While the ecology and evolution of partial migratory systems (defined broadly to include skip spawning) have been well studied, we are only beginning to understand how partial migratory populations are responding to ongoing environmental change. Environmental change can lead to differences in the fitness of residents and migrants, which could eventually lead to changes in the frequency of the strategies in the overall population. Here, we address questions concerning the life history of the endangered Gila cypha (humpback chub) in the regulated Colorado River and the unregulated tributary and primary spawning area, the Little Colorado River. We develop eight multistate models for the population based on three movement hypotheses, in which states are defined in terms of fish size classes and river locations. We fit these models to mark–recapture data collected in 2009–2012. We compare survival and growth estimates between the Colorado River and Little Colorado River and calculate abundances for all size classes. The best model supports the hypotheses that larger adults spawn more frequently than smaller adults, that there are residents in the spawning grounds, and that juveniles move out of the Little Colorado River in large numbers during the monsoon season (July–September). Monthly survival rates for G. cypha in the Colorado River are higher than in the Little Colorado River in all size classes; however, growth is slower. While the hypothetical life histories of life-long residents in the Little Colorado River and partial migrants spending most of its time in the Colorado River are very different, they lead to roughly similar fitness expectations when we used expected number of spawns as a proxy. However, more research is needed because our study period covers a period of years when conditions in the Colorado River for G. cypha are likely to have been better than has been typical over the last few decades.

The abundance of the Little Colorado River population of federally listed humpback chub Gila cypha in Grand Canyon has been monitored since the late 1980s by means of catch rate indices and capture–recapture‐based abundance estimators. Analyses of data from all sources using various methods are consistent and indicate that the adult population has declined since monitoring began. Intensive tagging led to a high proportion (>80%) of the adult population being marked by the mid‐1990s. Analysis of these data using both closed and open abundance estimation models yields results that agree with catch rate indices about the extent of the decline. Survival rates for age‐2 and older fish are age dependent but apparently not time dependent. Back‐calculation of recruitment using the apparent 1990s population age structure implies periods of higher recruitment in the late 1970s to early 1980s than is now the case. Our analyses indicate that the U.S. Fish and Wildlife Service recovery criterion of stable abundance is not being met for this population. Also, there is a critical need to develop new abundance indexing and tagging methods so that early, reliable, and rapid estimates of humpback chub recruitment can be obtained to evaluate population responses to management actions designed to facilitate the restoration of Colorado River native fish communities.

The lower perennial corridor of the Little Colorado River in Grand Canyon, Arizona, is numerically dominated by endemic desert fishes and therefore significant for conservation of these species. From 2000 to 2012, the U.S. Fish and Wildlife Service conducted monitoring of native fishes in the Little Colorado River near its confluence with the Colorado River. The primary focus of these efforts was to estimate the spring and fall abundance of native fishes, especially the federally endangered humpback chub Gila cypha. Because humpback chub in Grand Canyon are influenced by operations of Glen Canyon Dam, our efforts provide managers of the Glen Canyon Dam Adaptive Management Program with abundance estimates and trends of humpback chub in the Little Colorado River, the most important tributary in Grand Canyon for spawning and production of this species. From 2001 to 2006, the spring abundance estimates of humpback chub ≥150 and ≥200 mm remained relatively low (≤3,419 and ≤2,002 fish, respectively), thereafter significantly increasing to highs of 8,083 and 6,250, respectively, by spring 2010. Also from 2000 to 2006, the fall abundance estimates of humpback chub were substantially below those abundances estimated after 2006. In addition, flannelmouth sucker Catostomus latipinnis and bluehead sucker Catostomus discobolus showed post-2006 increases in relative abundance, suggesting a systemwide event occurred that was beneficial to native fishes. Most of the increases of humpback chub occurred during the spring season in the reaches of the Little Colorado River between 5 and 13.57 km upstream from the confluence. Successful production of age 0 year classes of humpback chub may be partially driven by hydrograph dynamics of the Little Colorado River, whereas water temperatures and predation pressures in the mainstem Colorado River likely influence survivorship of native fishes into subadult and adult life stages.