The index of biotic integrity (IBI). developed from information on the structure, composition, and functional organization of fish assemblages, is used to assess the health of aquatic ecosystems. We analyzed two large statewide data sets on stream fish assemblages to develop and test a version of the IBI for application to Wisconsin coldwater streams (maximum daily mean water temperature usually <22°C). This new IBI is needed because fish assemblages in Wisconsin coldwater streams differ significantly from those in warmwater streams (maximum daily mean temperature >24°C), for which an IBI already exists. High‐quality coldwater streams have few species, with salmonids and cottids dominating. and lack many of the taxonomic groups that are important in high‐quality warmwater streams. In contrast, high‐quality warmwater streams have numerous species, and cyprinids, catostomids, centrarchids, and percids typically dominate. Environmental degradation often causes an increase in species richness in coldwater fish assemblages, the opposite of what occurs in warmwater assemblages, as a small number of coldwater species are replaced by a larger number of more tolerant eurythermal and warmwater species. The new coldwater IBI has five metrics: (1) number of intolerant species, (2) percent of all individuals that are tolerant species, (3) percent of all individuals that are top carnivore species, (4) percent of all individuals that are native or exotic stenothermal coldwater or coolwater species, and (5) percent of salmonid individuals that are brook trout Salvelinus fontinalis. No regional or stream‐size adjustments in metric scoring criteria are needed. Relative coldwater IBI scores and ratings of stream sites throughout Wisconsin closely match independent rankings of environmental quality on the basis of physical habitat and water quality of the sites. Variation in IBI scores within and among years is gencrally low. The new coldwater IBI is not appropriate for coolwater streams (typical maximum summer daily mean temperature 22–24°C).

Methods used to estimate fish abundance in streams should be chosen based on the precision required by the study, the available time, and the number and kinds of species targeted. When entire assemblages of predominantly small, nongame fishes are to be sampled, most existing procedures have limitations. We compared estimates of species richness, abundance, and assemblage structure based on catch per effort (CPE) during a single tow‐barge electrofishing sample versus intensive tow‐bare electrofishing removal sampling procedures with block nets in paired, contiguous stations on nine streams in southern Wisconsin. Use of block nets had little effect on CPE during single upstream electrofishing passes; for stations approximately 35 times the mean stream width in length, the overall influence of fish entering and leaving the station appeared to be negligible. Estimates of abundance, based on total catch and based on the removal model, were higher in removal stations than in CPE stations. However, estimates of abundance between stations were correlated, and estimates of species richness and assemblage structure were similar. Relative to removal sampling, a single upstream CPE pass adequately assessed fish species richness, abundance, and assemblage structure in small streams.

Procedures for evaluating fish habitat in streams have focused largely on specific methods used to sample individual habitat variables, and studies ofsampling design are uncommon. We used data from 86 sites on 58 Wisconsin streams to determine the optimal number and spacing of habitat transects needed to characterize the means of commonly measured habitat variables. The optimal number of transects varied with stream width; approximately 13 transects, spaced every three mean stream widths (MSW), were required on narrow streams (<5 m wide), and approximately 20 transects, spaced every 2 MSWs, were needed on wider streams (5–35 m wide). Spacing transects in terms of MSW yields equal sample sizes regardless of stream width, is easier to apply than random spacing, and is logistically more reasonable than spacing transects at regular intervals without regard for stream width. Estimates based on transects spaced 2 MSWs apart within a stream reach of 35 MSWs were within 5% of the true values 95% of the time, Statistical differences that could be detected by means of 20 transects were reasonable and probably biologically meaningful.

To identify past successes and future opportunities for improved fisheries management in Wisconsin, we synthesized size‐structure information on 19 gamefish species from 1944 to 2012, incorporating data on more than 2 million measured individuals. Since the 1940s, mean and mean maximum sizes of five “gamefish” species (Lake Sturgeon Acipenser fulvescens, Largemouth Bass Micropterus salmoides, Smallmouth Bass M. dolomieu, Northern Pike Esox lucius, and Sauger Sander canadensis) have stayed fairly stable, and one (Muskellunge E. masquinongy) initially dropped and then rebounded—most likely as a product of increased catch‐and‐release fishing and restrictive harvest regulations. In contrast, four “panfish” species (i.e., Bluegill Lepomis macrochirus, Green L. cyanellus, Yellow Perch Perca flavescens, and Black Crappie Pomoxis nigromaculatus), which have not received the same conservation management attention, have experienced substantial and sustained erosions in size over the same period. Regulations for many species and species complexes have been cyclical over time, illustrating the challenge of consistently managing fisheries. Our long‐term retrospective analysis was effective at identifying new opportunities for improved fisheries management in Wisconsin (i.e., panfish management). We therefore encourage other big data retrospective approaches within and across regions to identify past successes and future opportunities in other fisheries management programs.

Conservation of genetic resources is a challenging issue for agencies managing popular sport fishes. To address the ongoing potential for genetic risks, we developed a comprehensive set of recommendations to conserve genetic diversity of muskellunge (Esox masquinongy) in Wisconsin, and evaluated the extent to which the recommendations can be implemented. Although some details are specific to Wisconsin's muskellunge propagation program, many of the practical issues affecting implementation are applicable to other species and production systems. We developed guidelines to restrict future broodstock collection operations to lakes with natural reproduction and to develop a set of brood lakes to use on a rotational basis within regional stock boundaries, but implementation will require considering lakes with variable stocking histories. Maintaining an effective population size sufficient to minimize the risk of losing alleles requires limiting broodstock collection to large lakes. Recommendations to better approximate the temporal distribution of spawning in hatchery operations and randomize selection of brood fish are feasible. Guidelines to modify rearing and distribution procedures face some logistic constraints. An evaluation of genetic diversity of hatchery‐produced fish during 2008 demonstrated variable success representing genetic variation of the source population. Continued evaluation of hatchery operations will optimize operational efficiency while moving toward genetic conservation goals.