Comment on “Assessing the potential for Smallmouth Bass population establishment in Grand Canyon”
No abstract available.
Arizona, Utah↗
Geology topics
Maria C. Dzul
Publications and source records attributed to Maria C. Dzul.
Growth of a threatened desert fish becomes resource dependent when released from temperature limitation in a regulated river
1. Growth of ectotherms typically positively correlates with increasing temperature towards an optimal temperature range, followed by a decline in growth when temperatures exceed the optimal temperature range for that organism. When temperature is within or close to the optimal range, food availability and other environmental factors can play important roles in modifying growth rates. River regulation often alters both environmental conditions (e.g., flow, turbidity and temperature) and aquatic food webs, modifying the quality and quantity of resources available to consumers. Here we aim to understand how food availability, water temperature and other environmental factors are associated with fish growth (defined here as a change in length) in a large, regulated desert river. 2. We measured growth of humpback chub (Gila cypha) at two river reaches located 240 km apart in the Colorado River within the Grand Canyon, Arizona, USA. We then fit Bayesian state-space models of growth that account for variable time at large to test environmental predictors such as water temperature, flow, turbidity (which increases during tributary flooding and can be a proxy for allochthonous inputs) and gross primary productivity (a proxy for autochthonous food) using an inclusion parameter approach. Both river reaches are located below Glen Canyon Dam, which regulates flow, alters seasonal water temperatures and traps sediment, nutrients, and organic carbon; however, merging tributaries and a greater distance from the dam lead to differences in environmental conditions. 3. In the upriver reach, where warm season water temperatures are below the optimal range for humpback chub most of the time, temperature was the primary driver of variation in growth according to inclusion parameter values and the strength of the standardised effect size. Turbidity was also included in the final model for the upper reach, but the inclusion parameter values and standardised effect size were smaller than for temperature. In the downriver, warmer reach, temperature still had the highest inclusion parameter value, but GPP had the highest standardised effect and nearly as high an inclusion parameter value. 4. We conclude that temperature is the primary limiting factor on growth of humpback chub in the Grand Canyon; however, as water temperatures increase, other factors, especially GPP, are associated with temporal variation in growth rates. Over the past two decades, declines in reservoir elevations and the volume of summer releases have increased downstream water temperatures. If warm temperatures persist into the future, other factors may have increasing roles in regulating interannual variability in chub growth. 5. Field studies of ectotherm growth often emphasise the role of water temperature; however, the role of resource availability is also increasingly recognised, especially in bioenergetics studies. Quantifying resource availability directly can be difficult, especially in large, remote rivers. Here, we show here that using proxies for resource availability (i.e., GPP as a proxy for autochthonous inputs) can yield useful insights regarding resource limitations with implications for management of federally listed fish species in a larger regulated river system.
Arizona↗
Integrating mark-recapture, catch, and expert habitat assessments to quantify recent increases in humpback chub abundance over a 200 km long river segment of the Colorado River in western Grand Canyon
Humpback chub, Gila cypha, were historically distributed throughout large portions of the Colorado River basin and were federally listed in 1967. In the Grand Canyon segment of the Colorado River, located below Glen Canyon Dam, chub abundances continued to decline through the early 2000s. Recently, catch has increased substantially, especially in the western Grand Canyon. Here, we integrate mark-recapture and catch data of subadult and adult humpback chub, with expert assessments of habitat suitability and an underlying model of spatial autocorrelation, to estimate abundance in western Grand Canyon from 2010 to 2024, a time of rapid population increase and expansion. Our model suggests that adult abundance grew ∼160 fold during this 15-year period, with a median adult population abundance of 70 000 (40 000–200 000; 95% credible interval) in 2024. Our approach identifies years with high population growth and indicates that the spatial distribution has changed over time. We test the sensitivity of our results to movement into sampling reaches during sampling with baited hoop nets. Despite rapid population growth, the resilience of humpback chub in western Grand Canyon is unknown.
Arizona↗
Status report on the Long-Term Experimental and Management Plan (LTEMP) Metrics for the Glen Canyon Dam adaptive management program
No abstract available.
Arizona, Nevada↗
Genetic structure of an expanding population of Humpback Chub in Grand Canyon
Objective Humpback Chub (HBC) Gila cypha in Grand Canyon declined in abundance and distribution over the latter part of the 20th century but have substantially increased in abundance and distribution over the past two decades. Although previous genetic work suggested that HBC in Grand Canyon belong to one genetic group, here we evaluate the genetic structure of HBC in Grand Canyon to determine whether relic populations in western Grand Canyon may have contributed unique variation to the recent population expansion or whether differences in behavior linked to migration in eastern Grand Canyon may promote assortative mating and heretofore unrecognized population structure. Methods Using fin clips collected from 167 individual HBC representing four sampling sites within Grand Canyon, we extracted DNA and developed data sets consisting of approximately 20,000 anonymous genomic loci. We quantified patterns of genetic diversity, and we accounted for outlier single-nucleotide polymorphisms to ensure that our interpretations of genetic patterns were not misled by adaptive processes and did not mask adaptively important genetic variation. Results Despite behavioral variation and the possibility that individuals with unique genetic variation survived in isolated warmwater sites within western Grand Canyon, HBC were not differentiated by sampling site or by differences in migratory behavior. Heterozygosity and nucleotide diversity were consistently high among sampling sites, and inbreeding coefficients were close to zero. Conclusions The HBC in Grand Canyon constitute a single genetic population. Our results do not preclude a genetic basis to migratory behavior, but our data suggest that this trait does not lead to assortative mating. Furthermore, while HBC may have survived in discontiguous warmwater refugia in western Grand Canyon during decades when the main stem was too cold for spawning, our data did not reveal any noticeable spatial variability in HBC genetics in the main stem after the recent HBC population expansion.
Arizona↗
The importance of sampling design for unbiased estimation of survival using joint live-recapture and live resight models
Survival is a key life history parameter that can inform management decisions and basic life history research. Because true survival is often confounded with emigration from the study area, many studies are forced to estimate apparent survival (i.e., probability of surviving and remaining inside the study area), which can be much lower than true survival for highly mobile species. One method for estimating true survival is the Barker joint live-recapture/live-resight (JLRLR) model, which combines capture data from a study area (hereafter the ‘capture site’) with resighting data from a broader geographic area. This model assumes that live resights occur throughout the entire area where animals can disperse to and this assumption is often not met in practice. Here we use simulation to evaluate survival bias from a JLRLR model under study design scenarios that differ in the site selection for resights: global, random, fixed including the capture site, and fixed excluding the capture site. Simulation results indicate that fixed designs that included the capture site showed negative survival bias, whereas fixed designs that excluded the capture site exhibited positive survival bias. The magnitude of the bias was dependent on movement and survival, where scenarios with high survival and frequent movement had minimal bias. In an effort to help minimize bias, we developed a multistate version of the JLRLR and demonstrated reductions in survival bias compared to the single-state version for most designs. Our results suggest minimizing bias can be accomplished by: 1) using a random resight design when feasible if global sampling is not possible, 2) using the multistate JLRLR model when appropriate, 3) including the capture site in the resight sampling frame when possible, and 4) reporting survival as apparent survival if fixed sites are used for resight with the single state JLRLR model.
Peer Community Journal↗
Estimating migration timing and abundance in partial migratory systems by integrating continuous antenna detections with physical captures
Many populations migrate between two different habitats (e.g. wintering/foraging to breeding area, mainstem–tributary, river–lake, river–ocean, river–side channel) as part of their life history. Detection technologies, such as passive integrated transponder (PIT) antennas or sonic receivers, can be placed at boundaries between habitats (e.g. near the confluence of rivers) to detect migratory movements of marked animals. Often, these detection systems have high detection probabilities and detect many individuals but are limited in their ability to make inferences about abundance because only marked individuals can be detected. Here, we introduce a mark–recapture modelling approach that uses detections from a double-array PIT antenna system to imply movement directionality from arrays and estimate migration timing. Additionally, when combined with physical captures, the model can be used to estimate abundances for both migratory and non-migratory groups and help quantify partial migration. We first test our approach using simulation, and results indicate our approach displayed negligible bias for total abundance (less than ±1%) and slight biases for state-specific abundance estimates (±1%–6%). We fit our model to array detections and physical captures of three native fishes (humpback chub [ Gila cypha ], flannelmouth sucker [ Catostomus latipinnis ] and bluehead sucker [ Catostomus discobolus ]) in the Little Colorado River (LCR) in Grand Canyon, AZ, a system that exhibits partial migration (i.e. includes residents and migrants). Abundance estimates from our model confirm that, for all three species, migratory individuals are much more numerous than residents. There was little difference in movement timing between 2021 (a year without preceding winter/spring floods) and 2022 (a year with a small flood occurring in early April). In both years, flannelmouth sucker arrived in mid-March whereas humpback chub and bluehead sucker arrivals occurred early- to mid-April. With humpback chub and flannelmouth sucker, movement timing was influenced by body size so that large individuals were more likely to arrive early compared to smaller individuals. With more years of data, this model framework could be used to evaluate ecological questions pertaining to flow cues and movement timing or intensity, relative trends in migrants versus residents and ecological drivers of skipped spawning.
Journal of Animal Ecology↗
U.S. Geological Survey Grand Canyon Monitoring and Research Center: Proceedings of the fiscal year 2023 annual reporting meeting to the Glen Canyon Dam Adaptive Management Program
This proceedings is prepared for the USBR and Glen Canyon Dam Adaptive Management Program (GCDAMP) to account for work conducted and products delivered in FY 2023 by SBSC's Grand Canyon Monitoring and Research Center (GCMRC) and to inform the Technical Work Group of science conducted by GCMRC and its cooperators in support of the GCDAMP. It includes a summary of accomplishments, modifications to work plans, and results related to projects included in GCMRC’s FY 2021-23 Triennial Work Plan. This work was done to support the 11 resource goals identified in the Glen Canyon Dam Long-Term Experimental and Management Plan (LTEMP) Environmental Impact Statement and Record of Decision.
Arizona, Nevada, Utah↗
Migration timing and tributary use of spawning flannelmouth sucker (Catostomus latipinnis)
Spawning phenology and associated migrations of fishes are often regulated by factors such as temperature and stream discharge, but flow regulation of mainstem rivers coupled with climate change might disrupt these cues and affect fitness. Flannelmouth sucker (Catostomus latipinnis) persisting in heavily modified river networks are known to spawn in tributaries that might provide better spawning habitat than neighboring mainstem rivers subject to habitat degradation (e.g., embedded sediments, altered thermal regimes, and disconnected floodplains). Passive integrative transponder (PIT) tag data and radio telemetry were used to quantify the timing and duration of flannelmouth sucker tributary spawning migrations in relation to environmental cues in McElmo Creek, a tributary to the San Juan River in the American Southwest. We also tested the extent of the tributary migration and assessed mainstem movements prior to and following tributary migrations. Additionally, multi-year datasets of PIT detections from other tributaries in the Colorado River basin were used to quantify interannual and cross-site variation in the timing of flannelmouth sucker spawning migrations in relation to environmental cues. The arrival and residence times of fish spawning in McElmo Creek varied among years with earlier migration and a three-week increase in residence time in relatively wet years compared to drier years. Classification tree analysis suggested a combination of discharge and temperature determined arrival timing. Of fish PIT tagged in the fall, 56% tagged within 10 km of McElmo Creek spawned in the tributary the following spring, as did 60% of radio-tagged fish, with a decline in its use corresponding to increased distance of tagging location. A broader analysis of four tributaries in the Colorado River basin, including McElmo Creek, found photoperiod and temperature of tributary and mainstem rivers were the most important variables in determining migration timing, but tributary and mainstem discharge also aided in classification success. The largest tributary, the Little Colorado River, had more residential fish or fish that stayed for longer periods (median = 30 days), while McElmo Creek fish stayed an average of just 10 days in 2022. Our results generally suggest that higher discharge, across years or across sites, results in extended use of tributaries by flannelmouth suckers. Conservation actions that limit water extraction and maintain natural flow regimes in tributaries, while maintaining open connection with mainstem rivers may benefit migratory species including flannelmouth suckers.
Journal of Fish Biology↗
Vital rates of a burgeoning population of Humpback Chub in western Grand Canyon
The Colorado River ecosystem has experienced habitat alterations and non-native species invasions, and as a result, many of its native species have experienced extirpations, abundance declines, and range constrictions. Despite these pitfalls, Humpback Chub, Gila cypha , have persisted and, in the last 10-15 years, expanded their range to become abundant in western Grand Canyon, a river segment in which it had been rare for the prior three decades. Here we analyze a 6-year mark-recapture study from a fixed monitoring reach in western Grand Canyon and provide the first estimates of survival and growth (vital rates) for this relatively ‘new’ group of Humpback Chub. We compare vital rates in western Grand Canyon to two life history forms (residents and migrants, which represent fast and slow life history trajectories, respectively) from the more established Little Colorado River (LCR) aggregation in eastern Grand Canyon. Compared to LCR-migrants and LCR-residents, Humpback Chub in western Grand Canyon had intermediate values for apparent survival, growth, and asymptotic length. Relatively high survival of subadults coupled with fast growth allows for rapid population growth in western Grand Canyon. However, a large cohort in 2017 failed to lead to noticeable increases in adults. Seasonal survival patterns were distinct in all three groups, and apparent survival was lowest in western Grand Canyon during spring months. Adult Humpback Chub in western Grand Canyon were mobile and had a high probability of transience (i.e., just passing through the reach) and temporary emigration, demonstrating the need for future movement studies in western Grand Canyon to better distinguish emigration from survival. We discuss how observations are related to disparate temperature regimes experienced by the three groups, and if(how) the relationship between metabolism and temperature influences vital rates within the river network.
Arizona↗
Proceedings of the Fiscal Year 2022 Annual Reporting Meeting to the Glen Canyon Dam Adaptive Management Program
(Hartwell) This report is prepared primarily to account for work conducted and products delivered in FY 2022 by GCMRC and to inform the Technical Work Group of science conducted by GCMRC and its cooperators in support of the Glen Canyon Dam Adaptive Management Program (GCDAMP). It includes a summary of accomplishments, modifications to work plans, results, and recommendations related to projects included in GCMRC’s FY 2021-23 Triennial Work Plan. This work was done to support the 11 resource goals identified in the Glen Canyon Dam Long-Term Experimental and Management Plan (LTEMP) Environmental Impact Statement and Record of Decision (Table 1).
Arizona↗
Incorporating antenna detections into abundance estimates of fish
Autonomous passive integrated transponder (PIT) tag antennas are commonly used to detect fish marked with PIT tags but cannot detect unmarked fish, creating challenges for abundance estimation. Here we describe an approach to estimate abundance from paired physical capture and antenna detection data in closed and open mark-recapture models. Additionally, for open models, we develop an approach that incorporates uncertainty in fish size, because fish size changes through time (as fish grow bigger) but is unknown if fish are not physically captured (e.g., only detected on antennas). Incorporation of size uncertainty allows for estimation of size-specific abundances and demonstrates a generally useful method for obtaining state-specific abundances estimates under state uncertainty. Simulation studies comparing models with and without antenna detections illustrate that the benefit of our approach increases as a larger proportion of the population is marked. When applied to two field data sets, our approach to incorporating antenna detections reduced uncertainty in abundance substantially. We conclude that PIT antennas hold great potential for improving abundance estimation, despite the challenges they present.
Canadian Journal of Fisheries and Aquatic Sciences↗
Assessing the population impacts and cost‐effectiveness of a conservation translocation
Managers often move, or translocate, organisms into habitats that are assumed to be suitable, however the consequences of these translocations are usually not rigorously assessed. Robust assessment of these management experiments should consider impacts to both donor and recipient populations and compare the cost‐effectiveness of translocations to other actions. Here we evaluate translocations of a federally listed fish species, humpback chub within a tributary to the Colorado River in its Grand Canyon reach (Arizona, USA). We analyze mark‐recapture data with multistate models to estimate vital rates (growth, survival, and movement) for the donor and recipient populations while accounting for substantial temporal variation in vital rates. We then use stochastic matrix projections to quantify the impact of translocations on adult population size. Lastly, we compare costs of translocations to another, legally required management action, non‐native fish removal, by modifying an existing bioeconomic model. We estimate that six of eight translocations during the study period positively impacted adult abundance and that the overall population impact was positive. Population projections suggest that each chub translocated per year increases the equilibrium adult population size by 1.2 (95% CI: 0.4 – 2.2) adults, lessening the need for non‐native fish removal. Continuation of translocations at the current rate is expected to save managers ~$50,000 per year by decreasing the annual probability of removals from 0.26 to 0.15. Further savings and decreases in removals could be attained by avoiding translocations in years when there has been no winter/spring runoff and modifying the number of translocated individuals based on estimates of juvenile production in the lower LCR. Synthesis and applications . Translocations that increase the abundance of a rare species can sometimes be viewed as a hedge against future declines that might necessitate more costly interventions. Quantifying population benefits and economic costs of management actions like translocations and comparing alternative actions can lead to cost effective conservation that is more easily sustained.
Arizona↗
Partial migration and spawning movements of humpback chub in the Little Colorado River are better understood using data from autonomous PIT tag antennas
Choosing whether or not to migrate is an important life history decision for many fishes. Here we combine data from physical captures and detections on autonomous passive integrated transponder (PIT) tag antennas to study migration in an endangered fish, the humpback chub (Gila cypha). We develop hidden Markov mark-recapture models with and without antenna detections and find that the model fit without antenna detections misses a large proportion of fish and underestimates migration and survival probabilities. We then assess survival and growth differences associated with life history strategy and migration for different demographic groups (small male, small female, large male, large female). We find large differences in survival according to life history strategy, where residents had much lower over-winter survival than migrants. However, within the migratory life history strategy, survival and growth were similar for active migrants and skipped migrants for all demographic groups. We discuss some common challenges to incorporating detections from autonomous antennas into population models and demonstrate how these data can provide insight about fish movement and life history strategies.
Arizona↗
Changes in prey, turbidity, and competition reduce somatic growth and cause the collapse of a fish population
Somatic growth exerts strong control on patterns in the abundance of animal populations via effects on maturation, fecundity, and survival rates of juveniles and adults. In this paper, we quantify abiotic and biotic drivers of rainbow trout growth in the Colorado River, AZ, and the resulting impact on spatial and temporal variation in abundance. Inferences are based on approximately 10,000 observations of individual growth grates obtained through an intensive mark‐recapture effort conducted over five years (2012‐2016) in a 130 km‐long study segment downstream of Glen Canyon Dam. Prey availability, turbidity‐driven feeding efficiency, and intra‐specific competition were the dominant drivers of rainbow trout growth. Discharge, water temperature, and solar insulation were also evaluated but had a smaller influence. Mixed‐effect models explained 79‐82% of the variability in observed growth rates, with fixed covariate effects explaining 79‐87% of the total variation in growth parameters across five reaches and 18 quarterly sampling intervals. Reductions in growth owing in part to a phosphorous‐driven decline in prey availability, led to substantive weight loss and poor fish condition. This in turn lowered survival rates and delayed maturation, which led to a rapid decline in abundance and later recruitments. Reductions in feeding efficiency, due to episodic inputs of fine sediment from tributaries, and warmer water temperatures, contributed to reduced growth in downstream reaches, which led to more severe declines in abundance. Somatic growth rates increased following the population collapse due to reduced competition, and in the absence of substantive increases in prey availability. Our study elucidates important linkages between abiotic and biotic factors, somatic growth, and vital rates, and demonstrates how variation in somatic growth influences temporal and spatial patterns in abundance.
Arizona↗
A need for speed in Bayesian population models: A practical guide to marginalizing and recovering discrete latent states
Bayesian population models can be exceedingly slow due, in part, to the choice to simulate discrete latent states. Here, we discuss an alternative approach to discrete latent states, marginalization, that forms the basis of maximum likelihood population models and is much faster. Our manuscript has two goals: 1) to introduce readers unfamiliar with marginalization to the concept and provide worked examples, and 2) to address topics associated with marginalization that have not been previously synthesized and are relevant to both Bayesian and maximum likelihood models. We begin by explaining marginalization using a Cormack-Jolly-Seber model. Next, we apply marginalization to multistate capture-recapture, community occupancy, and integrated population models and briefly discuss random effects, priors, and pseudo-R2. Then, we focus on recovery of discrete latent states, defining different types of conditional probabilities and showing how quantities such as population abundance or species richness can be estimated in marginalized code. Lastly, we show that occupancy and site abundance models with auto-covariates can be fit with marginalized code with minimal impact on parameter estimates. Marginalized code was anywhere from five to >1000 times faster than discrete code. Differences in inferences were minimal using marginalized code. Discrete latent states and fully conditional approaches provide the best estimates of conditional probabilities for a given site or individual. However, estimates for parameters and derived quantities such as species richness and abundance were minimally affected by marginalization and use of imperfect estimates of conditional probabilities. The results applied even when auto-covariates based on imperfect estimates of conditional probabilities were used. Understanding how marginalization works shrinks the divide between Bayesian and maximum likelihood approaches to population models. Some models that have only been presented in a Bayesian framework can easily be fit in maximum likelihood. On the other hand, factors such as informative priors, random effects, or pseudo-R2 values may motivate a Bayesian approach in some applications. An understanding of marginalization allows users to minimize the speed that is sacrificed when switching from a maximum likelihood approach. Widespread application of marginalization in Bayesian population models will facilitate more thorough simulation studies, comparisons of alternative model structures, and faster learning.
Ecological Applications↗
Inferring species interactions through joint mark–recapture analysis
Introduced species are frequently implicated in declines of native species. In many cases, however, evidence linking introduced species to native declines is weak. Failure to make strong inferences regarding the role of introduced species can hamper attempts to predict population viability and delay effective management responses. For many species, mark–recapture analysis is the more rigorous form of demographic analysis. However, to our knowledge, there are no mark–recapture models that allow for joint modeling of interacting species. Here, we introduce a two‐species mark–recapture population model in which the vital rates (and capture probabilities) of one species are allowed to vary in response to the abundance of the other species. We use a simulation study to explore bias and choose an approach to model selection. We then use the model to investigate species interactions between endangered humpback chub ( Gila cypha ) and introduced rainbow trout ( Oncorhynchus mykiss ) in the Colorado River between 2009 and 2016. In particular, we test hypotheses about how two environmental factors (turbidity and temperature), intraspecific density dependence, and rainbow trout abundance are related to survival, growth, and capture of juvenile humpback chub. We also project the long‐term effects of different rainbow trout abundances on adult humpback chub abundances. Our simulation study suggests this approach has minimal bias under potentially challenging circumstances (i.e., low capture probabilities) that characterized our application and that model selection using indicator variables could reliably identify the true generating model even when process error was high. When the model was applied to rainbow trout and humpback chub, we identified negative relationships between rainbow trout abundance and the survival, growth, and capture probability of juvenile humpback chub. Effects on interspecific interactions on survival and capture probability were strongly supported, whereas support for the growth effect was weaker. Environmental factors were also identified to be important and in many cases stronger than interspecific interactions, and there was still substantial unexplained variation in growth and survival rates. The general approach presented here for combining mark–recapture data for two species is applicable in many other systems and could be modified to model abundance of the invader via other modeling approaches.
Ecology↗
Estimating disperser abundance using open population models that incorporate data from continuous detection PIT arrays
Autonomous passive integrated transponder (PIT) tag antenna systems continuously detect individually marked organisms at one or more fixed points over long time periods. Estimating abundance using data from autonomous antennae can be challenging, because these systems do not detect unmarked individuals. Here we pair PIT antennae data from a tributary with mark-recapture sampling data in a mainstem river to estimate the number of fish moving from the mainstem to the tributary. We then use our model to estimate abundance of non-native rainbow trout Oncorhynchus mykiss that move from the Colorado River to the Little Colorado River (LCR), the latter of which is important spawning and rearing habitat for federally-endangered humpback chub Gila cypha. We estimate 226 rainbow trout (95% CI: 127-370) entered the LCR from October 2013-April 2014. We discuss the challenges of incorporating detections from autonomous PIT antenna systems into mark-recapture population models, particularly in regards to using information about spatial location to estimate movement and detection probabilities.
Colorado River↗