Failure to estimate capture efficiency, defined as the probability of capturing individual fish, can introduce a systematic error or bias into estimates of fish abundance. We evaluated the efficacy of multipass electrofishing removal methods for estimating fish abundance by comparing estimates of capture efficiency from multipass removal estimates to capture efficiencies measured by the recapture of known numbers of marked individuals for bull trout Salvelinus confluentus and westslope cutthroat trout Oncorhynchus clarki lewisi. Electrofishing capture efficiency measured by the recapture of marked fish was greatest for westslope cutthroat trout and for the largest size‐classes of both species. Capture efficiency measured by the recapture of marked fish also was low for the first electrofishing pass (mean, 28%) and decreased considerably (mean, 1.71 times lower) with successive passes, which suggested that fish were responding to the electrofishing procedures. On average, the removal methods overestimated three‐pass capture efficiency by 39% and underestimated fish abundance by 88%, across both species and all size‐classes. The overestimates of efficiency were positively related to the cross‐sectional area of the stream and the amount of undercut banks and negatively related to the number of removal passes for bull trout, whereas for westslope cutthroat trout, the overestimates were positively related to the amount of cobble substrate. Three‐pass capture efficiency measured by the recapture of marked fish was related to the same stream habitat characteristics that influenced (biased) the removal estimates and did not appear to be influenced by our sampling procedures, including fish marking. Simulation modeling confirmed our field observations and indicated that underestimates of fish abundance by the removal method were negatively related to first‐pass sampling efficiency and the magnitude of the decrease in capture efficiency with successive passes. Our results, and those of other researchers, suggest that most electrofishing‐removal‐based estimates of fish abundance are likely to be biased and that these biases are related to stream characteristics, fish species, and size. We suggest that biologists regard electrofishing‐removal‐based estimates as biased indices and encourage them to measure and model the efficiency of their sampling methods to avoid introducing systematic errors into their data.

List of boxes xi Preface xiii Acknowledgements xiv Guide to using this book xv Companion website xvii

We used strong inference with Akaike's Information Criterion (AIC) to assess the processes capable of explaining long-term (1984)(1985)(1986)(1987)(1988)(1989)(1990)(1991)(1992)(1993)(1994)(1995) variation in the per capita rate of change of mottled sculpin (Cottus bairdi) populations in the Coweeta Creek drainage (USA). We sampled two fourth-and one fifth-order sites (BCA [uppermost], BCB, and CC [lowermost]) along a downstream gradient, and the study encompassed extensive flow variation. Physical habitat availability varied significantly both within and among the sites.Sculpin densities in all sites were highly stable (coefficients of variation ϭ 0.23-0.41) and sampling variability was low (coefficients of variation ϭ 0.11-0.15). Population stability was positively associated with habitat stability, and the only significant correlations of population parameters among sites involved juveniles. Sculpin densities were significantly higher in BCB than in CC. The data suggest that, despite their proximity, the dynamics of populations within the sites are being determined by small-scale (i.e., 30-50 m) rather than broad-scale spatial processes.Both AIC and Dennis and Taper analyses indicated that simple density dependence had the greatest ability to explain variation in r for all life-history classes in all sites (AIC, seven of nine cases; Dennis and Taper, nine of nine cases). Multiprocess models had little explanatory power. When adults were removed from two sites, juvenile sculpin shifted into microhabitats formerly occupied by adults. No shifts occurred in control sites. Consequently, it is likely that the patterns of density dependence observed in all three sites were a consequence of intraspecific competition for space. Our findings argue for a multitiered approach to the study of population variation, one that encompasses long-term monitoring, spatial variation, and experimental testing of potential mechanisms.

Invasions of non-native brook trout (Salvelinus fontinalis) have the potential for upstream displacement or elimination of bull trout (Salvelinus confluentus) and other native species already threatened by habitat loss. We summarized the distribution and number of bull trout in samples from 12 streams with and without brook trout in central Idaho and used hierarchical regression analysis to consider whether brook trout have displaced bull trout along gradients of temperature and elevation. Brook trout generally were observed in higher numbers downstream of bull trout. Brook trout presence, number, and both temperature and elevation were important variables explaining the observed distributions and number of bull trout among streams. Our analyses support the hypothesis that brook trout have displaced bull trout, but results were highly variable and stream dependent. Although brook trout appeared to have displaced bull trout to higher elevations or colder temperatures, there was no clear influence on overall number of bull trout. Brook trout probably do influence bull trout populations and facilitate if not cause local extinctions, but threats probably vary strongly with environmental conditions. Bull trout in smaller streams could be more vulnerable than those in larger streams.

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Summary 1. Colonisation and population recovery are crucial to species persistence in environmentally variable ecosystems, but are poorly understood processes. After documenting movement rates for several species of stream fish, we predicted that this variable would influence colonisation rates more strongly than local abundance, per cent occupancy, body size and taxonomic family. We also predicted that populations of species with higher movement rates would recover more rapidly than species with lower movement rates and that assemblage structure would change accordingly. 2. To test these predictions, we removed fishes from a headwater and a mainstem creek in southwest Virginia and monitored colonisation over a 2‐year period. Using an information–theoretic approach, we evaluated the relative plausibility of 15 alternative models containing different combinations of our predictor variables. Our best‐supported model contained movement rate and abundance and was 41 times more likely to account for observed patterns in colonisation rates than the next‐best model. Movement rate and abundance were both positively related to colonisation rates and explained 88% of the variation in colonisation rates among species. 3. Population recovery, measured as the per cent of initial abundance restored, was also positively associated with movement rate. One species recovered within 3 months, most recovered within 2 years, but two species still had not recovered after 2 years. Despite high variation in recovery, the removal had only a slight impact on assemblage structure because species that were abundant in pre‐removal samples were also abundant in post‐removal samples. 4. The significance of interspecific variation in colonisation and recovery rates has been underappreciated because of the widely documented recovery of stream fish assemblages following fish kills and small‐scale experimental defaunations. Our results indicate that recovery of the overall assemblage does not imply recovery of each component species. Populations of species that are rare and less mobile will recover more slowly and will be more vulnerable to extinction in systems where chemical spills, hydrological alteration, extreme droughts and other impacts are frequent.

Introgressive hybridization threatens the persistence of several species of native salmonids in the western United States, but little is known about the factors influencing the establishment and maintenance of introgressed populations. We examined the occurrence of introgressive hybridization in westslope cutthroat (Oncorhynchus clarki lewisi) and rainbow trout (O. mykiss) populations in relation to physical characteristics of streams, trout density estimates, and the distance from stocking source. Trout were sampled from 80 stream sites in the Clearwater River Basin, Idaho, USA, and tissues from individual trout were analyzed to detect hybridization using noncoding sequences of nuclear DNA. We found a broad zone of hybridization detected at 64% of the sampled sites. The presence and degree of introgression was negatively related to elevation and positively related to stream width in our logistic regression model. Stream elevation and size likely influence hydrologic and thermal regimes. An interaction between the life history characteristics of the native and nonnative trout with these hydrologic and thermal stream gradients could explain the invasion success of rainbow trout and hence, the extent of the hybrid zone. Alternatively, the influence of elevation and stream width could be the result of habitat selection by the parental species, thereby reducing the opportunity for hybridization. Understanding the relationship between abiotic factors and introgressive hybridization will assist fisheries managers when evaluating the potential threat of introgression in different stream habitats and applying the necessary management actions to conserve the native cutthroat trout genotypes across broad landscapes. Corresponding Editor: K. D. Fausch

Stream fish managers often use fish sample data to inform management decisions affecting fish populations. Fish sample data, however, can be biased by the same factors affecting fish populations. To minimize the effect of sample biases on decision making, biologists need information on the effectiveness of fish sampling methods. We evaluated single-pass backpack electrofishing and seining combined with electrofishing by following a dual-gear, mark-recapture approach in 61 blocknetted sample units within first-to third-order streams. We also estimated fish movement out of unblocked units during sampling. Capture efficiency and fish abundances were modeled for 50 fish species by use of conditional multinomial capturerecapture models. The best-approximating models indicated that capture efficiencies were generally low and differed among species groups based on family or genus. Efficiencies of single-pass electrofishing and seining combined with electrofishing were greatest for Catostomidae and lowest for Ictaluridae. Fish body length and stream habitat characteristics (mean cross-sectional area, wood density, mean current velocity, and turbidity) also were related to capture efficiency of both methods, but the effects differed among species groups. We estimated that, on average, 23% of fish left the unblocked sample units, but net movement varied among species. Our results suggest that (1) common warmwater stream fish sampling methods have low capture efficiency and (2) failure to adjust for incomplete capture may bias estimates of fish abundance. We suggest that managers minimize bias from incomplete capture by adjusting data for site-and species-specific capture efficiency and by choosing sampling gear that provide estimates with minimal bias and variance. Furthermore, if block nets are not used, we recommend that managers adjust the data based on unconditional capture efficiency.