**3. Conservation implications**

Our study highlights three important fish conservation aspects in a river basin: (1) the consideration of multiple spatial scales for directing conservation, (2) the tradeoffs of assemblage level (i.e., multiple species) conservation, and (3) the implications of ignoring detection error. Although beyond the scope here, the minnow occurrence relationships can also be used for predictive simulations under different flow regime and fragmentation scenarios. For example, changes in species distributions could be predicted under different levels of dam removal or long-term changes in flow magnitude with increased drought (or both).

### **3.1 Multiscale fish conservation strategies**

The occurrence and relative abundance relationships for prairie chub can be used to identify target areas in the stream network with a higher chance of habitat restoration or reintroduction success. Spatial position has been shown to be strongly associated with the structure of fish populations and assemblages [5, 98, 99]. Prairie chub's distribution in the upper Red River basin is severely constrained by upstream dams (**Figure 2d**). There is essentially no probability of prairie chub occurring below heavily dammed HRUs, presumably due to connectivity requirements for pelagophil reproduction (see Section 1.3). Thus, finer-scale conservation actions (e.g., reintroduction or instream habitat enhancements) in these HRUs would be futile and waste available resources. The most favorable HRUs in the upper Red River stream network for prairie chub occurrence are along the mainstem or higher-order tributaries (i.e., higher long-term flow magnitude), with low upstream dam density and more constancy in rate of change. In particular, HRUs along the Wichita River without prairie chub detections had a high occurrence probability (**Figures 1** and **3c**). If feasible, increasing flow in HRUs with lower dam density could increase the range of the favorable area. Spatial position was also associated with reach-scale prairie chub relative abundance. All high adult counts were associated with reaches in the eastern portion of the study area and higher discharge (**Figure 4a** and **c**). Longitude and discharge were somewhat confounded, and we did not consider the effect of each with the other held constant (see Section 2.3). The number of low-flow days increases further east in the upper Red River basin [75]. However, stream discharge was variable at both the HRU and reach scale. Thus, management actions targeting prairie chub would likely be most effective at reaches in high occurrence probability HRUs in the eastern portion of the study area with higher average flow magnitude. Higher prairie chub relative abundance was also associated with intermediate salinity levels (**Figure 4c**). Salinity has been shown to be strongly associated with fish assemblage structure in Great Plains streams [100], and a quadratic relationship with population size makes sense ecologically for a freshwater species adapted to semiarid streams. However, salinity is highly variable across both space and time in the upper Red River basin [101]. There is also a salinity gradient at the ecotone with the Cross Timbers that constrains prairie chub's eastern distribution and forms a hybrid zone with shoal chub *Macrhybopsis hyostoma* [71]. Thus, to effectively implement a salinity target for prairie chub conservation, improved salinity monitoring would be needed. The findings for our study period are likely reflective of multiscale prairie chub ecological relationships in both wet and dry periods. Occurrence probability among HRUs has been shown to be similar in both wet and dry periods [56], and reach-scale adult counts were collected during a relatively wet period [97].

### **3.2 Assemblage-level fish conservation**

The mixed occurrence relationships among minnows with flow regime and fragmentation have implications for upper Red River basin conservation strategies. It is important that managers consider conservation actions that benefit target species without detrimental effects to other native fishes in the assemblage. Reducing variability in annual maxima timing and removing upstream dams might be beneficial for prairie chub. However, emerald shiner and suckermouth minnow have high occurrence probabilities in the northern portion of the study area where these changes might take place. Unless the mechanism(s) driving the distributions of emerald shiner and suckermouth minnow is better understood, it is possible for conservation actions designed to improve conditions for prairie chub to incidentally harm other species. Fragmentation might prevent prairie chub from successful upstream movement that is important for completing the pelagophil life cycle [58, 102]. However, emerald shiner and suckermouth minnow are more widespread and might be able to adapt to a wider variety of conditions including fragmented river systems (e.g., phenotypic plasticity, [103, 104]). Although prairie chub and emerald shiner are both pelagophils, there is evidence that emerald shiner is less sensitive to flow disturbances than some other pelagophil species [105] and portions of some pelagophil populations are residents that do not make upstream spawning movements [106, 107]. Emerald shiner is also adapted to lentic environments [108] and may benefit competitively in habitats near reservoirs. Because suckermouth minnow is not a pelagophil species, it might not require long unimpeded lengths of river for spawning. It is also possible that another unmeasured or confounding habitat metric is the driver of the emerald shiner and suckermouth minnow distributions. It is prudent to balance conservation efforts to benefit target species while maintaining habitat for other natives. For example, strategic dam removal in the northern portion of the upper Red River basin could benefit prairie chub while preserving habitat favorable to emerald shiner and suckermouth minnow. Also, consideration of flow-regime patterns that benefit numerous minnows (e.g., increased flow constancy) or may not affect other species (e.g., increasing flow magnitude) provide a balanced assemblage-level conservation approach.

### **3.3 Imperfect and variable detection**

Species occurrence is never perfectly observed (i.e., detection is imperfect), and detection probability varies differently among species and sampling methods across sampling conditions [86, 109, 110]. Thus, ignoring detection error results in only naïve occurrence and apparent species distributions (i.e., true distributions are always larger than observed). In addition to underestimating true occurrence, a high detection probability can be misinterpreted as high habitat suitability and lead to misinformed conservation strategies [110–112]. Species-specific fish detection probability varies in relation to numerous environmental characteristics (e.g., water depth,
