collected independently for each habitat type sampled. Additionally, to ensure complete spatial coverage of the preserve, vouchers of each species have been collected from the north, central, and southern regions of Big Cypress. Information regarding each voucher was entered into the project Access database, and each was assigned a unique identifier to link with related sampling information. Voucher collection is an ongoing process and will continue for the duration of the study. Specimens too large for preservation have been documented using a digital camera. Upon completion of this project, vouchers will be transferred to an NPS-identified repository.

Duever, M. J., J. E. Carlson, J. F. Meeder, L.C. Duever, L. H. Gunderson, L.A. Riopelle, T. R. Alexander, R. L. Myers, and D. P. Spangler. 1986. The Big Cypress National Preserve. National Audubon Society, New York pp 455.

National Park Service, U S Department of the Interior. 1991. Big Cypress National Preserve General Management Plan and Final Environmental Impact Statement. National Park Sevice, Ochopee, FL.

Methods for Big Cypress National Preserve Fish Monitoring and Assessment

The objectives of this program are to test and compare different sampling methods for aquatic animals in forested wetlands for use in the larger MAP program, and to collect data on aquatic animal communities in forested wetlands of BICY that will receive varying effects from Comprehensive Everglades Restoration Program (CERP) projects. Sampling is conducted at three forested-wetland sites located in the northeast, northwest, and central parts of the Preserve, respectively (Figure 1). Three replicate plots are sampled at each site. Each plot has a drift-fence/minnow-trap array and two 4-m2 drop traps. Drop traps are located within each plot to sample both deep- and shallow- water sections. Because one of the study's objectives is to test and evaluate techniques for sampling animals in the forest habitat, additional methods will be added to the sampling regime over time. This metadata description should be considered an evolving work.

Drift-fence/minnow-trap arrays were constructed from debris-barrier fencing in the shape of an "X" measuring approximately 10 meters along each wing. A square collection area was constructed from mesh netting at the center of the array, directing fish into four 3-mm mesh, metal minnow traps, each facing a different direction. The traps are inserted through slits in the mesh with one opening facing outwards and the opposite opening (inside of the array) plugged with cork. Minnow traps are passively fished without bait for 24 hours, then collected. Contents of each trap are identified and enumerated in the field, then placed on ice and returned to the lab for measurements.

Drop traps were constructed out of 13-mm iron rebar in the shape of a square two meters on a side. Traps were mounted onto PVC poles approximately 1.5-m tall and rigged with canvas nets approximately 1-m high. Traps are deployed by pulling support pins that allow the frame to drop quickly through the water column, extending the nets and trapping any fish inside the frame. Traps are cleared with rotenone and any contents were collected and enumerated. Fin-clipped fishes from outside the traps are introduced into the net prior to application of the rotenone to gauge the clearing efficiency. A second check for fishes missed during the first day of collection is performed after 24-h, before the nets were disassembled.

We recorded the location of each sampling site as universal transverse mercator coordinates using a Garmin Etrex Vista GPS. For each sample, all specimens are identified to species, and total catch per species recorded. Water temperature, pH, salinity, and dissolved oxygen are measured for each site using a Hydrolab 4a minisonde and datalogger borrowed from the BICY hydrology department.

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