Marine Resources Department 3 ). Extended periods of high 

 river flow in the Cooper River frequently dilute water in 

 Charleston Harbor and even in the vicinity of the harbor 

 mouth (U.S. Army Corps of Engineers, footnote 2). 



Coastal marshes cover approximately 20,230 ha in the entire 

 Charleston Harbor system. Of the total marsh area, salt 

 marshes compose about 48%, while freshwater marshes cover 

 approximately 36%, brackish marshes make up 6%, and 

 impoundment areas cover 10% (Tiner 1977). The marshes of 

 the Cooper River reflect strong freshwater inflow, dominated 

 by bulrushes (Scirpus sp.), cattail (Typha sp.), and giant cord- 

 grass, Spartina cynosuroides. Smooth cordgrass, Spartina 

 alterniflora, dominates the low salt-marsh habitats and is 

 mixed with black needlerush, Juncus roemerianus, in up- 

 stream locations where salinity transitions occur (South 

 Carolina Wildlife and Marine Resources Department, foot- 

 note 3). 



METHODS AND MATERIALS 



Data Collection 



We sampled six fixed stations in the channel of the Cooper 

 River-Charleston Harbor system (Fig. 1): C001 (The Tee), C002 

 (Big Island), C003 (North Charleston), C004 (Mouth of Cooper 

 River), J001 (Charleston Harbor), and J003 (Cummings Point). 

 Stations extended in a transect from the harbor mouth inland to 

 above permanent freshwater. Each station was sampled once a 

 month during the 5 yr from February 1973 through December 

 1977, with the following exceptions: C001 was sampled only dur- 

 ing 1973 and January 1974 and was discontinued because of un- 

 trawlable bottom; a new station, J001 , was established in January 

 1 975 . In addition, J003 was not sampled until May 1 973 . 



All collections were made with a 6 m (20-ft) semiballoon 

 otter trawl of 2.5 cm (1-in) stretch mesh. This net is particu- 

 larly selective toward capture of juvenile fishes and is less 

 effective in collection of older, larger fish and highly mobile 

 decapod crustaceans. Twenty-minute tows were made against 

 flood tide during daylight hours at a speed of 1 .3 m/s (2.5 kn), 

 resulting in a coverage of 1 .5 ± 0.4 km/tow. 



Bottom-water samples were collected 0.5 m above the bot- 

 tom with Van Dorn bottles at each station prior to trawling. 

 Water temperature was read from stem thermometers 

 mounted within the Van Dorn bottles. Salinity was measured 

 in the laboratory with a Beckman RS7B induction salinometer. 

 Dissolved oxygen was determined by the Winkler-Carpenter 

 method (Strickland and Parsons 1968). Turbidity was deter- 

 mined with a Hach Model 2100A turbidimeter. Winter sam- 

 pling encompassed January-March; spring sampling April- 

 June; summer July-September; and fall October-December. 



Specimens collected were either processed in the field or pre- 

 served in 10% Formalin and returned to the laboratory for 

 identification, counting, weighing (nearest 0.1 g), and mea- 

 suring (total length for Fishes; carapace width for crabs, mea- 

 sured as distance between tips of lateral spines; and total 

 length for shrimp from tip of rostrum to tip of telson). We 



recorded size measurements for all species numbering <50 

 specimens per tow. At stations where the trawl captured 

 larger numbers of organisms, we subsampled the catch as 

 follows: If >50 to <250 individuals were collected, a minimum 

 of 50 randomly selected specimens was measured; if >250 to 

 < 500 individuals were caught, a minimum of 20% was 

 measured; when >500 were caught, a minimum of 10% was 

 measured. 



Data Analysis 



The degree of similarity among collections and among 

 species was determined using normal and inverse cluster anal- 

 yses, employing the Bray-Curtis similarity coefficient and 

 "flexible sorting strategy" with the cluster intensity coeffi- 

 cient, p, set at the now standard value of -0.25 (Lance and 

 Williams 1967; Williams 1971; Stephenson et al. 1972; 

 Clifford and Stephenson 1975). Species which occurred in 

 only one or two collections during a sampling period and col- 

 lections which contained only one species were eliminated 

 from the analyses. Abundances were logarithmically trans- 

 formed (logio[AT + 1] where x is the number of individuals for a 

 given species) in order to lessen the tendency of extremely abun- 

 dant species to dominate the similarity matrix (Clifford and 

 Stephenson 1975). 



Two dendrograms were generated for each season: 1) A 

 dendrogram which indicated association of all sites by season 

 during the 5-yr sampling period based on faunal similarity, 

 and 2) a dendrogram which indicated association of all species 

 collected each season during the 5-yr sampling period based on 

 the abundance of species at sites where they were collected. 

 Nodal analysis (Williams and Lambert 1961; Lambert and 

 Williams 1962) was subsequently used to examine species 

 group and station coincidences based on patterns of constancy 

 and fidelity (Boesch 1977). 



An index of abundance (Musick and McEachran 1972; 

 Elliott 1977) was used to compare numbers and weights of 

 selected dominant species and is expressed as: 



Index of abundance 



N 



— Ilog,o(*+ 1) 



JVl 



where x = no. or weight of individuals of a given species in a 

 chosen frame and N = no. of collections in that time 

 frame 



We determined biomass and density estimates for fishes and 

 decapod crustaceans from computations of area swept by our 

 trawl gear. Estimates of area swept (a) were determined by 

 the following equation given by Klima": 



a = KM(0.6H) 

 10,000 mVha 



where K is speed in meters per hour, Mis time in hours fished, 

 and H is headrope length in meters. The constant 0.6 desig- 

 nates an effective swath of about 60% of the headrope length 

 as used by Roe (1969) and established by Wathne (1959). The 

 area swept by our 6 m otter trawl was estimated by this method 

 to be 0.54 ha/tow. 



•South Carolina Wildlife and Marine Resources Department. 1972. A study of 

 the Charleston Harbor estuary with special reference to deposition of dredged 

 sediments. Unpubl. manuscr., unpaginated. Office of Marine Conservation, 

 Management and Services, P.O. Box 12559, Charleston, SC 29412. 



'Klima, E. F. 1976. A review of the fishery resources in the western central 

 Atlantic. WECAF Studies No. 3, FAO No. 32975-76, 77 p. Available from 

 UN1PUB, 1180Avenue of the Americas, New York, NY 10036. 



