Damaged and immature specimens often result in macroinvertebrate data that contain ambiguous parent-child pairs (i.e., abundances associated with multiple related levels of the taxonomic hierarchy such as Baetis pluto and the associated ambiguous parent Baetis sp.). The choice of method used to resolve ambiguous parent-child pairs may have a very large effect on the characterization of invertebrate assemblages and the interpretation of responses to environmental change because very large proportions of taxa richness (73-78%) and abundance (79-91%) can be associated with ambiguous parents. To address this issue, we examined 16 variations of 4 basic methods for resolving ambiguous taxa: RPKC (remove parent, keep child), MCWP (merge child with parent), RPMC (remove parent or merge child with parent depending on their abundances), and DPAC (distribute parents among children). The choice of method strongly affected assemblage structure, assemblage characteristics (e.g., metrics), and the ability to detect responses along environmental (urbanization) gradients. All methods except MCWP produced acceptable results when used consistently within a study. However, the assemblage characteristics (e.g., values of assemblage metrics) differed widely depending on the method used, and data should not be combined unless the methods used to resolve ambiguous taxa are well documented and are known to be comparable. The suitability of the methods was evaluated and compared on the basis of 13 criteria that considered conservation of taxa richness and abundance, consistency among samples, methods, and studies, and effects on the interpretation of the data. Methods RPMC and DPAC had the highest suitability scores regardless of whether ambiguous taxa were resolved for each sample separately or for a group of samples. Method MCWP gave consistently poor results. Methods MCWP and DPAC approximate the use of familylevel identifications and operational taxonomic units (OTU), respectively. Our results suggest that restricting identifications to the family level is not a good method of resolving ambiguous taxa, whereas generating OTUs works well provided that documentation issues are addressed.

An index of biological integrity (IBI) was developed for streams in the Hudson, Delaware, and Susquehanna River drainages in the northeastern United States based on fish assemblage data from the Mohawk River drainage of New York. The original IBI, developed for streams in the U.S. Midwest, was modified to reflect the assemblage composition and structure present in Mid‐Atlantic Slope drainages. We replaced several of the Midwestern IBI metrics and criteria scores because fishes common to the Midwest are absent from or poorly represented in the Northeast and because stream fish assemblages in the Northeast are less rich than those in the Midwest. For all replacement metrics we followed the ecology‐based rationale used in the development of each of the metrics of the Midwestern IBI so that the basic theoretical underpinnings of the IBI remained unchanged. The validity of this modified IBI is demonstrated by examining the quality of streams in the Hudson, Delaware, and lower Susquehanna River basins. The relationships between the IBI and other indicators of environmental quality are examined using data on assemblages of fish and benthic macroinvertebrates and on chemical and physical stream characteristics obtained during 1993‐2000 by the U.S. Geological Survey's National Water Quality Assessment Program in these three river basins. A principal components analysis (PCA) of chemical and physical variables from 27 sites resulted in an environmental quality gradient as the primary PCA axis (eigenvalue, 0.41). Principal components analysis site scores were significantly correlated with such benthic macroinvertebrate metrics as the percentage of Ephemeroptera, Plecoptera, and Trichoptera taxa (Spearman R = −0.66, P < 0.001). Index of biological integrity scores for sites in these three river basins were significantly correlated with this environmental quality gradient (Spearman R = −0.78, P = 0.0001). The northern Mid‐Atlantic Slope IBI appears to be sensitive to environmental degradation in all three of the river basins addressed in this study. Adjustment of metric scoring criteria may be warranted, depending on composition of fish species in streams in the study area and on the relative effort used in the collection of fish assemblage data.

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Stream flow, chemical and biological data for the northern part of Swatara Creek, which drains a 112 km 2 area in the Southern Anthracite Field of eastern Pennsylvania, indicate progressive improvement in water quality since 1959, after which most mines in the watershed had been flooded. Drainage from the flooded mines contributes substantially to base flow in Swatara Creek. Beginning in 1995, a variety of treatment systems and surface reclamation were implemented at some of the abandoned mines. At Ravine, Pa., immediately downstream of the mined area, median SO 4 concentration declined from about 150 mg l −1 in 1959 to 75 mg l −1 in 1999 while pH increased from acidic to near-neutral values (medians: c.  pH 4 before 1975; c.  pH 6 after 1975). Fish populations rebounded from non-existent during 1959–1990 to 21 species identified in 1999. Nevertheless, recent monitoring indicates (1) episodic acidification and elevated concentrations and transport of Fe, Al, Mn, and trace metals during storm flow; (2) elevated concentrations of Fe, Mn, Co, Cu, Pb, Ni, and Zn in streambed sediments relative to unmined areas and to toxicity guidelines for aquatic invertebrates and fish; and (3) elevated concentrations of metals in fish tissue, notably Zn. The metals are ubiquitous in the fine fraction (<0.063 mm) of bed sediment in mining-affected tributaries and the main stem of Swatara Creek. As a result of scour and transport of streambed deposits, concentrations of suspended solids and total metals in the water column are correlated, and those for storm flow typically exceed base flow. Nevertheless, the metals concentrations are poorly correlated with stream flow because concentrations of suspended solids and total metals typically peak prior to peak stream stage. In contrast, SO 4 , specific conductance and pH are inversely correlated with stream flow as a result of dilution of poorly buffered stream water with weakly acidic storm runoff derived mainly from low-pH rainfall. Declines in pH to values approaching 5.0 during storm flow events or declines in redox potential during burial of sediment could result in the remobilization of metals associated with suspended solids and streambed deposits.

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The invasive shrub Japanese knotweed (Fallopia japonica) is spreading through riparian forests in Central Pennsylvania. There is concern that detritus from this species may impact adjacent aquatic ecosystems, as allocthonous material forms the basis for aquatic food webs and may impact benthic community structure. This study compares key ecosystem processes within Japanese knotweed leaf litter to leaf litter of a native riparian species, American sycamore (Platanus occidentalis). We assess benthic macroinvertebrate communities and decomposition rates within experimental Japanese knotweed and American sycamore leaf packs at three sites within the Susquehanna River. Japanese knotweed detritus hosted a similar macroinvertebrate community to American sycamore and their assemblages had similar representation of functional feeding groups. The similarity between the invertebrate communities occupying American sycamore and Japanese knotweed detritus indicates that macroinvertebrates are able to utilize non-native litter for habitat and potentially as an energy source. American sycamore decomposed at a faster rate than Japanese knotweed, lending support to the Novel Weapons Hypothesis, which suggests that non-native species like Japanese knotweed may inhibit microbial colonization and subsequent litter breakdown. Our results suggest that invasion of Japanese knotweed along riparian corridors of large river systems may not have severe ecological consequences on local ecosystem processes.

Government agencies frequently conduct benthic macroinvertebrate surveys for bioassessment at large spatial scales in a variety of aquatic habitats, including large rivers. However, these data are rarely used by investigators outside the specific regulatory agency. We used data from 150 benthic macroinvertebrate samples collected over a period of 20 y from 10 locations in a large, shallow river system (the Susquehanna River and 2 major tributaries) by personnel in 4 government agencies to explore broad spatial and temporal patterns in benthic assemblages. We standardized sample size and taxonomy to account for differences in sampling, processing, and identification methods among agencies. Invertebrate assemblages were dominated by mayflies and caddisflies (46-83%). Percent Ephemeroptera, Plecoptera, Trichoptera (EPT) and standard diversity measures were inversely correlated, indicating that traditional macroinvertebrate Index of Biotic Integrity (IBI) approaches might not be applicable to large rivers. These data showed differences in assemblage composition across sub-basins and revealed effects of the spread of invasive Asian clams and of black fly management on benthic assemblage structure in the river. Large-river invertebrates are understudied and, even with challenges of combining data sets from multiple agencies, we showed the potential utility of applying data from a large river system to reveal ecological patterns across space and time.