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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]

Land cover is an important determinant of aquatic habitat and is projected to shift with climate changes, yet climate-driven land cover changes are rarely factored into climate assessments. To quantify impacts and uncertainty of coupled climate and land cover change on warm-water fish species' distributions, we used an ensemble model approach to project distributions of 14 species. For each species, current range projections were compared to 27 scenario-based projections and aggregated to visualize uncertainty. Multiple regression and model selection techniques were used to identify drivers of range change. Novel, or no-analogue, climates were assessed to evaluate transferability of models. Changes in total probability of occurrence ranged widely across species, from a 63% increase to a 65% decrease. Distributional gains and losses were largely driven by temperature and flow variables and underscore the importance of habitat heterogeneity and connectivity to facilitate adaptation to changing conditions. Finally, novel climate conditions were driven by mean annual maximum temperature, which stresses the importance of understanding the role of temperature on fish physiology and the role of temperature- mitigating management practices. Si la couverture terrestre est un important determinant des habitats aquatiques et devrait changer dans la foulee des changements climatiques, les changements de couverture terrestre decoulant du climat sont rarement integres aux evaluations climatiques. Afin de quantifier les impacts et l'incertitude associes aux changements combines du climat et de la couverture terrestre sur la repartition d'especes de poissons d'eau chaude, nous avons employe une approche basee sur les modeles d'ensemble pour etablir des projections de la repartition de 14 especes. Pour chaque espece, les projections de l'aire de repartition actuelle ont ete comparees a 27 projections reposant sur des scenarios et regroupees afin de visualiser l'incertitude. Differentes techniques de regression et de selection de modeles ont ete utilisees pour determiner les facteurs de modification de la repartition. Des climats nouveaux, ou sans analogue, ont ete evalues afin de determiner la transferabilite des modeles. Les changements de la probabilite totale d'occurrence varient considerablement d'une espece a l'autre, allant d'une augmentation de 63 % a une diminution de 65 %. Les augmentations et diminutions des aires de repartition sont principalement causees par des variables associees a la temperature et au debit et elles font ressortir l'importance de l'heterogeneite et de la connectivite des habitats pour favoriser l'adaptation a des conditions changeantes. Enfin, les conditions climatiques nouvelles dependent de la temperature maximum annuelle moyenne, ce qui souligne l'importance de bien comprendre l'incidence de la temperature sur la physiologie des poissons et le role des pratiques de gestion visant a contrer les effets de la temperature. [Traduit par la Redaction], Introduction Changes in climate, a dominant control over the natural distribution of species, has and will continue to cause many species to shift their geographic range (Walther et al. 2002; [...]

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]

Macrophytes have recovered in rivers across the world, but long-term data and studies are lacking regarding community assembly and diversity changes coincident with macrophyte recovery. We investigated patterns of aquatic vegetation species composition and diversity in thousands of sites in the Upper Mississippi River, USA, spanning 21 y of monitoring and a period of vegetation recovery. We analyzed site-level compositional dissimilarity and environmental associations using non-metric multidimensional scaling, compared stability of lake-level assemblages over time with convex hulls, and assessed shared trends in assemblage dissimilarity at the pool scale using dynamic factor analysis. Site-level differences in aquatic vegetation assemblage structure were associated with water depth and substrate, and a gradient of species abundance and diversity was apparent. A common trend in assemblage dissimilarity over time and across contiguous floodplain lakes indicate that assemblage composition changed and diversity increased with considerable synchrony within the past 21 y. Shared trends across the 400-km study reach are indicative of 1 or more widespread, common drivers; however, neither hydrologic extremes nor turbidity explained vegetation assemblage patterns. Following several years of strong changes in composition and increased diversity, the vegetation assemblage displayed signs of increasing stability in some pools but not others. Further research is needed to identify drivers and mechanisms of aquatic vegetation assemblage expansion, assembly, and resilience, all of which will be applicable to the recovery of aquatic vegetation in floodplain systems worldwide. [ABSTRACT FROM AUTHOR]

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]

Continued large-scale public investment in declining ecosystems depends on demonstrations of "success". While the public conception of "success" often focuses on restoration to a pre-disturbance condition, the scientific community is more likely to measure success in terms of improved ecosystem health. Using a combination of literature review, workshops and expert solicitation we propose a generalized framework to improve ecosystem health in highly altered river basins by reducing ecosystem stressors, enhancing ecosystem processes and increasing ecosystem resilience. We illustrate the use of this framework in the Mississippi-Atchafalaya River Basin (MARB) of the central United States (U.S.), by (i) identifying key stressors related to human activities, and (ii) creating a conceptual ecosystem model relating those stressors to effects on ecosystem structure and processes. As a result of our analysis, we identify a set of landscape-level indicators of ecosystem health, emphasizing leading indicators of stressor removal (e.g., reduced anthropogenic nutrient inputs), increased ecosystem function (e.g., increased water storage in the landscape) and increased resilience (e.g., changes in the percentage of perennial vegetative cover). We suggest that by including these indicators, along with lagging indicators such as direct measurements of water quality, stakeholders will be better able to assess the effectiveness of management actions. For example, if both leading and lagging indicators show improvement over time, then management actions are on track to attain desired ecosystem condition. If, however, leading indicators are not improving or even declining, then fundamental challenges to ecosystem health remain to be addressed and failure to address these will ultimately lead to declines in lagging indicators such as water quality. Although our model and indicators are specific to the MARB, we believe that the generalized framework and the process of model and indicator development will be valuable in an array of altered river basins., Competing Interests: Conflict of interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.