Rehabilitation of large Anthropocene rivers requires engagement of diverse stakeholders across a broad range of sociopolitical boundaries. Competing objectives often constrain options for ecological restoration of large rivers whereas fewer competing objectives may exist in a subset of tributaries. Further, tributaries contribute toward building a “portfolio” of river ecosystem assets through physical and biological processes that may present opportunities to enhance the resilience of large river fishes. Our goal is to review roles of tributaries in enhancing mainstem large river fish populations. We present case histories from two greatly altered and distinct large-river tributary systems that highlight how tributaries contribute four portfolio assets to support large-river fish populations: 1) habitat diversity, 2) connectivity, 3) ecological asynchrony, and 4) density-dependent processes. Finally, we identify future research directions to advance our understanding of tributary roles and inform conservation actions. In the Missouri River United States, we focus on conservation efforts for the state endangered lake sturgeon, which inhabits large rivers and tributaries in the Midwest and Eastern United States. In the Colorado River, Grand Canyon United States, we focus on conservation efforts for recovery of the federally threatened humpback chub. In the Missouri River, habitat diversity focused on physical habitats such as substrate for reproduction, and deep-water habitats for refuge, whereas augmenting habitat diversity for Colorado River fishes focused on managing populations in tributaries with minimally impaired thermal and flow regimes. Connectivity enhancements in the Missouri River focused on increasing habitat accessibility that may require removal of physical structures like low-head dams; whereas in the Colorado River, the lack of connectivity may benefit native fishes as the disconnection provides refuge from non-native fish predation. Hydrologic variability among tributaries was present in both systems, likely underscoring ecological asynchrony. These case studies also described density dependent processes that could influence success of restoration actions. Although actions to restore populations varied by river system, these examples show that these four portfolio assets can help guide restoration activities across a diverse range of mainstem rivers and their tributaries. Using these assets as a guide, we suggest these can be transferable to other large river-tributary systems.

We designed a flexible protocol for monitoring fish species richness in nonwadeable rivers. Nine sites were sampled seasonally with six gears in two physiographic regions in Missouri (USA). Using resampling procedures and mixed-effects modeling, we quantified richness and compositional overlap among gears, identified efficient gear combinations, and evaluated protocol performance across regions and seasons. We detected 25–75 species per sample and 89 185 fish. On average, no single gear detected >62% of observed species, but an optimized, integrated-gear protocol with four complementary gears on average detected 90% of species while only requiring 51.9% of initial sampling effort. Neither season nor physiographic region explained low spatiotemporal variation in percent richness detected by the integrated-gear protocol. In contrast, equivalent effort with an electrofishing-only protocol was 53.5% less efficient, seasonally biased and imprecise (36.1%–82.3% of richness), and on average detected 15.9% less of observed richness. Altogether, riverine fish richness is likely underestimated with single-gear survey designs. When paired with existing wadeable-stream inventories, our customizable approach could benefit regional monitoring by comprehensively documenting riverine contributions to riverscape biodiversity.

Conservation practitioners increasingly recognize the conservation value of tributaries for supporting mainstem, large-river specialist fishes. A tributary's discharge at its mouth is a coarse indicator of the richness of large-river specialists found within the tributary, but the relative influences of regional dispersal and local habitat underpinning this species-discharge relationship are often unknown. We sampled large-river specialist fishes at sites within two nonwadeable tributaries of the Missouri and Mississippi rivers with contrasting prairie (Grand River) vs. upland (Meramec River) habitats to address four research questions: (1) Do alpha diversity (mean site-level species richness) and beta diversity (among-site species compositional differences) vary between tributaries? (2) Does mean annual discharge correlate with local habitat and downstream distance to mainstem rivers (i.e., mainstem connectivity)? (3) Are slopes of species-discharge relationships consistent between tributaries? And (4) Do local habitat and downstream distance explain residual richness at sites beyond variation already explained by species-discharge relationships? We detected 30 of 42 potential large-river specialist fishes, demonstrating most mainstem species use tributaries. Mean site richness was higher in the Grand River (12.5 species vs. 9.8 species in Meramec River), but partitioning of lower reaches (sites < 116 km from river mouth) and dispersal limitation in upper reaches (sites ≥ 145 km from river mouth) caused Meramec River beta diversity to be three times higher. Mean annual discharge correlated with habitat availability at sites and downstream distance to a mainstem. Although site-level alpha richness generally increased with discharge in both tributaries, slopes of species-discharge relationships varied between tributaries. Analyzing species-discharge residuals revealed downstream distance explained additional variation in site-level richness not accounted for by local discharge. For example, discharge alone underrepresented richness in lower-discharge sites accessible to dispersers (maximum underestimate = 8.7 species) and overrepresented richness in isolated sites (maximum overestimate = 5.8 species). Thus, predictive performance of species-discharge relationships can be improved by accounting for varying habitats among tributaries and downstream distance of sites to mainstems when valuing tributaries for fishes with dispersal-dependent life cycles.

Understanding relationships between habitat associations for individuals and habitat factors that limit populations is a primary challenge for managers of stream fishes. Although habitat use by individuals can provide insight into the adaptive significance of selected microhabitats, not all habitat parameters will be significant at the population level, particularly when distributional patterns partially result from habitat degradation. We used underwater observation to quantify microhabitat selection by an imperiled stream fish, the Candy Darter Etheostoma osburni, in two streams with robust populations. We developed multiple‐variable and multiple‐life‐stage habitat suitability indices (HSIs) from microhabitat selection patterns and used them to assess the suitability of available habitat in streams where Candy Darter populations were extirpated, localized, or robust. Next, we used a comparative framework to examine relationships among (1) habitat availability across streams, (2) projected habitat suitability of each stream, and (3) a rank for the likely long‐term viability (robustness) of the population inhabiting each stream. Habitat selection was characterized by ontogenetic shifts from the low‐velocity, slightly embedded areas used by age‐0 Candy Darters to the swift, shallow areas with little fine sediment and complex substrate, which were used by adults. Overall, HSIs were strongly correlated with population rank. However, we observed weak or inverse relationships between predicted individual habitat suitability and population robustness for multiple life stages and variables. The results demonstrated that microhabitat selection by individuals does not always reflect population robustness, particularly when based on a single life stage or season, which highlights the risk of generalizing habitat selection that is observed during nonstressful periods or for noncritical resources. These findings suggest that stream fish managers may need to be cautious when implementing conservation measures based solely on observations of habitat selection by individuals and that detailed study at the individual and population levels may be necessary to identify habitat that limits populations. Received March 30, 2016; accepted July 19, 2016Published online October 7, 2016