2 | METHODS
2.1 | Study system - river regulation and fish community changes
The San Juan River is the second largest tributary in the Colorado River Basin (Thompson, 1982) and has undergone severe hydrological alteration and fragmentation (Figure 1). Construction of Glen Canyon Dam in 1957 on the Colorado River created Lake Powell inundating lower reaches of the San Juan River. The upper reaches were further fragmented by Navajo Dam, completed in 1962; and altered the river’s natural flow regime by limiting spring peak flows and elevating summer base flows (Propst and Gido, 2004). Currently, the San Juan River consists of approximately 360 km of riverine habitat. In the 1990s, river ecologists began highlighting the importance of a river’s annual peak discharge in creating fish habitat as high flows can create and maintain fish habitat through increased channel heterogeneity (Poff, 1997; Van Steeter and Pitlick, 1998). This research supported the establishment of Navajo Dam flow recommendations developed to mimic the timing, frequency, and duration of the San Juan River’s natural hydrology albeit at reduced magnitudes (Holden, 1999; Pennock et al ., 2022). Although Navajo Dam operators attempted to meet these flow recommendations, continued significant deviations from the natural hydrograph and the establishment of nonnative vegetation likely continued to simplify and narrow the river’s channel which precluded inundation of the floodplain (Gidoet al ., 2013; Bassett, 2015; Franssen et al ., 2015).
The naturally depauperate San Juan River fish community experienced compositional changes prior to and after river regulation. Nonnative Channel Catfish (Ictalurus punctatus ) was stocked into the Colorado River Basin for food and recreation in the late 1800s and is the second most abundant large-bodied fish in the San Juan River (Franssen et al ., 2016, Fuller and Neilson, 2022). Common small-bodied nonnative fishes like Fathead Minnow (Pimephales promelas ) occupied the system prior to the closure of Navajo Dam but Red Shiner (Cyprinella lutrensis ), which is often the most abundant small-bodied fish, likely established a population in the 1980s (Franssen et al ., 2015; Nico et al ., 2022; accession records University of New Mexico Museum of Southwestern Biology [MSB]). The native fish community consists of five large-bodied endemic Colorado River Basin species: Bluehead Sucker (Catostomus discobolus ), Flannelmouth Sucker (Catostomus latipinnis ), endangered Razorback Sucker (Xyrauchen texanus ), Roundtail Chub (Gila robusta ), and endangered Colorado Pikeminnow (Ptychocheilus lucius ). The remaining two native species are small-bodied Speckled Dace (Rhinichthys osculus ) and Mottled Sculpin (Cottus bairdii ). Although there are no data on fish abundances prior to construction of Navajo Dam, monitoring of an application of a lethal chemical treatment downstream of Navajo Dam in the 1960s indicated the most common species collected in this location were Flannelmouth Sucker and Roundtail Chub (Olson, 1962). Due to a lack of natural recruitment, populations of Colorado Pikeminnow and Razorback Sucker only persist in the San Juan River through ongoing hatchery augmentation and Roundtail Chub is functionally extirpated (Franssenet al ., 2016).