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Traps are among the most common gears used to capture fish and crustaceans. When traps are deployed in surveys, the data gathered are often used to develop an index of abundance. However, trap catches are known to saturate over time for various reasons, such as space limitation of the gear or intraspecific interactions, and these features can dissociate the catch from local abundance. In this study, we develop a hierarchical state-space model of trap dynamics that is fit to data in a Bayesian framework. The model links trap catch to estimated local abundance, and additionally provides direct estimates of capture probability. For demonstration, we apply the model to data on black sea bass (Centropristis striata), which were collected using chevron traps combined with video cameras to give continuous-time observations of trap entries and exits. Results are consistent with the hypothesis that trap catch is generally proportional to local abundance. The model has potential application to surveys where animals not only enter a trap, but also may exit, such that the apparent trap saturation occurs because the system approaches equilibrium. [ABSTRACT FROM AUTHOR]

Occupancy models using incidence data collected repeatedly at sites across the range of a population are increasingly employed to infer patterns and processes influencing population distribution and dynamics. While such work is common in terrestrial systems, fewer examples exist in marine applications. This disparity likely exists because the replicate samples required by these models to account for imperfect detection are often impractical to obtain when surveying aquatic organisms, particularly fishes. We employ simultaneous sampling using fish traps and novel underwater camera observations to generate the requisite replicate samples for occupancy models of red snapper, a reef fish species. Since the replicate samples are collected simultaneously by multiple sampling devices, many typical problems encountered when obtaining replicate observations are avoided. Our results suggest that augmenting traditional fish trap sampling with camera observations not only doubled the probability of detecting red snapper in reef habitats off the Southeast coast of the United States, but supplied the necessary observations to infer factors influencing population distribution and abundance while accounting for imperfect detection. We found that detection probabilities tended to be higher for camera traps than traditional fish traps. Furthermore, camera trap detections were influenced by the current direction and turbidity of the water, indicating that collecting data on these variables is important for future monitoring. These models indicate that the distribution and abundance of this species is more heavily influenced by latitude and depth than by micro-scale reef characteristics lending credence to previous characterizations of red snapper as a reef habitat generalist. This study demonstrates the utility of simultaneous sampling devices, including camera traps, in aquatic environments to inform occupancy models and account for imperfect detection when describing factors influencing fish population distribution and dynamics. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Introductions of nonnative salmonids, such as rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta, have affected native fishes worldwide in unforeseen and undesirable ways. Predation and other interactions with nonnative rainbow trout and brown trout have been hypothesized as contributing to the decline of native fishes (including the endangered humpback chub Gila cypha) in the Colorado River, Grand Canyon. A multiyear study was conducted to remove nonnative fish from a 15-km segment of the Colorado River near the Little Colorado River confluence. We evaluated how sediment, temperature, fish prey availability, and predator abundance influenced the incidence of piscivory (IP) by nonnative salmonids. Study objectives were addressed through spatial (upstream and downstream of the Little Colorado River confluence) and temporal (seasonal and annual) comparisons of prey availability and predator abundance. Data were then evaluated by modeling the quantity of fish prey ingested by trout during the first 2 years (2003-2004) of the mechanical removal period. Field effort resulted in the capture of 20,000 nonnative fish, of which 90% were salmonids. Results indicated that the brown trout IP was higher (8-70%) than the rainbow trout IP (0.5-3.3%); however, rainbow trout were 50 times more abundant than brown trout in the study area. We estimated that during the study period, over 30,000 fish (native and nonnative species combined) were consumed by rainbow trout (21,641 fish) and brown trout (11,797 fish). On average, rainbow trout and brown trout ingested 85% more native fish than nonnative fish in spite of the fact that native fish constituted less than 30% of the small fish available in the study area. Turbidity may mediate piscivory directly by reducing prey detection, but this effect was not apparent in our data, as rainbow trout IP was greater when suspended sediment levels (range = 5.9-20,000 mg/L) were higher. [ABSTRACT FROM AUTHOR]

The federally endangered humpback chub Gila cypha in the Colorado River within Grand Canyon is currently the focus of a multiyear program of ecosystem-level experimentation designed to improve native fish survival and promote population recovery as part of the Glen Canyon Dam Adaptive Management Program. A key element of this experiment was a 4-year effort to remove nonnative fishes from critical humpback chub habitat, thereby reducing potentially negative interactions between native and nonnative fishes. Over 36,500 fish from 15 species were captured in the mechanical removal reach during 2003-2006. The majority (64%) of the catch consisted of nonnative fish, including rainbow trout Oncorhynchus mykiss (19,020), fathead minnow Pimephales promelas (2,569), common carp Cyprinus carpio (802), and brown trout Salmo trutta (479). Native fish (13,268) constituted 36% of the total catch and included flannelmouth suckers Catostomus latipinnis (7,347), humpback chub (2,606), bluehead suckers Catostomus discobolus (2,243), and speckled dace Rhinichthys osculus (1,072). The contribution of rainbow trout to the overall species composition fell steadily throughout the study period from a high of approximately 90% in January 2003 to less than 10% in August 2006. Overall, the catch of nonnative fish exceeded 95% in January 2003 and fell to less than 50% after July 2005. Our results suggest that removal efforts were successful in rapidly shifting the fish community from one dominated numerically by nonnative species to one dominated by native species. Additionally, increases in juvenile native fish abundance within the removal reach suggest that removal efforts may have promoted greater survival and recruitment. However, drought-induced increases in river water temperature and a systemwide decrease in rainbow trout abundance concurrent with our experiment made it difficult to determine the cause of the apparent increase in juvenile native fish survival and recruitment. Experimental efforts continue and may be able to distinguish among these factors and to better inform future management actions. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We present a new model to estimate capture probabilities, survival, abundance, and recruitment using traditional Jolly-Seber capture-recapture methods within a standard fisheries virtual population analysis framework. This approach compares the numbers of marked and unmarked fish at age captured in each year of sampling with predictions based on estimated vulnerabilities and abundance in a likelihood function. Recruitment to the earliest age at which fish can be tagged is estimated by using a virtual population analysis method to back-calculate the expected numbers of unmarked fish at risk of capture. By using information from both marked and unmarked animals in a standard fisheries age structure framework, this approach is well suited to the sparse data situations common in long-term capture-recapture programs with variable sampling effort. [ABSTRACT FROM AUTHOR]