Panama City Fisheries Resources Office: FY 2003 Annual Report

HIGHLIGHTS FOR FY 2003 1. Continued a 3-year threatened Gulf sturgeon population estimate in the Escambia River, Florida and conducted presence-absence surveys in 4 other Florida river systems and 1 bay. 2. Five juvenile Gulf sturgeon collected, near the mouth of the Choctawhatchee River, Florida, were equipped with sonic tags and monitored while over-wintering in Choctawhatchee Bay. 3. Continued to examine Gulf sturgeon marine habitat use. 4. Implemented Gulf Striped Bass Restoration Plan by coordinating the 20th Annual Morone Workshop, leading the technical committee, transporting broodfish, and coordinating the stocking on the Apalachicola-Chattahoochee-Flint (ACF) river system. 5. Over 73,000 Phase II Gulf striped bass were marked with sequential coded wire tags and stocked in the Apalachicola River. Post-stocking evaluations were conducted at 31 sites. 6. Three stream fisheries assessment s were completed to evaluate the fish community at sites slated for habitat restoration by the Partners for Fish and Wildlife Program (PFW). 7. PFW program identified restoration needs and opportunities for 10 areas. 8. Developed an Unpaved Road Evaluation Handbook. 9. Completed restoration of Chipola River Greenway, Seibenhener Streambank Restoration, Blackwater River State Forest, and Anderson Property. 10. Assessments for fluvial geomorphic conditions for design criteria were completed for 3 projects. 11. Geomorphology in Florida streams initiated development of Rosgen regional curves for Northwest Florida for use by the Florida Department of Transportation. 12. Developed a Memorandum of Understanding between partners for enhancing, protecting, and restoring stream, wetland, and upland habitat in northwest Florida 13. Completed aquatic fauna and fish surveys with new emphasis on integration of data from reach level into watershed and landscape scale and keeping database current. 14. Compliance based sampling of impaired waterbodies on Eglin Air Force Base in conjunction with Florida Department of Environmental Protection for Total Maximum Daily Load development support. 15. Surveyed 20 sites for the federally endangered Okaloosa darter, provided habitat descriptions, worked with partners to implement key recovery tasks and set priorities for restoration. 16. Worked with partners to develop a freshwater mussel survey protocol to provide standard operating procedures for establishing the presence/absence of federally listed mussel species within a Federal project area. 17. GIS database was created to identify all known freshwater mussel records from the northeast Gulf ecosystem. 18. Completed recovery plan for seven freshwater mussels and drafted candidate elevation package for seven additional mussels. Developed proposals to implement recovery plan. 19. Worked with Corps of Engineers and State partners to develop improved reservoir operating policies to benefit both riverine and reservoir fisheries for the ACF river system. 20. Multiple outreach projects were completed to detail aquatic resources conservation opportunities. 21. Multiple stream restoration and watershed management projects initiated or completed (see Appendix A).

Trapping success and population analysis of Siren lacertina and Amphiuma means

Siren and Amphiuma are two poorly known genera of aquatic salamanders that occur in the Southeastern United States. A primarily bottom-dwelling existence makes these salamanders difficult to detect with conventional sampling methodologies. Therefore, the current status of their populations is unknown. I compared the capture success of modified crayfish traps and plastic minnow traps in capturing these salamanders. In addition, a mark-recapture study of S. lacertina (Greater siren) and A. means (Two-toed amphiuma) was conducted at Okefenokee National Wildlife Refuge (southern Georgia) and at Katharine Ordway Preserve (north-central Florida) from August 2001 until September 2002. Crayfish traps were much more successful than minnow traps in catching siren and amphiuma. Crayfish traps yielded 270 captures for an overall capture success of 16%, whereas minnow traps yielded only 13 captures for an overall success rate of 0.05%. In addition, several marking techniques were evaluated, and of these, only passive integrated transponder (PIT) tags were retained for the duration of the study. Therefore, I recommend this marking technique for long-term monitoring of S. lacertina and A. means. Several variables were found to have significant effects on capture rates of salamanders. A. means were most often captured in summer and the number of captures was positively correlated with water temperature, water level, and rainfall. S. lacertina were most often captured during winter and spring. Number of captures was negatively correlated with water temperature, while no relationship was found with water level or rainfall. Trap day and baiting had no significant effect on number of A. means or S. lacertina captured. Recapture probabilities of both species were low, 0.025-0.03 for S. lacertina and 0.08-0.11 for A. means. Monthly survival rates were high, 0.77-0.97 for A. means and 0.88-1.00 for S. lacertina. Density estimates of 1.3 salamanders/m2 (S. lacertina) and 0.28 salamanders/m2 (A. means) were obtained for Lake Suggs using Jolly-Seber models. Siren and amphiuma make up a substantial part of wetland biomass and can impact many other wetland species. Thus, more attention must be focused on evaluating and monitoring their populations.

The Lune catchment abstraction management strategy. Consultation document September 2003

This consultation document sets out the proposed future licensing strategy for the Lune Catchment Abstraction Management Strategy (CAMS) area. Following the three month consultation period, the Environment Agency will determine the final licensing strategy and publish it in the CAMS document. The strategy will provide an indication of whether new abstraction licences are likely to be available and the conditions that should be expected on licences. Water plays a vital role in the Lune catchment, providing water for public supply, supporting recreation, such as angling and canoeing, and providing sustainable flows to preserve numerous designated sites. There is minimal abstraction throughout much of the catchment, apart from the lower reaches of the River Lune. The document is split into five sections relating to the CAMS process. Sections 1 to 4 outline the CAMS process, and Section 5 outlines the proposed licensing strategy for the Lune CAMS areas. It is important to note that this strategy deals with groundwater and surface water abstractions separately; Sections 4 and 5 are split to differentiate between the surface water and groundwater results and strategy.

River Wyre salmon action plan December 2003

In 1996 a Strategy for the Management of Salmon in England and Wales was launched by the National Rivers Authority setting out objectives for the management of Salmon fisheries. These objectives are to be met through local Salmon Action Plans which are to be produced for each of the 68 principal salmon rivers in England and Wales by December 2003. A consultation document was produced for the river Wyre and released publicly during October 2003. This document: • Determined an egg deposition figure of 1.27 million eggs which would allow maximum gain from the fisheries • Raised a number of issues which are though to limit existing salmon production. • Identified actions which may be undertaken by the Environment Agency and other bodies to improved stocks. The document looks at the issues in the consultation document and also highlights some important changes to historic egg deposition rates following further analysis of the data. Some of the major issues addressed in the plan are: • Severe low flows on specific tributaries • Reduced juvenile production caused by insufficient habitat. • Changes in flow regime resulting in the wash out of gravels and redds. • The impact of man made structures preventing access to suitable spawning areas, and preventing the downstream distribution of spawning gravels.

Front pages with contents of No. 62, 2003

Front cover. Information for supporters of the Charles Darwin Foundation. Table of Contents.

Back pages of No. 62, 2003

Charles Darwin Foundation for the Galapagos Islands. Map.

Spatial and temporal distribution of grouper larvae (Serranidae: Epinephelinae: Epinephelini) in the Gulf of Mexico and Straits of Florida

Little is known about the seasonality and distribution of grouper larvae (Serranidae: Epinephelini) in the Gulf of Mexico and Atlantic Ocean off the coast of the southeast United States. Grouper larvae were collected from a transect across the Straits of Florida in 2003 and 2004 and during the Southeast Area Monitoring and Assessment Program spring and fall surveys from 1982 through 2005. Analysis of these larval data provided information on location and timing of spawning, larval distribution patterns, and interannual occurrence for a group of species not easily studied as adults. Our analyses indicated that shelf-edge habitat is important for spawning of many species of grouper—some species for which data were not previously available. Spawning for some species may occur year-round, but two peak seasons are evident: late winter and late summer through early fall. Interannual variability in the use of three important subregions by species or groups of species was partially explained by environmental factors (surface temperature, surface salinity, and water depth). A shift in species dominance over the last three decades from spring-spawned species (most of the commercial species) to fall-spawned species also was documented. The results of these analyses expand our understanding of the basic distribution and spawning patterns of northwest Atlantic grouper species and indicate a need for further examination of the changing population structure of individual species and species dominance in the region.

Distributions and abundances of Pacific sardine (Sardinops sagax) and other pelagic fishes in the California Current Ecosystem during spring 2006, 2008, and 2010, estimated from acoustic–trawl surveys

The abundances and distributions of coastal pelagic fish species in the California Current Ecosystem from San Diego to southern Vancouver Island, were estimated from combined acoustic and trawl surveys conducted in the spring of 2006, 2008, and 2010. Pacific sardine (Sardinops sagax), jack mackerel (Trachurus symmetricus), and Pacific mackerel (Scomber japonicus) were the dominant coastal pelagic fish species, in that order. Northern anchovy (Engraulis mordax) and Pacific herring (Clupea pallasii) were sampled only sporadically and therefore estimates for these species were unreliable. The estimates of sardine biomass compared well with those of the annual assessments and confirmed a declining trajectory of the “northern stock” since 2006. During the sampling period, the biomass of jack mackerel was stable or increasing, and that of Pacific mackerel was low and variable. The uncertainties in these estimates are mostly the result of spatial patchiness which increased from sardine to mackerels to anchovy and herring. Future surveys of coastal pelagic fish species in the California Current Ecosystem should benefit from adaptive sampling based on modeled habitat; increased echosounder and trawl sampling, particularly for the most patchy and nearshore species; and directed-trawl sampling for improved species identification and estimations of their acoustic target stren

Abundance, distribution, and habitat of leatherback turtles (Dermochelys coriacea) off California, 1990−2003

Leatherback turtles (Dermochelys coriacea) are regularly seen off the U.S. West Coast, where they forage on jellyfish (Scyphomedusae) during summer and fall. Aerial line-transect surveys were conducted in neritic waters (<92 m depth) off central and northern California during 1990−2003, providing the first foraging population estimates for Pacific leatherback turtles. Males and females of about 1.1 to 2.1 m length were observed. Estimated abundance was linked to the Northern Oscillation Index and ranged from 12 (coefficient of variation [CV] =0.75) in 1995 to 379 (CV= 0.23) in 1990, averaging 178 (CV= 0.15). Greatest densities were found off central California, where oceanographic retention areas or upwelling shadows created favorable habitat for leatherback turtle prey. Results from independent telemetry studies have linked leatherback turtles off the U.S. West Coast to one of the two largest remaining Pacific breeding populations, at Jamursba Medi, Indonesia. Nearshore waters off California thus represent an important foraging region for the critically endangered Pacific leatherback turtle.

Geographic and seasonal variations in maturation and growth of female Pacific cod (Gadus macrocephalus) in the Gulf of Alaska and Bering Sea

This study investigates the temporal stability of length- and age-at-maturity estimates for female Pacific cod (Gadus macrocephalus) in the Gulf of Alaska and eastern Bering Sea. Females reached 50% maturity (A50) at 4.4 years in the Gulf of Alaska and at 4.9 years in the eastern Bering Sea. Total body length at 50% maturity (LT50) was significantly smaller (503 mm) in the Gulf of Alaska than in the eastern Bering Sea (580 mm). The estimated length- and age-at-maturity did not differ significantly between winter and spring in either the Gulf of Alaska (1999) or Bering Sea (2003) areas. The results of this study raised the spawning biomass estimate of female Alaskan Pacific cod from 298×103 t for 2005 to 499×103 t for 2006. The increased spawning biomass estimate resulted in an increased over-fishing limit for Pacific cod.

The fishery for California market squid (Loligo opalescens) (Cephalopoda: Myopsida), from 1981 through 2003

The California market squid (Loligo opalescens) has been harvested since the 1860s and it has become the largest fishery in California in terms of tonnage and dollars since 1993. The fishery began in Monterey Bay and then shifted to southern California, where effort has increased steadily since 1983. The California Department of Fish and Game (CDFG) collects information on landings of squid, including tonnage, location, and date of capture. We compared landings data gathered by CDFG with sea surface temperature (SST), upwelling index (UI), the southern oscillation index (SOI), and their respective anomalies. We found that the squid fishery in Monterey Bay expends twice the effort of that in southern California. Squid landings decreased substantially following large El Niño events in 1982−83 and 1997−98, but not following the smaller El Niño events of 1987 and 1992. Spectral analysis revealed autocorrelation at annual and 4.5-year intervals (similar to the time period between El Niño cycles). But this analysis did not reveal any fortnightly or monthly spawning peaks, thus squid spawning did not correlate with tides. A paralarvae density index (PDI) for February correlated well with catch per unit of effort (CPUE) for the following November recruitment of adults to the spawning grounds. This stock– recruitment analysis was significant for 2000−03 (CPUE=8.42+0.41PDI, adjusted coefficient of determination, r2=0.978, P=0.0074). Surveys of squid paralarvae explained 97.8% of the variance for catches of adult squid nine months later. The regression of CPUE on PDI could be used to manage the fishery. Catch limits for the fishery could be set on the basis of paralarvae abundance surveyed nine months earlier.

Stillwaters monitoring programme. Summary results 2001 and 2002

This is the Stillwaters monitoring programme. Summary results 2001 and 2002 from the Environment Agency North West. Until January 2001 the South Area Stillwaters Sampling Programme consisted of a rolling programme where five to six stillwaters were sampled three times a year (spring, summer and autumn). However, this method was not yielding the water quality information required for long term monitoring. Local weather conditions influence short-term water quality events, e.g. algal blooms, nutrient consumption, stratification, super-saturation etc, so results from one day sampling could only be regarded as individual ‘spot’ samples. Therefore year-on-year comparisons could not be made. It was decided that long-term water quality monitoring of the stillwaters would benefit more from sampling nutrient abundance over winter months. This would give an insight into the carry-over of nutrients available for algal growth the following year and so year-on-year productivity could be assessed. Survey results shown in this report were from: The Mere, Rostherne Mere, Melchett Mere, Tabley Mere, Tatton Mere, Hatchmere, Oak Mere, Black Lake, Chapel Mere, Bar Mere, Oss Mere, Marbury Big Mere, Comber Mere and Betley Mere.

Stillwaters monitoring programme.Summary results 2003 and 2004

This is the Stillwaters monitoring programme. Summary results 2003 and 2004 from the Environment Agency North West. This report is focuses in The Winter Monitoring of Stillwaters Programme, which began in January 2001 with the aim of gathering long term data on nutrient abundance over winter months. This allows assessment of nutrient ‘carry-over’ available for algal growth in the following year, plus year-on-year productivity. 14 stillwaters are monitored each year. The environmental issues associated with each Stillwater are summarised in the table below. Bank-side water samples are taken for nutrients (N, P and S) and chlorophyll. A YSI multi-parameter sonde measures temperature, pH, specific conductivity and dissolved oxygen (% saturation). Survey results shown in this report came from: Oak Mere and Bar mere.

Gunnislake Fish Counter Annual Report 2002

This is the Gunnislake Fish Counter Annual Report 2002 from the Environment Agency South West Region, which was held on March 2002. It presents the daily upstream counts of migratory salmonids recorded on the River Tamar at Gunnislake Weir fish counting station in 2002. The data within this report covers the period of the commercial migratory salmonid net buy-back scheme and the National Spring Salmon Bylaws. The report contains section on Net Buy-Back; Species Apportionment; Validation of counter efficiency; results as total number of migratory salmonid (salmon and Sea Trout) counted moving upstream in 2002 at Gunnislake; video validation and Counter Efficiency; and Discussion. The section Discussion includes Salmon and Sea Trout counts recorded on the River Tamar 1995-2002, other fish species observed as sea lamprey and Environmental Factors (river flows, water temperature, and barometric pressure).