Year 2 Data Summary Report: Nekton of Sarasota Bay and a Comparison of Nekton Community Structure in Adjacent Southwest Florida Estuaries

Year 2 Data Summary Report: Nekton of Sarasota Bay and a Comparison of Nekton Community Structure in Adjacent Southwest Florida Estuaries T.C. MacDonald; E. Weather; R.F. Jones; R.H. McMichael, Jr. Florida Fish and Wildlife Conservation Commission Fish and Wildlife Research Institute 1 Eighth Avenue Southeast St. Petersburg, Florida 3371-595 Prepared for Sarasota Bay Estuary Program 111 S. Orange Avenue, Suite 2W Sarasota, Florida 34236 June 4, 212

TABLE OF CONTENTS LIST OF FIGURES... iii LIST OF TABLES... v ACKNOWLEDGEMENTS... vii SUMMARY... ix INTRODUCTION... 1 METHODS... 2 Study Area... 2 Sampling Design... 3 Gear Specifications and Deployment... 6 Sample Processing... 7 Nekton Community Analysis... 9 Bray-Curtis similarity calculation... 12 Non-metric multidimensional scaling (MDS) and Similarity Percentage Analysis (SIMPER)... 12 Mercury Content Analysis... 13 RESULTS and DISCUSSION... 15 Physiochemical conditions... 15 Composition of overall nekton community... 18 Shallow water habitats sampled with 21.3-m seines... 19 Nearshore habitats sampled with 183-m seines... 22 Deeper-water habitats sampled with 6.1-m trawls... 26 Species Profiles... 29 Pink shrimp, Farfantepenaeus duorarum... 3 Blue crab, Callinectes sapidus... 33 Ladyfish, Elops saurus... 37 Bay anchovy, Anchoa mitchilli... 39 Common snook, Centropomus undecimalis... 41 Gray snapper, Lutjanus griseus... 43 Pinfish, Lagodon rhomboides... 46 Sheepshead, Archosargus probatocephalus... 51 Spotted Seatrout, Cynoscion nebulosus... 54 Striped mullet, Mugil cephalus... 56 Nekton Community Structure... 59 i

Intrabay Comparison... 59 Interbay Comparison... 68 Mercury Content Analysis... 77 Ladyfish, Elops saurus... 79 Common Snook, Centropomus undecimalis... 81 Sheepshead, Archosargus probatocephalus... 83 Gray Snapper, Lutjanus griseus... 85 Gag, Mycteroperca microlepis... 87 Spotted Seatrout, Cynoscion nebulosus... 89 Red Drum, Sciaenops ocellatus... 91 CONCLUSIONS... 93 Physiochemical conditions... 93 Composition of overall nekton community... 93 Nekton Community Structure... 94 Mercury Content Analysis... 95 LITERATURE CITED... 97 APPENDICES... 15 Appendix A. Animals designated as Selected Taxa because of their commercial or recreational importance.... 17 Appendix B. Summary of species collected, by sampling event, during Sarasota Bay nekton sampling, June 21 to April 211... 19 Appendix C. Summary of species collected, by gear and stratum, during Sarasota Bay nekton sampling, June 21 to April 211... 113 Appendix D. Summary of species collected, by embayment, during Sarasota Bay nekton sampling, June 21 to April 211... 117 Appendix E. Catch summary for taxa collected during both years, June 29 to April 211, of nekton sampling in Sarasota Bay with 21.3-m seines... 121 Appendix F. Catch summary for taxa collected during both years, June 29 to April 211, of nekton sampling in Sarasota Bay with 183-m seines... 125 Appendix G. Catch summary for taxa collected during both years, June 29 to April 211, of stratified-random sampling in Sarasota Bay with 6.1-m trawls... 129 Appendix H. Species overview plots for dominant taxa collected in 21.3-m seines in Sarasota Bay, June 29 to April 211... 133 Appendix I. Species overview plots for dominant taxa collected in 183-m haul seines in Sarasota Bay, June 29 to April 211... 155 Appendix J. Species overview plots for dominant taxa collected in 6.1-m otter trawls in Sarasota Bay, June 29 to April 211... 171 ii

LIST OF FIGURES Figure 1. Stations sampled between June 21 and April 211, and geographic strata in Sarasota Bay.... 5 Figure 2.Stations sampled between June 29 and April 211, and geographic strata in Tampa Bay and Charlotte Harbor.... 11 Figure 3. Temperature and total rainfall during each year of the study (29-21 and 21-211) and during a thirty year historical reference period (January 1979 to December 28)... 16 Figure 4. Mean water temperature, salinity, and dissolved oxygen by embayment, from nekton sampling in Sarasota Bay, June 29 April 211.... 16 Figure 5. Relative abundance and length-frequency distribution of pink shrimp collected with 21.3-m seine in Sarasota Bay, June 29 to April 211... 31 Figure 6. Relative abundance and length-frequency distribution of pink shrimp collected with 6.1-m trawl in Sarasota Bay, June 29 to April 211.... 32 Figure 7. Relative abundance and length-frequency distribution of blue crab collected with 21.3-m seine in Sarasota Bay, June 29 to April 211... 35 Figure 8. Relative abundance and length-frequency distribution of blue crab collected with 6.1-m trawl in Sarasota Bay, June 29 to April 211... 36 Figure 9. Relative abundance and length-frequency distribution of ladyfish collected with 183-m seine in Sarasota Bay, June 29 to April 211... 38 Figure 1. Relative abundance and length-frequency distribution of bay anchovy collected with 21.3-m seine in Sarasota Bay, June 29 to April 211... 4 Figure 11. Relative abundance and length-frequency distribution of common snook collected with 183-m seine in Sarasota Bay, June 29 to April 211... 42 Figure 12. Relative abundance and length-frequency distribution of gray snapper collected with 21.3-m seine in Sarasota Bay, June 29 to April 211... 44 Figure 13. Relative abundance and length-frequency distribution of gray snapper collected with 183-m seine in Sarasota Bay, June 29 to April 211... 45 Figure 14. Relative abundance and length-frequency distribution of pinfish collected with 21.3-m seine in Sarasota Bay, June 29 to April 211... 48 Figure 15. Relative abundance and length-frequency distribution of pinfish collected with 183-m seine in Sarasota Bay, June 29 to April 211... 49 Figure 16. Relative abundance and length-frequency distribution of pinfish collected with 6.1-m trawl in Sarasota Bay, June 29 to April 211... 5 Figure 17. Relative abundance and length-frequency distribution of sheepshead collected with 183- m seine in Sarasota Bay, June 29 to April 211... 52 Figure 18. Relative abundance and length-frequency distribution of sheepshead collected with 6.1- m trawl in Sarasota Bay, June 29 to April 211... 53 Figure 19. Relative abundance and length-frequency distribution of spotted seatrout collected with 21.3-m seine in Sarasota Bay, June 29 to April 211... 55 Figure 2. Relative abundance and length-frequency distribution of striped mullet collected with 183-m seine in Sarasota Bay, June 29 to April 211... 58 iii

Figure 21., by gear type, for nekton collected from each of the five embayments of Sarasota Bay during nekton sampling, June 29 April 211... 6 Figure 22. Non-metric Multidimensional Scaling ordination plot of nekton community structure in five embayments within Sarasota Bay for each gear type deployed during nekton sampling, June 29 April 211... 61 Figure 23., by gear type, for nekton collected from each bay segment in the Charlotte Harbor, Sarasota Bay and Tampa Bay estuaries during nekton sampling, June 29 April 211... 69 Figure 24. Non-metric Multidimensional Scaling ordination plot of nekton community structure in bay segments of three eastern Gulf of Mexico estuaries (Tampa Bay, Sarasota Bay and Charlotte Harbor) for each of gear type deployed during nekton sampling, June 29 April 211... 7 Figure 25. Relationship between natural log transformed total mercury concentration and standard length for ladyfish collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries.... 8 Figure 26. Comparison of sizes and total mercury concentration for ladyfish in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries... 8 Figure 27. Relationship between natural log transformed total mercury level and standard length for common snook collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries.... 82 Figure 28. Comparison of sizes and total mercury concentration for common snook collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries... 82 Figure 29. Relationship between natural log transformed total mercury level and standard length for sheepshead collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries.... 84 Figure 3. Comparison of sizes and total mercury concentration for sheepshead collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries... 84 Figure 31. Relationship between natural log transformed total mercury level and standard length for gray snapper collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries.... 86 Figure 32. Comparison of sizes and total mercury concentration for gray snapper collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries... 86 Figure 33. Relationship between natural log transformed total mercury level and standard length for gag collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries.... 88 Figure 34. Comparison of average sizes and total mercury concentration for gag collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries... 88 Figure 35. Relationship between natural log transformed total mercury level and standard length for spotted seatrout collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries.... 9 Figure 36. Comparison of average sizes and total mercury concentration for spotted seatrout collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries... 9 Figure 37. Relationship between natural log transformed total mercury level and standard length for red drum collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries.... 92 Figure 38. Comparison of average sizes and total mercury concentration for red drum collected in the Tampa Bay, Sarasota Bay and Charlotte Harbor estuaries... 92 iv

LIST OF TABLES Table 1. Description of sampling gears used during the Sarasota Bay stratified random sampling, June 21 April 211.... 4 Table 2. Summary of catch and effort for Sarasota Bay nekton sampling, June 21 to April 211.... 18 Table 3. Catch statistics for the 1 dominant taxa collected in 21.3-m bay seine samples in Sarasota Bay, June 21 to April 211..... 2 Table 4. Catch statistics for Selected Taxa collected in 21.3-m bay seine samples in Sarasota Bay, June 21 to April 211.... 21 Table 5. Catch statistics for the 1 dominant taxa collected in 183-m haul seine samples in Sarasota Bay, June 21 to April 211... 23 Table 6. Catch statistics for Selected Taxa collected in 183-m haul seine samples in Sarasota Bay, June 21 to April 211... 24 Table 7. Catch statistics for the 1 dominant taxa collected in 6.1-m trawl samples in Sarasota Bay, June 21 to April 211... 27 Table 8. Catch statistics for Selected Taxa collected in 6.1-m trawl samples in Sarasota Bay, June 21 to April 211... 28 Table 9. Similarity percentage analysis for Sarasota Bay embayment groupings identified in the MDS ordination for 21.3-m seine collections... 64 Table 1. Similarity percentage analysis for Sarasota Bay embayment groupings identified in the MDS ordination for 183-m seine collections... 65 Table 11. Similarity percentage analysis for Sarasota Bay embayment groupings identified in the MDS ordination for 6.1-m trawl collections... 66 Table 12. Similarity percentage analysis for Tampa Bay, Sarasota Bay, and Charlotte Harbor segment groupings identified in the MDS ordination for 21.3-m seine collections... 73 Table 13. Similarity percentage analysis for Tampa Bay, Sarasota Bay, and Charlotte Harbor segment groupings identified in the MDS ordination for 183-m seine collections... 74 Table 14. Similarity percentage analysis for Tampa Bay, Sarasota Bay, and Charlotte Harbor segment groupings identified in the MDS ordination for 6.1-m trawl collections... 75 Table 15. Summary of the number of fish, sizes, and mercury levels for fish tissue samples analyzed from the fisheries-independent sampling of Sarasota Bay... 78 v

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ACKNOWLEDGEMENTS We thank all the Fisheries-Independent Monitoring program personnel, too numerous to mention, who were involved in collecting and processing the many samples that make up this study. We also thank the Sarasota Bay Estuary Program for funding the study which provided a unique opportunity to collect data from a coastal lagoonal type system situated between Tampa Bay and Charlotte Harbor. Fisheries- Independent Monitoring program collections from Tampa Bay and Charlotte Harbor, which were analyzed for interbay species abundance and mercury concentration comparisons, were funded by State of Florida Recreational Saltwater Fishing License and the Department of the Interior, U.S. Fish and Wildlife Service, Federal Aid for Sportfish Restoration Project Number F-43 to the Florida Fish and Wildlife Conservation Commission (FWC). vii

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SUMMARY The Sarasota Bay Estuary Program s (SBEP) Comprehensive Conservation Management Plan stressed the importance of restoring and protecting juvenile fish habitats. Sarasota Bay has undergone considerable urbanization since the 195 s. An understanding of the distribution, abundance and habitat use of nekton (fish and macroinvertebrates) within Sarasota Bay is critical to protecting and restoring estuarine habitats. The Florida Fish and Wildlife Conservation Commission s (FWCC) Fisheries- Independent Monitoring (FIM) program has been monitoring nekton assemblages in Tampa Bay and Charlotte Harbor, estuaries that are adjacent to Sarasota Bay, since 1989. The goal of the FIM program is to provide timely, accurate, and consistent fisheries-independent data and analyses to fisheries managers for the conservation and protection of Florida s fisheries. The sampling design and data collected are intended to not only assess fishery stocks, but to also describe habitat utilization, biodiversity, nekton communities, and to document changes within Florida s estuarine systems. The general objectives of this study were to describe the nekton habitat utilization and community structure within Sarasota Bay, to compare nekton community structure between three adjacent estuaries (Tampa Bay, Sarasota Bay and Charlotte Harbor), and to assess mercury concentrations in edible fish tissues. Specifically, this study was designed to: 1) provide a database of fish and selected invertebrate species that inhabit Sarasota Bay; 2) examine spatial differences in species composition and relative abundance within Sarasota Bay; 3) examine spatial differences in species composition and relative abundance between three estuaries along Florida s Southwest Coast; and ix

4) develop baseline data on mercury content in fish from Sarasota Bay and compare those data to adjacent estuaries. The FIM program used a stratified-random sampling design to select sampling sites within each of the five Sarasota Bay embayments as defined by the Sarasota Bay Estuary Program. Samples were collected bi-monthly between June 29 and April 211 with 21.3-m seine, 183-m seine, and 6.1-m trawl. Water chemistry parameters (salinity, water temperature, dissolved oxygen and ph) and habitat assessments (bottom type, presence of submerged aquatic vegetation, shore habitat) were taken in association with each net deployment. The gear-specific nekton catch summary portion of this report has been limited to the second year of sampling (June 21 to April 211), while the analysis portions (meteorological patterns, community structure, species profiles, and total mercury concentrations) include data from both years of the study. Meteorological patterns during the two years of this study generally followed the 3 year trend from 1979 to 28, but monthly average temperatures and total rainfall occasionally deviated to extreme values. Monthly average air temperature during January to March 21 and December 21 to January 211 were lower than the 3 year average, with the extreme lows of winter 21 resulting in cold kills of many nekton species. Total rainfall during the study period was much higher than normal during the typically dry winter-spring months (January May) and lower than normal during the typical wet months (June September) of both years. The water temperatures and salinities observed during this study probably do not reflect the long-term average condition in Sarasota Bay and the nekton assemblage likely differs somewhat from that which would be expected from a longer-term sampling program. x

The nekton community in Sarasota Bay during the second year of this study was typical of most Florida estuaries and very similar to the first year of FIM program sampling in Sarasota Bay. The majority of the 13,88 nekton collected during year two were captured in 21.3-m seines (n=81,492) and just two taxa (bay anchovy and pinfish) represented over 62% of the total catch in this gear and almost 5% of the total catch from all gear types. Pinfish were also the dominant taxon collected in the 183-m seine (53.7%) and 6.1-m trawl (36.8%). Other estuarine dependent species such as spot, eucinostomus mojarra, silver jenny, silver perch, and scaled sardine were relatively abundant as well. Community analyses of the five embayments of Sarasota Bay (intrabay) and between the bay segments of three Southwest Florida estuaries (interbay) provided similar results. Nekton community structure, regardless of gear type, tended to differentiate into three groupings: 1) small Sarasota embayments, 2) larger bay segments closely linked to the Gulf of Mexico and receiving little direct freshwater inflow, and 3) larger bay segments not link closely to the Gulf and receiving relatively large amounts of freshwater inflow. The taxa that discriminated between the groupings tended to have higher abundance in smaller rather than in larger estuarine segments for both the intrabay and interbay analyses. The most obvious morphological differences between the grouping of small Sarasota embayments and the other bay segments is their relatively small surface area, relatively high freshwater inflow from Phillippi Creek, and absence of a direct connection to the Gulf of Mexico. In the interbay analyses, this grouping of small Sarasota embayments was least similar to the grouping of larger bay segments that received relatively high freshwater inflow and lacked direct xi

connections to the Gulf of Mexico. The smaller Sarasota Bay embayments are relatively close to the Gulf than are the larger bay segments with freshwater influence, possibly indicating that proximity to the Gulf of Mexico and/or embayment size were more important in determining nekton composition than was freshwater inflow. Mercury is a toxic element that has been shown to bio-accumulate in fish tissues and concentrations tend to increase with fish size, age and trophic level. Tissue samples for total mercury content analysis in Sarasota Bay have been taken from 468 individuals representing 25 taxa. About 9% of the collected tissue samples have been analyzed for total mercury concentration. Sample sizes were not large enough to perform linear regressions on any of the taxa collected from Sarasota Bay without combining with data from adjacent estuaries (Tampa Bay and Charlotte Harbor). The results of the mercury content analysis indicated that fish from Sarasota Bay do not contain higher concentrations of mercury than fish in adjacent estuaries and suggest that accumulation rates for Sarasota Bay nekton are similar to those found in Tampa Bay and Charlotte Harbor. xii

INTRODUCTION Sarasota Bay is an urbanized coastal lagoon system located on the southwest coast of Florida. Since the early 19s, dredge and fill activities have resulted in significant losses of ecologically important habitats, and historically semi-isolated tidal current regimes within embayments have been joined through the construction of an Intracoastal Waterway (ICW) channel that hydrologically links all embayments. Intense development occurred throughout the system starting in the late 195 s resulting in much of the natural shoreline being replaced by seawalls to retain dredge-and-fill material for housing sites and other construction projects. Mosquito ditching along with significant channelization of tidal creeks has altered historical patterns of surface water runoff to the bay and further exacerbated the problem of wetland habitat loss (Sarasota Bay National Estuary Program 23). A thorough understanding of the ecology of local nekton assemblages is imperative if the consequences of further anthropogenic or environmental changes are to be determined (Poulakis et. al. 24). In addition, the development of a baseline database documenting habitat use, recruitment and biodiversity can provide a broader understanding of the status of fish populations found within an estuary and help to guide the protection of estuarine-based fisheries and associated habitats (Paperno et. al. 21). The Sarasota Bay Estuary Program (SBEP) Comprehensive Conservation Management Plan (CCMP) stressed the importance of restoring and protecting juvenile fish habitat as well as the need to maintain fish populations while restoration efforts are pursued (Sarasota Bay National Estuary Program 1995). The objectives of this study are to: 1) provide a database of fish and selected invertebrate species that inhabit 1

Sarasota Bay; 2) examine spatial differences in species composition and relative abundance within Sarasota Bay; 3) examine spatial differences in species composition and relative abundance between three estuaries along Florida s Southwest Coast; and 4) develop baseline data on mercury content in fish from Sarasota Bay and compare those data to adjacent estuaries. METHODS Study Area Sarasota Bay is a coastal lagoon, located on the southwest coast of Florida, which stretches from Anna Maria Sound to the Venice Inlet. The bay is comprised of five embayments (Palma Sola, Sarasota, Roberts, Little Sarasota and Blackburn bays) which were formed behind a barrier island complex. This system is connected to the Gulf of Mexico through five inlets; Anna Maria Sound, Longboat Pass, New Pass, Big Sarasota Pass and Venice Inlet. Freshwater inflow enters the estuary through a series of creeks, bayous, and unnamed drainage ditches (Roat and Alderson 199). The main tributaries and receiving water bodies are Bowlees Creek and Whitaker and Hudson bayous (Sarasota Bay proper), Phillippi Creek (Roberts Bay), Clower and Catfish creeks (Little Sarasota Bay) and South Creek (Blackburn Bay). Shoreline vegetation consists largely of mangroves and marsh grasses, and bottom substrates are typically characterized as sand, mud, oysters, or a combination thereof (Flannery 1989). Seagrass meadows are the dominant vegetative cover in Sarasota Bay and are widely distributed throughout the bay (Haddad 1989). 2

Sampling Design The FIM program utilized a stratified-random sampling (SRS) design and a multigear approach to collect data on nekton (fish and select invertebrates) from a wide range of habitats and life history stages. This sampling design provides comprehensive data on size-specific, spatial and temporal patterns of abundance for the nekton community and for individual species. Specimens collected during this sampling are also used for various other assessments, such as fish health, mercury content, diet, age/growth, and reproduction. Three sampling gears (Table 1) were used: 1) 21.3-m seines; 2) 183-m seines; and 3) 6.1-m trawls. Generally speaking, the data gathered from seine hauls document habitat use by shallow-water shoreline-associated organisms whereas the data collected from trawls document habitat use in deeper areas. The dominant catch for the 21.3-m seine and 6.1-m trawl is juvenile fishes, although the adults of smaller species are also commonly caught. The 183-m seine is used to catch larger sub-adult and adult fishes. The seines and trawls also regularly collect some of the larger macroinvertebrate species from tidal rivers, most notably blue crabs (Callinectes sapidus), stone crabs (Menippe spp.) and pink shrimp (Farfantepenaeus duorarum). Sarasota Bay was divided into five geographically-defined zones (Zone A - Palma Sola Bay, Zone B - Sarasota Bay proper, Zone C - Roberts Bay, Zone D - Little Sarasota Bay and Zone E - Blackburn Bay; Figure 1). Each zone was further subdivided into 1-nm 2 grids. Within each grid, habitat and depth strata were identified, thereby designating the gear types that could be used in each. The number of samples collected in each zone with each gear was proportional to the number of grids in the zone that 3

could be sampled with a particular gear. Sites for each sampling event were chosen by randomly selecting grids and then randomly selecting a sampling site within each grid. A single collection was made at each selected site. Thirty primary samples consisting of six 183-m seines, eight 6.1-m trawls and sixteen 21.3-m seines were collected during each sampling event. Nine to 12 additional 21.3-m seine samples were collected during each sampling event as time allowed. Sampling events were scheduled with a bi-monthly periodicity in Sarasota Bay. Sampling began in June 29 and is ongoing with sampling currently scheduled to end in April 213. This report summarizes the data collected during year two of the study (June 21 to April 211) and assesses species distributions and abundance, and community structure from both years (June 29 to April 211). Table 1. Description of sampling gears used during the Sarasota Bay stratified random sampling, June 21 April 211. A more detailed description of each gear can be found in the FIM program s Procedure Manual. Gear Mesh Size (mm) Area Sampled Estimate (m 2 ) Description of use 21.3-m seine 3.2 14 used in near-shore and shoreline areas 1.5 m 183-m seine 38.1 4,12 used along shorelines 2.5 m 6.1-m trawl 38.1 (3.2-mm bag liner) 1,44 used in areas from 1.8-m to 7.6-m deep 4

Figure 1. Stations sampled (dots) between June 21 and April 211 (Year 2), and geographic strata (solid lines) in Sarasota Bay. 5

Gear Specifications and Deployment The gear type used to collect smaller nekton associated with shorelines and on offshore flats (>5 m from shore) was a 21.3-m center-bag seine with 3.2-mm mesh and leads spaced every 15 mm. The 21.3-m seine was pulled, with a crew member on each wing, for a distance of 9.1 m with the net wings separated by 15.5 m. The seine was deployed into the current and was landed by collapsing the seine around a pivot pole to close the wings and force the catch into the center bag. Each 21.3-m seine deployment sampled an estimated 14 m 2. Sampling sites for the 21.3-m seine were pre-stratified by the presence or absence of bottom vegetation or a shoreline. The 183-m haul seine was used to target larger sub-adult and adult nekton associated with shallow, nearshore habitats. Deployment of this gear occurred from the back of a boat in a standard rectangular shape along shorelines in relatively shallow waters (<2.5 m). Net wings were simultaneously hauled along the shoreline, keeping the lead lines close to the bottom, forcing the catch into the center bag portion of the gear. Each 183-m seine set enclosed an area of approximately 4,12 m 2. In Sarasota Bay proper, where two 183-m seine sets were collected during each sampling event, sites were pre-stratified by the presence or absence of overhanging shoreline vegetation. Too few samples were collected during each sampling event with 183-m seines in Palma Sola, Roberts, Little Sarasota and Blackburn bays to pre-stratify sampling sites by the presence or absence of overhanging shoreline vegetation. Juvenile and adult nekton that inhabit relatively deeper waters (1. 7.6-m) were collected in the 6.1-m otter trawl which had a 38-mm stretch mesh with a 3.2-mm mesh 6

cod-end liner. The trawl was towed from the back of a boat for 1 minutes. Tow speeds averaged.6-m/s; start and end locations for each trawl were marked using a global positioning system (GPS) so that the distance fished could be estimated. Each trawl deployment sampled an area of approximately 1,44 m 2. Salinity, temperature, ph, and dissolved oxygen were measured at the surface and at 1-m intervals to the bottom in association with each gear deployment. A variety of qualitative habitat assessments were also made, such as characteristics of the shoreline (e.g., vegetation type, inundation), substrate (e.g., sediment type, presence of submerged aquatic vegetation), and bycatch (i.e., total volume, type, and composition). All sampling was conducted during daylight hours (one hour after sunrise to one hour before sunset). Additional sampling details and habitat assessment procedures are described in the FIM program s Procedure Manual (FWC-FWRI 21). Sample Processing Sample work-up was similar for all samples, regardless of gear type. All fish and selected invertebrate species captured were identified to the lowest practical taxonomic level, generally species. Representative samples (three individuals of each species from the 21.3-m seines and 6.1-m trawls on each sampling trip) were brought back to the FWC-FWRI laboratory to confirm field identification. Species for which field identification was uncertain were also brought back to the laboratory. A maximum of 2 measurements (mm) were made per taxon, unless distinct cohorts were identifiable, in which case a maximum of 2 measurements were taken from each cohort; for certain economically valuable fish species (Selected Taxa, Appendix A), 4 individuals were measured. Standard length (SL) was recorded for fish (total length [TL] for seahorses 7

and disk width [DW] for rays), post-orbital head length (POHL) for shrimp, and carapace width (CW) for crabs. Animals that were not measured were identified and counted. When large numbers of individuals (>1,) were captured, the total number was estimated by fractional expansion of a sub-sampled portion of the total catch that had been split with a modified Motoda box splitter (Winner and McMichael 1997). Animals that did not require further laboratory examination were returned to the water. Additional details concerning sample work-up are described in the FIM program s Procedure Manual (FWC-FWRI 21). Due to frequent hybridization and/or extreme difficulty in the identification of smaller individuals, members of several abundant species complexes were not identified to species. Species of menhaden (Brevoortia spp.) were not identified to species. Brevoortia patronus and B. smithi frequently hybridize and juveniles of the hybrids and the parent species are difficult to identify (Dahlberg 197). Two abundant silverside species (Menidia beryllina and M. peninsulae) tend to hybridize, form allfemale clones, and occur in great abundance that renders identification to species impractical due to the nature of the diagnostic characters so they are represented in this report as Menidia spp. (Duggins et al. 1986; Echelle and Echelle 1997; Chernoff, personal communication). Species-level identification of mojarras (genus Eucinostomus) was limited to individuals 4 mm SL due to great difficulty in separating E. gula and E. harengulus below this size (Matheson, personal observation). The term eucinostomus mojarras is used for these small specimens. Species-level identification of gobies of the genus Gobiosoma (i.e., G. robustum and G. bosc) was limited to individuals 2 mm SL for the same reason; smaller individuals are hereafter referred to 8

as gobiosoma gobies. Similarly, needlefishes (Strongylura spp.) other than S. notata were only identified to species at lengths 1 mm SL. Gear-specific data summary tables for the numerically dominant and economically important taxa (Selected Taxa, Appendix A) were prepared with data from the second year of this study (June 21 to April 211). Summaries of all taxa collected by sampling event, gear and habitat, and embayment (sampling zone) were prepared using just the second year of the study period (Appendices B, C, and D, respectively). Appendices E, F and G contain catch summaries for all taxa collected with 21.3-m seines, 183-m seines, and 6.1-m trawls during both years of the study (June 29 April 211). Gear-specific catch overview plots (Appendices H, I, and J) for abundant ( 1 animals collected) and commonly collected ( 15% occurrence) taxa and species profiles for specific taxa were prepared using the two completed years of the study (June 29 to April 211). Abundance estimates for all gear types were calculated as the number of individuals/1 m 2. Nekton Community Analysis Nekton community structure was investigated using nonparametric multivariate analyses in PRIMER v6 software (Plymouth Routines in Multivariate Ecological Research; Clarke and Warwick 21). Analyses were based on pooled samples averaged by geographic area to investigate spatial patterns. Data from each gear type (21.3-m seines, 183-m seines, and 6.1-m trawl) were treated separately. Intrabay analyses were conducted to compare nekton assemblages in each of Sarasota Bay s embayments (Figure 1). Broader-scale geographic analyses (interbay analysis) were conducted to compare nekton assemblages in adjacent bay systems along the 9

southwest coast of Florida (Tampa Bay, Sarasota Bay and Charlotte Harbor; Figure 2). All nekton taxa collected, including species complexes (e.g., Eucinostomus spp. and Menidia spp.) and invertebrates were included in the community analyses. Taxa were subdivided into distinct size classes ( pseudo-species ) to address ontogenetic habitat shifts, immigration/emigration and mortality. 1

Figure 2.Stations sampled (dots) between June 29 and April 211, and geographic strata (solid lines) in Tampa Bay and Charlotte Harbor. 11

Bray-Curtis similarity calculation The basis of the multivariate analyses was an assessment of similarity in nekton community structure, calculated according to the method of Bray and Curtis (1957): where S jk is the Bray-Curtis similarity coefficient, y ij is the abundance of the ith species in the jth sample and y ik is the abundance of the same ith species in the kth sample. Abundance was standardized to number haul -1 for both seine types, and to number 1m -2 to account for varying tow lengths. Abundance data were square roottransformed prior to analysis to reduce the influence of highly abundant taxa. Non-metric multidimensional scaling (MDS) and Similarity Percentage Analysis (SIMPER) In order to provide a visual depiction of differences in nekton community structure non-metric multidimensional scaling (MDS) of the initial Bray-Curtis similarity matrices was conducted. This technique generates two-dimensional plots of distances between samples on the basis of their similarity in community structure (Clarke 1993). The MDS analysis uses an iterative procedure to attempt to map similarity of samples as closely as possible to the rank order of similarities from the input Bray-Curtis similarity matrix. The adequacy of this representation is judged by a stress value, for which zero is perfect representation, and values below ~.2 offer appropriate results for interpretation (Clarke and Warwick 21). MDS-plot axes do not have units, so the important 12

information in these plots is the distances between samples; samples close together on the plots are more similar in community structure than samples that are further apart. The MDS plots included samples that were averages of all data collected by geographic area. Similarity percentage analysis (SIMPER; Clarke and Warwick 21) was used to identify pseudo-species representative of dissimilarities between groups determined from MDS. Mercury Content Analysis Fish for mercury content analysis were placed directly on ice and returned to the laboratory, where standard length (SL) and sex were recorded. A clean stainless-steel knife was used to remove axial muscle tissue samples from the left dorsal area above the lateral line and anterior to the origin of the first dorsal fin for each fish. White muscle tissue taken from this region is representative of the portion of fish consumed by humans (Adams and McMichael 21). Care was taken to assure that the sample did not contact the outer layer of the specimen, blood, scales, or other surrounding surfaces during the extraction process. Tissue samples were immediately placed in sterile polyethylene vials and frozen at -2 C until analyzed. Total mercury concentration (THg) of each tissue sample was determined by EPA Method 7473 (Direct Mercury Analysis by Thermal Decomposition, Amalgamation, and Atomic Absorption Spectrometry [DMA], USEPA 27). Frozen tissue samples were thawed until ice crystals were no longer present on or within the sample, and approximately.2 g of clean unexposed muscle tissue was then excised with sterilized stainless steel instruments from the interior portion of the sample. The tissue sample was placed directly into a clean quartz sampling vessel, weighed to.1 g, and 13

analyzed for total mercury by FWC-FWRI with a calibrated DMA-8 Direct Mercury Analyzer (Milestone Inc., Shelton, CT). Quality control included analysis of laboratory method blanks, duplicate or triplicate tissue samples, and certified fish-tissue reference material (CRM; TORT-2, DOLT-4, obtained from the National Research Council of Canada) for each group of 1 or fewer fish samples analyzed. Matrix spike samples were processed for every 4 samples analyzed in a group. If CRM results were not within 1% of their certified value, all samples run subsequent to the last acceptable CRM result were re-analyzed. All total mercury levels were measured and reported as milligrams per kilogram (mg/kg) wet weight, rounded to three decimal points (.1). Linear regressions were used to describe relationships between fish length and total mercury concentration. Total mercury samples for individual species collected from within Sarasota Bay were not adequate to do estuary-specific models, so data from Sarasota Bay, Tampa Bay and Charlotte Harbor were combined. Total mercury concentrations from Tampa Bay and Charlotte Harbor prior to 26 were analyzed by EPA Method 245.6 (Determination of Mercury in Tissues by Cold Vapor Atomic Absorption Spectrometry [CVAAS]; USEPA 1991), which provides similar but not identical results to the DMA method. Therefore, THg values for all DMA-analyzed fish were converted into CVAAS values using equations developed by FWC from 1,566 split samples that were analyzed by both methods. Total mercury data were log transformed to approximate the normality and homoscedasticity requirements prior to regression analysis. Only species with at least 1 total animals collected, and at least 1 from Sarasota Bay, were analyzed using linear regression. 14

RESULTS and DISCUSSION Physiochemical conditions Monthly average air temperature and total rainfall measured at Tampa International Airport during this two year study period (June 29 April 211) and during a 3 year historical period (January 1979 to December 28) were compared. Generally, the monthly average temperature followed the 3 year historical trend, but with extreme cold and warm values during some months (Figure 3). The monthly average temperature tended to be slightly higher from May 21 to September 21 than the historical period (Figure 3). The average temperature was lower than the historic record during December 21, January 21 and 211, and February to March 21. Differences from the 3 year historic record for rainfall were also apparent (Figure 3). Rainfall totals in spring (March 21 and 211, April 21 and 211, and May 21) were higher than the historic totals, while some months during the summer and early fall were much lower (August 29, September 29 and 21, and October 21). Throughout the two years of this study, average monthly water temperature in each of the five embayments showed very similar trends with little difference between embayments (Figure 4). Water temperature followed the typical Florida pattern, with the warmest temperatures during the summer months, decreasing temperatures during the fall and winter, and rising temperatures in the spring. Each of the five embayments had similar salinity trends (Figure 4) but Little Sarasota and Roberts bays had a more obvious freshwater influence during both years than the other three embayments. Salinity maxima occurred in June 29 and 21 in 15

Average monthly temperature ( o C) 35 3 25 2 15 1 5 Air Temperature May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr Month May 29 - April 21 May 21 - April 211 Average 1979-28 Salinity (ppt) Temperature (*C) 3 25 2 15 35 3 25 Total Monthly Precipitation (cm) 35 3 25 2 15 1 5 Precipitation May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr Month May 29 - April 21 May 21 - April 211 Average 1979-28 Dissolved Oxygen (mg/l) 2 1 5 Jun-29 Oct-29 Feb-21 Jun-21 Oct-21 Palma Sola Bay Sarasota Bay Roberts Bay Little Sarasota Bay Blackburn Bay Feb-211 Figure 3. Temperature and total rainfall during each year of the study (29-21 and 21-211) and during a thirty year historical reference period (January 1979 to December 28). Data are from Tampa International Airport (Station 7221112842) and were downloaded from the National Climatic Data Center (http://www.ncdc.noaa.gov/cdoweb/search;jsessionid=ea4f1647269cf75676d248ca68eb77.lwf2). Figure 4. Mean (±standard deviation) water temperature, salinity, and dissolved oxygen (water column average) by embayment, from the nekton sampling in Sarasota Bay, June 29-April 211. 16

each of the embayments with average salinity values ranging from 34.3 to 37. ppt. Salinity was lowest in each embayment during April of both years, with two of the embayments (Roberts and Little Sarasota bays) having lower average salinity (<29 ppt) than the other three embayments (>31 ppt). Salinity minima occurring in April is not typical of Southwest Florida estuaries, in which salinity is usually higher toward the end of the dry season (April May). Rainfall totals, however, were unseasonably high in March of both 21 and 211 (Figure 3), with more than two times the long-term average rainfall occurring each year. This unseasonably high rainfall is responsible for this atypical salinity pattern. Water column average dissolved oxygen was above 5 mg/l in each of the embayments during the sampling period (Figure 4), except for Palma Sola Bay in August 29 (3.3 mg/l). The highest average dissolved oxygen concentration (1.76 mg/l) occurred in Little Sarasota Bay in June 29. The climatic and physiochemical conditions experienced during this two-year study of Sarasota Bay were not typical compared to the longer-term average condition for Southwest Florida. January, February, and December 21 had unseasonably cold temperatures with fish kills reported throughout Florida in January 21. Unseasonably heavy winter/spring precipitation was experienced during both 21 and 211, likely resulting in lower than average salinity values in the study area during April of both years. It is very likely that the nekton community sampled during this two year period was impacted by these climatic and physiochemical conditions and may differ from the nekton community that would be sampled over a longer time period. 17

Composition of overall nekton community A total of 13,88 fishes (16 taxa) and selected invertebrates (7 taxa) were collected from 248 samples collected between June 21 and April 211 (Table 2). Species lists with number of animals collected are provided by sampling event, gear and habitat strata, and geographic strata in Appendix B, C, and D, respectively. Sampling in Little Sarasota Bay accounted for 17% of the total sampling effort, yet accounted for almost a quarter of the total number of animals collected (24.2%; Table 2). Sarasota Bay proper, in which almost 33% of the sets were made, accounted for only 26.% of the total animals collected during the study period. The fewest number of animals (n=15,413, 14.9% of total catch) were collected in Roberts Bay. Table 2. Summary of catch and effort for Sarasota Bay nekton sampling, June 21 to April 211. 21.3-m seine 183-m seine 6.1-m trawl Totals Bay Segment (Zone) Animals Hauls Animals Hauls Animals Hauls Animals Hauls Palma Sola Bay (A) 15,185 29 4,846 6 349 6 2,38 41 Sarasota Bay (B) 2,243 45 4,915 12 1,787 24 26,945 81 Roberts Bay (C) 13,471 3 1,194 6 748 6 15,413 42 Little Sarasota Bay (D) 21,99 3 1,758 6 2,29 6 25,147 42 Blackburn Bay (E) 11,494 3 1,891 6 2,538 6 15,923 42 Totals 81,492 164 14,64 36 7,712 48 13,88 248 Bay anchovy (Anchoa mitchilli, n=32,559) was the most numerous taxon collected, representing 31.4% of the total catch (Appendix B, C, and D). Pinfish (Lagodon rhomboides, n=29,992) was the second most abundant taxon collected, accounting for an additional 28.9% of the total catch. The 23 Selected Taxa (n=13,634 18

animals) that were collected comprised 13% of the total catch. Spot (Leiostomus xanthurus, n=8,296, 8% of total catch) and striped mullet (Mugil cephalus, n=2,197, 2.1% of total catch) were the two most abundant Selected Taxa collected. Shallow water habitats sampled with 21.3-m seines A total of 81,492 animals, representing 79.5% of the overall catch, were collected from Sarasota Bay with 21.3-m seines (n=164 hauls; Table 2). Bay anchovy (A. mitchilli, n=31,339) was the most abundant taxon collected, accounting for 38.5% of the 21.3-m seine catch (Table 3). The taxa most frequently collected with 21.3-m seines were pinfish (Lagodon rhomboides, 81.7% occurrence) and eucinostomus mojarra (Eucinostomus spp., 65.2% occurrence). Animals collected with 21.3-m seines tended to be relatively small, ranging in length from 2 to 512 mm, with the mean length for each of the 1 dominant taxa ranging from 11 to 53 mm. A total of 11,351 animals from 15 Selected Taxa were collected, representing 13.9% of the entire 21.3-m seine catch (Table 4). Spot (L. xanthurus, n=7,635) was the most abundant Selected Taxon, accounting for 67.3% of the Selected Taxa collected by this gear. The Selected Taxon most frequently collected with 21.3-m seines was the pink shrimp (F. duorarum, 49.4% occurrence). 19

Table 3. Catch statistics for the 1 dominant taxa collected in 21.3-m bay seine samples in Sarasota Bay (n=164 hauls), June 21 to April 211. Percent (%) is the percent of the total catch represented by that taxon; percent occurrence (% Occur) is the percentage of samples in which that taxon was collected; CV is the coefficient of variation of the mean. Length is standard length for fish and post-orbital head length for shrimp. Taxa are ranked in order of decreasing mean catchper-unit-effort. Species of commercial or recreational importance (Selected Taxa) are denoted with an asterisk (*) after the species name. Scientific Name (Common Name) Number Catch-per-unit-effort (animals/haul) Length (mm) % No. % Occur Mean Stderr CV Max Mean Stderr Min Max Anchoa mitchilli (bay anchovy) 31,339 38.5 3.5 136.49 46.93 44.36 5,465. 29.3 15 53 Lagodon rhomboides (pinfish) 19,38 23.7 81.7 84.9 11.93 181.71 971.43 32.11 1 156 Eucinostomus spp. (eucinostomus mojarra) 9,347 11.5 65.2 4.71 5.2 163.55 34.71 25.7 1 47 Leiostomus xanthurus (spot) * 7,635 9.4 31.1 33.25 9.93 382.32 91. 22.8 1 172 Harengula jaguana (scaled sardine) 2,369 2.9 11.6 1.32 7.66 95.17 1,23.71 53.27 27 86 Mugil cephalus (striped mullet) * 2,124 2.6 13.4 9.25 5.45 754.52 65. 29.18 18 153 Bairdiella chrysoura (silver perch) 1,699 2.1 24.4 7.4 2.29 396.1 24. 53.42 13 141 Lucania parva (rainwater killifish) 1,673 2.1 22.6 7.29 2.74 481.82 35. 24.11 12 37 Farfantepenaeus duorarum (pink shrimp) * 1,19 1.4 49.4 4.83.92 244.4 72.86 11.12 2 25 Menidia spp. (menidia silversides) 731.9 18.3 3.18 1.5 64.23 227.14 39.51 14 9 Subtotal 77,334 95.1....... 2 172 Totals 81,492 1.. 354.93 5.8 183.28 5,715... 2 512 2

Table 4. Catch statistics for Selected Taxa collected in 21.3-m bay seine samples in Sarasota Bay (n=164 hauls), June 21 to April 211. Percent (%) is the percent of the total catch represented by that taxon; percent occurrence (% Occur) is the percentage of samples in which that taxon was collected; CV is the coefficient of variation of the mean. Length is standard length for fish, post-orbital head length for shrimp, and carapace width for crabs. Taxa are ranked in order of decreasing mean catch-per-unit-effort. Scientific Name (Common Name) Number Catch-per-unit-effort (animals/haul) Length (mm) % No. % Occur Mean Stderr CV Max Mean Stderr Min Max Leiostomus xanthurus (spot) 7,635 9.4 31.1 33.25 9.93 382.32 91. 22.8 1 172 Mugil cephalus (striped mullet) 2,124 2.6 13.4 9.25 5.45 754.52 65. 29.18 18 153 Farfantepenaeus duorarum (pink shrimp) 1,19 1.4 49.4 4.83.92 244.4 72.86 11.12 2 25 Cynoscion nebulosus (spotted seatrout) 131.2 22..57.15 339.73 2. 45 2.25 14 172 Sciaenops ocellatus (red drum) 112.1 6.1.49.23 599.42 25. 24 1.55 11 141 Callinectes sapidus (blue crab) 78.1 21.3.34.7 264.99 7.86 32 4.1 6 154 Lutjanus griseus (gray snapper) 6.1 19.5.26.6 272.53 4.29 59 7.9 9 284 Archosargus probatocephalus (sheepshead) 41.1 9.1.18.8 574.94 11.43 54 11.15 15 243 Paralichthys albigutta (Gulf flounder) 28. 9.8.12.5 575.23 8.57 85 17.84 16 351 Mugil gyrans (faintail mullet) 9. 1.8.4.3 1,14.33 5. 53 5.73 15 73 Mugil curema (white mullet) 9..6.4.4 1,28.62 6.43 87 1.52 78 93 Lutjanus synagris (lane snapper) 6. 1.2.3.2 1,87.4 3.57 35 8.83 2 65 Centropomus undecimalis (common snook) 4. 1.8.2.1 78.2 1.43 162 116.92 26 512 Elops saurus (ladyfish) 3. 1.8.1.1 734.82.71 245 7.88 236 261 Mycteroperca microlepis (gag) 2. 1.2.1.1 92.76.71 161 2. 141 181 Totals 11,351 13.9 84.1 49.44 11.9 38.21 1,28.57.. 2 512 21

Nearshore habitats sampled with 183-m seines A total of 14,64 animals were collected with 183-m seines (n=36 hauls), representing 14.1% of the overall catch (Table 2). Pinfish (L. rhomboides, n=7,843) was the most abundant taxon collected with 183-m seines, accounting for 53.7% of the total catch (Table 5). Pinfish were also the most frequently collected taxon, occurring in 94.4% of 183-m seine sets. Animals collected with 183-m seines tended to be much larger (mean size 215.2 mm) than those collected with either 21.3-m seines (37.5 mm) or 6.1-m trawls (41.1 mm). A total of 1,246 animals from 21 Selected Taxa were collected, representing 8.5% of the entire 183-m seine catch (Table 6). Leiostomus xanthurus (n=376) was the most abundant Selected Taxon, accounting for 3% of the Selected Taxa collected by this gear. Sheepshead (A. probatocephalus, 77.8% occurrence) was the most frequently collected Selected Taxa followed by spot and white mullet (Mugil curema), which occurred in 5% of the hauls. 22

Table 5. Catch statistics for the 1 dominant taxa collected in 183-m haul seine samples in Sarasota Bay (n=36 hauls), June 21 to April 211. Percent (%) is the percent of the total catch represented by that taxon; percent occurrence (% Occur) is the percentage of samples in which that taxon was collected; CV is the coefficient of variation of the mean. Length is standard length. Taxa are ranked in order of decreasing mean catch-per-unit-effort. Species of commercial or recreational importance (Selected Taxa) are denoted with an asterisk (*) after the species name. Scientific Name (Common Name) Number Catch-per-unit-effort (animals/haul) Length (mm) % No. % Occur Mean Stderr CV Max Mean Stderr Min Max Lagodon rhomboides (pinfish) 7,843 53.7 94.4 217.86 49.78 137.9 1,316. 1.34 45 21 Brevoortia spp. (menhaden) 2,159 14.8 25. 59.97 51.8 511.5 1,828. 9.28 5 236 Harengula jaguana (scaled sardine) 1,391 9.5 25. 38.64 29.9 464.37 1,44. 97.21 44 15 Orthopristis chrysoptera (pigfish) 53 3.6 52.8 14.72 5.61 228.72 182. 112 1.3 28 21 Leiostomus xanthurus (spot) * 376 2.6 5. 1.44 3.73 214.28 116. 133 1.77 73 24 Bairdiella chrysoura (silver perch) 312 2.1 38.9 8.67 4.6 318.14 155. 125 1.19 69 168 Strongylura notata (redfin needlefish) 297 2. 55.6 8.25 4.87 353.86 176. 361 1.51 292 427 Archosargus probatocephalus (sheepshead) * 23 1.4 77.8 5.64 1.41 149.59 4. 221 3.48 35 385 Diplodus holbrookii (spottail seabream) 161 1.1 13.9 4.47 4.3 54.8 145. 69.5 56 84 Nicholsina usta (emerald parrotfish) 152 1. 13.9 4.22 2.83 42.7 83. 122 1.47 84 162 Subtotal 13,424 91.8....... 28 427 Totals 14,64 1.. 45.67 99.1 146.57 3,29... 18 781 23

Table 6. Catch statistics for Selected Taxa collected in 183-m haul seine samples in Sarasota Bay (n=36 hauls), June 21 to April 211. Percent (%) is the percent of the total catch represented by that taxon; percent occurrence (% Occur) is the percentage of samples in which that taxon was collected; CV is the coefficient of variation of the mean. Length is standard length for fish and carapace width for crabs. Taxa are ranked in order of decreasing mean catch-per-uniteffort. Scientific Name (Common Name) Number Catch-per-unit-effort (animals/haul) Length (mm) % No. % Occur Mean Stderr CV Max Mean Stderr Min Max Leiostomus xanthurus (spot) 376 2.6 5. 1.44 3.73 214.28 116. 133 1.77 73 24 Archosargus probatocephalus (sheepshead) 23 1.4 77.8 5.64 1.41 149.59 4. 221 3.48 35 385 Mugil curema (white mullet) 141 1. 5. 3.92 1.16 177.25 28. 158 3.34 15 295 Elops saurus (ladyfish) 84.6 44.4 2.33 1.2 261.39 3. 276 4.98 225 462 Centropomus undecimalis (common snook) 74.5 36.1 2.6.89 258.72 27. 395 8.48 228 613 Mugil cephalus (striped mullet) 73.5 41.7 2.3.75 22.7 24. 33 1.68 113 444 Cynoscion nebulosus (spotted seatrout) 63.4 36.1 1.75.79 269.89 21. 169 9.9 82 538 Callinectes sapidus (blue crab) 53.4 41.7 1.47.4 162.76 1. 11 4.44 33 193 Sciaenops ocellatus (red drum) 47.3 33.3 1.31.56 259.47 19. 383 2.25 77 628 Paralichthys albigutta (Gulf flounder) 28.2 38.9.78.21 162.95 5. 153 12.8 55 34 Lutjanus griseus (gray snapper) 27.2 22.2.75.29 232.86 7. 177 9.24 89 251 Mycteroperca microlepis (gag) 26.2 13.9.72.37 38.3 11. 163 9.32 82 295 Mugil gyrans (fantail mullet) 25.2 19.4.69.47 49.93 17. 151 6.39 114 228 Scomberomorus maculatus (Spanish mackerel) 9.1 16.7.25.12 292.77 4. 256 26.49 132 321 Menticirrhus americanus (Southern kingfish) 5. 5.6.14.1 426.92 3. 243 18.84 19 3 Micropogonias undulatus (Atlantic croaker) 4. 5.6.11.9 47.26 3. 195 1.47 172 222 Continued 24

Table 6. Continued. Number % Catch-per-unit-effort (animals/haul) Length (mm) Scientific Name (Common Name) No. % Occur Mean Stderr CV Max Mean Stderr Min Max Pogonias cromis (black drum) 2. 5.6.6.4 418.16 1. 264 1.5 262 265 Farfantepenaeus duorarum (pink shrimp) 2. 2.8.6.6 6. 2. 19 1. 18 2 Trachinotus carolinus (pompano) 2. 2.8.6.6 6. 2. 222 6.5 215 228 Trachinotus falcatus (permit) 1. 2.8.3.3 6. 1. 185. 185 185 Menticirrhus littoralis (Gulf kingfish) 1. 2.8.3.3 6. 1. 184. 184 184 Totals 1,246 8.5 1. 34.61 5.57 96.55 168... 18 628 25

Deeper-water habitats sampled with 6.1-m trawls A total of 7,712 animals were collected in 6.1-m trawls (n=48 hauls), representing 7.4% of the overall catch (Table 2). Pinfish (L. rhomboides, n=2,841, 36.8% of total catch) was the most abundant taxon collected with this gear (Table 7). The taxon most frequently collected with 6.1-m trawls was also the pinfish (L. rhomboides), which occurred in over 7% of the trawl samples. Trawl collected animals tended to be similar in size to those collected with 21.3-m seines and smaller than those collected with 183- m seines. Eleven Selected Taxa (1,41 animals, 13.5% of the entire trawl catch) were collected with 6.1-m trawls (Table 8). Blue crab (Callinectes sapidus, n=382) accounted for 37% of the Selected Taxa collected with trawls. The Selected Taxon most frequently collected with 6.1-m trawls was the stone crab (Menippe spp.) which occurred in almost 6% of the trawl collections. 26

Table 7. Catch statistics for the 1 dominant taxa collected in 6.1-m trawl samples in Sarasota Bay (n=48 hauls), June 21 to April 211. Percent (%) is the percent of the total catch represented by that taxon; percent occurrence (% Occur) is the percentage of samples in which that taxon was collected; CV is the coefficient of variation of the mean. Length is standard length for fish and carapace width for crabs. Taxa are ranked in order of decreasing mean catch-per-uniteffort. Species of commercial or recreational importance (Selected Taxa) are denoted with an asterisk (*) after the species name. Scientific Name (Common Name) Number Catch-per-unit-effort (animals/1m 2 ) Length (mm) % No. % Occur Mean Stderr CV Max Mean Stderr Min Max Lagodon rhomboides (pinfish) 2,841 36.8 7.8 4.15 1.52 253.18 66.65 53.61 12 163 Orthopristis chrysoptera (pigfish) 1,23 15.9 5. 1.74 1.3 516.68 62.53 4 1.5 15 27 Anchoa mitchilli (bay anchovy) 1,22 15.8 1.4 1.71 1.67 674.91 8.21 29.11 21 38 Callinectes sapidus (blue crab) * 382 5. 52.1.56.21 26.77 9.31 57 1.93 12 172 Eucinostomus spp. (eucinostomus mojarra) 349 4.5 31.3.48.35 55.8 16.51 24.23 13 39 Leiostomus xanthurus (spot) * 285 3.7 25..42.26 43.7 11.69 55 2.58 13 175 Portunus spp. (swimming crab) 183 2.4 52.1.26.14 356.44 6.48 41.72 12 6 Menippe spp. (stone crab) * 143 1.9 58.3.22.5 149.1 1.48 33 1.73 5 112 Eucinostomus gula (silver jenny) 12 1.3 29.2.15.6 35.67 2.83 67 1.32 42 1 Farfantepenaeus duorarum (pink shrimp) * 78 1. 39.6.11.3 187.41.85 15.64 6 3 Subtotal 6,813 88.3....... 5 27 Totals 7,712 1.. 11.14 3.44 214.27 137.21.. 5 35 27

Table 8. Catch statistics for Selected Taxa collected in 6.1-m trawl samples in Sarasota Bay (n=48 hauls), June 21 to April 211. Percent (%) is the percent of the total catch represented by that taxon; percent occurrence (% Occur) is the percentage of samples in which that taxon was collected; CV is the coefficient of variation of the mean. Length is standard length for fish, post-orbital head length for shrimp, and carapace width for crabs. Taxa are ranked in order of decreasing mean catch-per-unit-effort. Scientific Name (Common Name) Number Catch-per-unit-effort (animals/1m 2 ) Length (mm) % No. % Occur Mean Stderr CV Max Mean Stderr Min Max Callinectes sapidus (blue crab) 382 5. 52.1.56.21 26.77 9.31 57 1.93 12 172 Leiostomus xanthurus (spot) 285 3.7 25..42.26 43.7 11.69 55 2.58 13 175 Menippe spp. (stone crab) 143 1.9 58.3.22.5 149.1 1.48 33 1.73 5 112 Farfantepenaeus duorarum (pink shrimp) 78 1. 39.6.11.3 187.41.85 15.64 6 3 Archosargus probatocephalus (sheepshead) 73.9 14.6.11.9 611.56 4.54 178 3.86 2 247 Paralichthys albigutta (Gulf flounder) 59.8 45.8.9.3 212.9 1.14 141 8.75 3 256 Lutjanus griseus (gray snapper) 13.2 8.3.2.1 368.76.32 151 12.99 34 233 Lutjanus synagris (lane snapper) 3. 4.2.. 58.24.14 69 11.98 5 91 Cynoscion nebulosus (spotted seatrout) 3. 6.3.. 391.75.7 159 81.82 22 35 Cynoscion arenarius (sand seatrout) 1. 2.1.. 692.82.7 157. 157 157 Mycteroperca microlepis (gag) 1. 2.1.. 692.82.6 95. 95 95 Totals 1,41 13.5 91.7 1.54.37 166.42 12.7.. 5 35 28

Species Profiles The following sections provide profiles on various abundant and frequently occurring species in terms of seasonal abundance, sizes collected, spatial distribution, and bottom habitat preference. Species included in these profiles are numerically dominant or economically important (i.e., recreationally or commercially fished species, such as spotted seatrout, common snook and pink shrimp). Summary statistics of catch for both completed years of this study are included in Appendices E, F and G for the 21.3-m seines, 183-m seines and 6.1-m trawls, respectively. Summary graphs for all taxa that were identified to species, had at least a 15% occurrence, and for which 1 or more individuals were collected during bi-monthly sampling in Sarasota Bay between June 29 and April 211 are provided in Appendices H, I and J. The abundance and size distribution results presented in these appendices and in the following species profiles are based on a limited time series (two years of bi-monthly sampling) with a relatively small sample size, so there is considerable variability in the data. 29

Pink shrimp, Farfantepenaeus duorarum Pink shrimp range from the Chesapeake Bay to the Yucatan Peninsula and are of great commercial importance, especially in the Gulf of Mexico (Carpenter 22). Catches in Florida were valued at nearly $21M in 25 (FWRI, unpublished data). They spawn offshore and enter estuaries as postlarvae (Allen et al. 198). They probably use selective tidal stream transport (i.e., ascend into the water column on flood tides and descend towards the substrate on ebb tides [Hughes 1969]) to recruit to nursery grounds. Different life stages of pink shrimp exhibit a broad range of salinity tolerance, although salinities from approximately 12 to 45 ppt seem to be preferred (Pattillo et al. 1997). Pink shrimp did not comprise a large proportion of the catch in the 183-m seines (Appendix F) but were commonly collected in both 21.3-m seines (52% of the hauls, Appendix E) and 6.1-m trawls (35%, Appendix G). Pink shrimp collected in 21.3-m seines tended to be smaller (median post-orbital head length of 11 mm; Figure 5) than those collected in 6.1-m trawls (15 mm; Figure 6). In the shallow water habitats sampled with the 21.3-m seine abundance of pink shrimp was higher during June and October than in the other months (Figure 5). Pink shrimp in shallow water habitats were more abundant in the vegetated areas of Little Sarasota and Blackburn bays (Figure 5). Although mean abundance in the deeper water sampled with 6.1-m trawls was higher in February and June, and in Roberts and Little Sarasota bays, variability in the abundance estimates was too high to discern any real trends (Figure 6). 3

Farfantepenaeus duorarum (pink shrimp) 21.3-m seine 7 6 6 (53) (56) (56) (54) (54) (52) 5 (59) (92) (59) (59) (56) (animals.1 m -2 ± 95% CL) 5 4 3 2 (animals.1 m -2 ± 95% CL) 4 3 2 1 1 Feb Apr Jun Aug Oct Dec Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment 2 3. 7 (animals.1 m -2 ± 95% CL) 18 16 14 12 1 8 6 4 2 (5) (182) (15) (33) (252) (73) 2.5 2. 1.5 1..5 Number of individuals 6 5 4 3 2 1 Total = 2,542 Mud Mud-sand Sand Structure Some None. 1 2 3 4 5 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 5. Relative abundance and length-frequency distribution of pink shrimp collected with 21.3-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 31

Farfantepenaeus duorarum (pink shrimp) 6.1-m trawl.35.6.3 (16) (16) (16) (16) (16) (16).5 (12) (48) (12) (12) (12) (animals.1 m -2 ± 95% CL).25.2.15.1 (animals.1 m -2 ± 95% CL).4.3.2.5.1. Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment 25 2 Total = 144 Number of individuals 15 1 5 5 1 15 2 25 3 35 Size-class mid-point (mm) Figure 6. Relative abundance and length-frequency distribution of pink shrimp collected with 6.1-m trawl in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 32

Blue crab, Callinectes sapidus Blue crabs occur in the western Atlantic from Canada to Argentina, including Bermuda and the Antilles, and have been successfully introduced in Europe and Japan (Carpenter 22). This species supports large commercial fisheries in Florida, valued at nearly $12M in 25 (FWRI, unpublished data), and is an important predator and prey species in inshore waters (Steele and Bert 1994). Blue crabs are transients in estuaries: spawning and larval development occur in marine waters, but juveniles and adults spend most of their time in estuaries (Steele and Bert 1994). Larval blue crabs recruiting into the estuary and adult females leaving the estuary to spawn use selective tidal stream transport (Olmi 1994; Tankersley et al. 1998). Chemical cues emanating from estuarine and freshwater watersheds promote settlement by triggering metamorphosis in larvae (Wolcott and De Vries 1994; Forward et al. 1994 and 1997). Blue crabs tolerate salinities from freshwater to at least 5 ppt. Optimal salinities differ among lifehistory stages: 12 36 ppt for larvae, 2 21 ppt for juveniles, less than 1 ppt for adult males, and 23 33 ppt for egg-bearing females (Pattillo et al. 1997). Blue crabs were collected in all three gear types deployed during this study (Appendix E, F, and G), but were only commonly collected and abundant in the collections made with 21.3-m seines (Appendix E) and 6.1-m trawl (Appendix G). They were collected during all months sampled with the highest abundance during winter and spring months (December to April) in the shallow-water habitats sampled with the small seine (Figure 7). In deeper-water habitats sampled with 6.1-m trawls, blue crabs had their highest abundance in February with a steady decline through the remainder of the year (Figure 8). Blue crabs were collected from each of the sampled embayments with 33

both gear types; although there was not clear abundance trend between embayments for the shallow water habitats, blue crabs using the deeper-water habitats were more abundant in Little Sarasota Bay and least abundant in Sarasota Bay. Sizes captured with 6.1-m trawls ranged from 12 mm to 172 mm carapace width (CW) with a bimodal distribution (modes at 15 and 9 mm CW). Blue crabs captured with 21.3-m seines tended to be smaller than those in trawls (single mode at 1mm, range 6 to 154 mm CW). 34

Callinectes sapidus (blue crab) 21.3-m seine.7.4.6 (53) (56) (56) (54) (54) (52) (59) (92) (59) (59) (56) (animals.1 m -2 ± 95% CL).5.4.3.2 (animals.1 m -2 ± 95% CL).3.2.1.1. Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment.35.25 18.3 (5) (182) (15) (33) (252) (73) 16 Total = 17 (animals.1 m -2 ± 95% CL).25.2.15.1.2.15.1.5 Number of individuals 14 12 1 8 6 4.5 2. Mud Mud-sand Sand Structure Some None. 2 4 6 8 1 12 14 16 18 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 7. Relative abundance and length-frequency distribution of blue crab collected with 21.3-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 35

Callinectes sapidus (blue crab) 6.1-m trawl 1.4 2.5 (12) (48) (12) (12) (12) (animals.1 m -2 ± 95% CL) 1.2 1..8.6.4 (16) (16) (16) (16) (16) (16) (animals.1 m -2 ± 95% CL) 2. 1.5 1..5.2. Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment 6 Total = 489 5 Number of individuals 4 3 2 1 2 4 6 8 1 12 14 16 18 2 Size-class mid-point (mm) Figure 8. Relative abundance and length-frequency distribution of blue crab collected with 6.1-m trawl in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 36

Ladyfish, Elops saurus Ladyfish inhabit estuarine and nearshore waters throughout Florida. Larval and juvenile ladyfish can be found in a variety of nearshore habitats, including coastal beaches, canals, rivers, and mosquito impoundments (Gilmore et al. 1982; McBride et al. 21). Length-frequency analysis suggests that ladyfish grow to 2 3 mm standard length by age 1. Their diet consists mainly of fish with decapod crustaceans being of secondary importance (Darnell 1958; Sekavec 1974). Florida landings were just over 1 million pounds in 27 with over 75% being landed by the commercial fishery (FWC-FWRI 28). Ladyfish were captured with both the 21.3-m and 183-m seine during this study (Appendices E and F, respectively). They were only common and abundant, however, in the larger seine where they comprised.8% of the total catch (n=183) and occurred in 4.3% of the hauls. The majority of captured ladyfish were between 225 and 3 mm SL (Figure 9), with the largest ladyfish collected measuring 462 mm SL. Variability in the abundance data was too high to discern spatial or temporal patterns. 37

Elops saurus (ladyfish) 183-m seine.3.3.25 (12) (12) (12) (12) (12) (12).25 (12) (24) (12) (12) (12) (animals.1 m -2 ± 95% CL).2.15.1 (animals.1 m -2 ± 95% CL).2.15.1.5.5. Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment.14.3 8.12 (3) (48) (16) (5) (66) (6).25 Total = 183 (animals.1 m -2 ± 95% CL).1.8.6.4.2.15.1 Number of individuals 6 4 2.2.5. Mud Mud-sand Sand Structure Some None. 1 2 3 4 5 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 9. Relative abundance and length-frequency distribution of ladyfish collected with 183-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 38

Bay anchovy, Anchoa mitchilli Bay anchovies range from Maine to the Yucatan Peninsula and are of great importance in estuarine food chains due to their trophic position, small size, and extreme abundance (Pattillo et al. 1997; Carpenter 22). They spawn in nearshore marine waters and estuaries (Peebles et al. 1996; Pattillo et al. 1997). Larvae use selective tidal stream transport to travel to upstream nursery areas (Schultz et al. 23). Although each life stage of bay anchovy exhibits a broad range of salinity tolerance (Pattillo et al. 1997), each tends to distribute differently in relation to salinity: spawning adults, eggs, and newly hatched larvae are found at higher salinities than are laterstage larvae and juveniles (Peebles et al. 1991). Bay anchovies were collected in 21.3-m seine and 6.1-m trawl hauls (Appendices E and G, respectively), but not with 183-m seine (Appendix F). They were only abundant and frequently collected in the 21.3-m seine hauls in which they comprised 32.7% (n= 71,33) of the total catch and were present in 31.7% of the hauls. With the exception of very low abundance in February, there were no obvious seasonal trends in abundance for bay anchovy (Figure 1) collected from the shallow waters sampled with 21.3-m seines. Bay anchovies were less abundant in Palma Sola, Sarasota, and Blackburn bays than in Roberts and Little Sarasota bays. Bay anchovies collected in 21.3-m seines ranged in size from 15 to 56 mm SL, with a mode at 25 mm SL. 39

Anchoa mitchilli (bay anchovy) 21.3-m seine 12 35 (53) (56) (56) (54) (54) (52) 1 3 (59) (92) (59) (59) (56) (animals.1 m -2 ± 95% CL) 8 6 4 (animals.1 m -2 ± 95% CL) 25 2 15 1 2 5 Feb Apr Jun Aug Oct Dec Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment 3 (252) (73) 5 4 (animals.1 m -2 ± 95% CL) 25 2 15 1 5 (5) (182) (15) (33) 4 3 2 1 Number of individuals 3 2 1 Total = 71,33 Mud Mud-sand Sand Structure Some None Substrate Vegetation Dominant Bottom Habitat 1 2 3 4 5 Size-class mid-point (mm) 6 7 Figure 1. Relative abundance and length-frequency distribution of bay anchovy collected with 21.3-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 4

Common snook, Centropomus undecimalis Common snook occur in tropical and subtropical estuarine systems of the western Atlantic (Rivas 1986). In Florida, they occur principally from Cape Canaveral on the Atlantic coast southward around the peninsula to Cedar Key on the Gulf of Mexico coast (Taylor et al. 2). Common snook are popular sport fish that support a large recreational fishery throughout much of coastal south and central Florida (Muller and Taylor 22). Spawning occurs primarily in ocean passes and secondary embayments (Taylor et al. 1998). Small juveniles are found in quiet shallow-water creeks, canals, and lagoons in both low-salinity (riverine) and high-salinity (mangrove and saltmarsh) environments (McMichael et al. 1989; Peters et al. 1998). As juvenile common snook grow to about 15 mm SL, marked changes in their tolerance of high temperature and low dissolved oxygen occur (Peterson and Gilmore 1991), and juveniles are no longer abundant at the sites described above. Larger juveniles and adult common snook are found in a wide variety of estuarine habitats. Common snook were not collected in 6.1-m trawls (Appendix G), were rarely collected in 21.3-m seines (Appendix E), but were encountered in over 4% of the 183- m seine sets (Appendix F). There were no obvious seasonal trends in common snook abundance (Figure 11) probably the result of low sample size (6 hauls per sampling event). Common snook had much higher abundance in samples over seagrass, but the number of hauls over unvegetated bottom types was very low. Common snook collected in 183-m seines ranged in size from 228 to 75 mm SL with a mode at 4 mm SL. 41

Centropomus undecimalis (common snook) 183-m seine.35.25 (animals.1 m -2 ± 95% CL).3.25.2.15.1 (12) (12) (12) (12) (12) (12) (animals.1 m -2 ± 95% CL).2.15.1.5 (12) (24) (12) (12) (12).5. Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment.3.12 5 (animals.1 m -2 ± 95% CL).25.2.15.1.5 (3) (48) (16) (5) (66) (6).1.8.6.4.2 Number of individuals 4 3 2 1 Total = 21. Mud Mud-sand Sand Structure Some None. 2 4 6 8 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 11. Relative abundance and length-frequency distribution of common snook collected with 183-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 42

Gray snapper, Lutjanus griseus Gray snapper are a reef species found along the western Atlantic from Massachusetts south to Rio de Janeiro, Brazil. Adults spawn during summer (June September) near areas of bottom structure in offshore waters (Stark 1971; Domeier and Colin 1997). Juvenile gray snapper recruit to estuarine areas including seagrass beds and mangrove shorelines (Nagelkerken et al. 2; Cocheret de la Moriniere et al. 22; Serafy et al. 23; Whaley et al. 27; Faunce and Serafy 28) where they typically spend the first year or two of their lives. Juvenile gray snapper feed primarily on penaeid shrimp and crabs (Rutherford et al.1989) and adults feed on fish, shrimp, and crabs (Harrigan et al. 1989; Hettler 1989). Gray snapper are an economically important species with Florida landings totaling 2,23,737 pounds in 27 (FWC-FWRI 28). Gray snapper were collected in all three gear types deployed in Sarasota Bay, but were more frequently encountered with the 21.3-m (18.8%; Appendix E) and 183-m (3.6%; Appendix F) seines than with the 6.1-m trawl (9.4%; Appendix G). The 21.3-m seine collected smaller gray snapper (mode at 3 mm SL; Figure 12) than did the 183- m seine (modes at 14 and 2 mm SL; Figure 13). Gray snapper were absent from collections made with both seine type in February, and were absent (183-m seine) or present in very low abundance (21.3-m seine) during April. With both seine types, gray snapper were less abundant in Palma Sola Bay than any of the other embayments and had higher abundance in collections at sites with some bottom vegetation. 43

Lutjanus griseus (gray snapper) 21.3-m seine 1.6.8 1.4 (53) (56) (56) (54) (54) (52) (59) (92) (59) (59) (56) (animals.1 m -2 ± 95% CL) 1.2 1..8.6.4 (animals.1 m -2 ± 95% CL).6.4.2.2. Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment 2.5.4 3 (animals.1 m -2 ± 95% CL) 2. 1.5 1..5 (5) (182) (15) (33) (252) (73).3.2.1 Number of individuals 25 2 15 1 5 Total = 187. Mud Mud-sand Sand Structure Some None. 5 1 15 2 25 3 35 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 12. Relative abundance and length-frequency distribution of gray snapper collected with 21.3-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 44

Lutjanus griseus (gray snapper) 183-m seine.25.18 (12) (12) (12) (12) (12) (12).16 (12) (24) (12) (12) (12) (animals.1 m -2 ± 95% CL).2.15.1.5 (animals.1 m -2 ± 95% CL).14.12.1.8.6.4.2. Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment.25.1 4 Total = 137 (animals.1 m -2 ± 95% CL).2.15.1.5 (3) (48) (16) (5) (66) (6).8.6.4.2 Number of individuals 3 2 1. Mud Mud-sand Sand Structure Some None. 5 1 15 2 25 3 35 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 13. Relative abundance and length-frequency distribution of gray snapper collected with 183-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 45

Pinfish, Lagodon rhomboides Pinfish range from Cape Cod to the Yucatan Peninsula, including Bermuda and northern Cuba. They are most abundant from Cape Hatteras through the northern Gulf of Mexico (Pattillo et al. 1997; Carpenter 22). Florida s pinfish landings in 27 were 2,22,492 pound with 96% of the total being landed by recreational fisherman and 83% coming from the gulf coast (FWRI-FWC 28). Their high abundance in estuaries and their trophic placement have led some to suggest that they play a more important role in structuring epibenthic communities (Pattillo et al. 1997) than they do in the fishery. Spawning occurs offshore and larvae use selective tidal stream transport to travel to nursery areas (Pattillo et al. 1997; Forward et al. 1998). Pinfish have been recorded in salinities ranging from to >4 ppt, but may avoid the lower end of this range (Pattillo et al. 1997). Pinfish were one of the two most abundant taxa collected in each of the three gear types, comprising 25.%, 55.8%, and 26.6% of the total catch in 21.3-m seines, 183-m seines, and 6.1-m trawls, respectively (Appendices E, F, and G, respectively). Pinfish were also one of the most commonly collected taxa, occurring in over 75% of the samples collected with each gear type. Pinfish collected in 21.3-m seine (mode at 2 mm SL, range 9 to 18 mm; Figure 14) and 6.1-m trawl (modes at 15, 3 and 8 mm SL, range 11 to 163 mm; Figure 16) samples were smaller than those collected in 183- m seines (modes at 75 and 135 mm SL, range 43 to 213 mm; Figure 15). Pinfish were most abundant in the winter and spring (February to April) in both 21.3-m seines and 6.1-m trawl collections (Figure 14 and Figure 16), and were most abundant in 183-m seine hauls from April to October (Figure 15). Pinfish did not show 46

any strong distributional trends among the five embayments for any of the gear types. Pinfish were more abundant in 21.3-m seine collections that sampled some seagrass (Figure 14), whereas pinfish collected in 183-m seines did not show an abundance trend related to bottom vegetation (Figure 15). 47

Lagodon rhomboides (pinfish) 21.3-m seine 25 6 (animals.1 m -2 ± 95% CL) 2 15 1 5 (53) (56) (56) (54) (54) (52) (animals.1 m -2 ± 95% CL) 5 4 3 2 1 (59) (92) (59) (59) (56) Feb Apr Jun Aug Oct Dec Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment 25 5 14 (5) (182) (15) (33) (animals.1 m -2 ± 95% CL) 2 15 1 5 (252) (73) 4 3 2 1 Number of individuals 12 1 8 6 4 Total = 54,5 2 Mud Mud-sand Sand Structure Some None 5 1 15 2 25 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 14. Relative abundance and length-frequency distribution of pinfish collected with 21.3-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 48

Lagodon rhomboides (pinfish) 183-m seine 18 1 16 (12) (12) (12) (12) (12) (12) (12) (24) (12) (12) (12) (animals.1 m -2 ± 95% CL) 14 12 1 8 6 4 (animals.1 m -2 ± 95% CL) 8 6 4 2 2 Feb Apr Jun Aug Oct Dec Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment 6 8 35 5 (3) (48) (16) (5) (66) (6) 3 Total = 12,775 (animals.1 m -2 ± 95% CL) 4 3 2 6 4 2 Number of individuals 25 2 15 1 1 5 Mud Mud-sand Sand Structure Some None 5 1 15 2 25 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 15. Relative abundance and length-frequency distribution of pinfish collected with 183-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 49

Lagodon rhomboides (pinfish) 6.1-m trawl 14 12 (animals.1 m -2 ± 95% CL) 12 1 8 6 4 (16) (16) (16) (16) (16) (16) (animals.1 m -2 ± 95% CL) 1 8 6 4 (12) (48) (12) (12) (12) 2 2 Feb Apr Jun Aug Oct Dec Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment 16 Total = 5,925 14 12 Number of individuals 1 8 6 4 2 2 4 6 8 1 12 14 16 18 Size-class mid-point (mm) Figure 16. Relative abundance and length-frequency distribution of pinfish collected with 6.1-m trawl in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 5

Sheepshead, Archosargus probatocephalus Sheepshead, Archosargus probatocephalus, are found in coastal estuarine and inner- to mid-shelf waters from Cape Cod to Brazil (Jennings 1985). Larval sheepshead are pelagic and metamorphose into juveniles at about 8 mm (Parsons and Peters 1989; Tucker and Alshuth 1997). Juvenile sheepshead are most abundant in grass flats and over mud bottoms (Springer and Woodburn 196, Odum and Heald 1972, Jennings 1985). In late summer, juvenile sheepshead begin to congregate with adults around stone jetties, breakwaters, piers, wrecks, and bulkheads (Jennings 1985). Recreational and commercial fishermen commonly harvest sheepshead, with the recreational fishery accounting for almost 9% of the total pounds landed in recent years (Munyandorero et al. 26). Sheepshead were collected in almost 7% of the hauls made with the 183-m seine (Appendix F), but occurred much less frequently in 6.1-m trawl (15.6%; Appendix G) and 21.3-m seine hauls (11.4%; Appendix E). Sheepshead collected in the 21.3-m seine did not meet the abundance criteria for inclusion (n<1 and <15% occurrence) in this section. Sheepshead collected with 183-m seines tended to be larger (mode at 23 mm SL, range 35 to 385 mm SL; Figure 17) than those collected with trawls (mode at 17 mm SL, range 13 to 36 mm SL; Figure 18). There were no obvious seasonal trends for sheepshead collected with either gear (Figure 17 and Figure 18). Abundance of sheepshead collected in 183-m seines was highest in Little Sarasota Bay and from collections that sampled at least some bottom vegetation (Figure 17). 51

Archosargus probatocephalus (sheepshead) 183-m seine.35.6 (12) (24) (12) (12) (12).3 (12) (12) (12) (12) (12) (12).5 (animals.1 m -2 ± 95% CL).25.2.15.1 (animals.1 m -2 ± 95% CL).4.3.2.5.1. Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment.6.2 1 (animals.1 m -2 ± 95% CL).5.4.3.2.1 (3) (48) (16) (5) (66) (6).18.16.14.12.1.8.6.4 Number of individuals 8 6 4 2 Total = 362.2. Mud Mud-sand Sand Structure Some None. 1 2 3 4 5 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 17. Relative abundance and length-frequency distribution of sheepshead collected with 183-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 52

Archosargus probatocephalus (sheepshead) 6.1-m trawl.5 (16) (16) (16) (16) (16) (16) 1.2 (animals.1 m -2 ± 95% CL).4.3.2.1 (animals.1 m -2 ± 95% CL) 1..8.6.4.2 (12) (48) (12) (12) (12). Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment 5 4 Total = 149 Number of individuals 3 2 1 1 2 3 4 5 Size-class mid-point (mm) Figure 18. Relative abundance and length-frequency distribution of sheepshead collected with 6.1-m trawl in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 53

Spotted Seatrout, Cynoscion nebulosus Spotted seatrout occur along the U.S. east coast from New York south to Florida and in the Gulf of Mexico from Florida to Laguna Madre (Carpenter 22). Over much of its range, spotted seatrout are the target of important recreational and commercial fisheries (Bortone 23). Spawning occurs within estuaries or near passes into estuaries (Brown-Peterson, 23). Spotted seatrout have been collected at salinities ranging from to 75 ppt, but juveniles may prefer 8-25 ppt, with 2-25 ppt possibly representing the physiological optimum for larger juveniles and adults (Pattillo et al. 1997). Spotted seatrout were collected in each of the gear types (Appendix E, F, and G), but were only abundant (n=259) and frequently collected (2.6% of samples) in the 21.3-m seine hauls. The 21.3-m seine tended to collect small-sized seatrout (mode at 25 mm SL; Figure 19), which represent early young-of-the-year animals. Abundance was higher during the summer and fall months (June, August and October; Figure 19) than during other months (February, April and December), and none were collected during April. They were most abundant in collections that sampled some bottom vegetation and although present in all embayments, the mean abundance was slightly higher in Roberts and Little Sarasota bays (Figure 19). 54

Cynoscion nebulosus (spotted seatrout) 21.3-m seine 1.2.8 1. (53) (56) (56) (54) (54) (52) (59) (92) (59) (59) (56) (animals.1 m -2 ± 95% CL).8.6.4 (animals.1 m -2 ± 95% CL).6.4.2.2. Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment 1.8.6 5 1.6 (5) (182) (15) (33) Total = 259 (animals.1 m -2 ± 95% CL) 1.4 1.2 1..8.6.4.2 (252) (73).5.4.3.2.1 Number of individuals 4 3 2 1. Mud Mud-sand Sand Structure Some None. 2 4 6 8 1 12 14 16 18 2 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 19. Relative abundance and length-frequency distribution of spotted seatrout collected with 21.3-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 55

Striped mullet, Mugil cephalus Striped mullet are a cosmopolitan species; in the Western Atlantic, they range from Nova Scotia to Argentina (Carpenter 22). This species supports large fisheries in many areas, including Florida. Landings in Florida were valued at over $5M in 25; this value was less than half of the value in 1994 (FWRI, unpublished data), the year before the constitutional restriction on entangling nets was initiated. Striped mullet are a major prey item for many fishes and birds (Pattillo et al. 1997; Withers and Brooks 24; Bacheler et al. 25; Blewett et al. 26). They spawn on the continental shelf and recruit to estuaries as slender, silvery pelagic juveniles (Pattillo et al. 1997; McDonough and Wenner 23). Recruiting juveniles are strong swimmers capable of traversing long distances to locate nursery habitats, perhaps aided by olfactory cues (Etnier and Starnes 1993; Peters and Matheson, pers. obs.). Juvenile and adult striped mullet exhibit a broad range of salinity tolerance and can be extremely abundant in tidal rivers (Pattillo et al. 1997; Paperno and Brodie 24; Idelberger and Greenwood 25). Adults sometimes move hundreds of miles inland in major river systems such as the Mississippi, but juveniles are most common at salinities higher than freshwater (Etnier and Starnes 1993; Boschung and Mayden 24). Striped mullet were not collected in 6.1-m trawls (Appendix G), but were relatively abundant in 21.3-m seines (Appendix E) and 183-m seines (Appendix F). Frequency of occurrence, however, was only high enough (38.9%) to assess trends from the 183-m seine collections. Striped mullet length-frequency distributions were bimodal (modes at 15 and 325 mm SL and range from 113 to 444; Figure 2). There 56

were no obvious seasonal, embayment or habitat trends in abundance for striped mullet collected in 183-m seine samples. 57

Mugil cephalus (striped mullet) 183-m seine.2 (12) (12) (12) (12) (12) (12).18.16 (12) (24) (12) (12) (12) (animals.1 m -2 ± 95% CL).15.1.5 (animals.1 m -2 ± 95% CL).14.12.1.8.6.4.2. Feb Apr Jun Aug Oct Dec. Palma Sola Sarasota Roberts Little Sarosota Blackburn Month Bay Segment.8.7 25 (3) (48) (16) (5) (66) (6).6 Total = 117 (animals.1 m -2 ± 95% CL).6.4.2.5.4.3.2 Number of individuals 2 15 1 5.1. Mud Mud-sand Sand Structure Some None. 1 2 3 4 5 Substrate Vegetation Dominant Bottom Habitat Size-class mid-point (mm) Figure 2. Relative abundance and length-frequency distribution of striped mullet collected with 183-m seine in Sarasota Bay, June 29 to April 211. Numbers in parenthesis along the top of each abundance graph represent the number of samples collected within each category. 58

Nekton Community Structure Intrabay Comparison Significant differences in abundance (Analysis of Variance, Tukey post hoc test) between embayments, but not sampling years, were identified for nekton sampled with the 21.3-m seine (P<.1, n=325, df=9, Model SS=113.52, Error SS=1,34.94) and the 6.1-m trawl (P<.5, n=96, df=9, Model SS=29.45, Error SS=138.53). There were no significant differences (Analysis of Variance) in abundance between either embayments or years for nekton collected with the 183-m seine (P=.47, n=72, df=9, Model SS=1.9, Error SS=75.86). Nekton abundance for both the 21.3-m seine and 6.1-m trawl was significantly higher in Little Sarasota Bay than in Palma Sola Bay and Sarasota Bay proper (Figure 21), while abundance in Roberts and Blackburn bays were not significantly different from any of the other three embayments. The non-metric multi-dimensional scaling (MDS) plots show embayment groupings of nekton community structure in Sarasota Bay for each of the gear types sampled between June 29 and April 211 (Figure 22). Two of the embayments (Little Sarasota and Roberts bays) grouped together at a Bray-Curtis similarity of 6% or greater for each of the gear types, indicating that they were consistently more similar to each other than to any of the other three embayments. While the remaining three embayments had nekton communities that were distinct from each other for the 183-m seines and 6.1-m trawls, the 21.3-m seine had an additional grouping of the two northern embayments (Sarasota and Palma Sola bays) at 72% similarity. 59

7 6 21.3-m bay seine a a a,b b a,b 5 4 3 2 1 (animals.1 m -2 ± 95% CL) 14 12 1 8 6 4 2 5 4 183-m haul seine 6.1-m otter trawl a a a,b b a,b 3 2 1 Palma Sola Bay Sarasota Bay Roberts Bay Little Sarasota Bay Blackburn Bay Figure 21., by gear type, for nekton collected from each of the five embayments of Sarasota Bay during nekton sampling, June 29 April 211. Letters above bars in 21.3-m seine and 6.1-m trawl plot represent significant differences (ANOVA, P<.5, Tukey post hoc test, b > a); significant differences were not found for 183-m seines. 6

Figure 22. Non-metric Multidimensional Scaling (MDS) ordination plot of nekton community structure in five embayments within Sarasota Bay for each gear type deployed during nekton sampling, June 29 April 211. Ellipses, labeled with capital letters (A, B, C, or D), group embayments that had similar nekton communities as determined by Bray-Curtis similarities of 72% (a. 21.3-m seines), 65% (b. 183-m seines) and 6% (6.1-m trawls) from hierarchical agglomerative cluster analysis. 61

Similarity percentage analyses (SIMPER) on the 21.3-m seine data indicated that differences in abundance, not taxa, determined differences in community structure; only one of the top 25 pseudo-species that determined community structure between embayment groupings was unique to a specific group (Opisthonema oglinum, 31 to 5mm SL; Table 9). Fifteen of the top 25 pseudo-species were more abundant in Group A (Little Sarasota and Roberts bays) than in the other two embayment groupings. Three of the top 25 pseudo-species had their highest abundance in Group B (Palma Sola Bay and Sarasota Bay proper) and seven were most abundant in Blackburn Bay. Four of the top 25 pseudo-species are Selected Taxa, with three having their highest abundance in Blackburn Bay (L. xanthurus, <31mm SL; M. cephalus, <31mm SL; and F. duorarum, <31mm POH) and the fourth (M. cephalus, 31-5mm SL) being most abundant in embayment Group B (Palma Sola Bay and Sarasota Bay proper). Differences in abundance also distinguished the embayment groupings for the 183-m seine collections (SIMPER analysis; Table 1). None of the top 25 pseudospecies that differentiated community structure between embayment groupings for the 183-m seine was unique to a single group. Fourteen of the top 25 pseudo-species had higher abundance in Sarasota Bay proper (Group C) than any of the other embayment groupings. Only two of the 25 top pseudo-species had their highest abundance in Blackburn Bay (Group D). Peak abundance for the six Selected Taxa in the top 25 were distributed between the Little Sarasota and Roberts bays group (Group A: A. probatocephalus, >1mm SL; L. griseus, >1mm SL; and S. ocellatus, >1mm SL), Palma Sola Bay (Group B: L. xanthurus, >1mm SL; and E. saurus, >1mm SL), and 62

Sarasota Bay proper (Group C: L. xanthurus, >1mm SL; and M. microlepis, >1mm SL). With only one of the top 25 pseudo-species (L. xanthurus, 31-5mm SL; Table 11) being unique to a single embayment grouping in the similarity percentage analyses (SIMPER), abundance differences defined the MDS embayment groupings for the 6.1- m trawl collections. Peak abundance occurred in embayment group A (Little Sarasota and Roberts bays) for 14 of the top 25 pseudo-species, which included three Selected Taxa (seven pseudo-species: L. xanthurus at <31mm SL, 31-5mm SL, and <1mm SL; C. sapidus at <31mm CW, 31-5mm CW, and 51-1mm CW; and L. griseus at >1mm SL). Two, three, and six pseudo-species each had peak abundance in Palma Sola Bay (Group B), Sarasota Bay proper (Group C) and Blackburn Bay (Group D), respectively. 63

Table 9. Similarity percentage (SIMPER) analysis for Sarasota Bay embayment groupings identified in the MDS ordination for 21.3-m seine collections (Figure 21). Mean abundance (Group Abundance) and percent contribution to dissimilarity between groups (Group Dissimilarity) for the top 25 pseudo-species that distinguished embayment groupings are listed. Group A included Little Sarasota and Roberts bays, Group B included Sarasota and Palma Sola bays, and Group C consisted of only Blackburn Bay. Taxa are listed in decreasing order of relative contribution to overall differences between groups. Group Abundance (animals/1m 2 ) 1/2 Group Dissimilarity % contribution Scientific name Common name Size Class A B C A to B A to C B to C Anchoa mitchilli Bay anchovy <31mm 5.3 2.34.7 3.14 15.83 13.98 Anchoa mitchilli Bay anchovy 31-5mm 4.77 1.82.58 3.54 9.53 6.4 Harengula jaguana Scaled sardine 31-5mm 1.1.54.92 4.27 3.11 2.77 Anchoa cubana Cuban anchovy 31-5mm.69.4.13 4.53 4.37.69 Eucinostomus spp. Eucinostomus mojarra <31mm 4.1 3.12 5.67 3.22 1.33 4.48 Leiostomus xanthurus 1 Spot <31mm 2.54 1.75 2.96 2.1 2.6 4.8 Menidia spp. Silverside 31-5mm.88.49 1.6 1.69 1.9 3.38 Lucania parva Rainwater killifish <31mm.91 1.83.74 3.42. 3.35 Mugil cephalus 1 Striped mullet <31mm.31.47.61 2.8 2.31 1.89 Lagodon rhomboides Pinfish <31mm 4.17 4.3 4.89 1.18 2.9 1.74 Lagodon rhomboides Pinfish 31-5mm 3.76 3.18 3.36 2.27 1.46 1.19 Farfantepenaeus duorarum 1 Pink shrimp <31mm 1.7.84 1.94 1.52.82 2.7 Harengula jaguana Scaled sardine 31-5mm.54.4.25 1.45 1.65 1.27 Eucinostomus spp. Eucinostomus mojarra 31-5mm 2.38 1.78 1.84 2.17 1.62.54 Mugil cephalus 1 Striped mullet 31-5mm..16.6 1.75.69 1.75 Opisthonema oglinum Atlantic thread herring 31-5mm.25.. 2.4 1.96. Bairdiella chrysoura Silver perch 31-5mm.69.26.66 1.82.7 1.18 Menidia spp. Silverside 31-5mm.32.37.66.63 1.82 1.24 Opisthonema oglinum Atlantic thread herring 31-5mm.33.2.2 1.85 1.8. Lucania parva Rainwater killifish 31-5mm.9.36.4 1.55.31 1.64 Lagodon rhomboides Pinfish 51-1mm 2.12 1.81 1.96 1.73.69 1. Eucinostomus gula Silver jenny 31-5mm 1.18.66 1.5 1.72.89.78 Menidia spp. Silverside <31mm.23.14.7.92 1.46.87 Microgobius gulosus Clown goby <31mm.93.25.16 1.22 1.57.41 Floridichthys carpio Goldspotted killifish 31-5mm.13.28.31 1.42.77.69 1 Species of direct economic importance (Selected Taxa). 64

Table 1. Similarity percentage (SIMPER) analysis for Sarasota Bay embayment groupings identified in the MDS ordination for 183-m seine collections (Figure 21). Mean abundance (Group Abundance) and percent contribution to dissimilarity between groups (Group Dissimilarity) for the top 25 pseudo-species that distinguished embayment groupings are listed. Group A included Little Sarasota and Roberts bays, while groups B, C and D were each comprised of a single embayment (Palma Sola, Sarasota, and Blackburn, respectively). Taxa are listed in decreasing order of relative contribution to overall differences between groups. Group Abundance (animals/1m 2 ) 1/2 Group Dissimilarity % contribution Scientific name Common name Size Class A B C D A to B A to C A to D B to C B to D C to D Brevoortia spp. Menhaden 51-1mm.1.59.1.1 17.7 2.13 2.79 15.9 18.93. Lagodon rhomboides Pinfish >1mm.89 1.66 1.4.45 11.39 1.4 5.88 7.47 15.64 5.8 Harengula jaguana Scaled sardine 51-1mm.4.12.21.39 3.47 3.62 14.25.79 8.85 7.35 Lagodon rhomboides Pinfish 51-1mm.74 1.24 1.54 1. 8.46 7.7 4.44.89 4.14 4.92 Harengula jaguana Scaled sardine >1mm.4.2.31.21.87 5.77 6.77 5.39 5.79.95 Bairdiella chrysoura Silver perch >1mm.6.3.41.14. 6.65 2. 6.13 1.64 5.7 Opisthonema oglinum Atlantic thread herring >1mm.2..12.1.6 3.62.65 3.81.45 4.7 Brevoortia spp. Menhaden >1mm.13.3.4. 3.19 2.8 4.7.52 1.1 1.56 Diplodus holbrookii Spottail pinfish 51-1mm...17.2. 3.82.75 3.54.64 3.58 Ariopsis felis Hardhead catfish >1mm.27.12.9.1 2.4 1.49 4.54. 1.94 1.97 Leiostomus xanthurus 1 Spot >1mm.14.17.17.4 1.49 1.18 2.7.74 2.19 2.92 Elops saurus 1 Ladyfish >1mm.17.21.12.3 1.4.69 2.27 1.1 2.9 1.52 Orthopristis chrysoptera Pigfish 51-1mm.12.8.28.19 1.21 2. 1.35 2.17.83 1.79 Nicholsina usta Emerald parrotfish >1mm.1.1.15.. 3.2. 2.62. 3.52 Bairdiella chrysoura Silver perch 51-1mm.3.4.1.14.35 1.79 2.67 1.56 2.14. Archosargus probatocephalus 1 Sheepshead >1mm.42.15.17.15 2.95 2.15 3.3... Strongylura notata Redfin needlefish >1mm.1.14.18.17 1.7 2.6.99 1.62. 2.6 Lutjanus griseus 1 Gray snapper >1mm.17.1.9.6 2.42.33 1.79 1.49.75 1.6 Orthopristis chrysoptera Pigfish >1mm.15.25.3.13 1.68 1.86..48 1.51 1.98 Mycteroperca microlepis 1 Gag >1mm.1..13.3. 1.85 1.4 1.9 1.11 1.2 Opisthonema oglinum Atlantic thread herring 51-1mm.1.1.7..42 1.88.47 1.7. 2.43 Eucinostomus harengulus Tidewater mojarra 51-1mm.3.9.2.3 1.96.47.65 1.33 1.49. Stephanolepis hispidus Planehead filefish 51-1mm.1..9.1. 1.53. 1.67.45 1.55 Lagodon rhomboides Pinfish 31-5mm..2.4.1.85 1.6.57.85. 1.3 Sciaenops ocellatus 1 Red drum >1mm.1.7.2.8.46.85.52.44.83 1.3 1 Species of direct economic importance (Selected Taxa). 65

Table 11. Similarity percentage (SIMPER) analysis for Sarasota Bay embayment groupings identified in the MDS ordination for 6.1-m trawl collections (Figure 21). Mean abundance (Group Abundance) and percent contribution to dissimilarity between groups (Group Dissimilarity) for the top 25 pseudo-species that distinguished embayment groupings are listed. Group A included Little Sarasota and Roberts bays, while groups B, C and D were each comprised of a single embayment (Palma Sola, Sarasota, and Blackburn, respectively). Taxa are listed in decreasing order of relative contribution to overall differences between groups. Group Abundance (animals/1m 2 ) 1/2 Group Dissimilarity % contribution Scientific name Common name Size Class A B C D A to B A to C A to B A to B A to B A to B Leiostomus xanthurus 1 Spot <31mm 1.61..1.4 18.7 17.11 17.22.43.64.38 Lagodon rhomboides Pinfish <31mm 1.32.22.8.76 8.46 8.29 3.45.98 5.93 6.64 Orthopristis chrysoptera Pigfish <31mm.5...66.64.6 8.5. 11.23 11.42 Lagodon rhomboides Pinfish 31-5mm.47.2.5.82 3.89 2.88 3.88 1.58 9.83 9.2 Leiostomus xanthurus 1 Spot 31-5mm.56... 7.57 7. 7.16... Eucinostomus spp. Eucinostomus mojarra <31mm.4.2.15.54 2.35 1.16 2.3 2.23 5.89 4.6 Anchoa mitchilli Bay anchovy <31mm.34.7.9.3 3.85 3.68 3.65 2.95.64 2.48 Anchoa mitchilli Bay anchovy 31-5mm.32.2.7.2 3.17 3.2 3.3 2.12. 1.39 Archosargus probatocephalus 1 Sheepshead >1mm.11.6..41..8 2.33 1.75 3.2 4.16 Lagodon rhomboides Pinfish 51-1mm.32.6.67.24 1.12 1.46.68.94 2.24 2.86 Gobiosoma robustum Code goby <31mm.12.29.8.2 1.39..61 3.17 2.51.58 Eucinostomus gula Silver jenny 51-1mm.66.21.2.13 2.46 2.7 2.33.46..28 Gobiosoma spp. Gobiosoma gobies <31mm.18.17.8.2.44.83 1.33 2.32 2.4.63 Callinectes sapidus 1 Blue crab 51-1mm.4.17.5.21 1.16 1.56.55 1.4.96 1.62 Eucinostomus spp. Eucinostomus mojarra 31-5mm.18..5.15 1.6.97. 1.12 1.84 1.17 Orthopristis chrysoptera Pigfish >1mm.43.3.21.14.84 1.1 1.53.69.95.53 Callinectes sapidus 1 Blue crab 31-5mm.2.16.3.3 1.11.98 1.1 1.52 1.. Callinectes sapidus 1 Blue crab <31mm.15.13.2.3 1.16 1.5 1.6.95.9.33 Lagodon rhomboides Pinfish >1mm.43.54.43.16.73.41.62.57 1.7 1.37 Menippe spp. 1 Stone crab <31mm.4.25.29.24 1.19 1.47.88.8..83 Orthopristis chrysoptera Pigfish 51-1mm.21.15.18.8 1.23 1.15 1.14..64.83 Leiostomus xanthurus 1 Spot >1mm.11.2.5..84.49 1.8 1.4.38 1.3 Orthopristis chrysoptera Pigfish 31-5mm.4..3.9.49.5.54 1.35 1.25.44 Eucinostomus gula Silver jenny >1mm..2.8.. 1.13. 1.85. 1.52 Lutjanus griseus 1 Gray snapper >1mm.9...8.93.86.34. 1.2 1.4 1 Species of direct economic importance (Selected Taxa). 66

Within each gear type, there was considerable overlap in the taxa and pseudospecies that comprised the nekton community structure in each embayment grouping. Differences in abundance, therefore, defined embayment grouping differences. The two gear types that target smaller-bodied nekton (21.3-m seine and 6.1-m trawl) had a higher percentage of the top 25 pseudo-species with peak abundance in embayment group A (Little Sarasota and Roberts bays), while the 183-m seine had a higher percentage of pseudo-species with peak abundance in Sarasota Bay proper. Little Sarasota and Roberts bays grouped together for each of the gear types. Little Sarasota and Roberts bays are geographically smaller than Palma Sola Bay and Sarasota Bay proper and are not directly linked to the Gulf of Mexico through a pass as are Blackburn Bay and Sarasota Bay proper. Little Sarasota and Roberts bays also receive more freshwater inflow, from Phillippi Creek, than any of the other three embayments and experienced lower average salinity than other embayments during the study period (June 29 to April 211; Figure 4). It is likely that embayment size, freshwater inflow, and connectivity to the Gulf of Mexico are important factors in determining the nekton community structure within Sarasota Bay. 67

Interbay Comparison Analysis of variance (ANOVA, Tukey post hoc test) identified significant difference in abundance between bay segments, but not sampling years, for the nekton community sampled with 21.3-m seines (P<.1, n=1,141, df=27, Model SS=487.59, Error SS=4,299.93), 183-m seines (P<.1, n=516, df=27, Model SS= 91.83, Error SS= 545.37), and 6.1-m trawls (P<.1, n=564, df=27, Model SS= 98.58, Error SS= 7.47). Regardless of gear type, the bay segment with the highest abundance was in Sarasota Bay (Little Sarasota Bay for 21.3-m seines and 6.1-m trawl, and Sarasota Bay proper for 183-m seines; Figure 23). Bay segments for Sarasota Bay (Figure 1), and Tampa Bay and Charlotte Harbor (Figure 2) were included in the nekton community structure analyses of these three estuaries. The non-metric multi-dimensional scaling (MDS) plots produced similar groupings of bay segments regardless of the gear type (Figure 24). Little Sarasota and Roberts bays grouped together (Group C) for all three gear types, with this grouping including Blackburn Bay for 21.3-m seines and 6.1-m trawls. Old Tampa Bay, Hillsborough Bay and Upper Charlotte Harbor grouped together (Group A) for each of the gear types. Regardless of estuary and gear type, the bay segments with passes to the Gulf of Mexico (Gasparilla Sound, Pine Island Sound, Sarasota Bay proper and Lower Tampa Bay North and South; Group B) grouped together with Middle Charlotte Harbor. Palma Sola Bay grouped with the lower estuary bay segments (Group B) for two of the three gear types, but for the 183-m seines, Palma Sola Bay formed its own group at the 6% similarity level. 68

12 1 8 21.3-m seine a b b b a,b b a,b,c c b,c a,b a,b a b,c a 6 4 2 (animals.1 m -2 ± 95% CL) 25 2 15 1 5 183-m seine a c b c b,c c a,b,c a,b,c a,b,c b,c a,b,c b,c b,c b,c 6.1-m trawl 6 a,b b,c a a,b a,b,c a,b b,c c a,b,c a,b,c a,b a,b b a 4 2 Upper CH Middle CH Gasparilla Sound Pine Island Sound Palma Sola Bay Sarasota Bay Roberts Bay Little Sarasota Bay Blackburn Bay Upper TB Middle TB Hillsborough Bay Lower TB North Lower TB South Bay Segment Figure 23., by gear type, for nekton collected from each bay segment in the Charlotte Harbor (magenta), Sarasota Bay (light green) and Tampa Bay (dark green) estuaries during nekton sampling, June 29 April 211. Letters above bars represent significant differences (ANOVA, P<.5, Tukey post hoc test, c>b>a). Embayments, within each estuary, are generally listed from North to South and East to West. 69

Figure 24. Non-metric Multidimensional Scaling (MDS) ordination plot of nekton community structure in bay segments of three eastern Gulf of Mexico estuaries (Tampa Bay, Sarasota Bay and Charlotte Harbor) for each of gear type deployed during nekton sampling, June 29 April 211. Ellipses, labeled with capital letters (A, B, C, or D), group bay segments that had similar nekton communities as determined by Bray-Curtis similarities of 69% (a. 21.3-m seines), 6% (b. 183-m seines) and 45% (6.1-m trawls) from hierarchical agglomerative cluster analysis. 7