An ecological characterization of Salt River Bay National Historical Park and Ecological Preserve, U.S. Virgin Islands

Salt River Bay National Historical Park and Ecological Preserve (hereafter, SARI or the park) was created in 1992 to preserve, protect, and interpret nationally significant natural, historical, and cultural resources (United States Congress 1992). The diverse ecosystem within it includes a large mangrove forest, a submarine canyon, coral reefs, seagrass beds, coastal forests, and many other natural and developed landscape elements. These ecosystem components are, in turn, utilized by a great diversity of flora and fauna. A comprehensive spatial inventory of these ecosystems is required for successful management. To meet this need, the National Oceanic and Atmospheric Administration (NOAA) Biogeography Program, in consultation with the National Park Service (NPS) and the Government of the Virgin Islands Department of Planning and Natural Resources (VIDPNR), conducted an ecological characterization. The characterization consists of three complementary components: a text report, digital habitat maps, and a collection of historical aerial photographs. This ecological characterization provides managers with a suite of tools that, when coupled with the excellent pre-existing body of work on SARI resources, enables improved research and monitoring activities within the park (see Appendix F for a list of data products).

Effects of reducing nutrient loads to surface waters within the Mississippi River Basin and the Gulf of Mexico: Topic 4 Report for the Integrated Assessment on Hypoxia in the Gulf of Mexico

The overall goal of this assessment was to evaluate the effects of nutrient-source reductions that may be implemented in the Mississippi River Basin (MRB) to reduce the problem of low oxygen conditions (hypoxia) in the nearshore Gulf of Mexico. Such source reductions would affect the quality of surface waters—streams, rivers, and reservoirs—in the drainage basin itself, as well as nearshore Gulf waters. The task group’s work was divided into addressing the effects of nutrient-source reductions on: (1) surface waters in the MRB and (2) hypoxia in the Gulf of Mexico.

Flux and sources of nutrients in the Mississippi-Atchafalaya River Basin: Topic 3 Report for the Integrated Assessment on Hypoxia in the Gulf of Mexico.

Ths report addresses the following two questions: 1) What are the loads (flux) of nutrients transported from the Mississippi-Atchafalaya River Basin to the Gulf of Mexico, and where do they come from within the basin? 2) What is the relative importance of specific human activities, such as agriculture, point-source discharges, and atmospheric deposition in contributing to these loads? These questions were addressed by first estimating the flux of nutrients from the Mississippi-Atchafalaya River Basin and about 50 interior basins in the Mississippi River system using measured historical streamflow and water quality data. Annual nutrient inputs and outputs to each basin were estimated using data from the National Agricultural Statistics Service, National Atmospheric Deposition Program, and point-source data provided by the USEPA. Next, a nitrogen mass balance was developed using agricultural statistics, estimates of nutrient cycling in agricultural systems, and a geographic information system. Finally, multiple regression models were developed to estimate the relative contributions of the major input sources to the flux of nitrogen and phosphorus to the Gulf of Mexico.

1987 ecosystem view of management research in the Myakka River: review of Phase I and Phase II reports

This memorandum has four parts. The first is a review and partial synthesis of Phase 1 and Phase 2 Reports by Dr. Ernest Estevez of the Mote Marine Laboratory to the Board of County Commissioners of Sarasota County, Florida. The review and synthesis emphasizes identification of the most important aspects of the structure of the Myakka system in terms of forcing functions, biological components, and major energy flows. In this context, the dominant primary producers, dominant fish species and food habits, and major environmental variables were of articular interest. A major focus of the review and synthesis was on the river zonations provided in the report and based on salinity and various biological indicators. The second part of this memorandum is a review of a draft report by Mote Marine Laboratory on evaluation of potential water quality impacts on the Myakka River from proposed activities in the watershed. This Memorandum's third part is a review of resource-management related ecosystem models in the context of possible future models of the Myakka River Ecosystem. The final part of this memorandum is proposed future work as an extension of the initial reports.

Examination of the foraging habits of Pacific harbor seal (Phoca vitulina richardsi) to describe their use of the Umpqua River, Oregon, and their predation on salmonids

The increase in harbor seal (Phoca vitulina richardsi) abundance, concurrent with the decrease in salmonid (Oncorhynchus spp.) and other fish stocks, raises concerns about the potential negative impact of seals on fish populations. Although harbor seals are found in rivers and estuaries, their presence is not necessarily indicative of exclusive or predominant feeding in these systems. We examined the diet of harbor seals in the Umpqua River, Oregon, during 1997 and 1998 to indirectly assess whether or not they were feeding in the river. Fish otoliths and other skeletal structures were recovered from 651 scats and used to identify seal prey. The use of all diagnostic prey structures, rather than just otoliths, increased our estimates of the number of taxa, the minimum number of individuals and percent frequency of occurrence (%FO) of prey consumed. The %FO indicated that the most common prey were pleuronectids, Pacific hake (Merluccius productus), Pacific stag-horn sculpin (Leptocottus armatus), osmerids, and shiner surfperch (Cymatogaster aggregata). The majority (76%) of prey were fish that inhabit marine waters exclusively and fish found in marine and estuarine areas (e.g. anadromous spp.) which would indicate that seals forage predominantly at sea and use the estuary for resting and opportunistic feeding. Salmonid remains were encountered in 39 samples (6%); two samples contained identifiable otoliths, which were determined to be from chi-nook salmon (O. tshawytscha). Because of the complex salmonid composition in the Umpqua River, we used molecular genetic techniques on salmonid bones retrieved from scat to discern species that were rare from those that were abundant. Of the 37 scats with salmonid bones but no otoliths, bones were identified genetically as chinook or coho (O. kisutch) salmon, or steelhead trout (O. mykiss) in 90% of the samples.

Multidirectional movements of sportfish species between an estuarine no-take zone and surrounding waters of the Indian River Lagoon, Florida

We examined movement patterns of sportfish that were tagged in the northern Indian River Lagoon, Florida, between 1990 and 1999 to assess the degree of fish exchange between an estuarine no-take zone (NTZ) and surrounding waters. The tagged f ish were from seven species: red drum (Sciaenops ocellatus); black drum (Pogonias cromis); sheepshead (Archosargus probatocephalus); common snook (Centropomus undecimalis); spotted seatrout (Cynoscion nebulosus); bull shark (Carcharhinus leucas); and crevalle jack (Caranx hippos). A total of 403 tagged fish were recaptured during the study period, including 65 individuals that emigrated from the NTZ and 16 individuals that immigrated into the NTZ from surrounding waters of the lagoon. Migration distances between the original tagging location and the sites where emigrating fish were recaptured were from 0 to 150 km, and these migration distances appeared to be influenced by the proximity of the NTZ to spawning areas or other habitats that are important to specific life-history stages of individual species. Fish that immigrated into the NTZ moved distances ranging from approximately 10 to 75 km. Recapture rates for sportfish species that migrated across the NTZ boundary suggested that more individuals may move into the protected habitats than move out. These data demonstrated that although this estuarine no-take reserve can protect species from fishing, it may also serve to extract exploitable individuals from surrounding fisheries; therefore, if the no-take reserve does function to replenish surrounding fisheries, then increased egg production and larval export may be more important mechanisms of replenishment than the spillover of excess adults from the reserve into fishable areas.

The geographic basis for population structure in Fraser River chinook salmon (Oncorhynchus tshawytscha)

We surveyed variation at 13 microsatellite loci in approximately 7400 chinook salmon sampled from 52 spawning sites in the Fraser River drainage during 1988–98 to examine the spatial and temporal basis of population structure in the watershed. Genetically discrete chinook salmon populations were associated with almost all spawning sites, although gene flow within some tributaries prevented or limited differentiation among spawning groups. The mean FST value over 52 samples and 13 loci surveyed was 0.039. Geographic structuring of populations was apparent: distinct groups were identified in the upper, middle, and lower Fraser River regions, and the north, south, and lower Thompson River regions. The geographically and temporally isolated Birkenhead River population of the lower Fraser region was sufficiently genetically distinctive to be treated as a separate region in a hierarchial analysis of gene diversity. Approximately 95% of genetic variation was contained within populations, and the remainder was accounted for by differentiation among regions (3.1%), among populations within regions (1.3%), and among years within populations (0.5%).Analysis of allelic diversity and private alleles did not support the suggestion that genetically distinctive populations of chinook salmon in the south Thompson were the result of postglacial hybridization of ocean-type and stream-type chinook in the Fraser River drainage. However, the relatively small amount of differentiation among Fraser River chinook salmon populations supports the suggestion that gene flow among genetically distinct groups of postglacial colonizing groups of chinook salmon has occurred, possibly prior to colonization of the Fraser River drainage.

Evaluation and application of microsatellites for population identification of Fraser River chinook salmon (Oncorhynchus tshawytscha)

Variation at 13 microsatellite loci was previously surveyed in approximately 7400 chinook salmon (Oncorhynchus tshawytscha) sampled from 50 localities in the Fraser River drainage in southern British Columbia. Evaluation of the utility of the microsatellite variation for population-specific stock identification applications indicated that the accuracy of the stock composition estimates generally improved with an increasing number of loci used in the estimation procedure, but an increase in accuracy was generally marginal after eight loci were used. With 10–14 populations in a simulated fishery sample, the mean error in population-specific estimated stock composition with a 50-popula-tion baseline was <1.4%. Identification of individuals to specific populations was highest for lower Fraser River and lower and North Thompson River populations; an average of 70% of the individual fish were correctly assigned to specific populations. The average error of the estimated percentage for the seven populations present in a coded-wire tag sample was 2% per population. Estimation of stock composition in the lower river commercial net fishery prior to June is of key local fishery management interest. Chinook salmon from the Chilcotin River and Nicola River drainages were important contributors to the early commercial fishery in the lower river because they comprised approximately 50% of the samples from the net fishery prior to mid April.

Modeling the effect of striped bass (Morone saxatilis) on the population viability of Sacramento River winter-run chinook salmon (Onchorhynchus tshawytscha)

We estimated the impact of striped bass (Morone saxatilis) predation on winter-run chinook salmon (Oncorhynchus tshawytscha) with a Bayesian population dynamics model using striped bass and winter-run chinook salmon population abundance data. Winter-run chinook salmon extinction and recovery probabilities under different future striped bass abundance levels were estimated by simulating from the posterior distribution of model parameters. The model predicts that if the striped bass population declines to 512,000 adults as expected in the absence of stocking, winter-run chinook salmon will have about a 28% chance of quasi-extinction (defined as three consecutive spawning runs of fewer than 200 adults) within 50 years. If stocking stabilizes the striped bass population at 700,000 adults, the predicted quasi-extinction probability is 30%. A more ambitious stocking program that maintains a population of 3 million adult striped bass would increase the predicted quasi-extinction probability to 55%. Extinction probability, but not recovery probability, was fairly insensitive to assumptions about density dependence. We conclude that winter-run chinook salmon face a serious extinction risk without augmentation of the striped bass population and that substantial increases in striped bass abundance could significantly increase the threat to winter-run chi-nook salmon if not mitigated by increasing winter chinook salmon survival in some other way.

Larval development of the southern sea garfish (Hyporhamphus melanochir) and the river garfish (H. regularis) (Beloniformes: Hemiramphidae) from South Australian waters

Larval development of the southern sea garfish (Hyporhamphus melanochir) and the river garfish (H. regularis) is described from specimens from South Australian waters. Larvae of H. melanochir and H. regularis have completed notochord flexion at hatching and are characterized by an elongate body with distinct rows of melanophores along the dorsal, lateral, and ventral surfaces; a small to moderate head; a heavily pigmented and long straight gut; a persistent pre-anal finfold; and an extended lower jaw. Fin formation occurs in the following sequence: caudal, dorsal and anal (almost simultaneously), pectoral, and pelvic. Despite the similarities between both species and among hemiramphid larvae in general, H. melanochir larvae are distinguishable from H. regularis by 1) having 58–61 vertebrae (vs. 51–54 for H. regularis); 2) having 12–15 melanophore pairs in longitudinal rows along the dorsal margin between the head and origin of the dorsal fin (vs. 19–22 for H. regularis); and 3) the absence of a large ventral pigment blotch anteriorly on the gut and isthmus (present in H. regularis). Both species can be distinguished from similar larvae of southern Australia (other hemiramphids and a scomberosocid) by differences in meristic counts and pigmentation.

Genetic analysis of juvenile coho salmon (Oncorhynchus kisutch) off Oregon and Washington reveals few Columbia River wild fish

Little is known about the ocean distributions of wild juvenile coho salmon off the Oregon-Washington coast. In this study we report tag recoveries and genetic mixed-stock estimates of juvenile fish caught in coastal waters near the Columbia River plume. To support the genetic estimates, we report an allozyme-frequency baseline for 89 wild and hatchery-reared coho salmon spawning populations, extending from northern California to southern British Columbia. The products of 59 allozyme-encoding loci were examined with starch-gel electrophoresis. Of these, 56 loci were polymorphic, and 29 loci had P0.95 levels of polymorphism. Average heterozygosities within populations ranged from 0.021 to 0.046 and averaged 0.033. Multidimensional scaling of chord genetic distances between samples resolved nine regional groups that were sufficiently distinct for genetic mixed-stock analysis. About 2.9% of the total gene diversity was due to differences among populations within these regions, and 2.6% was due to differences among the nine regions. This allele-frequency data base was used to estimate the stock proportions of 730 juvenile coho salmon in offshore samples collected from central Oregon to northern Washington in June and September-October 1998−2000. Genetic mixed-stock analysis, together with recoveries of tagged or fin-clipped fish, indicates that about one half of the juveniles came from Columbia River hatcheries. Only 22% of the ocean-caught juveniles were wild fish, originating largely from coastal Oregon and Washington rivers (about 20%). Unlike previous studies of tagged juveniles, both tag recoveries and genetic estimates indicate the presence of fish from British Columbia and Puget Sound in southern waters. The most salient feature of genetic mixed stock estimates was the paucity of wild juveniles from natural populations in the Columbia River Basin. This result reflects the large decrease in the abundances of these populations in the last few decades.

The phytoplankton species composition and abundance of Ogun River, Abeokuta, southwestern Nigeria

The phytoplankton species composition and abundance in Ogun River, Ogun state, Southwest Nigeria was studied for a period of seven months (December, 2011 - June, 2012), a total of forty-one genera belonging to five taxonomic groups were recorded from Ogun River. The phytoplankton species composition was surpassed by Chrysophyta with 15 species consisting of 36.6% followed by Chlorophyta with 14 consisting of 34.1%. This was followed by Cyanophyta (7 species) consisting of 17.1%, Euglenophyta with 3 species consisting of 7.3% and Pyrrophyta with 2 species consisting 4.92%. Cyanophyta was the highest in abundance consisting of 41% while the lowest in abundance was Pyrrophyta consisting of 1.5%. The low nature of phytoplankton abundance and diversity observed in this study must have been caused by the polluted nature of the water due to the anthropogenic activities carried out around its shores The dominance of Cyanophyta in this river is similar to findings from Lake Victoria, Lake Bishoftu, Lake Chaohu and the temple pond of Thirupour.

The zooplankton species composition and abundance in Ogun River, Abeokuta, Ogun State, southwestern Nigeria

Investigation on the species composition and abundance of zooplankton in Ogun River, Abeokuta, Ogun state, Southwestern Nigeria was carried out for a period of seven months (December, 2011-June, 2012), Using hand trawling method, 55 µm mesh size plankton net was trawled horizontally ten times to capture zooplankton. The zooplankton samples were put into properly labeled plastic containers and preserved in 4% formalin solution. A total of sixteen genera from five taxonomic groups were recorded from Ogun River. Cladocera predominated both in terms of species composition and abundance. Five species of Cladocera was recorded consisting of 31.25%. Protozoa and Rotifera recorded four species each consisting of 25%. Copepoda recorded two species consisting of 12.5%, and Ostracoda with one species consisting of 6.25%. The low nature of zooplankton abundance and species composition observed in this study must have been caused by the polluted nature of the water due to the anthropogenic activities carried out around its shores The dominance of Cladocera in this river is similar to findings from River Echara and River Imo, Southeastern Nigeria.

Assessment of some physico-chemical parameters of River Ogun (Abeokuta, Ogun State, southwestern Nigeria) in comparison with national and international standards

This study assessed the physico-chemical quality of River Ogun, Abeokuta, Ogun state, Southwestern Nigeria. Four locations were chosen spatially along the water course to reflect a consideration of all possible human activities that are capable of changing the quality of river water. The water samples were collected monthly for seven consecutive months (December 2011 – June 2012) at the four sampling stations. pH, air temperature (℃), water temperature (℃), conductivity (µs/cm) and total dissolved solids (mg/L) were conducted in-situ with the use of HANNA Combo pH and EC multi meter Hi 98129 and Mercury-in-glass thermometer while dissolved oxygen (mg/L), nitrate (mg/L), phosphate (mg/L), alkalinity (mg/L) and hardness (mg/L) were determined ex-situ using standard methods. Results showed that dissolved oxygen, hydrogen ion concentration, total hardness and nitrate were above the maximum permissible limit of National Administration for Food, Drugs and Control (NAFDAC), Standard Organization of Nigeria (SON), Federal Environmental Protection Agency (FEPA), United States Environmental Protection Agency (USEPA), European Union (EU) and World Health Organization (WHO) for drinking water during certain months of the study period. Results also showed that water temperature and conductivity were within the permissible limits of all the standards excluding FEPA. However, total dissolved solids and alkalinity were within the permissible limits of all the standards. Adejuwon and Adelakun, (2012) also reported similar findings on Rivers Lala, Yobo and Agodo in Ewekoro local government area of Ogun state, Nigeria. Since most of the parameters measured were above the maximum permissible limits of the national and international standards, it can be concluded that the water is unfit for domestic uses, drinking and aquacultural purposes and therefore needs to be treated if it is to be used at all. The low dissolved oxygen values for the first four months was too low i.e. < 5 mg/L. This is most likely as a result of the amount of effluents discharged into the river. To prevent mass extinction of aquatic organisms due to anoxic conditions, proper regulations should be implemented to reduce the organic load the river receives.