110 FWRI Technical Report TR-11

Introduction

Question 5—What is the relationship between environmental and habitat change and the recruitment, growth,

and survivorship of animals in Florida Bay?

In the context of the Florida Bay Science Program,

higher-trophic-level species (HTLS) include zooplankton; benthic invertebrates such as sponges, mollusks, crustaceans (particularly decapods); fishes;

marine mammals; marine reptiles; and water birds. Scientific input about HTLS in the bay is critical to the successful restoration of Florida Bay and associated coastal

ecosystems because HTLS are both ecologically and

economically important and are viewed as important

by the public. Performance measures based on HTLS

are essential to protecting and restoring Florida Bay in

the Comprehensive Everglades Restoration Plan

(CERP) implementation process.

HTLS integrate the condition of the ecosystem

and reflect it in their responses to environmental

change. Question 5 investigates how HTLS respond to

changes in the characteristics of the ecosystem, such

as benthic communities, water quality, and circulation, and exchange with adjacent ecosystems and the

effect of human activities on these characteristics.

Question 5 also investigates how HTLS are affected by

fishing. Some HTLS play a critical role in regulating

ecosystem functions, so changes due to fishing or other

causes, anthropogenic or natural, can have repercussions on the entire Florida Bay ecosystem.

The higher-trophic-levels component of the Florida

Bay Science Program has approached Question 5 by addressing the following questions: 

• How do human activities (e.g., water management,

fishing) and major natural factors influence biological processes affecting growth, survival, and recruitment of fishery species, protected species, and

keystone species in Florida Bay?

• How do HTLS community composition and trophic

structure vary in time and space, what factors are responsible, and what processes are affected by the

variation?

• What major processes influence transport of presettlement stages of fish and invertebrates to and into

Florida Bay, what is their schedule, what parts of

the bay are most affected, and what is their importance to recruitment to fisheries inside and outside

of the bay?

• What animals affect major ecological processes in the

bay, such as primary productivity and nutrient cycling, and what is the magnitude of this role?

Substantial progress has been made on these topics but much remains to be done. This chapter synthesizes recent results, examines historical information

relevant to the central question, and identifies needed

future work.

Description of Higher-Trophic-Level

Species in Florida Bay

The HTLS component of the Florida Bay Science Program encompasses all the animals of the system. Recent work on higher trophic levels in Florida Bay builds

on prior research in coastal waters of Everglades National Park (ENP) before or in the 1950s and 1960s,

summarized by Tilmant (1989) and Tabb and Roessler

(1989); in the 1970s by Schmidt (1979); and in the 1980s

by Thayer and Chester (1989), Powell et al. (1989), Sogard et al. (1989), Holmquist et al. (1989), Robblee et al.

(1991), and Ley et al. (1994). More than 250 fish species

are known to occur in Everglades National Park coastal

waters (Loftus, 2000), although Schmidt (1979) found

only 128 fish species in Florida Bay. Tabb (1966) concluded that individuals of most species left ENP waters for unknown seaward spawning areas when they

reached sexual maturity.

A synthesis of past research for the March 1998

Chapter 8

Higher-Trophic-Level Species

Lead Author Joan A. Browder

Contributors Cynthia Yeung, Thomas Schmidt, Mark J. Butler, IV, Maria Criales, Allyn Powell, 

Don DeAngelis, David Evans, Larry Settle, Bill Sharp, Craig Faunce, Jerald Ault, Anne Marie Eklund, 

G. Lynn Wingard, Gordon Thayer, Darlene Johnson, David Rumbold, Jeffrey Chanton, C. Chasar, 

Jerome Lorenz, Ed Matheson, James Colvocoresses, Michael Robblee, Laura Engleby, 

Chris Koenig, Samantha Whitcraft
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 111

HTLS Group Report (Browder et al., 1998) organized the

animals of the bay into a generalized food web (Figure

8.1). The primary producers at the food-web base include phytoplankton, epiphytes, benthic algae, seagrass, and mangroves. The Florida Bay fauna is made

up of herbivores, detritivores, planktivores, and piscivores at three or four trophic levels.Within the bay, the

food web has two major branches: pelagic (water-column) and benthic (on or near the bottom), which may

converge at the highest trophic levels. Most of the following information is summarized from Browder et al.

(1998), but new information has been added as cited.

In the pelagic branch of the food web, filter-feeding planktonic stages of fishes, crustaceans, mollusks,

and other taxa feed on phytoplankton (e.g., diatoms,

dinoflagellates) in the water column and are preyed

upon by small, schooling pelagic fish such as bay anchovies and hardhead silversides.The benthic branch

includes filter feeders (e.g., sponges, bivalve mollusks,

ascidians, polychaetes) and demersal grazers or detritivores, such as amphipods, harpacticoid copepods,

polychaetes, striped mullet, and post-settlement stages

of mollusks and other invertebrates.The next level of

benthic consumers includes a host of small demersal

fish and macroinvertebrates that feed on small invertebrates. Dominant members of this group include

gulf toadfish, goldspotted killifish, rainwater killifish,

dwarf seahorse, dusky pipefish, gulf pipefish, spotfin

mojarra, silver jenny, white grunt, pigfish, pinfish, and

silver perch (Thayer et al., 1999). Pink shrimp and many

taxa of small caridean and penaeoidean shrimp also are

numerically abundant in the bay (Holmquist et al.,

1989; Robblee, personal communication). Juvenile spiny

lobsters are abundant in the southwestern portion of

Figure 8.1 Trophic levels in Florida Bay.

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

112 FWRI Technical Report TR-11

the bay south of major mud bank barriers (Field and

Butler, 1994; Herrnkind et al., 1997). The limited research in the bay and nearby areas suggests that the

demersal fish in the bay are generalists that eat a variety of benthic invertebrates (Zieman, 1981; Schmidt,

1993a; Ley et al., 1994).

Florida Bay supports several highly sought-after

game fish, including red drum, spotted seatrout, gray

snapper, snook, tarpon, and bonefish (Schmidt et al.,

2001, 2002). Sharks are commonly seen during aerial

surveys (S. Bass, personal communication) and include nurse sharks, bonnethead sharks, and lemon

sharks. Rays (e.g., sting rays and manta rays) are commonly seen on aerial surveys. Small fish and macroinvertebrates are the prey of these larger fish.Within the

Florida Bay area, gray snapper and red drum principally eat shrimp and crabs, whereas barracuda,

seatrout, and snook eat more fish than crustaceans

(Marshall, 1954; Croker, 1960; Yokel, 1966; Fore and

Schmidt, 1973; Rutherford et al., 1983; Schmidt, 1986,

1989; Harrigan et al., 1989; Hettler, 1989). Of the abundant forage fish, those that appear to be important in

the diet of some piscivorous fishes are gulf toad fish

(lemon sharks, red drum, and bonefish), pinfish (lemon

sharks and snook), hardhead silversides (snook),

goldspotted killifish (barracuda), and rainwater killifish (barracuda and spotted seatrout) (Schmidt, 1986,

1989; Crabtree et al., 1998; Koenig et al., 2001). In southern Florida Bay, juvenile lobsters constitute a large

fraction of the diets of a variety of fish: nurse sharks,

bonnethead sharks, southern stingrays, bonefish, permit, and gulf toadfish (Smith and Herrnkind, 1992).

Small mollusks are abundant in Florida Bay and are

probably fed on by rays and fish such as sheepshead.

The pink shrimp, Farfantepenaeus duorarum, is a key

component of trophic webs.This species is an important prey of game fish (Croker, 1960; Stewart, 1961,

Yokel, 1966; Rutherford et al., 1983; Schmidt, 1986, 1989;

Hettler, 1989) and wading birds (Palmer, 1962), linking

them to small grazers and detritivores supported by

algae and seagrass and mangrove detritus (Fry et al.,

1999).The abundant small caridean shrimps in Florida

Bay are the principal prey of juvenile pink shrimp

(Schwamborn and Criales, 2000).

The many piscivorous water birds that live in the

bay seasonally or year-round eat small fish and

macroinvertebrates such as crabs and shrimps, although this is poorly documented. Piscivorous birds in

the bay include double-crested cormorants, brown

pelicans, red-breasted mergansers, laughing gulls,

ring-billed gulls, royal terns, many wading bird species,

and bald eagles and ospreys.The most abundant wading bird species in the bay seasonally are white ibis and

great egrets (Browder and Bass, unpublished data).

The bay is a major habitat for the great white heron,

roseate spoonbill, and reddish egret. All of these species

feed in Florida Bay proper or in shallow ponds on the

bay’s islands.

The bottlenose dolphin is another high-level predator in Florida Bay and, based on studies elsewhere in

south Florida, probably feeds on fish at several trophic

levels.The American crocodiles that occur in the northern bay and the American alligators that penetrate

the northern bay during wet years are also predators

on the bay’s small-fish populations.

Two large grazing animals, the West Indian manatee and the adult green sea turtle, may have once

been more abundant in Florida Bay than they are

today. They also may have influenced the structure

and productivity of seagrasses as a result of their grazing. A review by Thayer et al. (1984) described the dietary importance of seagrass to various herbivores

and the influence of herbivory on seagrass systems.

Green turtles once were the primary consumers of

seagrasses in the Caribbean, but they are now few in

number everywhere. In a major feeding area in

Nicaragua,Thalassia testudinum made up 87% of the diet

of green sea turtles, and other seagrasses (Syringodium

filiforme and Halodule wrightii) made up another 5%.

Grazing by green sea turtles may have profound influences on the seagrass community that are different

from the effects of grazing by other herbivores. Green

sea turtles may feed on Thalassia preferentially. They

are known to maintain discrete grazing plots in a Thalassia bed and feed repeatedly on the new growth in

these plots until food quality deteriorates. It is possible that the presence of grazing sea turtles might prevent the type of high-biomass Thalassia monoculture

that preceded the seagrass die-off in Florida Bay of the

late 1980s.The possible impact of loss of sea turtles on

Florida Bay was discussed by Jackson et al. (2001). Grazing by manatees may have a more disruptive effect than

that by turtles because the rhizophore is disturbed

and might jeopardize recovery (Thayer et al., 1984).

The density of large herbivores in Florida Bay today

may be too low for them to have much influence on the

present ecosystem.

Seagrass is the main diet of the caridean seagrass

shrimp (Schwamborn and Criales, 2000). Seagrass is

also important in the diet of sea urchins and has been

reported to be in the diets of some fishes (Thayer et al.,

1984). Even where grazing animals are more abundant, it is likely that more energy travels from seagrass to consumers through the detrital than the

grazing food web. In Florida Bay today, only the detrital food web is significant.

A conceptual model developed to help guide

Florida Bay HTLS research is shown in Figure 8.2.The

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 113

model incorporates the following major concepts:

• Critical ecosystem characteristics (i.e., salinity, water

quality, and biological benthic habitat) directly influence HTLS at the individual species level. Speciesand community-level response represents the

aggregate influence of these characteristics integrated over HTLS populations;

• Changes in HTLS at the species and community

level occur as the result of driving processes acting

on Florida Bay as a whole.These processes influence

HTLS by their effect on critical ecosystem characteristics and by controlling the movement of HTLS

into and out of Florida Bay;

• At the shelf scale, potentially influencing factors include temperatures on spawning grounds, larval

transport processes, and fishing;

• The scope of research on HTLS of Florida Bay must

include within-bay, cross-boundary, and greater

coastal ecosystem processes, and these processes

should be examined at time scales from seasons to

decades; 

• Higher-trophic-level processes and patterns potentially affected by water management occur at the

population, community/trophic, and ecosystem level; 

• HTLS responses to water management are expected

to occur through water management effects on salinity, the area of co-occurrence of biologically favorable

salinity and habitat, the condition of biological habitat (e.g., seagrass, sponge, coral), animal movements,

and loading of nutrients or toxicants; 

• Intrinsic factors potentially influencing responses

to water management include physiological salinity

requirements, dietary and energy requirements,

and trophic relationships, all of which may differ

by species, life stage, and spawning and migration

characteristics; 

• At the bay scale, other factors with the potential to

influence HTLS include salinity-temperature interactions, toxicant concentrations in freshwater inflow, and fishing.

Processes Driving Change in the 

Ecosystem 

Preceding chapters describe some major ecosystem

characteristics that influence higher-trophic-levelspecies in Florida Bay: salinity, water quality, and benthic habitat. All are subject to change, and an

understanding of how they might change is being developed in other parts of the Florida Bay program. Determining how their change might affect these species

is being determined by HTLS research. Relationships

between processes driving change, ecosystem characteristics, and characteristic species and communities of

Florida Bay are highly relevant to the CERP, which will

influence the change-driving processes. Defining and

quantifying these relationships is crucial to preparing

performance measures to restore or protect Florida Bay.

Augmenting the descriptions of ecosystem characteristics in the preceding chapters are studies on mercury.

These studies are defining previously unknown spatial

patterns of mercury and methylmercury concentrations

in Florida Bay waters, sediments, and biota.

The quest for answers to Question 5 must extend

beyond Florida Bay to include the greater ecosystem

that supports the movements of species into and out

of the bay and the processes that affect these movements. Animal movements, as well as the flow of water,

connect Florida Bay not only to the upstream Everglades and coastal mangrove areas but also to the

Florida Keys, the reef tract, the southwestern Florida

shelf, and the Dry Tortugas. Many higher-trophic-level

species range between the bay and the coastal reefs

during their life cycle.The processes driving change in

the Florida Bay ecosystem extend beyond the bay both

upstream and downstream.

The principal anthropogenic processes potentially

driving change in the Florida Bay ecosystem are water

management, contaminant and nutrient inputs, causeway and bridge construction in the Florida Keys, and

Figure 8.2 Conceptual model of factors affecting higher-trophiclevel species in Florida Bay.

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

114 FWRI Technical Report TR-11

fishing. Climatic variation and oceanographic processes

are other instruments of change in the Florida Bay

ecosystem and may cause year-to-year and long-term

variation.

WATER MANAGEMENT

By affecting freshwater inflow to Florida Bay, water

management can affect Florida Bay’s HTLS through the

effects of freshwater inflow on salinity patterns, nutrients, organic detritus, and contaminant loads. Salinity directly affects physiological processes that

determine growth, survival, and reproductive rates of

many higher-trophic-level-species.The area in which

a favorable salinity range overlaps with other favorable

conditions (i.e., shoreline, depth, or bottom habitat) in

areas accessible to appropriate life stages determines

the productive capacity of the bay for a given species.

Salinity gradients may provide orientation cues that

promote the successful immigration into the bay of

postlarvae spawned offshore that use the bay as a

nursery ground. Nutrients and organic detritus may

have positive or negative effects depending on concentration. In excess, they degrade habitat (via reduced water clarity, low dissolved oxygen, etc.).

Effects of water management on salinity patterns,

nutrients, and contaminant loads are being studied in

other parts of the Florida Bay science program. A major

emphasis of the HTLS science plan is determining the

possible effect of changes in salinity on animal species

and communities. Water management may affect

higher-trophic-level organisms through effects on important living benthic habitat such as seagrass and

sponges (e.g., through salinity, nutrient, turbidity, or

other effects on the organisms that form living benthic

habitat), and these potential effects are also being evaluated through studies of relationships of HTLS to living benthic habitat.

FISHING

Many coastal fisheries in south Florida have ecological connections to Florida Bay. Especially notable of

these are the commercial fishery for pink shrimp and

the commercial and recreational fisheries for gray

snapper and spiny lobster. These species and others

(sparids, grunts, other snapper, and even groupers)

found on the Florida Keys reef tract and in the waters

near the Dry Tortugas spend part of their life cycle in

Florida Bay. Reef waters near Marathon in the middle

Keys are an important spawning ground for gray snapper (Rutherford, 1989). Shelf waters near the Dry Tortugas islands are the most important commercial

fishing grounds for pink shrimp in Florida, and Florida

Bay is the major pink shrimp nursery ground. Florida

Bay also contains important spiny lobster nursery

habitat, and Everglades National Park is a fishing-free

sanctuary for spiny lobster. Nearby areas and parts of

Florida Bay outside of ENP support recreational and

commercial fishing for Spanish mackerel, spiny lobster,

and other species.

Recreational fishing is an expanding sport in the

Florida Keys, the Tortugas waters, and Florida Bay, both

within and outside ENP boundaries.The number of fishing trips in ENP in 2001 was the highest ever reported

(Schmidt et al., 2002). ENP began phasing out commercial fishing in the bay in the early 1980s, when

analyses of recreational and commercial fishery data

suggested that overfishing might be occurring. Since

then, recreational fishing regulations have been

strengthened. Later analyses have suggested that environmental factors affect abundance (Tilmant et al.,

1989; Schmidt et al., 2002).The ratio of kept fish to total

fish caught changed dramatically from the 1980s to the

1990s. This may be an artifact of regulatory changes

(legal size limits, bag limits, seasonal closures); however,

it may be indicative of an increased catch of sizes that

were too small to keep (i.e., below legal size limits).

This issue will be addressed in current and future

analyses of size-frequency distributions in the creel

census data by ENP and the Fish and Wildlife Research

Institute.

The growing demand for fish and the popularity

of fishing have increased the pressure on fishery populations in south Florida. Fishing pressure is especially reflected in declining size and density of snappers

and groupers and changes in the trophic structure of

fish assemblages on reefs (Ault et al., 1998). These

changes are apparent even in the Tortugas area and are

consistent with similar changes previously detected in

the Florida Keys (Ault et al., 1998; Bohnsack et al., 1999;

Schmidt et al., 1999).The observed decline in fish abundance may be due to loss of coral habitat. For example,

the total area of Caribbean reef-building corals Acropora palmata and Acropora cervicornis has declined by

93% and 98% respectively since 1983 (Miller et al.,

2002).

OCEANOGRAPHIC PROCESSES

The Loop Current and Florida Current and their countercurrents, the Tortugas Gyre, and coastal eddies are

oceanographic features that may influence the migration of postlarvae to Florida Bay and to the Florida

Keys reef tract from offshore spawning areas. These

processes may affect the timing of abundance peaks

and year-class strength in fish and macroinvertebrate

populations in the bay and on the reef tract.

The Florida Keys reef tract extends almost without

interruption along the entirety of the Florida Keys and

is the core component of the Florida Keys National MaHigher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 115

rine Sanctuary. Florida Bay is connected to the reef tract

through interisland channels. Regional-scale and localscale oceanic processes that affect the reef tract likely

also affect Florida Bay. Reef tract populations are replenished not only by their spawning locally but also

by their spawning upstream of the reef tract. The upstream distance of sites contributing larvae is principally determined by current velocity and larval

development rate, which ranges from 2 weeks in some

invertebrates and fish to up to 12 months in spiny lobster. Recruitment of some species to the Florida Keys

reef tract from as far away as the western Caribbean

has been postulated. The argument for multiple upstream larval sources for the Florida spiny lobster population is especially strong, given the wide geographic

range of the species and its extraordinarily long planktonic larval life (Lyons, 1980; Yeung et al., 2000; Yeung

and Lee, 2002), and is supported by mtDNA analysis

(Silberman et al., 1994).

Having more local sources of larvae may be important to most populations. The lower southwest

Florida shelf in the vicinity of the Dry Tortugas is one

potential source of recruitment to the Florida Keys

reef tract and Florida Bay. The islands of the Dry Tortugas and their surrounding shallow waters lie roughly

150 km (70 miles) west of Key West and are known for

remoteness and relatively unspoiled marine richness

(Ault et al., 2002b; Franklin et al., 2003). The coastal

shelf in the vicinity of the Dry Tortugas is the major

spawning ground for pink shrimp in Florida. Recent

research is discovering luxuriant, previously unknown

and unmapped coral reefs near the Dry Tortugas and

near the Marquesas, which lie between the Dry Tortugas and Key West (Miller et al., 2001).

CAUSEWAY/BRIDGE CONSTRUCTION

The flow connecting Florida Bay to the Atlantic Ocean

through Lignum Vitae, Indian Key, and Teatable Key

channels was reduced by the construction of the Flagler railroad, which became the Overseas Highway.This

construction, which occurred in the early 1900s, partially blocked tidal passages and affected bay circulation and associated water quality (Healy, 1996). By

affecting transport between the bay and the Gulf of

Mexico and Atlantic Ocean, the construction areas

may also have affected the immigration of postlarvae

and early juveniles into Florida Bay.The U.S. Corps of

Engineers is leading a study to determine whether

Keys passes should be enlarged to restore the health

of Florida Bay. The Corps is planning a pilot study of

the effect of enlarging passes that have been restricted

by the highway. The pilot study will be performed in

passes located between Fat Deer (Marathon) and

Grassy keys.

Research Approaches

A major focus of Florida Bay HTLS research has been

to characterize the responses of species and species

groups to environmental and habitat conditions that

vary in space and time.The topic has been approached

via modeling, statistical analyses, experiments, and

field measurements. Modeling, supported by laboratory experiments, was used to characterize the response of individual organisms and was applied to

pink shrimp, spiny lobster, sponges, and spotted

seatrout to examine functional responses to salinity and

temperature and their consequences for populations.

Separately, statistical analyses of historical resource survey data were used to characterize the response of 11

forage species and 9 fishery species to environmental

variables at the population and community level. Field

studies were conducted to characterize the spatial and

temporal patterns of immigration of early life stages

into Florida Bay from offshore spawning grounds and

the density of juveniles on Florida Bay nursery grounds.

Most work has included an examination of the possible effects of salinity because salinity is likely to be affected by inland water management.

A more recent focus of Florida Bay HTLS research

has been to examine the effect of HTLS on critical

ecosystem characteristics, such as water quality and

benthic habitat, that determine habitat quality and

define distinct communities. In this regard, sponges are

a major interest because of the recent decline in sponge

biomass in the bay. Sponges are capable of regulating

water clarity through their filter feeding, and the volume of water filtered is largely determined by sponge

biomass density, which has declined substantially in

recent years.

Field sampling and comparative analysis of data

from fished and unfished areas provided information

on the effect of fishing on individual species and species

composition.

Comparative studies provided evidence that fishing in ENP affects size distribution within species (gray

snapper) and the species composition of communities.

Underwater visual resource surveys on the reef tract

and near the Dry Tortugas have found signs of overfishing of fish species that occur both on the reef tract

and in Florida Bay.

One approach to examining the effect of water

management on HTLS has been through statistical

analyses relating fishery catch or catch per unit effort

to indices of freshwater inflow to Florida Bay and

nearby southwestern Florida coastal waters. Another

approach, already mentioned above, has been to examine the effect of salinity on processes that affect

the abundance of these species.

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116 FWRI Technical Report TR-11

Summary of Recent Results

The following summary of recent results, presented as

bullets, is organized under specific research questions

(subsets of the four topic questions identified above)

to provide an overview of progress. Table 8.1 organizes research activities into specific topics, and these

topics provide a general framework for a series of sections synthesizing recent results and conclusions, by

specific research topic.

Does salinity affect survival and growth, do salinity patterns affect faunal abundance and distributions, and

will changes in salinity patterns affect the bay’s nursery function? 

• Five species of sponges found in Florida Bay expeTable 8.1 Research topics defined by Question 5 (cells in the matrix) and key references to the associated research.

Population Level— Individual Level—

Research Topic Species Abundance and Community Growth and Survival

General Read et al., 2001; Limouzy-Paris et al., 1997; Settle et al., 2001; Powell et al., 2004

Characteristics Costello et al., 1986; Robblee et al., 1991;

Thayer and Chester, 1989; Powell et al., 1989;

Chester and Thayer, 1990; Thayer et al., 1999;

Powell, 2002, 2003; Powell et al., 2004; 

Schwamborn and Criales, 2000;

Stevely and Sweat, 2001

Salinity Pattern Schmidt et al., 2001; Browder et al., 1999, 2002; Browder et al., 1999, 2001b, 2002; 

Brewster-Wingard et al., 2001; Camp et al., Butler et al., 2001a; Butler, 1999, 2003;

2001; Matheson et al., 2001; Field and Butler, Field and Butler, 1994; Wuenschel,

1994; Lorenz, 2001a 2001; Richards and DeAngelis, 2001

Water Quality Water quality effect on HTLS: Water quality effects on

(No results reported) contaminants and humans,

piscivorous birds, mammals, and

HTLS effect on water quality: reptiles: Evans and Crumley, 2000; 

Stevely and Sweat, 2001; Peterson and Sepulveda et al., 1998;

Fourqurean, 2001 Effects on invertebrates: Scott et al., 2002

Biological Habitat effect on HTLS: Habitat effect on HTLS: Butler et al.,

Benthic Habitat Dennis and Sulak, 2001; Robblee et al., 1995; Butler, 2003

2001; Matheson et al., 2001; Powell et al.,

2001a,b; Ortner et al., 2001; Robblee et al., 2001;

Chanton et al., 2001; Herrnkind and Butler,

1994; Field and Butler, 1994; Butler et al.,

1995; Butler, 2003; Koenig et al., 2001

HTLS effect on habitat:

Rose et al., 1999; Peterson and 

Fourqurean, 2001

Coastal Transport Field and Butler, 1994; Yeung et al., 2001; Settle et al., 2001; Yeung and Lee, 2002;

(Larval) Process Yeung and Lee, 2002; Jones et al., 2001; Acosta and Butler, 1997; Criales and 

Browder et al., 2001a, 2002; Lee, 1995; Criales and McGowan, 1993,

Butler et al., 2001b; Criales et al., 2003 1994; Jones et al., 2001; Jones et al., 1970;

Tabb et al., 1962; Roessler et al., 1969; 

Smith, 2000; Butler et al., 2001

Water Management Browder, 1985; Sheridan, 1996 Lorenz, 2001a, 2001b

and Hydrology Browder, 2000; Johnson et al., 2002a

Fishing Faunce et al., 2002; Bohnsack et al., 2001;

Schmidt et al., 2001

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FWRI Technical Report TR-11 117

rience high mortality rates at low salinity. None survived at 15 practical salinity units (psu) (laboratory

experiments).

• Pink shrimp from Florida Bay are more sensitive to

low salinity than to high salinity.The salinity of maximum physiological survival varies with temperature.

Pink shrimp are more tolerant of high salinity at

high temperature and low salinity at low temperature. Acclimation improves survival at high salinity

(55 psu) but not at low salinity (5–10 psu). Growth of

pink shrimp is optimal at a salinity of 30 psu (laboratory).

• A salinity optimum of 35 psu has been reported for

postlarval Caribbean spiny lobster. The extreme

salinities that sometimes occur in portions of Florida

Bay are lethal to lobster postlarvae (laboratory).

• Larval and juvenile spottedseatrout survival and

growth are low at salinities over 45 psu (laboratory).

• Temperature and salinity have an interactive effect

on the metabolic rate of young spotted seatrout.Their

metabolic rate in relation to size is biphasic and

changes isometrically with body mass in early stages,

approximating an exponential relationship near unity,

but changes isometrically thereafter (laboratory).

• Spotted seatrout catch rates in the recreational fishery are negatively related to indices of freshwater inputs to Florida Bay (analyses of creel census data).

• Western Florida Bay is a major nursery ground for

spotted seatrout (field study). The high density of

planktonic postlarvae suggests that central Florida

Bay may also be a major nursery ground when conditions allow. Salinities greater than 45 psu have frequently occurred in central Florida Bay in the past,

which may limit this area’s nursery value.

• Pink shrimp recruitment from Florida Bay could

differ between years, seasons, and regions of the

bay due solely to observed salinity and temperature variation (simulation model).

• Observed salinities during a wet and a dry year

caused a predicted decline in lobster recruitment of

approximately 25% in the area of Florida Bay directly affected by salinity variation (individual-based

model).

• Habitat, tidal amplitude, freshwater inflow to Florida

Bay, and salinity were the most widely influential

variables explaining density in 11 forage species in

a meta-analysis of data from historical surveys. Seagrass density and tidal amplitude each were significant for 10 species, seagrass type and freshwater

inflow each were significant for 9 species, and salinity was significant for 7 species (statistical analyses

of combined data sets).

Does water management affect the productive

capacity of Florida Bay?

• When used in alternative testing to select the preferred plan for CERP, a statistical model relating an

abundance index of pink shrimp in the Tortugas

fishery to freshwater inflow to ENP at the Tamiami

Trail during certain months predicted that “natural

system”flows (as compared to the 1995-base case or

any alternative) consistently produced highest

shrimp abundance over a 31-yr period.The selected

alternative was predicted to lead to abundances intermediate between predictions for the natural system and 1995-base case.

• Remnants of molluscan faunas obtained in cores

suggest that molluscan faunal diversity and absolute

abundance in eastern and central Florida Bay began

a decline in the 1960s or earlier and reached a low

in the 1970s. The low species diversity and the increased abundance of Brachidontes exustus are evidence of a system under stress.

• Fish density in the wet season is positively related

to water depth in coastal marshes and the length of

time during which water depths are greater than

12.5 cm. Maximum concentration (to roughly twice

dry-down density) in low spots (e.g., creeks and shallow pans) occurs when water depths decline below

12.5 cm in adjacent marshes. Successful roseate

spoonbill nesting occurred in past years during dry

season when mean water depths in the coastal

marshes were less than 12.5 cm. Nesting failures in

recent years can be explained by out-of-season water

releases from the C-111 Canal.

What affects the balance between benthic and pelagic

trophic networks in Florida Bay? 

• The seagrass die-off was a suspected cause of a shift

from benthic to pelagic dominance in the fish community, because bay anchovy abundance was much

greater in 1995 than in 1984–1985. Recent findings discount this possible cause.The abundance of bay anchovy in the western bay has fluctuated since it

reached a maximum in 1995.The diversity and overall abundance of canopy-dwelling fauna have increased since 1995 without a return to the original

Thalassia-dominated seagrass canopy.

• Bay anchovy abundance may be related to the presence of salinity fronts. Bay anchovy abundance was

negatively correlated with salinity and positively

correlated with salinity standard deviation, chlorophyll, and an index of freshwater inflow in an analysis of historic data. A study in the Manatee River

associated low mean salinity and high salinity standard deviation with the presence of fronts and found

a relationship between anchovy egg abundance and

these indicators of fronts.

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

118 FWRI Technical Report TR-11

• Seagrass diversity may determine faunal density. A

principal components analysis suggested that faunal

species have affinities to certain seagrass types—

Thalassia, Halodule, or Syringodium—or with macroalgae. Seagrass type was a significant explaining

variable in a meta-analysis of faunal density in

Florida Bay, and faunal density in relation to seagrass

type varied differently depending on faunal species.

No faunal species was identified that had pure

Thalassia as its sole affinity.

Do bottom and shoreline habitats affect abundance and

community composition?

• Mangrove prop-root habitat in northeastern Florida

Bay had significantly more fish larvae than did

nearby open-water sites or nearshore areas without

mangroves, but it had a lower density and diversity

of both forage fish and juvenile predator fishes than

found in similar habitat in the Bahamas and Puerto

Rico, leading to the hypothesis that the low densities were caused by isolation from offshore sources

of larvae or juveniles.

• Seagrass density was a significant explaining variable for density for 10 of 11 key forage species

examined, and seagrass type was a significant explaining variable for density of 9 of the 11 species.

Does fishing affect fish populations?

• According to a comparison of the length-frequency

distributions inside and outside of an area in the park

protected from fishing, recreational fishing in Everglades National Park affects the size structure of

gray snapper.

• Evidence of overfishing is seen in gray snapper and

other species on the reef tract.

Is spatial variation in influencing factors (e.g., freshwater inflow, tidal mixing) reflected in distinct regional

patterns in species distributions and community and

trophic composition in Florida Bay? 

• Peak concentrations of postlarval pink shrimp are

roughly an order of magnitude greater in passes

leading into western Florida Bay than in channels to

Florida Bay through the Florida Keys. Movement

into the bay occurs on the flood tide. The timing of

high immigration rates is more predictable when

shrimp immigrate from the west than from the east.

• Based on stable isotope analyses, the central bay

has a strongly seagrass-based trophic structure,

whereas the western bay has a more plankton-dominated trophic structure. The eastern bay offers a

non-seagrass-based diet (likely more water-column

based).The trophic structure of the southwestern bay

is based on macroalgae.

• Northern Florida Bay is probably not a significant

nursery area for red drum.

Is temporal variation in recruitment strength of spiny lobster, snapper, and pink shrimp related to oceanographic

processes, especially to the Tortugas gyres?

• Spiny lobster postlarvae that recruit throughout the

year had peaks of influx into the bay at the Middle

Keys coinciding with the presence of eddy and countercurrent conditions.

• Larval duration of gray snapper varied from one

year to the next and, within the first year, ranged from

35.50 to 41.45 days.

• Peak abundance of gray snapper larvae in Florida

Keys channels occurred in summer 1997 and was coincident with a well-developed Loop Current (high latitudinal extent) favoring gyre formation off the Dry

Tortugas, where gray snapper spawning aggregations occur.

• Temporal variability was observed in the influx of

pink shrimp postlarvae through two channels in the

Middle Keys and may be related to the position of

the leading edge of the cyclonic eddies relative to the

channels. Pink shrimp larvae at the spawning

grounds seem to be retained by the circulation of the

Tortugas gyre.

Are urban and agricultural sources, carried by the C111 canal, responsible for high methylmercury in

Florida Bay and its biota?

• Sources of elevated mercury concentrations in fish

from northeastern Florida Bay include (1) methylmercury in runoff from the Everglades and (2) in situ mercury methylation in sediments from both the

mangrove transition zone and the open bay itself.

• Mercury concentrations were higher along a Taylor

River–Little Madeira Bay sampling transect than

along a C-111 canal–Joe Bay transect, suggesting

that the urban and agricultural runoff that more

strongly influences the C-111 canal–Joe Bay transect is not the most important source of mercury to

the bay and its biota.

Did the former density of sponges in Florida Bay influence water quality to the extent that the sponge

die-off that followed seagrass die-off led to waterquality conditions that impeded the recovery of seagrass?

• At pre-die-off (before 1992) densities, sponges in

Florida Bay may have been capable of filtering the

entire water column in 24 hours. Recovery of the

largest and most abundant species has been extremely slow. At present densities, filtering takes an

estimated four days. Sponges are efficient filters of

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 119

small (<5 μm) planktonic particles. Loss of sponges

may have reduced water clarity and affected seagrass

recovery.

Do predators seek areas of higher prey abundance?

• Bottlenose dolphin were found in areas of highest

density of potential prey, supporting the working hypothesis that they search out feeding areas with

higher prey concentrations. Dolphin and prey densities are higher in the east-central and south-central bay than they are in the northeastern bay.

However, densities of both dolphin and prey are

lower in the east-central and south-central bay than

they are in other coastal areas.

Distribution of Species and 

Patterns of Abundance

Spatial variation in the influence of environmental

and physical factors shaping Florida Bay, especially

substrate, freshwater inflow, and degree of mixing

with waters of the Atlantic and the Gulf of Mexico, have

led to substantial regional differences in animal distributions within the bay. For example, the southern bay

is prime habitat for juvenile spiny lobster, which are

found in few other parts of the bay. On the other hand,

juvenile pink shrimp occur most densely in the western bay. Animal distributions have been used to define

distinct subregions of the bay, beginning with Turney

and Perkins’ (1972) delineations based on mollusks.

Subregional delineations based on animals roughly

correspond to those based on seagrasses (Zieman et al.,

1989) and water quality (Boyer, 1997). Short-term and

long-term temporal variations in environmental variables accentuate regional differences in bay habitat (for

example, the northeastern bay has the most seasonally

variable salinities). Temporal variation also undermines efforts to better describe and understand regional differences (for example, the northcentral bay

can be hypersaline one summer and mesohaline another, creating an entirely different environment for animals during the same time of year). Recent research

has expanded our understanding of how animal distributions vary spatially and temporally and the most

likely reasons for the variation. Results of studies that

address the spatial and temporal variations of a number of parameters follow.

Field studies have expanded the knowledge of

spawning areas and spawning periods. Powell (2003)

and Powell et al. (2002, 2004) determined that spotted

seatrout spawning occurs primarily in western Florida

Bay. Spawning at Bradley Key and Palm Key had been

observed historically, but spawning at Whipray Basin

and Little Madeira Bay was determined for the first time

in 1994–1995 sampling. Based on collections and hatchdate estimates from 1995 collections, they determined

that spawning occurred principally during the summer,

with spawning peaks in May and June. Larvae were collected over a wide range of bottom types with and

without seagrass, in waters with temperatures between 20°C and 35°C (majority 26°–34°C) and salinities between 12 psu and 41 psu (majority 25–40 psu).

Consistently high densities of larvae were collected at

Whipray Basin, which is located in the central portion

of the bay and is a valuable juvenile nursery area despite low seagrass above-ground standing crop and occasional (two occasions during sampling—40 psu and

41 psu) hypersaline conditions in 1998 and 1999.

Nursery grounds of several other gamefish species

that occur in Florida Bay as adults are not yet documented in Florida Bay. Recently Powell et al. (2002) attempted to locate Florida Bay nursery grounds of red

drum, which occur in Florida Bay and spawn in the

nearby Gulf of Mexico. Based on the work of Peters and

McMichael (1987) in Tampa Bay, Powell et al. (2002)

concluded that northern Florida Bay was the only suitable nursery habitat for red drum in the bay. Powell et

al. (2002) sampled intensively there, and concluded

that limitations on larval transport from offshore waters was preventing red drum from using this part of

the bay as nursery habitat. Colvocoresses (unpublished data) found young juvenile red drum in the

East River of Little Madeira Bay and near the mouth

of McCormick Creek, but the Powell et al. (2002) work

suggests that the occurrence of red drum juveniles in

northern Florida Bay is not a seasonally regular event.

Read et al. (2001) studied bottlenose dolphin in the

eastern half of Florida Bay and found that densities of

prey organisms in trawl samples were higher in areas

where bottlenose dolphin had been feeding than in

samples taken elsewhere. This supported their hypothesis that dolphin seek out feeding areas with higher

prey concentrations.These investigators found a greater

abundance of dolphins in the east-central and southcentral parts of the bay than they found in the northeastern bay. (Their study did not include the western

bay.) They suggested that the low abundance of dolphins

in the northeastern bay might be related to the lower

fish densities that have been reported there by other investigators. In 20 surveys conducted in all four seasons, they encountered 23 groups of bottlenose

dolphins, consisting of 133 individuals.They concluded

that the entire bay area they surveyed contained relatively few dolphins, corresponding to the low density

and diversity of potential prey items overall. In all seasons and areas, Read et al.’s (2001) trawl catches were

dominated by mojarras (family Gerreidae).

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

120 FWRI Technical Report TR-11

Effect of Ecosystem Characteristics

on Growth and Survival

Work on this topic addresses the principal question:

How do growth and survival of individuals in each

HTLS vary through the range of environmental conditions defined by salinity, water quality, and benthic

habitat found in Florida Bay? Major working hypotheses are as follows: 

• Salinity directly affects the growth and survival of

HTLS;

• The carrying capacity of Florida Bay nursery areas

is related to the overlap of favorable salinity and favorable bottom or shoreline habitat.

Effect of Salinity on Growth and Survival

Simulation models and associated experimental trials

suggest that several Florida Bay species, each with optimal habitat in a different part of the bay, can be affected by changes in freshwater inflow and the resultant

changes in salinity patterns. Both pink shrimp and

spiny lobster could be adversely affected by the extreme

high salinity that often occurs in the north-central part

of the bay and sometimes spreads westward into optimal shrimp nursery habitat and southward into optimal lobster habitat. Lobster and shrimp could both

be adversely affected by low salinities in otherwise

suitable habitat and locations.

The effects of salinity and temperature on the

growth, survival, and subsequent recruitment and harvest of pink shrimp (Farfantepenaeus duorarum) were examined via laboratory experiments and a simulation

model (Browder et al., 2002). The pink shrimp is an

ecologically and economically important species that

has major nursery grounds in Florida Bay. Experiments were conducted to determine the response of juvenile growth and survival to temperature (15°–33°C)

and salinity (2–55 psu), and the results were used to refine an existing model (Browder et al., 1999). Results of

these experiments (Figure 8.3a,b) (Browder et al., 2002)

indicated that juvenile pink shrimp can tolerate a wide

range of salinities in their optimal temperature range

(20°–25°C), but the salinity tolerance range narrows

with distance from that range. Acclimation improved

survival at extremely high salinity (55 psu) but not at

extremely low salinities (i.e., 5–10 psu). Analyses of

the laboratory data suggested that growth rate increases with temperature until tolerance is exceeded

beyond approximately 35°C. Growth is optimal in the

midrange of salinity (30 psu) and decreases as salinity increases or decreases. Potential recruitment and

harvests from regions of Florida Bay were simulated

Figure 8.3 Response curves of survival, growth, and potential offshore harvest of pink shrimp in relation to salinity and temperature (Browder et al., 2002).

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 121

based on locally observed daily temperatures and

salinities.The simulations predicted that potential harvests might differ between years, seasons, and regions

of the bay solely on the basis of temperature and salinity. Results indicated that harvests on the Tortugas

shrimp grounds could be affected by spatial extent, location relative to suitable bottom habitat, and duration

of unfavorable temperatures within a favorable salinity range.

Butler et al. (2001a) explored the effect of changing

salinity on lobster and hard-bottom habitat, especially

as it might relate to lobster microhabitat (i.e., various

species of sponges and octocorals). Salinity experiments at winter temperatures have recently been completed for several sponge species (Figure 8.4). The

results indicate that there is reduced survival for an increasing number of species as salinity decreases (Butler et al., 2001a). None of the five species tested survived

at 15 psu. Field and Butler’s (1994) results concerning

salinity and temperature effects on postlarval lobsters

suggested a salinity optimum of 35 psu. Survival rates

at salinities other than 35 psu were low below 18°C and

above 33°C.

Powell et al. (2004) examined temperature-related

spatial and temporal variation in growth and survival

of spotted seatrout between areas and months. They

found a strong parabolic relationship between temperature and the growth of juveniles (22–60 d) but no

significant relationship between temperature and the

growth of larvae. They did not have an appropriate

distribution of samples to look at spatial and temporal variation in relation to salinity.

In a laboratory experiment, Wuenschel et al.(2001,

2002) found a significant interactive effect of temperature and salinity on routine metabolic rates of spotted seatrout.They found a biphasic metabolic rate that

changed isometrically with body mass in early stages

of larval growth, approximating the exponential relationship near unity proposed in previous studies, and

changed allometrically thereafter. Response surfaces

describing the effects of temperature and salinity on

maximum consumption and growth rates were also developed from laboratory experiments.

The optimal salinity for spotted seatrout may differ for each life stage. Schmidt et al., 2001, 2002) found

a negative correlation between annual average spotted seatrout catch rates and indices of freshwater inputs to the bay. Johnson et al. (2002a) found a low but

significant negative correlation between spotted

seatrout catch rates and bay salinity but thought it

could be the spurious result of fish concentrating during hypersaline events in more limited favorable habitat with increased vulnerability to fishing. There is

indirect evidence that hypersaline conditions reduce

survival of spotted seatrout in the early-settlement

stage. Although larval concentrations suggest that central Florida Bay is a major spawning ground for spotted seatrout (Powell, 2003), juvenile spotted seatrout

appeared to extend their range into the central portion

of the bay when hypersaline conditions were absent

(Thayer et al., 1999; Powell, personal communication),

but this has to be tested more rigorously. Citing Alshuth

and Gilmore (1994), Powell (2003) noted that spotted

seatrout eggs do not float at salinities less than 15 psu,

so egg survival might be virtually zero percent at 0–15

psu. On the other hand, laboratory experiments of

spotted seatrout in Texas suggest that the species does

not spawn at salinities greater than 30 psu (Wakeman

and Wolschlag, 1977; Taniguchi, 1980).

Effect of Water Quality on 

Growth and Survival

The staff of Everglades National Park maintain a record

of fish kills in Florida Bay (Schmidt, 1993b; Schmidt and

Robblee, 1994).These deaths are believed to occur because of low dissolved oxygen in the water column.The

mass mortalities are usually reported in the Snake

Bight area, where episodic low dissolved oxygen may

be caused by a combination of extremely shallow water,

high summer temperatures, poor tidal and wind mixing, and high respiration rates. High ammonia levels

recently reported by Boyer (personal communication)

are another possible source of mortality.

Contaminants in Florida Bay biota have been investigated previously. Tissues of fish, macroinvertebrates, and birds were analyzed for concentrations of

heavy metals, pesticides, and polychlorinated biphenyls

(PCBs) in fish and macroinvertebrates (Ogden et al.,

1974). Concentrations of DDT, arsenic, and methylmercury in marine animals were high enough to warrant

Figure 8.4 Survival of five sponge species at four salinities at winter

water temperatures for four weeks (Butler, 2005).

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

122 FWRI Technical Report TR-11

further investigation and led to later air-quality studies in ENP. As part of a larger study of the possible effects of mosquito control in Monroe County, the

Environmental Protection Agency (Anonymous, 1980)

examined fish and shellfish tissues and water for concentrations of certain pesticides, including Naled and

Batex.They found negligible amounts of Naled in fish

and shellfish, although oysters accumulated an average of 0.007 ppb of Naled. Batex was not found in detectable amounts in either fish or shellfish. Results

may have been biased on the low side by the dry-season conditions that prevailed.

A multiyear study in the C-111 canal and associated sites in Florida Bay was undertaken in order to determine other contaminant risks that may exist in south

Florida (Scott et al., 2002). According to extensive surface-water data and results from analyses of sediment,

tissue, and semipermeable membrane devices, canal

contamination seems to be derived from the extensive

agricultural production that drains into the C-111

canal. The results of this study indicate that runoff

from agricultural fields led to quantifiable pesticide

residues found in both canal and bay surface water, at

levels that occasionally exceeded current water-quality criteria. The major pesticide of concern was endosulfan, which was detected at 100% of the sites sampled.

The decision to alter the C-111 canal flow and allow increased freshwater flow into the adjacent Everglades

may result in discharges of pesticides through Everglades National Park and into Florida Bay. Endosulfan

concentrations are highest in the northeastern part of

Florida Bay, where the special sensitivity of pink shrimp

could cause mortalities. Low pink shrimp densities in

northeastern Florida Bay have been documented since

at least the 1960s (Costello et al., 1986). Other factors (e.g.,

extreme and variable salinities, absence of broad banks,

sparse seagrass coverage) may limit the presence of

pink shrimp in the northeastern bay, but no investigation of the possible effect of endosulfan on pink

shrimp in the bay has been made.

Health advisories are now posted in eastern Florida

Bay warning of elevated levels of mercury in some

higher-trophic-level fish. Thirty percent of spotted

seatrout sampled from eastern Florida Bay exceed

Florida’s no-consumption advisory level of 1.5 μg/g–1

(Evans et al., 2001). Jack crevalles also contain comparably high mercury concentrations (Evans, personal

communication). Other species of gamefish and forage

fish, although not as high in mercury as these two

species, have concentrations several times those found

in the western bay or elsewhere in Florida.These high

concentrations may put humans, other mammals,

birds, and reptiles at risk. Reduction in body burdens

of mercury in top carnivores is one of the success criteria listed by the South Florida Ecosystem Restoration

Task Force. Work is underway by Marnie Billie at FIU

to assess the ecological risk of consumption of Florida

Bay fish by piscivorous ospreys in the bay. Planned

restoration activities in the Everglades will change

freshwater deliveries to Florida Bay. These deliveries

could alter the existing high levels of mercury in some

Florida Bay gamefish through enhanced mercury fluxes

as well as altered productivity and food web structure, which influence mercury bioaccumulation.

Effect of Benthic Habitat on 

Growth and Survival

This issue has generally been approached by relating

benthic habitat to animal densities, which implies survival and growth, rather than by measuring habitat

effects on growth and survival directly.The fact that faunal densities are correlated with certain benthic habitats suggests that growth and survival are highest in

the appropriate habitat. See section on effect of benthic habitat on abundance.

Immigration, Growth, and Survival of 

Offshore-Spawning Fishes that Use

Florida Bay as a Nursery

In an effort to understand spatial and temporal patterns

of variability in immigration, growth, and survivorship of upper-trophic-level fishes, Settle (unpublished

data) examined these life history attributes in several

important species in the bay. Juvenile great barracuda

using the bay as nursery habitat are the product of protracted spawning, which is centered during the summer but with nearly 15% occurring from late fall and

winter. Spawning during these later periods has not

been previously reported in south Florida and may

suggest that either some spawning does occur in the

region during those times or that some barracuda in

the bay originate from elsewhere in the species’ distribution.The youngest individuals are found in the Atlantic transition, gulf transition, and western subregions

of the bay, suggesting ingress from both the Atlantic

channels and the open Gulf of Mexico. Cohort-specific

growth rates of young fish (age 30–150 d) ranged from

1.44 to 2.65 mm d–1 during the 1990s. Over the same period, growth was significantly slower in two faunally

depauperate subregions, the eastern and the turbid

western bay. Relative condition (weight/length) of this

species over the period 1973 to 2000 declined during

the early to mid-1990s and appears to be returning to

values observed during the 1970s and mid-1980s.The

overall instantaneous natural mortality rate was 0.02656.

Average survival was 97.38% d–1.Cohort-specific growth

Higher-Trophic-Level Species
rates of juvenile lane snapper (age 30–242 d), which primarily inhabit the gulf transition and western subregions, showed significant intra- and interannual

variation and ranged from 0.59 to 0.93 mm d–1. Snappers spawned during the spring and summer grew

faster than those spawned during fall and winter, and

fish spawned during 1998 grew faster than those

spawned in 1997. Instantaneous natural mortality both

years was 0.03636, and average survival was 96.43% d–1.

Effect of Ecosystem Characteristics

on Species Distribution and 

Community and Trophic Structure

Work on this topic addresses the major questions: Do

HTLS’ community composition or trophic structure

in Florida Bay vary in time and space, what factors are

responsible for this variation, and what processes are

affected? Major working hypotheses are as follows: 

• The abundance of HTLS is low in the northeastern

portion of Florida Bay because of high-amplitude

variation in salinity, low density of seagrass, lack of

extensive banks, restrictions on the immigration of

postlarvae, or a combination of all of these factors; 

• Changes in community composition are related to

changes in salinity, which can be influenced by water

management, although the effect of benthic habitat,

tidal exposure, rainfall, and oceanographic events

may need to be filtered out to see these effects; 

• Changes have occurred in the species composition

of mollusks, foraminifera, and other sessile species

in Florida Bay, and these changes reflect changes in

salinity, water quality, and the cover and composition of benthic vegetation;

• Spatial and temporal patterns in trophic pathways

vary depending on salinity, water quality, and abundance and type of benthic vegetation; 

• Widespread sponge mortalities may affect both

hard-bottom and seagrass communities;

• Fishing reduces the number and size of some apex

predators, causing shifts in community structure;

and

• Changes in community composition are related directly to changes in benthic habitat.

Effect of Salinity on Species Abundance

and Community Structure

Several studies suggest that hypersalinity affects the

benthic fauna of Florida Bay. Schmidt (1977) reported

lower forage fish diversity, biomass, and numbers in

northcentral Florida Bay in salinities greater than 45

psu. Johnson et al. (2002a,b) noted that “evenness”(an

index of community structure) among 11 dominant

species, as estimated from statistical model predictions, was lower in 1990, a year of extreme high salinity in the bay, than in 1995, a wet year. Lyons (1999)

observed fewer species in the molluscan community

in the hypersaline part of Florida Bay. A simulation

model based on experimental data (Browder et al.,

2002) predicted lower juvenile pink shrimp densities

and fewer potential recruits to the Tortugas fisheries

from the hypersaline central part of Florida Bay. Based

on relative concentrations of smallest-stage seatrout

postlarvae, Powell (2003) determined that central

Florida Bay is a major spawning ground for spotted

seatrout; however, there is evidence that at salinities

greater than 45 psu, survival and growth of larval and

juvenile spotted seatrout could be diminished (Wuenschel, 2002). The frequency and duration of hypersaline events in the central bay might, therefore, affect

survival and growth of young seatrout and, consequently, the abundance of this species. Powell (2002)

noted that densities of the postlarvae of many species

collected with an epibenthic sled were higher in the

central bay, indicating that many species may be disproportionately exposed to hypersaline conditions in

an otherwise favorable nursery area. Sogard et al. (1989)

found lower species richness of both epibenthic and

water-column fishes. Holmquist et al. (1989) found a

lower species richness of macroinvertebrates in the

central bay, which was characterized by low tidal range

and hypersaline conditions during their studies.They

concluded that water circulation and salinity patterns

were influential in structuring Florida Bay’s epibenthic

faunal communities.

HISTORICAL DISTRIBUTIONS OF MOLLUSKS

AS INDICATORS OF PAST SALINITY 

PATTERNS

Historical records of salinity and bottom vegetation

were reconstructed based on molluscan assemblages

in shallow sediment cores. An analysis by BrewsterWingard et al. (2001) suggested that molluscan assemblages in Florida Bay have undergone distinct

changes over the past 100–200 years. Brachidontes exustus, a euryhaline species tolerant of diminished water

quality and a wide range of salinities, accounts for

more than 80% of the molluscan fauna in the upper

portions of six cores. Four cores from central and eastern Florida Bay and one from Featherbed Bank in Biscayne Bay suggest decreases in molluscan faunal

diversity and absolute abundance that began perhaps

in the 1960s or earlier and reached a low in the early

1970s (Figure 8.5).

The dominance of Brachidontes and the decreases

in faunal richness and abundance are indicative of a

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 123

Higher-Trophic-Level Species
system under stress. Interestingly, the transition-zone

cores from the mouth of Taylor Creek and in Manatee

Bay do not show the decline in faunal diversity and absolute abundance exhibited in the other cores. Based

on their analysis of molluscan epiphytic species within

the cores, Brewster-Wingard et al. (2001) concluded

that common factors are affecting the faunas and their

associated bottom vegetation across eastern and central Florida Bay, despite the isolation of some of the

basins.

Effect of Water Quality on Species 

Abundance and Community Structure

Ortner et al. (2001), who examined possible relationships between chlorophyll, zooplankton, and anchovy

from January 1994 through January 1999, found no evidence that phytoplankton blooms were causing a fundamental shift in community structure and trophic

dynamics in Florida Bay. Copepod concentrations were

not related to chlorophyll concentrations, and anchovy

density was not related to copepod concentrations.

On the other hand, Johnson et al. (2002a) found a significant relationship between bay anchovy density and

chlorophyll a concentrations. Intermittent high anchovy densities might be due to the attraction of anchovies to unvegetated bottoms and high turbidity

(Patillo et al., 1997). Peebles’ (2002) study of bay anchovy egg densities in the Manatee River suggests

that structured, spatially and temporally intensive

sampling of bay anchovy eggs may reveal relationships with prey abundance, salinity fronts, and freshwater inflow not obvious from previous sampling in

Florida Bay.

Effect of Benthic Habitat on Species

Abundance and Community Structure

FISH DISTRIBUTIONS IN MANGROVE 

PROP–ROOT HABITAT

Dennis and Sulak (2001) found that prop-root sites in

northeastern Florida Bay had significantly more fish larvae than did nearby open-water sites or nearshore

areas without mangroves. However, the densities of

both forage fish and juvenile predator fishes were

lower among mangrove prop-root habitats in Little

Madeira Bay, Trout Cove, and Manatee Bay than in

prop-root habitats in the Bahamas and Puerto Rico.

They proposed that isolation from offshore sources of

larvae or juveniles was the reason for the low densities. In support of this conclusion, they found that the

concentration of larval fish was much greater on the leeward side of Key Largo than at their northeastern

Florida Bay mangrove prop-root sites. Fish density

and biomass were greater in mangrove prop-root habitats than in adjacent fringing seagrass areas. In a previous study by Thayer et al. (1987), they determined that

the mangrove prop-root habitat in Florida Bay and

nearby areas was occupied by a distinct faunal assemblage.

CANOPY–DWELLING FISH AND 

MACROINVERTEBRATE ASSEMBLAGES 

IN RELATION TO SEAGRASS

Densities of many macroinvertebrate and fish species

in Florida Bay are higher inside seagrass beds than outside them (Holmquist et al., 1989; Sogard et al., 1989;

Thayer and Chester, 1989; Thayer et al., 1999; Matheson

et al., 2001). Johnson et al. (2002a) analyzed the combined

data of 6 field studies (including those cited above) and

quantified the relationship between animal density

and seagrass density for 11 key forage species. They

found that of the 10 species whose densities were significantly related to seagrass, 5 were densest in dense

Florida Bay Synthesis Hunt and Nuttle

124 FWRI Technical Report TR-11

Figure 8.5 Historical view of the dominance of a molluscan

water-quality indicator in the molluscan fauna (Brewster-Wingard

et al., 2001) at three Florida Bay locations. Brachidontes tolerates conditions that other mollusks cannot. Experiments are underway to better define the conditions tolerated by Brachidontes.

Higher-Trophic-Level Species
seagrass, 4 were densest in moderately dense seagrass, and 1 was densest in sparse seagrass. Bottom or

seagrass type was a significant variable explaining the

densities of 10 forage species.Three species were densest in Syringodium, three were densest in Halodule, two

were densest in mixed grasses with Syringodium, and

one was densest in mixed grasses with Thalassia. One,

bay anchovy, was densest in areas without seagrass.

SHIFTS BETWEEN BENTHIC AND PELAGIC

ZOOPLANKTIVORES

A prevailing hypothesis has been that the seagrass

die-offs and phytoplankton blooms experienced beginning in the late 1980s provoked a trophic shift in

western Florida Bay from a system based principally

on benthic production to one based principally on

water-column production.This hypothesis grew out of

comparisons of the fish and macroinvertebrate community compositions in 1984–1985 to those in 1994–1995.

Thayer et al. (1999) compared the fish assemblages of

1984–1985 to those of 1994–1995 in three regions of the

bay and found that canopy-dwelling species had declined and that pelagic zooplanktivores dominated

the fauna. Robblee et al. (2001) compared benthic vegetation, fish, and macroinvertebrate assemblages found

in Johnson Key Basin in 1985 to those found there in

1995. They observed a decrease in Thalassia and Syringodium and an increase in Halodule and bare bottom.

They found a decrease in Farfantepenaeus duorarum

(pink shrimp), seagrass-associated caridean shrimps

(–65%), and seagrass-associated fishes (–81%) and concluded that the decline in seagrass-associated species

was a result of seagrass die-off.

The hypothesis that loss of seagrass would result

in a trophic shift of fish was discounted by sampling

data beyond 1995.The juvenile and small-resident fish

assemblage in collections of Powell et al. (2001b) made

during 1996–2000 (especially 1998) differed markedly

from that in 1994–1995 and resembled the assemblage

observed in 1984–1985. The change from canopydwelling to pelagic zooplanktivores from 1984–1985

to 1994–1995 was followed by a change back to canopy

dwellers in 1998–1999. The investigators concluded

that the recovery of an assemblage of fish species dominated by seagrass canopy dwellers cannot be wholly

explained by recovery of seagrasses because there is

no evidence of seagrass recovery on a subdivisionwide basis in 1999–2000 relative to 1994–1995. In fact,

seagrass densities in 1999–2000 were much lower than

in 1984–1985 (Powell et al., 2001b).

Ortner et al. (2001) also refuted the hypothesis of

a trophic shift related to loss of seagrass coverage and

an increase in phytoplankton blooms.They concluded

that the recent history (1994–2000) of phytoplankton,

zooplankton, and planktivorous fish abundances provides little or no support for the concept of a fundamental, persistent shift from a demersal benthic-based

food web to a pelagic water-column-based food web.

Furthermore, there seems to be no clear relationship

between plankton bloom incidence or intensity and the

abundance of zooplanktonic herbivores, nor is there a

relationship between the abundance of the bay anchovy and its preferred copepod prey.

An alternative hypothesis for the observed fluctuation in dominance between demersal and water-column species is that the density of the small-juvenile

and small-resident canopy-dwelling fish assemblage

is influenced by the sporadic dominance of pelagic

zooplanktivorous clupeiforms that might be related to

water column chlorophyll a concentrations (Powell et

al., 2001b).

Another alternative hypothesis is that the establishment of a more heterogeneous bottom habitat, occupied by Halodule and Syringodium as well as some

Thalassia, might be responsible for the recovery of

canopy-associated species after 1995 (Robblee, personal communication) An exploratory principal component analysis revealed four PCs, each of which could

be interpreted to relate to a vegetation component:

Thalassia (PC1), Halodule (PC2), Syringodium (PC3), and

macroalgae (PC4) (Robblee et al., 2001). Pink shrimp correlated with PC2 and PC3.The rainwater killifish was

correlated with PC1. Affinities of various species to

certain types of seagrass habitat might lead to greater

overall abundance if seagrass habitat diversity increases.This is supported by the work of Johnson et al.

(2002a), who found that densities of various species varied, depending upon the type of seagrass they were

found in and that no species was found at highest

density in pure Thalassia beds.This result is especially

valuable because Somerfield et al. (2002) concluded

that even large faunal effects of seagrass habitat heterogeneity might be difficult to detect. This hypothesis might explain the recovery of canopy-dwelling

species after 1995 but not the fluctuations in bay anchovy density.

Peebles’ (2002) study of bay anchovy egg abundance in the Manatee River provides insight on the bay

anchovy fluctuations in Florida Bay. Using a spatially

and temporally intense sampling strategy, Peebles

(2002) found that nighttime bay anchovy egg abundance in Manatee Bay was positively related to Acartia tonsa abundance the previous day. Bay anchovy

appeared to spawn immediately upstream from salinity fronts (which he defined as a change of 1 psu/km)

that concentrated their prey. The effect of freshwater

inflow on bay anchovy egg abundance was non-linear.

Peak abundance occurred when salinity fronts formed

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 125

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

126 FWRI Technical Report TR-11

near the river mouth. Egg abundance declined when

these fronts advanced seaward of the river mouth but

was lowest when fronts were weak or absent during

low-flow periods.The presence of a salinity front was

associated with relatively low mean salinity and high

standard deviation in salinity. In their analysis of a

data set compiled from several studies, Johnson et al.

(2002a) found a significant relationship between bay anchovy density and salinity (negative relationship), standard deviation in salinity (positive relationship), and

freshwater inflow index (positive relationship) in

Florida Bay. Peebles’ (2002) study might explain the

mechanisms behind these relationships.

EFFECTS OF MACROALGAE ON 

ANIMAL ABUNDANCE

The pattern of settlement of spiny lobster postlarvae

in southwestern Florida Bay may be highly dependent on the location of red macroalgae (Laurencia),

crevice shelters and planktonic postlarval abundance

(Herrnkind and Butler, 1994). Mud banks that restrict

transport, unfavorable salinity, and scarcity of hard-bottom settlement habitat may severely restrict the presence of spiny lobster in the interior bay (Field and

Butler, 1994).

EFFECT OF SPONGES ON 

JUVENILE SPINY LOBSTER

Butler et al. (1995) documented widespread sponge

mortality coinciding with months-long, extensive

cyanobacterial blooms in the south-central part of

Florida Bay in the early 1990s (1991, 1992, 1994). They

showed with field experiments that the loss of sponges

affected the distribution of spiny lobster juveniles,

which use crevices beneath sponges as nursery habitat. Use of artificial shelters increased following the

sponge decline. Juvenile spiny lobster abundance declined 23% at sites without artificial substrates and increased 76% at sites with artificial substrates. The

long-term effect of sponge mortality on lobster abundance is not known, but shelter such as that provided

by sponges reduces the risk of predation (Herrnkind

and Butler, 1994). Based on their results, the authors

suggested that loss of shelter might lead to increased

predation on animals that remain in areas without

shelter or are in search of shelter. Loss of area with shelter may cause crowding and resource limitation in

areas of remaining shelter (Butler et al., 1995). Other animals that use sponges as habitat include stone crabs

(Menippe mercenaria), spider crabs (Mithrax spp.), toadfish (Opsanus beta), and octopus (Octopus spp.).

SPATIAL VARIABILITY IN 

TROPHIC RELATIONSHIPS 

The relative importance of seagrass and phytoplankton in food webs differs across the bay, and neither is

important in certain parts of the bay. Chanton et al.’s

(2001) evaluation of stable carbon (C), nitrogen (N), and

sulfur (S) (δ13C, δ15N, δ34S) data for producers and consumers in Florida Bay indicated that the interior of

the bay has a strongly seagrass-based trophic structure,

whereas the gulf (outer or western) sites in the bay shift

toward a more plankton-dominated trophic system

(Figure 8.6). It is not yet certain whether the shift in Figure 8.6 reflects natural spatial variation or a temporal

trend forced by changing environmental conditions in

the bay. Stable carbon, nitrogen, and sulfur data in

Figure 8.7 from Evans et al. (2001) confirm Chanton et

al.’s (2001) description of the trophic structure of the

interior and western bay. In addition, the data suggest

a nonseagrass-based diet (likely a more pelagic-, or

water-column-, based food web) in the eastern bay.

Predominant food webs in the hard-bottom communities of Florida Bay (mainly the southwestern bay)

and bayside hard-bottom communities in the Florida

Figure 8.6 Summary comparison of consumer tissue δ13C vs δ34S

from several Florida coastal ecosystems. Data illustrate the gradient

in stable isotope values as trophic dependence shifts from seagrass

beds “benthic”, δ13C-enriched, δ34S-depleted) to the water-column

(“planktonic”) (δ13C-depleted, δ34S-enriched) (Chanton and Lewis,

2002).

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 127

Keys are based on macroalgae rather than seagrass, according to stable-isotope analyses (C, N, and S) conducted by Behringer and Butler (1999).They sampled

macroalgae, seagrass, suspended particulate organic

matter (POM), sediment POM, sponges, gastropods,

holothurians, bivalves, and spiny lobsters. With the

exception of suspension feeders, the hard-bottom animals were trophically independent of seagrass.

Koenig et al. (2001) found spatial, temporal, and ontogenetic dietary shifts in the major prey of red drum.

They speculated that the differences were due to differences in prey availability. This is consistent with

observations about the abundance of various prey,

which differs by region. They were not able to detect

spatial or seasonal differences in the diet of snook,

possibly because of the lower resolution of the snook

diet data.

Variation in Ecosystem 

Characteristics

Effects of Animals on the Ecosystem

Specific questions being addressed by this research are

as follows: (1) how do animals affect their ecosystem,

and what are the consequences of change in animal

abundance or distribution for the rest of the system?

(2) What is the ecological role of sponges in the ecosystem, and what does the loss of sponges in southwestern Florida Bay and an increasing fishery for some

sponge species portend? 

EFFECTS OF ANIMALS ON BENTHIC HABITAT

Benthic grazing animals in exceptionally high densities can adversely affect benthic vegetation in Florida

Bay. A dense aggregation of the variegated sea urchin

(Lytechinus variegatus) caused severe, localized defoliation of a seagrass bed in outer Florida Bay during

1997–1998 (Rose et al., 1999). Macia and Lirman (1999)

described the population dynamics of this aggregation

and Rose et al. (1999) described the short-term effect

of this aggregation on the benthic community. Subsequent monitoring of the aggregation during 1998–1999

revealed that urchin densities progressively declined,

as did their effect on seagrass biomass. However, as of

2002, seagrass biomass in the area of the meadow that

underwent the most severe defoliation remained drastically reduced compared to areas that had not been

damaged by urchins (W. Sharp, personal communication).

ROLE OF SPONGES IN REGULATING 

WATER QUALITY

The working hypothesis is that the large-scale loss of

suspension-feeding sponges may have rendered the

Florida Bay ecosystem susceptible to recurring phytoplankton blooms (Peterson and Fourqurean, 2001).

Sponges are capable of filtering large volumes of water

when feeding.Widespread sponge mortalities occurred

in Florida Bay from 1992 to 1994. By 1995, total sponge

biomass was a fraction of its former level: there had

been a 70% decline in the Long Key area and an 84.6%

decline in the Marathon area (Stevely and Sweat, 2001).

Loss of sponge biomass in Florida Bay may be having

major ecological effects on water quality (Stevely and

Sweat, 2001; Peterson and Fourqurean, 2001) 

Sponges are a particularly dominant structural

feature of Florida Bay seagrass and hard-bottom habitats, functioning as efficient filters of small (less than

5 μm) planktonic particles. Previous studies have illustrated that the grazing pressure of filter-feeding

bivalves may control phytoplankton abundance. If the

presence of sponges increases light availability to the

benthic plant communities, then sponges may reduce

the shading effects of phytoplankton blooms, and the

loss of sponges in Florida Bay may have cascading effects on the associated seagrass community (Peterson

and Fourqurean, 2001).

Since the initial seagrass die-off in the late 1980s,

blooms have swept over extensive portions of the bay

Figure 8.7 Stable isotope analysis of Florida Bay gamefish to

support methylmercury studies in Florida Bay (Evans et al., 2001).

The analysis complements the view of the bay in the previous

figure by adding information on the bay’s eastern and northern transition zones.

Higher-Trophic-Level Species
north of the middle Keys and have persisted for

months.The proliferation of the cyanobacterium (Synechococcus) and diatom (Rhizosolenia) blooms has caused

widespread concern among scientists and water managers.These blooms have the potential for disrupting

the ecology of the bay and harming benthic plant communities by depleting oxygen, producing toxins, and

reducing the light levels in the bay. Some regions of

Florida Bay exhibit high levels of algal and/or nonalgal suspended solids, resulting in low light penetration.

Although phytoplankton blooms were not likely the

cause of the initial seagrass die-off, the reduction in

light caused by high phytoplankton standing crops

may have contributed to poor seagrass recovery and

more recent seagrass die-offs.

Prior to the widespread sponge mortalities that occurred from 1992 to 1994, Stevely and Sweat (2001)

collected data on the abundance of commercial sponges

(Spongia and Hippospongia) and the entire sponge community at 15 locations in the Middle and Upper Keys

(4 locations were within Everglades National Park).

They have been evaluating the recovery of the sponge

community annually since 1994 and have identified to

family, genus, or species level approximately 95% of the

sponges counted. In general, recovery of the largest and

most abundant sponge species (in the genera Spheciospongia and Ircinia) has been extremely slow.The first

significant indication of recovery of these species was

found at Marathon in 1999 and 2000, but recovery was

still not apparent at Long Key by April of 2001. These

large species represented 70% of the sponge community biomass prior to the mortalities.

Based on their data prior to the 1992–1994 mortalities, Stevely and Sweat (2001) estimated that the mean

sponge abundance was 0.725 sponges/m2 and mean

sponge biomass volume was 364 ml/m2. Based on a

sponge pumping rate of 10,000 times the sponge volume per day (Reiswig, 1974; Reiswig, personal communication), the sponge biomass could therefore pump

3,640 liters of seawater per square meter per day. Since

the water column in the study area was approximately

three meters deep, sponge biomass could be expected

to pump the equivalent of the entire water column in

24 hours (Stevely and Sweat, 2001).The loss of 75% of

sponge biomass might be expected to lengthen the

time required to pump the water column from one day

to four days.

Peterson and Fourqurean (2001) speculate that

system-wide trophic dysfunction caused by the sponge

die-off has potentially contributed to the magnitude of

the nuisance phytoplankton blooms, and that the loss

of these organisms can explain why this system remains

susceptible to recurrent blooms of phytoplankton and

cyanobacteria.

Oceanographic Effects on 

Larval Transport and Recruitment

Major questions related to this topic are (1) What

processes are involved in the transport of presettlement

stages of fish and invertebrates to the boundaries of

Florida Bay, and what are their schedules? and (2)

What pathways do early life stages of offshore-spawned

HTLS use to enter Florida Bay, what is the relative importance and extent of penetration into the bay’s interior by these pathways, and what factors influence

transport and settlement?

Many species associated with the reef tract and the

southwestern Florida shelf spend some part of their

life cycle in Florida Bay. For example, Florida Bay is a

major nursery ground for pink shrimp that are harvested in waters off the Dry Tortugas, the most economically important pink shrimp fishing ground in the

state. Florida Bay also contains important spiny lobster nursery habitat, and Everglades National Park is

a fishing-free sanctuary for spiny lobster. Water flows

and animal movements connect Florida Bay not only

to the upstream Everglades and coastal mangrove

areas but also to the Florida Keys, the reef tract, the

southwest Florida shelf, and the Dry Tortugas. Many

HTLS range between the bay and coastal reefs within

their life cycle. The development of scientific knowledge about HTLS of the bay, therefore, must extend

beyond Florida Bay to address the greater ecosystem

that supports these species and the processes that

affect their movements. For example, research should

include the Loop and Florida currents and countercurrents, the Tortugas Gyre, and coastal eddies.The effect of these processes on larval transport and the

distribution and abundance of HTLS in the bay must

be addressed to improve the ability to distinguish

effects of changes in freshwater inflow.

Florida Bay lies between the Atlantic Ocean and the

Gulf of Mexico and is connected to both of these bodies through regional-scale circulation and exchange

processes and the oceanic boundary currents that influence these processes. The southwest Florida Shelf

to the west and the Keys coastal zone to the east and

south of Florida Bay interact with each other and the

bay through the tidal channels between the Keys and

also by means of their boundary currents (Herrnkind

and Butler, 1994; Lee et al., 2001). A dominant process

potentially affecting water transport and the transport of eggs and larvae to Florida Bay is the strong, coherent response to alongshore wind-forcing coupled

with seasonal stratification in response to variations in

wind-mixing, air-sea exchange, and river runoff along

the nearshore western shelf. Boundary current dynamics and eddy processes are also critical larval transFlorida Bay Synthesis Hunt and Nuttle

128 FWRI Technical Report TR-11

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 129

port mechanisms that operate both on the regional

and local scales.Transport response to prevailing easterly winds may vary along the Florida Keys as a result

of the curvature of the coastline (Lee and Williams,

1999), but they are expected to favor onshore larval

transport between the Lower Keys and the Dry Tortugas, where the coastline is east-west oriented. Onshore convergence of the Florida Current can also

facilitate transport into the coastal zone of the Keys, and

this occurs mainly in the upper Keys where the shelf

narrows and curves northwards (Yeung and Lee, 2002).

The area of the Dry Tortugas is an important spawning site for penaeid shrimps, spiny lobsters, and some

species of snappers and groupers (Limouzy-Paris et al.,

1997). Pink shrimp larvae were retained by the Tortugas gyre circulation for a period of two weeks (Criales

and Lee, 1995). Coastal eddies originating from the

Dry Tortugas and propagating downstream may be a

mechanism to deliver presettlement stages from

spawning site to nursery sites on the reef tract and in

Florida Bay (Yeung et al., 2001; Criales et al., 2003).The

lower southwestern shelf in the vicinity of the Dry

Tortugas is a potential source of recruitment to the

Florida Keys reef tract and Florida Bay for both reef fish

and pink shrimp.

Frontal eddies of the Loop Current in the Gulf of

Mexico that propagate southward along the outer edge

of the western shelf may be trapped and develop into

persistent gyres off the Dry Tortugas (Fratantoni et al.,

1998; Yeung and Lee, 2002). The subsequent arrival of

another frontal eddy or the abrupt retreat of the Loop

Current may dislodge the gyre, which then moves

eastward along the southeastern shelf off the Florida

Keys in the form of a transient coastal eddy. The Tortugas gyre provides a mechanism for retaining larvae

for periods of weeks to up to three months (Lee et al.,

1994).

EDDIES AND GYRES

Working hypotheses about the transport of larvae to

the boundaries of the bay are as follows: (1) Presettlement stages are transported and detrained into the

coastal zone of the Florida Keys by coastal eddies. (2)

Spawning and nursery sites for pink shrimp, spiny

lobsters, and some snappers are linked through the

evolution of the coastal eddies from the Tortugas gyre.

(3) The formation of the Tortugas gyre is enhanced by

a well-developed Loop Current (high latitudinal intrusion) whose dynamics may be modulated by climatic

shift. (4) Snapper larvae entering Florida Bay originate from spawning stocks that form seasonal aggregations off the Dry Tortugas. (5) Year-class strength of

six snapper species is enhanced by increased larval retention and nutrient-enrichment of the pelagic larval

habitat via gyre-induced upwelling during spawning

season off the Dry Tortugas (Criales and McGowan,

1994; Criales and Lee, 1995; Jones et al., 2001; Yeung et

al., 2001; Yeung and Lee, 2002).

Supply of early-life-stage recruits is a major limiting factor of the year-class strength of aquatic species.

Presettlement stages of the spiny lobster, snapper, and

pink shrimp that inhabit Florida Bay as juveniles and/or

adults enter the bay from the ocean through interisland

channels.

The eddy hypothesis of regional recruitment has

important implications over larger temporal and spatial scales. Because coastal eddies originate from the

Dry Tortugas, they may constitute the essential transport link between the spawning and nursery grounds.

Moreover, eddy formation at the Dry Tortugas is associated with Loop Current frontal dynamics, which are

in turn modulated by long-term climatic variability

(Yeung et al., 2001; Yeung and Lee, 2002).

Observed larval distribution patterns of some crustaceans in the Florida Keys coastal zone corroborate

many of the predictions based on key coastal transport

processes. Early-stage phyllosomata (less than 2 months

old) were concentrated within or at the boundaries of

a gyre in the pattern hypothesized for passive drifters

(Yeung and Lee, 2002).The abundance of strong-swimming spiny lobster postlarvae was not highly correlated

with wind-driven currents that can affect the coastal

transport of more passive drifters (Acosta and Butler,

1997). High concentrations of pink shrimp larvae were

found in the Tortugas Gyre in late spring–early summer (Criales and Lee, 1995). High densities of larvae and

postlarvae of 10 different shrimp families were found

Figure 8.8 Monthly mean influx density of spiny lobster postlarvae

observed at Long Key and the predicted density (densityLK) using

an index of countercurrent magnitude in a simple regression model

(r2 = 0.50, F1,16 = 17.90, P < 0.0006) (Yeung et al., 2001).The index

is the average magnitude of the countercurrent component for the

periods two weeks prior to and three days during sampling taken

at a current meter moored at Tennessee Reef in the middle Keys.

Satellite imagery confirmed that in most cases, enhanced coastal

countercurrents coincided with the presence of a cyclonic mesoscale

eddy in the vicinity.

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

130 FWRI Technical Report TR-11

off Looe Key during the presence of a gyre (Criales and

McGowan, 1993, 1994).

Variability in the supply of larvae may be related

to the development of mesoscale eddies and their associated countercurrents on the oceanside of the channels. Peak influx of spiny lobster postlarvae into the bay

through the middle Keys coincided with the presence

of eddy and countercurrent conditions (Figures 8.8,

8.9) (Yeung et al., 2001; Yeung and Lee, 2002).

Temporal and spatial variability in the supply of

spiny lobster postlarvae to Florida Bay nursery grounds

may interact with local nursery-habitat structure to

influence recruitment and year-class strength. Butler

et al. (2001b) used an individual-based model to address

this question. They tested eight scenarios of variability describing postlarval supply (Uniform, Volumetric, Gradient, Broken Stick–Static, Broken Stick–

Variable, Pulsed, Aggregated, and Random).Their results indicated that random variation in the arrival of

postlarvae among regions of the Florida Keys leads to

the highest recruitment, whereas persistently patchy

settlement (i.e., pulsed and aggregated scenarios) yields

the lowest. Analyses of field data suggested that the random supply was the most realistic scenario. Field data

were based on artificial collectors positioned at eight

sites in the Florida Keys.

Eddy transport processes may also affect supply

and nutritional condition of pink shrimp and snapper

presettlement stages entering Florida Bay through the

Florida Keys. Influx of early-life-stage recruits was

monitored monthly on the new moon for two years at

two tidal channels on opposite ends of the middle

Keys: Whale Harbor (east end) and Long Key Channel

(west end). Back-counted birth dates based on counts

Figure 8.9 Example of a sequence of satellite SST images used to infer gyre displacement and progression down the Straits of Florida

(Yeung et al., 2001). Warmer waters are red, cooler waters are blue. The centers of each of two gyres (1 and 2) present during this period

are indicated. On March 5, a gyre (1) was centered off the Dry Tortugas; by March 14, it had begun moving downstream; and by March

25, the upstream frontal eddy (2) responsible for its displacement is clearly evident.

Higher-Trophic-Level Species
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FWRI Technical Report TR-11 131

of otolith daily increments suggested that snapper larval duration during the first year varied across species

and ranged from 35.50 to 41.45 days (Jones et al., 2001).

Preliminary analyses of Year-2 samples suggested that

larval durations differed from those of Year 1. Peak

abundance of snapper larvae in the channels occurred

in the summer of 1997 and was coincident with a welldeveloped Loop Current (high latitudinal extent) favoring gyre formation off the Dry Tortugas, where

snapper spawning aggregations occur. Criales et al.

(2003) showed that the temporal pattern of immigration of postlarval pink shrimp differed substantially between Long Key Channel and Whale Harbor Channel

(Figure 8.10).The influx of postlarvae at Long Key channel was lower in magnitude but steadier than the influx at Whale Harbor. Long Key channel showed the

highest postlarval influx in late spring–summer,

whereas the postlarval influx through Whale Harbor

(downstream from Long Key in terms of the Gulf

Stream and associated shelf gyre processes) showed

both spring–summer and winter peaks. The winter

peak may be associated with the countercurrent generated by eddies (Figure 8.10). This high variability

over small spatial scales suggests the influence of

mesoscale processes.

MOVEMENT INTO AND WITHIN 

FLORIDA BAY

Other working hypotheses that relate principally to

movement of postlarvae into the bay are as follows: (1)

Pink shrimp postlarvae enter Florida Bay from two directions: west (across the southwestern shelf) and

southeast (through the Lower Keys).The western and

southeastern pathways vary in importance and are affected differently by physical oceanographic factors and

tides. (2) Sufficient numbers of pink shrimp larvae

enter the bay’s interior for the interior bay to be a significant nursery ground and source of recruits to the

fishery during years of favorable conditions. (3) Snappers settle outside Florida Bay but near the boundary

and enter Florida Bay as juveniles. (4) The abundance

of bay-dependent species that are spawned offshore

is lower in northeastern Florida Bay because of weak

transport across the bay.

Transport across the lower and middle Keys has

previously been the most recognized pathway of larval transport to Florida Bay because past studies (Criales and McGowan, 1994; Yeung, 2001) have shown

that local winds, Florida Current flow, and coastal eddies interact to influence the onshore transport and recirculation of larvae in the Florida Keys. New work,

based on synchronized sampling of postlarvae on both

sides of Florida Bay, indicates that the dominant pathway of influx of postlarval pink shrimp into Florida Bay

is from the west (Browder et al., 2002). Peak concentrations of pink shrimp postlarvae in water moving

into the bay from the west (through Sandy Key and

Middle Ground channels) were substantially larger

than in water moving into the bay from the southeast

(Whale Harbor Channel). The temporal pattern from

the west consisted of one large, sustained summer

peak (Figure 8.11). In contrast, peak concentrations at

Whale Harbor were observed in February, May, and

July and were smaller (Figure 8.11). Prior studies examined the influx of pink shrimp postlarvae from the

southeast (Allen et al., 1980) and west (Tabb et al., 1962;

Roessler et al., 1969; Robblee et al., 1991), but these

studies were not designed in a way that would allow

us to make comparisons now.

Pink shrimp nursery grounds are on the western

Figure 8.10 Mean monthly postlarval influx of pink shrimp has

different temporal patterns in channels of the middle Florida Keys

(Criales et al., 2003). At Long Key Channel (the two upper graphs),

larval concentrations are associated with surface temperature. At

Whale Harbor Channel, larval concentrations were associated

with the coastal countercurrent flow.

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

132 FWRI Technical Report TR-11

side of the bay (Robblee et al., 1991), not in the east

(Costello et al., 1986).The larvae spawned north of the

Dry Tortugas on the relatively shallow shelf may escape

from the strong flow of the Florida Current and move

northeast toward the bay with the winds and tidal

currents.

Effect of Human Activities

This topic was approached by addressing three major

questions: 

• What are the potential effects of water management

and other human activities on recruitment, growth,

and survivorship of HTLS? 

• What is the potential effect of water management on

bioaccumulation of mercury?

• How does fishing, both within the bay and outside

the bay, affect fishery populations and our ability to

detect effects of water management on recruitment,

growth, and survival? 

Some critical working hypotheses relative to these

questions were as follows:

• The timing and amount of freshwater releases to

coastal wetlands adjacent to Florida Bay affect the

nesting success of wading birds in northeastern

Florida Bay.

• Changes in water management that affect the spatial coverage, intensity, and duration of hypersalinity affect shrimp, lobster, and other species.

• Abrupt and out-of-season releases of large volumes

of fresh water into Florida Bay and coastal waters adversley affect benthic fauna and fish, shrimp, and lobster recruitment.

• Increased freshwater inflow to northeastern Florida

Bay will increase the load of mercury entering the bay

and the body burden of mercury in bay HTLS.

• Fishing on the reef tract, in the Tortugas, and throughout the bay affects the population structure and

abundance of predator fish species in Florida Bay.

WATER MANAGEMENT AND 

WADING–BIRD NESTING SUCCESS

Linkages of water management, fish production, and

roseate spoonbill nesting success in wetlands adjacent to northern Florida Bay have been quantified in

studies by Lorenz (2001a,b). Other investigators have

proposed that fish availability to wading birds during

their nesting season in south Florida is influenced by

two main factors: the extent to which water covers

wetlands during the wet season and the consistency of

the decrease in water depth and water coverage during the following dry season. Lorenz (2001b) demonstrated the effectiveness of the process of expansion and

contraction of water area in enhancing prey availability to wading birds in the coastal marshes immediately

north of eastern Florida Bay. He determined that fish

density during the wet season is positively related to

water depth in the marsh and the length of time in

which depths in the marsh are greater than 12.5 cm. He

found that concentrations of fish in topographic lows

occur—and reach roughly twice dry-down density—

when water depths in the adjacent marsh decline

below 12.5 cm. Roseate spoonbills that nest on islands

in northeastern Florida Bay feed in these coastal

marshes during the nesting season, which coincides

with the usual dry season. Lorenz (2001b) examined

their nesting record in relation to water-level data and

determined that, in general, mean water levels at his

Figure 8.11 The temporal pattern of monthly pink shrimp postlarval influx on the western side of the bay (upper-graph) differs from

the Middle Florida Keys stations (lower-graph) but is similar to that at Long Key Channel the two previous years (Figure 10, upper graphs,

(Criales et al., 2003).

Higher-Trophic-Level Species
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FWRI Technical Report TR-11 133

fish-sampling sites in the coastal marshes were lower

than 12.5 cm during successful roseate spoonbill nesting periods and higher than 12.5 cm during failed

nesting periods. Furthermore, prey availability at the

sites during successful nesting periods was twice that

during failed nesting periods. On the other hand, nesting failed to occur during several recent years that

might have been expected to support successful nesting. This failure may be explained by out-of-season

water releases from the nearby C-111 canal.These releases have been shown to raise water levels in the

coastal wetlands. Such releases during spoonbill nesting periods could cause prey to become dispersed and

result in nesting failure.

The coastal marshes north of Florida Bay were

principally oligohaline prior to the extensive drainage

and water diversion that occurred with water management (Egler, 1952). Since the time that hydrologic

modification was begun, mangroves have encroached

inland, and there are other indications that the coastal

marshes have become more saline (Ross et al., 2000).

Lorenz’s (2001a) study of coastal fish populations

demonstrated that fish densities were substantially

greater and that community composition in the coastal

wetlands immediately north of northeastern Florida

Bay resembled that of an oligohaline marsh in recent

years of exceptionally high rainfall, when conditions

approximated predrainage conditions. Fish densities

were substantially greater in the years of oligohaline

conditions.This study demonstrated that it is possible

to regain wetland productivity with restoration of more

natural hydrologic responses to rainfall.

Several time series are being developed for birds

in Florida Bay.The database on nesting activity in bald

eagles extends back to the late 1950s and continues.The

osprey database is also lengthy, albeit interrupted, and

continues. Monthly data on the abundance and activity of water birds in Florida Bay is five years in length

and still growing.These databases provide the opportunity to analyze bird activity in the bay in relation to

freshwater inflow and other conditions that might affect these birds’ food supply. This information also is

available for use in trophic network models. Information on the diet of water birds in Florida Bay is very limited and largely anecdotal.

EFFECTS OF WATER RELEASES ON 

RECRUITMENT AND BENTHIC FAUNA

Some statistical studies have directly connected abundance indices from fishery data to indices of freshwater flow to Florida Bay and the southwestern coast.

These freshwater flows are affected by water releases

to ENP at the Tamiami Trail and by the management

of water levels and releases in the South Dade Conveyance system on the eastern border of ENP. Changes

in catch rates in fisheries can provide a rough index of

change in relative abundance. In an analysis of ENP

catch and effort data, Schmidt et al. (2001) found that

an index of freshwater runoff to Florida Bay and adjacent coastal waters was positively related to snook

catch rates but negatively related to spotted seatrout

catch rates. Change in harvests can provide a rough

index of abundance when change in effort is taken

into account. Browder (1985) found a positive relationship between pink shrimp harvests in the Tortugas

fishery and a freshwater inflow index (water levels at

P35 in ENP). Analyses by Browder (2000) and Sheridan

(1996) suggested that freshwater inputs as either rainfall or runoff influence pink shrimp catch rates. Browder’s (1985, 2000) work suggested that the timing of

freshwater inputs affects harvests and catch rates.

Johnson et al. (2002a) found that water releases at the

Tamiami Trail were a significant variable explaining the

density of 9 of 11 dominant species in Florida Bay’s forage fish assemblage (Table 8.2).

SPATIAL PATTERNS OF MERCURY AND

METHYLMERCURY 

Widespread patterns of elevated mercury (Hg) concentrations in game fish and forage fish have been observed in eastern Florida Bay (Evans et al., 2001).Within

this region, highest concentrations of both methylmercury and total mercury have been observed in water

and sediments in the mangrove transition zone near

the inflows of Everglades freshwater through Joe Bay

and Little Madeira Bay (Rumbold et al., 2003). Incubation studies with stable mercury isotopes revealed

substantial in situ methylation in open-water bay sediments as well. Inputs of bioavailable Hg(II) may be a

critical-determining factor driving this methylation.

Concurrent seasonal variations in both methylmercury and total mercury concentrations were observed

in sediment, water, and forage fish, with peak concentrations occurring during the warm rainy season

near the coast, where Everglades runoff enters the

bay. No significant long-term temporal trends in mercury levels in gamefish can be observed as yet for the

period 1996–2001. From these results, it has been concluded that the sources of elevated mercury concentrations in fish from northeastern Florida Bay include

(1) methylmercury in runoff from the Everglades and

(2) in situ mercury methylation in sediments from both

the mangrove transition zone and the open bay itself

(Rumbold et al., 2003). Mercury concentrations seem to

be higher along a Taylor River–Little Madeira Bay sampling transect than along a C-111 canal–Joe Bay transect, suggesting that the urban and agricultural runoff

that most strongly influences the C-111 canal–Joe Bay

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

134 FWRI Technical Report TR-11

transect is not the most important source of mercury

to the bay and its biota. All of these processes could

change with restored Everglades freshwater flows and

might be further altered by changes in nutrient inputs and trophic processing.

EFFECT OF FISHING ON AGE STRUCTURE

AND ABUNDANCE OF PREDATORS

Faunce et al. (2002) provided evidence that fishing in

areas of northern Florida Bay open to recreational fishing affects target fish populations there. The modal

length of gray snapper (Lutjanus griseus) along mangrove shorelines is substantially larger in the Crocodile Sanctuary of Everglades National Park, where

fishing has been excluded since 1980, than in other parts

of Florida Bay in Everglades National Park and the

nearby Biscayne National Park, where fishing is allowed. Modal lengths were 25–30 cm TL in the Crocodile Sanctuary vs. 15–20 cm TL elsewhere. Future work

may be needed to clearly separate effects of fishing from

effects of differences in habitat. Ley et al. (1999) found

a similar pattern. Other studies (Bohnsack et al., 2001;

Ault et al., 2002a,b) suggest that fishing affects reef

fish populations, some of which spend part of their life

cycle in Florida Bay. On the other hand, Schmidt et

al.’s (2001, 2002) recent analyses of Everglades National Park creel census data shows that catch rates were

positively correlated with fishing rates for four target

species—spotted seatrout, red drum, snook, and gray

snapper—suggesting that fishing pressure was not affecting overall abundance.

Modeling Change in 

Higher-Trophic-Level Species

Two types of models have thus far been applied to

HTLS research in Florida Bay. Empirical, statistical

models have been used to explore data for patterns that

suggest the major processes driving variation in species

abundance and community structure. Complementing

these models are simulation models, often incorporating population dynamics, to examine the sensitivity of individual organisms to varying characteristics

of their habitat, such as bottom cover and salinity.

Statistical Models

EXPLORATORY GENERAL ADDITIVE MODELS

Johnson et al. (2001, 2002a,b) assembled a database for

Florida Bay that integrated six independent forage

fish/macroinvertebrate studies conducted between

1974 and 1997.The database was used to examine the

dynamics of 11 key forage species. General additive

models were used to determine which major forcing

functions and habitat factors control the abundance and

distribution of these key forage species. The most

widely influential variables explaining abundance and

Table 8.2 Summary of forage fish models and significant factors. S = the factor was significant for that species.

NS = factor was not significant. A number following an S means the significant effect was lagged by that many months.

The bottom row represents the number of species where that factor is statistically significant.

Seagrass Seagrass Tidal

Species Gear Month Temp. Depth Salinity Habitat Type Density Amplitude Sea Level Wind Rain Flow

Transitory species

F. duoraram S NS S NS NS S S* S S S-3 NS NS NS

L. rhomboides NS S S S NS NS S S S NS NS S-1 S-1

Mojarras S NS S NS NS S S* S S S-2 S-2 S-2 S-2

Pelagic species

A. mitchilli S S S S S S S S S NS S-2 NS S

Resident species

O. beta NS S S NS S S NS S S NS S-3 NS S-3

G. robustum S S NS S NS S S S S NS NS S-2 S-1

F. carpio S NS NS NS S S NS NS NS NS S NS S-2

S. scovelli S S S SS S S S S NS NS NS S-2

M. gulosus S NS NS NS S S S S S NS NS NS S-2

L. parva S NS NS NS S S S S S NS NS S-3 NS

H. zosterae NS S NS NS S S S S S NS NS NS S-2

Significance 8 6 6 4 7 10 9 10 10 2 4 4 9

* The significant effect occurred only between presence vs. absence of seagrass.

Higher-Trophic-Level Species
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FWRI Technical Report TR-11 135

distribution were seagrass density, habitat, and tidal

amplitude, which were significant variables for 10

species, followed by seagrass type and freshwater inflow to the bay (9 species), salinity (7 species), and

temperature and month (6 species). Depth, wind, and

rainfall (4 species each) and sea level (2 species) were

less important variables in predicting the abundances

of forage species (Table 8.2).The U-shaped relationships

of three species (Gobiosoma robustum, Floridichthys carpio, and Lucania parva) to salinity suggested they might

be adapted to extreme conditions (high and low salinities).The majority of species were positively correlated

with seagrass density, with the exception of the pelagic

bay anchovy (Anchoa mitchilli), F. carpio, the toadfish (Opsanus beta), and the gobies Microgobius gulosus and G.

robustum, which were more abundant in sparse seagrass.The specific types of bottom cover were important for seven animal species, as follows: Syringodium

(M. gulosus, Lagodon rhomboides, Hippocampus zosterae,

and L. parva), Halodule (Farfantepenaeus duorarum, Syngnathus scovelli),Thalassia (G.robustum), and no seagrass

(A. mitchilli).Three taxa (F. duorarum, L. rhomboides, and

Eucinostomus spp.) that spawned outside of the bay

showed relationships with tidal amplitude, sea level,

and/or wind, which suggests that transport mechanisms may affect abundance.

FORECASTS OF THE TORTUGAS 

SHRIMP FISHERY

Several empirical statistical models have been used to

relate Tortugas catches or catch rates to indices of

freshwater inputs to Florida Bay. Browder (1985) found

a statistical relationship between quarterly Tortugas

catches and the average water level in ENP monitoring well P35. Later, Sheridan (1996) developed a statistical model that related annual Tortugas catches to

Everglades well data, rainfall data, and air temperature and sea level measured at Key West the previous

spring and summer. The Sheridan model, which was

updated every year with new data, successfully predicted Tortugas catches for the upcoming year for a

number of years.

More recently, Browder (2000) developed a statistical model relating annual average Tortugas catch

rates to the rainfall of several prior months.Two models were developed, one for recruits to the fishery (assumed to be shrimp in the 68-count per pound

category) and another for larger shrimp. These models were designed to make rainfall-based predictions

of catch rates that could be compared with observed

catch rates to separate effects of south Florida’s highly

variable rainfall from effects of change in water management. Modeling results suggested that timing as

well as quantity of rainfall influence catch rates.The two

rainfall-based models, which were based on data for

biological years (July–June) 1964–1965 through

1994–1995, had high r 2 (0.89 and 0.76, respectively), but

their predictions differed greatly from observations

in five subsequent years, when few if any water management changes had occurred (Browder, 2001, unpublished report).

A second empirical model was prepared (Browder, 2000) to test alternative configurations of the water

management system proposed in the “Restudy”that

developed the CERP.This model related Tortugas catch

rates of recently recruited shrimp to releases of fresh

water into Everglades National Park at its northern

boundary immediately downstream from the leveed

Everglades Water Conservation Areas. The model,

based on data for the period 1964–1965 through

1994–1995, explained 92% of the variation in average

annual catch rate. Total monthly water releases for

several months of the year explained more than 57%

of the variation in catch rate.The rest of the explained

variance was due to other variables. These included

large-shrimp catch rates the previous year and

monthly average Key West air temperature (as a proxy

for water temperature) for several months. The relationship between catch rate and water flow was positive for some months and negative for others,

suggesting that timing as well as volume is important.

When used in alternative testing, the model predicted

consistently higher annual catch rates for the “Natural

System”than for the “1995 base case”or any alternative, suggesting that south Florida’s predrainage hydrologic system provided the best conditions for pink

shrimp production. To make these predictions, the

output of hydrologic models served as input to the

shrimp model.

Another analysis examined pink shrimp recruitment to the Tortugas grounds in relation to observed

salinity in the western and central bay (Browder, 2000).

Because of limitations in available salinity data, the time

series analyzed was very short compared to that available for relating recruitment to rainfall and water releases to Everglades National Park. A weak, but

significant, relationship was found between monthly

recruitment and time-lagged monthly average salinity in both areas.

Simulation Models

A simulation model was developed to predict survival,

growth of juvenile pink shrimp cohorts, and potential

harvests from these cohorts as a function of temperature and salinity in Florida Bay (Browder et al., 1999).

The model was recently refined with data from new laboratory experiments (Browder et al., 2002).The model

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

136 FWRI Technical Report TR-11

structure consists of three algorithms, which govern (1)

physiological survival as a function of temperature

and salinity; (2) growth as a function of temperature,

salinity, and total length; and (3) survival from predation as a function of total length. The model is driven

by observed daily temperatures and salinities from

specific locations in Florida Bay.The model simulates

juvenile densities in that part of the bay and potential

recruitment (and related harvests) to the Tortugas fishery from that part of the bay.

A spatially explicit individual-based model for

Caribbean spiny lobster (Panulirus argus) was developed in 1993 (Butler, 1994). Reformulations of the

same model have been used to investigate a variety of

issues, including (1) the potential effect on lobster recruitment of a massive loss of nursery habitat structure that was due to a sponge die-off (Butler, 2003), (2)

the consequences of temporal and spatial variation in

postlarval supply on recruitment (Butler et al., 2001b),

(3) the effect of nursery habitat structure and geographic specificity on recruitment (Butler et al., 2001b),

and (4) the direct and indirect consequences of altered salinity on recruitment (M. Butler, personal communication). The ecological aspects of recruitment

included in this model start with the arrival of spiny

lobster postlarvae in the nearshore nursery and terminate when larger juveniles begin to enter fishermen’s traps. The recruitment process is explicitly

incorporated into this model by superimposing on

the model’s spatial landscape the daily ecological

processes faced by juvenile spiny lobsters: settlement,

growth, shelter, selection, mortality, and movement.

The model tracks each hypothetical lobster from settlement until recruitment to 50-mm carapace length.

Settlement occurs once every 28 days, corresponding

to the lunar cycle. Growth is a discontinuous process

involving molts. Daily mortality is a function of various aspects of habitat and lobster-habitat interactions. Simulations with the model were run for

observed extreme conditions: a wet year (1995) and a

dry year (1993).The direct effects of salinity were limited to approximately 20% of the lobster nursery area,

where salinity varies naturally. Simulation results suggested that lobster recruitment during a very wet or

dry year would be similar. In both cases, recruitment

declined by approximately 25% in the area directly affected by salinity changes, which resulted in an approximately 5% decline in recruitment over the entire

Florida Keys region, as compared to control simulations where salinity was stable at 35 psu. Other simulations predicted that the lobster population would

be surprisingly resilient to sponge die-off. Although

nearly the entire sponge community was decimated

over approximately 20% of the nursery area, this loss

of habitat was predicted to result in only a 16% decline

in lobster recruitment in the perturbed region and a

2% decline over the entire Florida Keys region. The

model allowed a follow-up analysis of “why this is

so.” Apparently the effect was not just because the

supply of postlarvae was three times higher in the

post-die-off year simulated, but mainly because juvenile lobster movement to nearby unaffected areas

and shifts in shelter use on sites affected by sponge dieoff, a response supported by field evidence (Butler et

al., 1995; Herrnkind et al., 1997).

Richards (2003) examined the relationships of temperature and salinity to growth rates in crocodiles

(Crocodylus acutus) by tracking 30 radio-tagged hatchlings in the vicinity of the Turkey Point Power Plant for

up to several weeks.Water temperatures in habitats in

which the hatchlings were tracked were within the

range 29°–35°C, a range in which temperature is not expected to have a detrimental effect on growth (Mazzotti

et al., 1986). Richards found that temperature had no

effect on most measures of growth. Although laboratory work has shown that salinity has a strong negative effect on mass in hatchling American crocodiles

(Dunson, 1982), field observations suggest that they can

survive and grow in highly saline areas (Lang, 1975;

Mazzotti, 1983). Richards also found that salinity did

not significantly affect growth rates, supporting these

field observations.Two of the individuals in very high

salinities (approximately 60 psu) grew at the same rate

as most individuals in low-salinity water. In the laboratory, Mazzotti and Dunson (1984) showed that hatchling C. acutus maintained in seawater (35 psu) grew well

if given periodic access to brackish water (4 psu).

Richards observed that hatchlings used hollows in the

banks of canals and ponds and also that four individuals on five occasions (sometimes accompanied by

other hatchlings) moved out of their low-salinity pond

and into the hypersaline canal areas at night and returned to their pond the following day. These observations support the hypothesis that crocodiles may

have behavioral adaptations for escaping adverse effects of salinity.

Substantial progress has been made in the development of a bioenergetically based individual larval

spotted seatrout model to simulate metabolic rate,

consumption, and growth as a function of temperature

and salinity (Wuenschel et al., 2004).The model follows

the basic energy budget equation in which consumption equals the sum of metabolism, excretion, and

growth, and each component is a function of fish size,

temperature, and salinity, where appropriate.The final

model will incorporate variability for each component,

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FWRI Technical Report TR-11 137

which will enable researchers to model a population

of individuals, rather than just the average individual.

Laboratory experiments (n = 779, SL 4.5–39.5 mm) provided the basic information for the model.

A spatially explicit prey-predator model for spotted seatrout and pink shrimp coupled to physical

processes was developed for Biscayne Bay (Ault et al.,

1999, 2003; Wang et al., 2003).The spotted seatrout component of the model was individual-based.

Ongoing Research

Projects

At the time of the 2001 Florida Bay Conference, five new

(or continuing) HTLS projects funded for two years by

the NOAA Coastal Oceans Program had barely started.

Although these studies have made substantial progress

to now, their results were not presented at the Florida

Bay Conference, and only a portion of these results

were available for this synthesis. These projects are

briefly described below.

MODELING PINK SHRIMP RECRUITMENT

FROM FLORIDA BAY

In this project, we are continuing to develop a simulation model and the associated performance measures to evaluate the potential effect that upstream

water-management changes resulting from efforts to

restore the Greater Everglades ecosystem have had

upon Florida Bay.This work seeks to (1) clarify the effects of freshwater inflow and seagrass habitat on

Florida Bay’s pink shrimp nursery function, (2) determine the major influences of meteorological and

oceanographic processes on postlarval pink shrimp

and their recruitment to the fishery, and (3) improve

the ability to predict recruitment to the Tortugas fishery in response to changes in water management. As

part of this work, a spatially explicit recruitment model

will be developed from the existing unit model; postlarval immigration pathways, transport rates, and influencing factors will be described and quantified; and

historical data on pink shrimp density will be analyzed and used to further refine and verify the model.

REGIONAL ASSESSMENT OF SPONGE 

DYNAMICS AND SPONGE FISHERY IMPACTS

This project is part of a multiyear investigation of the

hard-bottom communities of Florida Bay and the Florida

Keys. It combines modeling, laboratory experiments,

and fieldwork to explore the relationship of spiny lobster population dynamics to spatiotemporal patterns in

the structure of bottom habitat and environmental variables.The current project focuses on sponges, but some

elements also pertain to spiny lobsters and octocorals.

The four principal objectives of the project are (1) to describe size-specific population dynamics information

(e.g., growth and reproductive status) needed to model

and manage commercial sponge species, (2) to determine the effects of commercial fishing on sponges and

the bycatch of the sponge fishery, (3) to experimentally test the tolerance (e.g., survival, susceptibility to

disease, changes in behavior) of selected hard-bottomdwelling species (e.g., five sponge species, two octocoral species, and three size-classes of spiny lobster) to

different salinities and periods of exposure at winter

(18°C) and summer (28°C) water temperatures, and (4)

to incorporate new and existing information into a spatially explicit simulation model to quantitatively compare the effects of potential management strategies on

the sustainability of the sponge fishery and its effects

on hard-bottom community structure in the Florida

Keys National Marine Sanctuary.

POPULATION STUDIES, ABUNDANCE,

HABITAT USE, TROPHIC DESCRIPTIONS,

AND REPRODUCTIVE STATUS OF MARINE

TURTLES INHABITING FLORIDA BAY

The purposes of this study are (1) to capture and tag

sea turtles in Florida Bay to continue long-term monitoring of individual growth rates, foraging-site fidelity, residency rates, health status, and trends in

abundance, (2) to elucidate the trophic role of loggerheads as apex predators in Florida Bay, (3) to provide detailed descriptions of loggerhead habitat use

and behavior, and (4) to examine the sexual maturity

and reproductive frequency of adult-sized loggerheads inhabiting Florida Bay.The principal study area

is the central-western region.

REEF–FISH COMMUNITY DYNAMICS AND

LINKAGES WITH FLORIDA BAY

This continuing project will apply a visual sampling

strategy to quantify coral-reef fish community changes.

The project has the following goals: (1) to provide intensive and precise spatial and habitat-specific fisheryindependent assessment of reef fish communities; (2)

to document trends in reef fish size and abundance

within and outside no-take zones in the Florida Keys

reef tract; (3) to test specific hypotheses predicting

continuing changes in reef fish communities as the

result of no-take protection; (4) to provide a precise and

spatially explicit database for assessing any future reef

fish population changes resulting from Everglades

restoration actions; (5) to provide managers with options for optimizing long-term survey design strategies

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

138 FWRI Technical Report TR-11

to identify reef-fish population changes; and (6) to correlate the linkages between reef fish communities and

fishing, habitat, oceanographic, and other physical

processes to guide appropriate experimental studies

on dynamic mechanisms and to develop predictive

models.

DEVELOPMENT OF SPATIALLY EXPLICIT

MODELS TO PREDICT GROWTH–POTENTIAL

OF AGE–0 GRAY SNAPPER, LUTJANUS

GRISEUS, IN FLORIDA BAY DURING

RESTORATION OF FRESHWATER FLOWS

The general goal is to examine patterns of growth in

juvenile gray snapper and develop a bioenergetic

model of growth that is a function of temperature,

salinity, and fish size.This model will be extended into

a spatially explicit calculation of potential fish growth

using historical environmental data as well as predicted changes in the environment of Florida Bay

under different water-management strategies. Specific objectives are (1) to quantify patterns in juvenile

gray snapper growth through a retrospective analysis

of previously collected samples, (2) to examine the relationships between juvenile gray snapper growth and

temperature and salinity using previously collected

samples and historical monitoring data, (3) to develop

an individual-based bioenergetic model for juvenile

gray snapper under a range of temperature and salinity conditions, (4) to recalibrate and validate the bioenergetic model by comparing predicted growth with

observed growth, and (5) to develop a spatially explicit model that predicts growth-potential of young

snapper throughout Florida Bay under various freshwater flow regimes.

UPSTREAM LARVAL SUPPLY TO FLORIDA

BAY—THE DRY TORTUGAS CONNECTION

This project explores the pathways and transport

processes for migration of larval fish, shrimp, and lobster from the Dry Tortugas to Florida Bay. Emphasis is

on the role of episodic, mesoscale events, such as those

involving eddies and the Tortugas gyre.The hypothesis to be tested is that the presence of a coastal eddy

enhances the influx of presettlement recruits into

Florida Bay. Densities of incoming recruits in the middle and lower Keys during the presence and absence

of an eddy are being compared.This is a continuation

of a previous south Florida program project for which

substantial progress has been made in relating spiny

lobster larval transport to eddies and gyres (Yeung et

al., 2001). Planned work seeks to determine what happens closer to the origin of eddies at the Dry Tortugas

and lower Keys and the importance of the western recruitment pathway in connecting the Dry Tortugas

with Florida Bay over the southwestern Florida shelf.

Coordinated sampling at Southwest Channel in the Dry

Tortugas and bayside at Northwest Channel will attempt to link the newly spawned snapper larvae to subsequent early-settlement stages.

ATLAS OF LIFE HISTORIES OF JUVENILE AND

SMALL RESIDENT SPECIES IN FLORIDA BAY

The atlas will include information on the range, reproduction, diet, spatial and temporal abundance and

distribution, and length-frequency distributions in the

bay. This work is being conducted with NMFS base

funding.

ATLSS MODEL OF 

COASTAL WETLAND FISHES

A spatially explicit model of the resident fishes of the

coastal wetlands is being developed by Cline et al.

(2001) to further explore the relationships determined

by Lorenz (2001a,b). The model uses the object-oriented modeling framework provided by the Across

Trophic Level System Simulation (ATLSS), which is now

being applied to the Everglades. Development of the

coastal fish model will extend ATLSS into the coastal

marshes and provide a basis for expanding the wading bird elements of ATLSS into the coastal zone.

Unresolved Issues and Questions: 

Research Needs 

Criteria used to propose future research topics were

as follows: (1) follow-up of promising recent research

expected to sharpen or broaden answers to Question

5; (2) addressing promising new hypotheses that replace failed hypotheses; (3) development of performance measures based on species and communities

most likely to be affected by CERP changes; and (4) addressing gaps in the current program when new information suggests higher priority should be assigned.

The following series of topic areas fit one or more of

these criteria.

LOCATION OF NURSERY AREAS OF 

MAJOR GAME FISH SPECIES 

Many sought-after game fish species are found in

Florida Bay as preadults and adults, but the current

nursery grounds of most their populations are not delineated.This includes red drum, snook, tarpon, bonefish, and gray snapper. Recently, Powell (2003)

delineated nursery grounds for spotted seatrout in

central and western Florida Bay. Colvocoresses (unpublished data) found red drum juveniles in the East

River of Little Madeira Bay at a salinity of 6 psu; however, efforts by Powell (2002) to find red drum nursery

Higher-Trophic-Level Species
grounds in northern Florida Bay were unsuccessful,

possibly because the appropriate salinity was not present during sampling. Efforts need to be directed at the

southwestern mangrove estuaries of Everglades National Park, the most likely place to find the type of red

drum habitat described by Peters and McMichael (1987)

(i.e., low-energy, low-salinity [range = 0–25 psu, mean

= 7 psu], turbid, backwater environments “...of a river

at the head of the bay”). Odum and Heald (1972) collected many red drum juveniles in the Whitewater

Bay system (North River), and this system could be a

nursery area for red drum found as adults and subadults in Florida Bay.Tabb et al. (1962) found early-settlement-stage bonefish and tarpon in the Buttonwood

Canal–Flamingo area.There has been no follow-up to

better define the nursery areas of these species. Earlysettlement-stage snook have not been found south of

Chokoloskee (T. Schmidt, personal communication), although similar habitat appears to occur between

Chokoloskee and Cape Sable.The settlement grounds

for gray snapper that enter the bay are not well defined,

although Rutherford et al. (1989) identified mixed seagrass beds of Syringodium-Thalassia-Halodule in western Florida Bay as best settling-out habitats for juvenile

gray snapper. The nursery areas of some of these

species are likely to be in the front lines of changes

caused by new water-management structure and operations.These nursery areas need to be delineated so

that the potential effect of water-management changes

on salinity patterns, nutrient inputs, and other conditions in these areas can be predicted.

INFLUENCE OF HABITAT AND 

ENVIRONMENTAL VARIABLES ON SPECIES

COMPOSITION AND TROPHIC DYNAMICS

The following nonmutually exclusive hypotheses about

factors influencing the abundance and relative abundance of water column and seagrass canopy species

should be explored:

Hypothesis 1—Density and abundance of bay anchovy is related to salinity fronts.

Hypothesis 2—Density and abundance of canopy

species is related to seagrass diversity.

Regional trophic-web models should be developed to integrate existing and future information on

food webs and trophic structure in Florida Bay. Information on water birds and large marine vertebrates

(sharks, rays, bottlenose dolphins, and sea turtles)

should be incorporated into the models.The trophicweb models should be viewed as precursors to an

ecosystem model to be developed in a subsequent

funding phase. The work should include the use of

stable isotope analyses, including use of museum specimens (assuming the work to develop methods for

processing museum material has been completed).

Statistical analyses of historical resource survey

data should be expanded and the results used to design and quantify trophic-web and ecosystem models.

The database assembled by Johnson et al. (2001) provides the opportunity to develop trophic network models for Florida Bay. As a result of major differences in

the food-web base, separate network models should be

prepared for each of the bay’s subregions (Butler et al.,

2001b; Chanton et al., 2001; Evans et al., 2001; ). Network

models previously prepared for the bay by R. Ulanowicz (University of Maryland) and A. Acosta (Florida’s

Fish and Wildlife Research Institute) would provide a

starting point for a new effort. Acosta (personal communication) observed that network modeling suffered

from a lack of biomass information on benthic organisms. This is still a serious deficiency, although some

data on sponge biomass have been gathered. Molluscan samples collected by W. Lyons and archived at the

Fish and Wildlife Research Institute could be used to

develop data on molluscan biomass. Analyses and

comparisons of trophic structure in the various regions of the bay could be used to organize information

about HTLS and assess effects of salinity changes resulting from changes in water management.

FACTORS AFFECTING 

POSTLARVAL IMMIGRATION

IMMIGRATION INTO THE BAY’S INTERIOR

HTLS researchers, building on the work of physical

oceanographers, have gained some knowledge about

the pathways, mechanisms, and oceanographic factors influencing immigration of offshore-spawned larvae and postlarvae to the eastern edge of Florida Bay.

However, little information exists on physical processes

that influence the immigration of postlarvae onto potential nursery grounds in the bay’s interior. This information is highly relevant because it would better

elucidate the ecological importance and potential economic importance of reducing the frequency, duration, and intensity of hypersaline conditions in the

interior of the bay.To what extent is and how much of

the interior of the bay is accessible to offshore-spawned

species? What factors cause the accessibility of the

inner bay to vary? This information would allow researchers to determine what benefits of improved conditions might bring to these species. Greater

coordination of biological and physical research on

the movement of water and early-life stages into the

bay’s interior is needed. Physical research in the interior of the bay was initiated last year, opening new

opportunities for collaboration.

Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 139

Higher-Trophic-Level Species
Florida Bay Synthesis Hunt and Nuttle

140 FWRI Technical Report TR-11

IMMIGRATION TO FLORIDA BAY

Recent research suggests that the major pathway for

transport of pink shrimp postlarvae from the Tortugas

to Florida Bay may be across the southwestern Florida

shelf. Research on larval immigration to Florida Bay

nursery grounds from the west is hampered by a lack

of physical oceanographic work that addresses questions biological researchers need to answer. For example, what dynamic, physical structures might enable

early-life stages spawned near the Dry Tortugas to

reach the bay from the west? Net flows across a hypothetical boundary of the bay stretching from Cape

Sable to Marathon have been described (Smith, 2000),

but the flow characteristics along the bay boundary

(boundary of the bay proper) that stretches from Cape

Sable to Long Key are less known. Water movement

across this boundary from both the west and the south

needs to be studied by oceanographers in integrated

studies with biologists studying immigration of earlylife stages onto Florida Bay nursery grounds.

EFFECT OF LARVAL BEHAVIOR AND 

FRESHWATER INFLOW ON LARVAL 

IMMIGRATION RATES

Freshwater inflow may provide directional cues or otherwise influence the rate of larval immigration from offshore spawning grounds to nearshore nursery grounds.

This topic has not been explored with respect to Florida

Bay species since Hughes (1969a,b) conducted experiments suggesting that presettlement pink shrimp postlarvae move vertically in the water column in response

to salinity gradients. He proposed that this behavioral

response resulted in net shoreward transport of postlarvae on flood tides. Hughes’results raise questions that

have never been addressed regarding the possible role

of freshwater inflow in postlarval immigration of pink

shrimp and other species: Do the volume and timing

of freshwater inflow influence the magnitude of influx

of postlarvae to Florida Bay?

EFFECT OF SALINITY ON SURVIVAL 

AND GROWTH 

Integrated studies that might include models, supporting field studies, laboratory experiments, and statistical analyses should be conducted to determine

the relationships between salinity, survival, growth,

and other biological processes. For example, the shrimp

model should be applied to assessing potential nursery grounds in the mangrove estuaries of ENP and examining the possible effects of alternative management

strategies on the larger Florida Bay system that includes these areas. Another needed application is in

interpreting juvenile density data in relation to postlarval immigration and fisheries data. A spotted

seatrout individual-based model should be developed

to integrate all the recently acquired new information

about this species in the bay. Questions about the impact of hypersaline conditions in the central bay on

year-class strength of spotted seatrout need to be addressed.The lobster model should be expanded to integrate new information on salinity tolerance of lobster

and living components of lobster habitat. Following up

on modeling results, field experiments should attempt

to quantify the effect on growth and survival of movements away from undesirable conditions (i.e., hypersalinity or hyposalinity).

QUANTIFICATION OF SIZE–RELATED 

PREDATION MORTALITY

Better quantification of size-related predation mortality is needed to adequately address the effects of

salinity on survival through the effect of salinity on

growth.This issue is especially pertinent to pink shrimp,

spotted seatrout, gray snapper, and lobster. Results

are needed to refine and quantify simulation models.

EFFECTS OF WATER QUALITY ON SURVIVAL

AND GROWTH

This question has not been specifically addressed in

current research in Florida Bay. Effects of both nutrient enrichment and common chemical contaminants

on Florida Bay fish and macroinvertebrates may be

relevant to determining the effects of changes in water

management.

EFFECTS OF BENTHIC HABITAT ON 

SETTLEMENT, SURVIVAL, AND GROWTH

What characteristics of habitat lead to initial settlement?

How do characteristics of settlement habitat affect survival and growth? How faithful are animals to the location of first settlement? What causes movement and

where do animals go? Information on these questions

is needed to further refine simulation models.

IDENTIFICATION OF OTHER SOUTH

FLORIDA COASTAL AREAS WITH ENHANCED

MERCURY BIOACCUMULATION IN FISH

Previous work (Rumbold et al., 2003) identified the

transitional mangrove ecotone in northeastern Florida

Bay as a region of enhanced mercury and methylmercury concentrations in water, sediments, and fish. In unpublished data, Evans found concentrations of mercury

in red drum and crevalle jack from Whitewater Bay that

were comparable to those found in the same species

in northeastern Florida Bay.Whitewater Bay is a mangrove-dominated embayment just north of western

Florida Bay that receives some runoff from the Shark

River, an area of known mercury contamination in

Higher-Trophic-Level Species
Hunt and Nuttle Florida Bay Synthesis

FWRI Technical Report TR-11 141

fish. It seems likely that other estuarine recipients of

Shark River drainage could support fish with high

mercury concentrations.The sensitivity of fish from the

mangrove ecotone of the entire Ten Thousand Islands

complex of southwestern Florida suggests the need for

a monitoring program to establish mercury concentrations in susceptible fish species. A research effort to

determine the mercury sources and responses to future CERP changes in the volume and timing of freshwater flows should be made.

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