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Effective management and conservation of fishes requires understanding habitat use across multiple life stages while ensuring necessary habitats are both available and accessible. Tributary habitats may play an important role in recruitment and dispersal of fishes in anthropogenically modified rivers such as the Mississippi and Illinois Rivers of the Midwest U.S.A. Identifying source locations that contribute to recruitment of fish populations can determine the importance of connectivity within river networks and pinpoint critical habitats that sustain fish populations. In the Upper Mississippi River System (UMRS), the environments that fish use in early life stages (i.e., natal origin) can be identified using otolith trace element analysis due to stability and distinctness in water chemistry (strontium: calcium [Sr:Ca]) among water bodies that is reflected in otoliths.Here, we used trace element analysis to determine natal origin of six small‐bodied fishes including bullhead minnow (Pimephales vigilax), emerald shiner (Notropis atherinoides), gizzard shad (Dorosoma cepedianum), bluegill (Lepomis macrochirus), orangespotted sunfish (Lepomis humilis), and yellow perch (Perca flavescens) across six reaches of the UMRS (Pools 4, 8, 13, 26, the Open River of the Middle Mississippi River, and the La Grange Pool of the Illinois River). Otolith core Sr:Ca for fishes was quantified using laser ablation inductively coupled plasma mass spectrometry. Using the resulting Sr:Ca chemical signatures of otolith cores, natal origin (tributary, immigrant, or potential resident) was determined for individual fish based on family‐specific relationships between otolith and water chemistries.We found that all species originated from tributaries and other reaches (i.e., were immigrants) to varying extents, which acted as evidence for network connectivity. Specifically, tributaries contributed up to 48% of individuals at a given reach. In certain reaches, Pool 26 and the Open River reach, up to 80% of individuals in a species immigrated from another mainstem river reach. Network connectivity was also important in both upstream and downstream directions. Contributions from network connectivity varied among species: bullhead minnow used less whereas orangespotted sunfish used more network connectivity than when all species were combined. Further, the use of network connectivity varied spatially where individuals captured in Pool 8 and the La Grange Pool less often and those from Pool 26 and the Open River more often originated from network connectivity compared to the whole assemblage across reaches.These results indicate that species' life history traits probably interacted with the physical environment, which differs spatially, to yield observed recruitment source patterns. Our results show that network connectivity contributes to established assemblages of native small‐bodied fishes throughout the UMRS and underscore the role of interjurisdictional management in maintaining network connectivity to sustain fish populations. [ABSTRACT FROM AUTHOR]

Understanding how gene flow influences adaptive divergence is important for predicting adaptive responses. Theoretical studies suggest that when gene flow is high, clustering of adaptive genes in fewer genomic regions would protect adaptive alleles from recombination and thus be selected for, but few studies have tested it with empirical data. Here, we used restriction site‐associated sequencing to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We used four differentiation‐based outlier tests and three genotype–environment association analyses to define neutral single nucleotide polymorphisms (SNPs) and outlier SNPs that were putatively under selection. We then examined the distribution of outlier SNPs along the genome and investigated whether these SNPs were found in genomic islands of differentiation and inversions. We found that gene flow varied among species, and outlier SNPs were clustered more tightly in species with higher gene flow. The two species with the highest overall FST (0.0303–0.0720) and therefore lowest gene flow showed little evidence of clusters of outlier SNPs, with outlier SNPs in these species spreading uniformly across the genome. In contrast, nearly all outlier SNPs in the species with the lowest FST (0.0003) were found in a single large putative inversion. Two other species with intermediate gene flow (FST ~ 0.0025–0.0050) also showed clustered genomic architectures, with most islands of differentiation clustered on a few chromosomes. Our results provide important empirical evidence to support the hypothesis that increasingly clustered architecture of local adaptation is associated with high gene flow. see also the Perspective by Sara M. Schaal and Sara J. Smith [ABSTRACT FROM AUTHOR]

Floodplains of large rivers are exploited for agricultural production, industrial and municipal development, and transportation infrastructure. Recently, increased frequency of costly floods has prompted consideration of whether offsetting benefits might accrue from management of floodplains for ecosystem services. We employed a simple inundation model for 800 km of the Lower Missouri River, USA, to evaluate spatial and temporal distributions of ecological floodplain inundation metrics and how those distributions might vary with levee removal and climatic change. The model evaluates inundation at 30 × 30 m resolution on a daily basis over 82 years of record. We quantified provisioning of waterfowl habitat and potential denitrification. Spatial variability is affected by ongoing geomorphic adjustments that affect floodplain connectivity. Statistical models indicate that available floodplain area and recent aggradation are predictive of most inundation metrics. Connectivity is sensitive to climate‐change scenarios that predict increased floodplain inundation during spring waterfowl migrations; the greatest sensitivity to future climate exists where channel‐floodplain geomorphology presently enhances floodplain connectivity. Evaluation of floodplain denitrification indicates that on average, the nonleveed part of the floodplain could denitrify 0.05%–1.7% of the mean annual nitrogen load of the river. Levee removal could increase this rate to only 3.6% of the nitrogen load. The capacity of floodplain connectivity to influence certain ecosystem services is highly variable in space along the Lower Missouri River and may be appreciably influenced by climate change. Hence, decisions to optimize management of large‐river floodplains are likely to be highly location dependent. Plain Language Summary: Increased flooding on large, highly engineered rivers has prompted reconsideration of how to increase resiliency to flooding while also increasing net socioeconomic benefits. These concerns have prompted managers to consider how ecosystem services—such as provision of wildlife habitat or nutrient processing—may contribute to bottom‐line decisions about levee system designs. On the Lower Missouri River, USA, ongoing erosion and deposition along the channel exert a strong control on flooding patterns. Recognition of where and when floodplain areas flood, and a full accounting of costs and benefits of flooding, can be a useful component of floodplain management, especially when flooding potential varies substantially along the river. Key Points: Resiliency of large‐river floodplains to floods can be highly spatially variable, dependent on geomorphic channel adjustmentsFloodplain habitat for waterfowl increases significantly in areas of decreased channel conveyance and increased floodplain areaDenitrification potential, on average, is only 3.6% of N flux, showing that nutrient mitigation strategies in the floodplain are limited [ABSTRACT FROM AUTHOR]

Functional composition of communities across scales is increasingly used to infer resilience of biotic communities to environmental change. To assess the relevance of these concepts to management of large rivers, analyses were applied to fish community data of the Upper Mississippi River. First, to evaluate whether there was evidence for structural patterns in fish size distributions, a discontinuity analysis was performed. Using long-term fish data, consistent discontinuities were identified across 14 reaches, suggesting similar structuring processes occur throughout the nearly 1300 river kilometers represented by those reaches. Increased variability in species abundance in relation to proximity to edges of body size aggregations supports the discontinuity hypothesis that body size aggregations are structured by key processes. Functional richness and redundancy were quantified within and across identified scales for each of 14 river reaches. Diversity of trophic and spawning guilds was generally greater in the upstream reaches in comparison with downstream reaches, with the exception of the diversity of large-bodied spawning guilds. Evidence of functional shifts in the composition of fishes occurred, but differed by size aggregations, likely reflecting scale-specific resource availability. Redundancy of spawning and trophic groups across body size aggregations suggested downstream reaches of this system may be less resilient to disturbances and were weakly associated with reduced habitat diversity. These findings suggest that discontinuities in large river fish assemblages do occur and may provide indication of shifting resource availability. Further investigation of the underlying processes and scales that support resource availability will be critical to managing for resilience in large river ecosystems. [ABSTRACT FROM AUTHOR]

Detecting nuisance species at low abundance or in newly established areas is critical to developing pest management strategies. Due to their sensitivity to disturbance and erratic jumping behavior, Silver CarpHypophthalmichthys molitrixcan be difficult to collect with traditional sampling methods. We compared catch per unit effort (CPUE) of all species from a Long Term Resource Monitoring (LTRM) electrofishing protocol to an experimental electrofishing technique designed to minimize Silver Carp evasion through tactical boat maneuvering and selective application of power. Differences in CPUE between electrofishing methods were detected for 2 of 41 species collected across 2 years of sampling at 20 sites along the Illinois River. The mean catch rate of Silver Carp using the experimental technique was 2.2 times the mean catch rate of the LTRM electrofishing technique; the increased capture efficiency at low relative abundance emphasizes the utility of this method for early detection. The experimental electrofishing also collected slightly larger Silver Carp (mean: 510.7 mm TL versus 495.2 mm TL), and nearly four times as many Silver Carp independently jumped into the boat during experimental transects. Novel sampling approaches, such as the experimental electrofishing technique used in this study, should be considered to increase probability of detection for aquatic nuisance species. Received June 9, 2016; accepted September 19, 2016 Published online January 3, 2017 [ABSTRACT FROM PUBLISHER]

Over the past century, channelization, agricultural tiling, and land use changes have resulted in significant stream channel degradation of the Cache River in southern Illinois. With the increasing interest in restoration of the watershed's bottomland forests and swamps, we sought to characterize geomorphic change over the past 110 years to inform restoration and management. A previously surveyed stretch of river was resurveyed in the fall of 2011, following a record flood in the spring of that year. Results suggest that the slope of the channel in this section of the river has increased 345% between 1903 and 1972 ( p < 0.01), but has not changed significantly since ( p = 0.12). Within that same time period, bank heights increased between 1 and 7 m and bed elevation decreased between 1 and 5 m. Changes in resurveyed cross sections appear to be primarily due to recent flood scour. It appears as though early 20th Century stream channel modifications had immediate effects on the geomorphology of the channel; however, channel geometry is now at or near equilibrium. This case study of the Cache River watershed demonstrates how and why successful restoration will require integration of geomorphic processes of the system. [ABSTRACT FROM AUTHOR]