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).