Long-term Dynamics of Large-bodied Fishes Assessed from Spatially Intensive Monitoring of a Managed Desert River

Imperilment of native fishes worldwide, and particularly in the American Southwest, has prompted management actions to protect and recover threatened populations. Implementation of management activities, however, often proceeds without clear understandings of ecological interactions between native fishes and other biotic and physical components of the environment. Using data obtained in a 19-year, intensive monitoring effort across 288 km of the San Juan River in NM and UT, USA, we quantified relationships among large-bodied fishes and longitudinal environmental gradients, tested for faunal breaks of fishes and habitat structure along the river's course, and assessed the response of fishes to mechanical removal of non-native fishes and stocking of endangered fishes. Mesohabitat variation was not strongly linked to densities of large-bodied fishes, but we found strong and temporally consistent longitudinal patterns of native and non-native fishes: Native fish densities were highest upstream while non-native fish densities where highest downstream, potentially driven by differential responses to temperature regimes. Two breaks in the longitudinal structure of large-bodied fishes were identified and were associated with a man-made barrier and changes in the width of the river's floodplain. While densities of common native fishes were relatively constant during the study, non-native fish removal apparently reduced densities of one of two targeted species and densities of two endangered fishes increased as a result of stocking hatchery-reared fish. Results of this study suggest that large-bodied fishes of the San Juan River are responding to large-scale longitudinal gradients rather than small-scale habitat variation and management activities have altered densities of target species with limited responses by other fishes in the system. Copyright © 2014 John Wiley & Sons, Ltd.