EXECUTIVE SUMMARY In 1967, the humpback chub (Gila cypha) (HBC) was added to the federal list of endangered species and is today protected under the Endangered Species Act of 1973. Only six populations of humpback chub are currently known to exist, five in the Colorado River Basin above Lees Ferry, Arizona, and one in Grand Canyon, Arizona. The majority of Grand Canyon humpback chub are found in the Little Colorado River (LCR)-the largest tributary to the Colorado River in Grand Canyon-and the Colorado River near its confluence with the Little Colorado River. Monitoring and research of the Grand Canyon humpback chub population is overseen by the U.S. Geological Survey's (USGS) Grand Canyon Monitoring and Research Center (GCMRC) under the auspices of the Glen Canyon Dam Adaptive Management Program (GCDAMP), a Federal initiative to protect and improve resources downstream of Glen Canyon Dam. This report provides updated information on the status and trends of the LCR population in light of new information and refined assessment methodology. An earlier assessment of the LCR population (Coggins and others, 2006a) used data collected during 1989?2002; the assessment provided here includes that data and additional data collected through 2006. Catch-rate indices, closed population mark-recapture model abundance estimates, results from the original age-structured mark recapture (ASMR) model (Coggins and others, 2006b), and a newly refined ASMR model are presented. This report also seeks to (1) formally evaluate alternative stock assessment models using Pearson residual analyses and information theoretic procedures, (2) use mark-recapture data to estimate the relationship between HBC age and length, (3) translate uncertainty in the assignment of individual fish age to resulting estimates of recruitment and abundance from the ASMR model, and (4) evaluate past and present stock assessments considering the available data sources and analyses, recognizing the limitations inherent in both. A major task of this study was to improve the overall methodology used to conduct HBC stock assessment by addressing concerns identified in an independent review conducted in 2003 (Kitchell and others, 2003). The review report identified that the current technique of assigning age to individual fish based on length was a potential source of bias in ASMR estimates of abundance and recruitment, and called for a more complete examination of this potential error source. Additionally, the review suggested that further work to develop procedures to better arbitrate among alternative assessment models (e.g., ASMR 1?3) would be beneficial. To address the first of the concerns identified by the independent review, this study uses mark-recapture data to develop a temperature-dependent growth model to characterize the relationship between HBC age and length. This model attempts to account for temperature differences resulting from both ontogenetic habitat shifts between the Little Colorado and the mainstem Colorado Rivers as well as seasonal variation in water temperature within the LCR. The resulting growth model is then used to characterize the error in assigning age to individual fish based on length. Results presented in this study suggest that ageing error does not result in large bias in either abundance or recruitment estimates from the ASMR model. However, incorporating ageing error into the assessment does result in less precise estimates, particularly for recruitment. To address the second concern brought forward in the review report related to model selection procedures, this study arbitrated among the competing models by both examining model fit using Pearson residual analyses and considering information theoretic measures. Although adult abundance estimates and trend varied little among all models considered, these procedures identified ASMR 3 as the model whose underlying assumptions were most consistent with the data. Because ASMR 3 is