Publications by Colleges and Departments (MSU - Bozeman)
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Item The Importance of Phenology and Thermal Exposure to Early Life History Success of Nonnative Smallmouth Bass in the Yellowstone River(Wiley, 2022-07) Voss, Nicholas S.; Al‐Chokhachy, Robert; Sepulveda, Adam J.; Verhille, Christine E.; Ruggles, Michael P.; Zale, Alexander V.Knowledge of potential spread by introduced species is critical to effective management and conservation. The Smallmouth Bass Micropterus dolomieu is an example of a fish that has been introduced globally, often spreads after introduction, and has substantial predatory impacts on fish assemblages. Nonnative Smallmouth Bass in the free-flowing Yellowstone River, Montana, have expanded from warmer, downstream sections of river into colder, upstream sections containing socio-economically valuable trout fisheries. We sought insight into mechanisms controlling upstream spread by evaluating whether progressively colder upstream climates physiologically constrained successful recruitment by limiting age-0 growth and preventing overwinter survival (i.e., population establishment). We documented the phenology, growth, and overwinter survival of age-0 Smallmouth Bass across a temperature gradient leading to their upstream extent in the Yellowstone River. The upstream extent of population establishment did not appear limited by water temperature alone. Age-0 body size at the onset of winter did not differ significantly between colder, upstream reaches and warmer, downstream reaches. Instead, the earlier hatch timing exhibited by some age-0 individuals in upstream sections allowed them to experience longer growing seasons than many individuals in downstream sections. This counter-intuitive hatching phenology mediated much of the expected decreases in growth in colder, upstream climates. Furthermore, evidence of successful overwinter survival and simulations of age-0 starvation mortality indicated that age-0 individuals at the upstream extent of their distribution successfully recruited to the age-1 year-class during four consecutive years. However, age-0 individuals were rare or absent throughout the uppermost upstream distribution of adults, suggesting that something other than temperature limits or discourages reproduction farther upstream. Taken together, our results suggest that Smallmouth Bass have not yet reached the thermal limit of their upstream distribution in the Yellowstone River and that future spread may challenge fisheries managers tasked with management of coldwater trout fisheries in this river.Item Msocc: Fit and analyse computationally efficient multi‐scale occupancy models in r(2020-07) Stratton, Christian; Sepulveda, Adam J.; Hoegh, Andrew1. Environmental DNA (eDNA) sampling is a promising tool for the detection of rare and cryptic taxa, such as aquatic pathogens, parasites and invasive species. Environmental DNA sampling workflows commonly rely on multi-stage hierarchical sampling designs that induce complicated dependencies within the data. This complex dependence structure can be intuitively modelled with Bayesian multi-scale occupancy models. However, current software for such models are computationally demanding, impeding their use. 2. We present an r package, msocc, that implements a data augmentation strategy to fit fully Bayesian, computationally efficient multi-scale occupancy models. The msocc package allows users to fit multi-scale occupancy models, to estimate and visualize posterior summaries of site, sample and replicate-level occupancy, and to compare different models using Bayesian information criterion. Additionally, we provide a supplemental web application that allows users to investigate study design for multi-scale occupancy models and acts as a graphical user interface to the msocc package. 3. The utility of the msocc package is illustrated on a published dataset and the functions in msocc are compared to the primary Bayesian toolkit for multi-scale occupancy modelling, eDNAoccupancy, using various computational benchmarks. These benchmarks indicate that msocc is capable of fitting models 50 times faster than eDNAoccupancy. 4. We hope that access to software that efficiently fits, analyses and conducts study design investigations for multi-scale occupancy models facilitates their implementation by the research and wildlife management communities.Item Potential utility of environmental DNA for early detection of Eurasian watermilfoil (Myriophyllum spicatum)(2016-01) Newton, Jeremy; Sepulveda, Adam J.; Sylvester, Kevin; Thum, Ryan A.Considering the harmful and irreversible consequences of many biological invasions, early detection of an invasive species is an important step toward protecting ecosystems (Sepulveda et al. 2012). Early detection increases the probability that suppression or eradication efforts will be successful because invasive populations are small and localized (Vander Zanden et al. 2010). However, most invasive species are not detected early because current tools have low detection probabilities when target species are rare and the sampling effort required to achieve acceptable detection capabilities with current tools is seldom tractable (Jerde et al. 2011). As a result, many invasive species go undetected until they are abundant and suppression efforts become costly.