The flood-pulse concept (FPC) states that annual inundation is the principal force responsible for productivity and biotic interactions in river-floodplain systems. Somatic growth is one component of production, and we hypothesized that, if the FPC applies, growth of fishes that use the moving littoral zone should differ among years with differing flood pattern, whereas nonlittoral fishes would show no such response. Growth of largemouth bass (Micropterus salmoides) and bluegill (Lepomis macrochirus), species that exploit littoral resources, increased during a year having an unusual warm-season flood in the Upper Mississippi River system and was reduced during low-water years. Growth of white bass (Morone chrysops), which do not rely heavily on the littoral zone, did not differ significantly between the extreme-flood and low-water years. Patterns of growth of black crappie (Pomoxis nigromaculatus), which have intermediate dependence on the moving littoral zone, were somewhat ambiguous. These results are consistent with the hypothesis that the FPC applies, at least under certain conditions, to this temperate river system. Our results can also provide an important basis from which to assess some costs and benefits of water level management strategies in large regulated temperate rivers.

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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 among-population recombination and thus be selected for, but few studies have tested this hypothesis with empirical data. Here, we used RADseq to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We then conducted genome scans for genomic islands of divergence to examine the distribution of adaptive loci and investigated whether these loci were found in inversions. We found that gene flow varied among species, and adaptive loci were clustered more tightly in species with higher gene flow. For example, the two species with the highest overall F ST (0.03 -0.07) and therefore lowest gene flow showed little evidence of clusters of adaptive loci, with adaptive loci spread uniformly across the genome. In contrast, nearly all adaptive loci in the species with the lowest F ST (0.0004) were found in a single large putative inversion. Two other species with intermediate gene flow (F ST ~ 0.004) also showed clustered genomic architectures, with most islands of divergence clustered on a few chromosomes. These results provide important empirical evidence to support the hypothesis that increasingly clustered architectures of local adaptation are associated with high gene flow. Our study utilized a unique system with species spanning a large gradient of life histories to highlight the importance of gene flow in shaping adaptive divergence.

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 among-population recombination and thus be selected for, but few studies have tested this hypothesis with empirical data. Here, we used RADseq to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We then conducted genome scans for genomic islands of divergence to examine the distribution of adaptive loci and investigated whether these loci were found in inversions. We found that gene flow varied among species, and adaptive loci were clustered more tightly in species with higher gene flow. For example, the two species with the highest overall FST (0.03 - 0.07) and therefore lowest gene flow showed little evidence of clusters of adaptive loci, with adaptive loci spread uniformly across the genome. In contrast, nearly all adaptive loci in the species with the lowest FST (0.0004) were found in a single large putative inversion. Two other species with intermediate gene flow (FST ~ 0.004) also showed clustered genomic architectures, with most islands of divergence clustered on a few chromosomes. These results provide important empirical evidence to support the hypothesis that increasingly clustered architectures of local adaptation are associated with high gene flow. Our study utilized a unique system with species spanning a large gradient of life histories to highlight the importance of gene flow in shaping adaptive divergence.

We applied an Index of Biotic Integrity (IBI) used on Wisconsin/Minnesota waters of the upper Mississippi River (UMR) to compare data from two systemic sampling programmes. Ability to use data from multiple sampling programmes could extend spatial and temporal coverage of river assessment and monitoring efforts. We normalized for effort and tested fish community data collected by the Environmental Monitoring and Assessment Program‐Great Rivers Ecosystems (EMAP‐GRE) 2004–2006 and the Long Term Resource Monitoring Program (LTRMP) 1993–2006. Each programme used daytime electrofishing along main channel borders but with some methodological and design differences. EMAP‐GRE, designed for baseline and, eventually, compliance monitoring, used a probabilistic, continuous design. LTRMP, designed primarily for baseline and trend monitoring, used a stratified random design in five discrete study reaches. Analysis of similarity indicated no significant difference between EMAP‐GRE and LTRMP IBI scores (n = 238; Global R = −0.052; significance level = 0.972). Both datasets distinguished clear differences only between ‘Fair’ and ‘Poor’ condition categories, potentially supporting a ‘pass–fail’ assessment strategy. Thirteen years of LTRMP data demonstrated stable IBI scores through time in four of five reaches sampled. LTRMP and EMAP‐GRE IBI scores correlated along the UMR's upstream to downstream gradient (df [3, 25]; F = 1.61; p = 0.22). A decline in IBI scores from upstream to downstream was consistent with UMR fish community studies and a previous, empirically modelled human disturbance gradient. Comparability between EMAP‐GRE (best upstream to downstream coverage) and LTRMP data (best coverage over time and across the floodplain) supports a next step of developing and testing a systemic, multi‐metric fish index on the UMR that both approaches could inform. Copyright © 2011 John Wiley & Sons, Ltd.