A summary report on juvenile salmonid populations of the River Lune catchment, 1981 to 1991

This report summarises the fisheries electrofishing survey work undertaken on the River Lune, England, in the period 1981-85 and 1991. As part of a long term monitoring programme by the National Rivers Authority, juvenile surveys, with the emphasis on salmonids, have been carried out on the River Lune on a number of occasions since 1981. The latest survey in 1991 now gives the opportunity to assess what, if any, changes have occurred in the juvenile populations across the last 11 years and how future fisheries management may impact on the River Lune as a fishery. The areas of trout and salmon, fry and parr production will be considered in detail, as will adult trout populations. Water quality issues will be mentioned briefly as will habitat issues, where they are deemed to be important in affecting fish densities.

Extreme events and ecological forecasting

Almost all extreme events lasting less than several weeks that significantly impact ecosystems are weather related. This review examines the response of estuarine systems to intense short-term perturbations caused by major weather events such as hurricanes. Current knowledge concerning these effects is limited to relatively few studies where hurricanes and storms impacted estuaries with established environmental monitoring programs. Freshwater inputs associated with these storms were found to initially result in increased primary productivity. When hydrographic conditions are favorable, bacterial consumption of organic matter produced by the phytoplankton blooms and deposited during the initial runoff event can contribute to significant oxygen deficits during subsequent warmer periods. Salinity stress and habitat destruction associated with freshwater inputs, as well as anoxia, adversely affect benthic populations and fish. In contrast, mobile invertebrate species such as shrimp, which have a short life cycle and the ability to migrate during the runoff event, initially benefit from the increased primary productivity and decreased abundance of fish predators. Events studied so far indicate that estuaries rebound in one to three years following major short-term perturbations. However, repeated storm events without sufficient recovery time may cause a fundamental shift in ecosystem structure (Scavia et al. 2002). This is a scenario consistent with the predicted increase in hurricanes for the east coast of the United States. More work on the response of individual species to these stresses is needed so management of commercial resources can be adjusted to allow sufficient recovery time for affected populations.

Spatial and temporal variation in otolith chemistry for tautog (Tautoga onitis) in Narragansett Bay and Rhode Island coastal ponds

The elemental composition of otoliths may provide valuable information for establishing connectivity between fish nursery grounds and adult fish populations. Concentrations of Rb, Mg, Ca, Mn, Sr, Na, K, Sr, Pb, and Ba were determined by using solution-based inductively coupled plasma mass spectrometry in otoliths of young-of-the year tautog (Tautoga onitis) captured in nursery areas along the Rhode Island coast during two consecutive years. Stable oxygen (δ18O) and carbon (δ13C) isotopic ratios in young-of-the year otoliths were also analyzed with isotope ratio mass spectrometry. Chemical signatures differed significantly among the distinct nurseries within Narragansett Bay and the coastal ponds across years. Significant differences were also observed within nurseries from year to year. Classification accuracy to each of the five tautog nursery areas ranged from 85% to 92% across years. Because accurate classification of juvenile tautog nursery sites was achieved, otolith chemistry can potentially be used as a natural habitat tag.

Fish Habitat Utilization Patterns and Evaluation of the Efficacy of Marine Protected Areas in Hawaii: Integration of NOAA Digital Benthic Habitat Mapping and Coral Reef Ecological Studies

Over the past four decades, the state of Hawaii has developed a system of eleven Marine Life Conservation Districts (MLCDs) to conserve and replenish marine resources around the state. Initially established to provide opportunities for public interaction with the marine environment, these MLCDs vary in size, habitat quality, and management regimes, providing an excellent opportunity to test hypotheses concerning marine protected area (MPA) design and function using multiple discreet sampling units. NOAA/NOS/NCCOS/Center for Coastal Monitoring and Assessment’s Biogeography Team developed digital benthic habitat maps for all MLCD and adjacent habitats. These maps were used to evaluate the efficacy of existing MLCDs for biodiversity conservation and fisheries replenishment, using a spatially explicit stratified random sampling design. Coupling the distribution of habitats and species habitat affinities using GIS technology elucidates species habitat utilization patterns at scales that are commensurate with ecosystem processes and is useful in defining essential fish habitat and biologically relevant boundaries for MPAs. Analysis of benthic cover validated the a priori classification of habitat types and provided justification for using these habitat strata to conduct stratified random sampling and analyses of fish habitat utilization patterns. Results showed that the abundance and distribution of species and assemblages exhibited strong correlations with habitat types. Fish assemblages in the colonized and uncolonized hardbottom habitats were found to be most similar among all of the habitat types. Much of the macroalgae habitat sampled was macroalgae growing on hard substrate, and as a result showed similarities with the other hardbottom assemblages. The fish assemblages in the sand habitats were highly variable but distinct from the other habitat types. Management regime also played an important role in the abundance and distribution of fish assemblages. MLCDs had higher values for most fish assemblage characteristics (e.g. biomass, size, diversity) compared with adjacent fished areas and Fisheries Management Areas (FMAs) across all habitat types. In addition, apex predators and other targeted resources species were more abundant and larger in the MLCDs, illustrating the effectiveness of these closures in conserving fish populations. Habitat complexity, quality, size and level of protection from fishing were important determinates of MLCD effectiveness with respect to their associated fish assemblages. (PDF contains 217 pages)

The Affects of acid mine drainage on the water quality, and benthic macroinvertebrate and fish population in streams in Maryland

The purpose of this study was to measure and evaluate relationships between populations of benthic macroinvertebrates and fish, as well as variations in water quality in streams affected by acid Mine drainage. (PDF contains 21 pages)

Population connectivity among Dry Tortugas, Florida, and Caribbean populations of mutton snapper (Lutjanus analis), inferred from multiple microsatellite loci

Determining patterns of population connectivity is critical to the evaluation of marine reserves as recruitment sources for harvested populations. Mutton snapper (Lutjanus analis) is a good test case because the last known major spawning aggregation in U.S. waters was granted no-take status in the Tortugas South Ecological Reserve (TSER) in 2001. To evaluate the TSER population as a recruitment source, we genotyped mutton snapper from the Dry Tortugas, southeast Florida, and from three locations across the Caribbean at eight microsatellite loci. Both Fstatistics and individual-based Bayesian analyses indicated that genetic substructure was absent across the five populations. Genetic homogeneity of mutton snapper populations is consistent with its pelagic larval duration of 27 to 37 days and adult behavior of annual migrations to large spawning aggregations. Statistical power of future genetic assessments of mutton snapper population connectivity may benefit from more comprehensive geographic sampling, and perhaps from the development of less polymorphic DNA microsatellite loci. Research where alternative methods are used, such as the transgenerational marking of embryonic otoliths with barium stable isotopes, is also needed on this and other species with diverse life history characteristics to further evaluate the TSER as a recruitment source and to define corridors of population connectivity across the Caribbean and Florida.

Assessment of fish populations and habitat on Oculina Bank, a deep-sea coral marine protected area off eastern Florida

A portion of the Oculina Bank located off eastern Florida is a marine protected area (MPA) preserved for its dense populations of the ivory tree coral (Oculina varicosa), which provides important habitat for fish. Surveys of fish assemblages and benthic habitat were conducted inside and outside the MPA in 2003 and 2005 by using remotely operated vehicle video transects and digital still imagery. Fish species composition, biodiversity, and grouper densities were used to determine whether O. varicosa forms an essential habitat compared to other structure-forming habitats and to examine the effectiveness of the MPA. Multivariate analyses indicated no differences in fish assemblages or biodiversity among hardbottom habitat types and grouper densities were highest among the most complex habitats; however the higher densities were not exclusive to coral habitat. Therefore, we conclude that O. varicosa was functionally equivalent to other hardbottom habitats. Even though fish assemblages were not different among management areas, biodiversity and grouper densities were higher inside the MPA compared to outside. The percentage of intact coral was also higher inside the MPA. These results provide initial evidence demonstrating effectiveness of the MPA for restoring reef fish and their habitat. This is the first study to compare reef fish populations on O. varicosa with other structure-forming reef habitats and also the first to examine the effectiveness of the MPA for restoring fish populations and live reef cover.

Changes in a benthic megafaunal community due to disturbance from bottom fishing and the establishment of a fishery closure

Trawling and dredging on Georges Bank (northwest Atlantic Ocean) have altered the cover of colonial epifauna, as surveyed through in situ photography. A total of 454 photographs were analyzed from areas with gravel substrate between 1994 and 2000 at depths of 40–50 m and 80–90 m. The cover of hydroids, bushy bryozoans, sponges, and tubeworms was generally higher at sites undisturbed by fishing than at sites classified as disturbed. The magnitude and significance of this effect depended on depth and year. Encrusting bryozoans were the only type of colonial epifauna positively affected by bottom fishing. Species richness of noncolonial epifauna declined with increased bottom fishing, but Simpson’s index of diversity typically peaked at intermediate levels of habitat disturbance. Species that were more abundant at undisturbed sites possessed characteristics that made them vulnerable to bottom fishing. These characteristics include emergent growth forms, soft body parts, low motility, use of complex microhabitats, long life spans, slow growth, and larval dispersal over short distances. After the prohibition of bottom fishing at one site, both colonial and noncolonial species increased in abundance. Populations of most taxa took two years or more to increase after the fishing closure. This finding indicates that bottom fishing needs to be reduced to infrequent intervals to sustain the benthic species composition of Georges Bank at a high level of biodiversity and abundance.

Abundance of adult horseshoe crabs (Limulus polylphemus) in Delaware Bay estimated from a bay-wide mark-recapture study

Estimates of the abundance of American horseshoe crabs (Limulus polyphemus) are important to determine egg production and to manage populations for the energetic needs of shorebirds that feed on horseshoe crab eggs. In 2003, over 17,500 horseshoe crabs were tagged and released throughout Delaware Bay, and recaptured crabs came from spawning surveys that were conducted during peak spawning. We used two release cohorts to test for a temporary effect of tagging on spawning behavior and we adjusted the number of releases according to relocation rates from a telemetry study. The abundance estimate was 20 million horseshoe crabs (90 % confidence interval: 13−28 million), of which 6.25 million (90% CI: 4.0−8.8 million) were females. The combined harvest rate for Delaware, New Jersey, Virginia, and Maryland in 2003 was 4% (90% CI: 3−6%) of the abundance estimate. Over-wintering of adults in Delaware Bay could explain, in part, differences in estimates from ocean-trawl surveys. Based on fecundity of 88,000 eggs per female, egg production was 5.5×1011 (90% CI: 3.5×1011, 7.7×1011), but egg availability for shorebirds also depended on overlap between horseshoe crab and shorebird migrations, density-dependent bioturbation, and wave-mediated vertical transport.

A History of Benthic Research in the NMFS Northeast Fisheries Science Center

The Northeast Fisheries Science Center of NOAA's National Marine Fisheries Service has a long history of research on benthic invertebrates and habitats in support of the management of living marine resources. These studies began in the 1870's under Spencer F. Baird's guidance as part of an effort to characterize the Nation's fisheries and living marine resources and their ecological interactions. This century and a quarter of research has included many benthic invertebrate studies, including community characterizations, shellfish biology and culture, pathology, ecosystem energy budget modeling, habitat evaluations, assessments of human impacts, toxic chemical bioaccumulation in demersal food webs, habitat or endangered species management, benthic autecology, systematics (to define new species and species population boundaries), and other benthic studies. Here we review the scope of past and current studies as a background for strategic research planning and suggest areas for further research to support NOAA's goals of sustainable fisheries management, healthy coastal ecosystems, and protected species populations.

A geo-referenced benthic habitat survey in support of natural resource management: Port Graham Bay, Alaska

The impact of recent changes in climate on the arctic environment and its ecosystems appear to have a dramatic affect on natural populations (National Research Council Committee on the Bering Sea Ecosystem 1996) and pose a serious threat to the continuity of indigenous arctic cultures that are dependent on natural resources for subsistence (Peterson D. L., Johnson 1995). In the northeast Pacific, winter storms have intensified and shifted southward causing fundamental changes in sea surface temperature patterns (Beamish 1993, Francis et al. 1998). Since the mid 1970’s surface waters of the central basin of the Gulf of Alaska (GOA) have warmed and freshened with a consequent increase in stratification and reduced winter entrainment of nutrients (Stabeno et al. 2004). Such physical changes in the structure of the ocean can rapidly affect lower trophic levels and indirectly affect fish and marine mammal populations through impacts on their prey (Benson and Trites 2002). Alaskan natives expect continued and perhaps accelerating changes in resources due to global warming (DFO 2006).and want to develop strategies to cope with their changing environment.

Ontogenetic shifts in natural diet during benthic stages of American lobster (Homarus americanus), off the Magdalen Islands

The natural diet of 506 American lobsters (Homarus americanus) ranging from instar V (4 mm cephalothorax length, CL) to the adult stage (112 mm CL) was determined by stomach content analysis for a site in the Magdalen Islands, Gulf of St. Lawrence, eastern Canada. Cluster and factor analyses determined four size groupings of lobsters based on their diet: <7.5 mm, 7.5 to <22.5 mm, 22.5 to <62.5 mm, and ≥62.5 mm CL. The ontogenetic shift in diet with increasing size of lobsters was especially apparent for the three dominant food items: the contribution of bivalves and animal tissue (flesh) to volume of stomach contents decreased from the smallest lobsters (28% and 39%, respectively) to the largest lobsters (2% and 11%, respectively), whereas the reverse trend was seen for rock crab Cancer irroratus (7% in smallest lobsters to 53% in largest lobsters). Large lobsters also ate larger rock crabs than did small lobsters.

The genetic diversity of Acipenser stellatus populations in the Caspian Sea was studied using microsatellite technique

A total of 361 caudal fin samples were collected from adult A. stellatus specimens caught in the north Caspian Sea, including specimens from Kazakhstan (Ural River), Russia (Volga River), Azerbaijan (Kura River), specimens caught in the south Caspian Sea including specimens from Fishery Zone 1 (from Astara to Anzali), Fishery Zone 2 (from Anzali to Ramsar), Fishery Zone 3 (from Nowshahr to Babolsar), Fishery Zone 4 (from Miyankaleh to Gomishan) as well as from specimens caught in Turkmenistan (all specimens were collected during the sturgeon stock assessment survey). About 2 g of fin tissue was removed from each caudal fin sample, stored in 96% ethyl alcohol and transferred to the genetic laboratory of the International Sturgeon Research Institute. Genomic DNA was extracted using phenol-chloroform method. The quality and quantity of DNA was assessed using 1% Agarose gel electrophoresis and Polymerase Chain Reaction (PCR) was conducted on the target DNA using 15 paired microsatellite primer. PCR products were electrophoresed on polyacrylamide gels (6%) that were stained using silver nitrate. Electrophoretic patterns and DNA bands were analyzed with BioCapt software. Allele count and frequency, genetic diversity, expected heterozygosity and observed heterozygosity allele number, and the effective allele number, genetic similarity and genetic distance, FST and RST were calculated. The Hardy Wienberg Equilibrium based on X2 and Analysis of Molecular Variance (AMOVA) at 10% confidence level was calculated using the Gene Alex software. Dendrogram for genetic distances and identities were calculated using TFPGA program for any level of the hierarchy. It is evident from the results obtained that the 15 paired primers studied, polymorphism was observed in 10 pairs in 12 loci, while one locus did not produce DNA bands. Mean allele number was 13.6. Mean observed and expected heterozygosity was 0.86 and 0.642, respectively. It was also seen that specimens from all regions were not in Hardy Wienberg Equilibrium in most of the loci (P≤0.001). Highest Fst (0.063) was observed when comparing specimens from Fishery Zone 2 and Fishery Zone 4 (Nm=3.7) and lowest FST (0.028) was observed when comparing specimens from the Volga River and those from the Ural River (8.7). Significant differences (P<0.01) were observed between RST recorded in the specimens studied. Highest genetic distance (0.604) and lowest genetic resemblance (0.547) were observed between specimens from Fishery zones 2 and 4. Lowest genetic distance (0.311) and highest genetic resemblance (0.733) was observed between specimens from Turkmenistan and specimens from Fishery zone 1. Based on the genetic dendrogeram tree derived by applying UPGMA algorithm, A. stellatus specimens from Fishery zone 2 or in other words specimens from the Sepidrud River belong to one cluster which divides into two clusters, one of which includes specimens from Fishery zones 1, 3 and 4 and specimens from Turkmenistan while the other cluster includes specimens from Ural, Volga and Kura Rivers. It is thus evident that the main population of this species belongs to the Sepidrud River. Results obtained from the present study show that at least eight different populations of A. stellatus are found in the north and south Caspian Sea, four of which are known populations including the Ural River population, the Volga River population, the Kura River population and the Sepidrud River populations. The four other populations identified belonging to Fishery zones 1, 3, and 4 and to Turkmenistan are most probably late or early spawners of the spring run and autumn run of each of the major rivers mentioned. Specific markers were also identified for each of the populations identified. The Ural River population can be identified using primers Spl-68, 54b and Spl-104, 163 170, 173, the Volga River population can be identified using primers LS-54b and Spl-104, 170, 173 113a and similarly the population from the Kura River can be identified using primers LS-34, 54b and Spl-163, 173 and that from the Sepidrud River can be identified using primers LS-19, 34, 54b and Spl-105, 113b. This study gives evidence of the presence of different populations of this species and calls for serious measures to be taken to protect the genetic stocks of these populations. Considering that the population of A. stellatus in Fishery zone 2 is an independent population of the Sepidrud River in the Gilan Province, the catch of these fishes in the region needs to be controlled and regulated in order to restore the declining stocks of this species.

The genetic structure and phylogenetics of pikeperch (Sander lucioperca) Anzali and Amirkolaye wetlands and perch (Perca fluviatilis) populations in Aras Dam and south-west of the Caspian Sea

The genetic structure of pikeperch (Sander lucioperca) and perch (Perca fluviatilis) populations was studied using microsatellite technique. A total of 207 specimens of adult pikeperch were collected from Aras dam (57 specimens), Anzali wetland (50 specimens), Talesh (50 specimens) and Chaboksar (50 specimens) coasts. Also a total of 158 specimens of adult perch were collected from Anzali (Abkenar (50 specimens)and Hendekhale(48 specimens)) and Amirkolaye(60 specimens) wetlands. About 2 g of each specimen's dorsal fin was removed, stored in 96% ethyl alcohol and transferred to the genetic laboratory of the International Sturgeon Research Institute. Genomic DNA was extracted using ammonium-acetate method. The quality and quantity of DNA was assessed using 1% agarose gel electrophoresis. Polymerase Chain Reaction (PCR) was conducted on the target DNA using 15 pairs of microsatellite primers. PCR products were electrophoresed on poly acryl amide gels (6%) that were stained that were stained using silver nitrate. DNA bands were analyzed with BioCapt software. Allele count and frequency, genetic diversity, expected and observed heterozygosity , allele number and the effective allele number, genetic similarity and genetic distance, Fst, Rst, Hardy Weinberg Equilibrium based on X2 and Analysis of Molecular Variance (AMOVA) at 10% confidence level was calculated using the Gene Alex software. Dendogram for genetic distances and identities were calculated using TFPGA program for any level of hierarchy. The results for P. fluviatilis showed that from 15 pair of primers that were examined 6 polymorphic and 7 monomorphic loci were produced, while 2 loci didn't produce any DNA bands. Mean allele number was 4.1±1.1 and mean observed and expected heterozygosity was 0.56±0.12 and 0.58±0.14 respectively. It was also seen that specimens from all regions were not in Hardy Weinberg Equilibrium in some of loci (P<0.001). Highest Fst (0.095) with Nm=2.37 was observed between Hendekhale and Amirkolaye and the lowest Fst (0.004) with Nm=59.31 was observed between Abkenar and Hendekhale. According to AMOVA Significant difference (P<0.05) was observed between recorded Rst in the studied regions in Anzali and Amirkolaye lagoons. In another words there are two distinct populations of this species in Anzali and Amirkolaye lagoons. The highest genetic distance (0.181) and lowest genetic resemblance (0.834) were observed between specimens from Hendekhale and Amirkolaye and the lowest genetic distance (0.099) and highest genetic 176 resemblance (0.981) were observed between specimens from Abkenar and Hendekhale. Based on the genetic dendogram tree derived by applying UPGMA algorithm, specimens from Anzali and Amirkolaye wetlands have the same ancestor. On the other hand there is no noticeable genetic distance between the specimens of these two regions. Also the results for S. lucioperca showed that from 15 pair of primers that were examined 6 polymorphic and 7 monomorphic loci were produced, while 2 loci didn't produce any DNA bands. Mean allele number was 3.0±0.6 and mean observed and expected heterozygosity was 0.52±0.21 and 0.50±0.14 respectively. It was also seen that specimens from all regions were not in Hardy Weinberg Equilibrium in some of loci (P<0.001). Highest Fst (0.093) with Nm=2.43 was observed between Aras dam and Anzali wetland and the lowest Fst (0.022) with Nm=11.27 was observed between Talesh and Chaboksar coasts. Significant differences (P<0.05) were observed between recorded Rst in the studied regions exept for Talesh and Chaboksar Coasts. In another words there are three distinct populations of this species in Caspian sea, Anzali wetland and Aras dam. Highest genetic distance (0.110) and lowest genetic resemblance (0.896) were observed between specimens from Aras dam and Anzali wetland and the lowest genetic distance (0.034) and highest genetic resemblance (0.966) were observed between specimens from Talesh and Chaboksar coasts. Based on the genetic dendogram tree derived by applying UPGMA algorithm, specimens from Talesh and Chaboksar coasts have the lowest genetic distance. On the other hand the main population of this species belongs to Anzali wetland. Phylogenetic relationship of these two species was inferred using mitochondrial cytochrome b gene sequencing. For this purpose 2 specimens of P. fluviatilis from Anzali wetland, 2 specimens of S. lucioperca from Aras dam and 2 specimens of S. lucioperca from Anzali wetland were sequenced and submitted in Gene Bank. These sequences were aligned with Clustal W. The phylogenic relationships were assessed with Mega 4. The results of evolutionary history studies of these species using Neighbor-Joining and Maximum Parsimony methods showed that the evolutionary origin of pikeperch in Aras Dam and Anzali wetland is common. On the other hand these two species had common ancestor in about 4 million years ago. Also different sequences of any region specimens are supposed as different haplotypes. 177 As a conclusion the results of this study showed that microsatellite and mtDNA sequencing methods respectively are effective in genetic structure and phylogenic studies of P. fluviatilis and S. lucioperca.

Variation in composition of macro-benthic invertebrates as an indication of water quality status in three bays in Lake Victoria

Knowledge of how biota can be used to monitor ecosystem health and assess impacts by human alterations such as land use and management measures taken at different spatial scales is critical for improving the ecological quality of aquatic ecosystems. This knowledge in Uganda is very limited or unavailable yet it is needed to better understand the relationship between environmental factors at different spatial scales, assemblage structure and taxon richness of aquatic ecosystems. In this study, benthic invertebrate community patterns were sampled between June 2001 and April 2002 and analysed in relation to water quality and catchment land use patterns from three shallow near-shore bays characterized by three major land uses patterns: urban (Murchison Bay); semi-urban (Fielding Bay); rural (Hannington Bay). Variations in density and guild composition of benthic macro-invertebrates communities were evaluated using GIS techniques along an urban-rural gradient of land use and differences in community composition were related to dissolved oxygen and conductivity variation. Based on numerical abundance and tolerance values, Hilsenhoff's Biotic Index ofthe invertebrates was determined in order to evaluate the relative importance of water quality in the three bays. Murchison Bay supported a relatively taxa-poor invertebrate assemblage mainly comprising stenotopic and eurytopic populations of pollution-tolerant groups such as worms and Chironomus sp. with an overall depression in species diversity. On the contrary, the communities in Fielding and Hannington bays were quite similar and supported distinct and diverse assemblages including pollution-intolerant forms such as Ephemeroptera (mayflies), Odonata (dragonflies). The Hilsenhoff Biotic Index in Murchison Bay was 6.53. (indicating poor water quality) compared to 6.34 for Fielding Bay and 5.78 for Hannington Bay (both indicating fair water quality). The characterization of maximum taxa richness balanced among taxa groups with good representation of intolerant individuals in Hannington Bay relative to Fielding and Murchison bays concludes that the bay is the cleanest in terms of water quality. Contrary, the dominance of few taxa with many tolerant iqdividuals present in Murchison Bay indicates that the bay is degraded in terms of water quality. These result are ofimportance when planning conservation and management measures, implementing large-scale biomonitoring programs, and predicting how human alterations (e.g nutrient loading) affect water ecosystems. Therefore, analysis of water quality in relation to macro-invertebrate community composition patterns as bio-indicators can lead to further understanding of their responses to environmental manipulations and perturbations.