Executive Summary: Our project combined field surveys of fish communities and habitat characteristics with estimates of population genetic structure to identify and evaluate critical factors influencing fish communities in the Gila River basin of New Mexico. Fish communities were structured along a strong habitat gradient associated with stream size, with distinct differences in the distribution of native and nonnative fishes. Nonnative warm-water species generally occurred in mainstem habitats, whereas coldwater nonnative salmonids occurred in high elevation tributaries. Habitat affinities of native species varied, with some occurring in mainstem habitats and others in tributaries. Several native species, such as desert sucker Pantosteus clarkii, Sonora sucker Catostomus insignis, and longfin dace Agosia chrysogaster, were abundant across a broad range
of habitats. Characterizing differences of dispersal among species was attempted with tagging studies (via passive integrated transponder PIT tagging) and otolith microchemistry. Contrasting movement patterns among species with different life history traits was hampered by low abundances and limited recaptures of most species. Unexpected variability in otolith crystalline
structure also confounded the use of otoliths to identify differences in natal and adult habitat. Nevertheless, we were able to make inferences on dispersal by investigating patterns of genetic structure. For our genetic analyses, we first used the conceptual framework developed by Winemiller and Rose (1992) to classify fishes based on key ecological traits and then matched those trait classifications with patterns of genetic diversity. Genetic assays identified different patterns of genetic structure and diversity that were somewhat related to species life history characteristics. These patterns ranged from moderate levels of spatial structure in small-bodied, short-lived species indicating dispersal limitation to almost no spatial structure in large-bodied species without dispersal limitation. Nonnative equilibrium strategists had limited distributions, indicating limited dispersal, strong habitat preference, or both. Finally, we used Bayesian networks to visualize the associations between the persistence of federally endangered species and measures of nonnative predator biomass, system productivity, wildfire and distance from source populations. Both distance from source populations and the presence of nonnative predators could negatively influence the persistence of these species. Combined, the experiments conducted during this project emphasize the importance of both habitat heterogeneity and dispersal processes as major structuring factors of Gila River fish communities. Conservation actions should aim to maintain connectivity among diverse habitats within the upper Gila River basin.
