Theses and Dissertations at Montana State University (MSU)
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Item Improving genomic resources for the study of invasiveness in Eurasian watermilofil (Myriophyllum spicatum) and their hybrids(Montana State University - Bozeman, College of Agriculture, 2021) Pashnick, Jeffrey John; Chairperson, Graduate Committee: Ryan Thum; This is a manuscript style paper that includes co-authored chapters.Genomics has revolutionized the way biologists ask fundamental questions about evolution. The thousands to tens of thousands of molecular markers generated through modern genomics increase the likelihood of detecting traits associated with a phenotype of interest. While genomics provides ever increasing evidence detecting these traits, they must be developed in each new system. Myriophyllum spicatum L. (Eurasian watermilfoil, EWM) and their hybrids with native Myriophyllum sibiricum Komorov (northern watermilfoil, NWM) are heavily managed aquatic plants in the United States. Genotypes both within and across these taxa and their hybrids can differ in their growth and herbicide response, prompting interest in determining which specific genotypes and genes will respond best to specific control tactics. However, because genotypes are unable to be distinguished by morphology, distinguishing genotypes requires molecular markers. EWM, NWM, and their hybrid are hexaploid (2n=6x=42) and developing these molecular markers requires accurately genotyping in a hexaploid with unknown chromosomal inheritance. The first manuscript of this dissertation empirically tested the genotyping information obtained from three commonly used molecular marker types, AFLPs, microsatellites, and GBS data. We found that while GBS markers have the lowest error rate, all molecular marker types provide the same genotype information. In the second chapter we used a mapping population, GBS data, and likelihood models to determine if watermilfoil was an allohexaploid, autohexaploid, or a mix between them. We found overwhelming evidence that watermilfoil is an allohexaploid across the genome. Finally, using the characteristics of each molecular marker type, the third chapter developed a cost-effective and information dense panel of microhaplotypes to genotype in watermilfoil. Microhaplotyping data can be shared across laboratories and promotes collaboration with weed managers by informing management with genetic information. Together, the work in this dissertation provides diploidized molecular markers and polyploid mode of inheritance to begin to connect genotype to herbicide response traits in watermilfoil.Item Assessment of the Yellowstone Lake food web during lake trout suppression and Yellowstone cutthroat trout recovery informs conservation benchmarks(Montana State University - Bozeman, College of Letters & Science, 2022) Glassic, Hayley Corrine; Chairperson, Graduate Committee: Christopher S. Guy; This is a manuscript style paper that includes co-authored chapters.The collapse of native Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri (hereafter cutthroat trout) in Yellowstone Lake was caused by predation by invasive lake trout Salvelinus namaycush. As an ecosystem with a low-diversity fish assemblage and several longterm data sets, Yellowstone Lake provided a unique opportunity to evaluate the influence of an invasive salmonid population undergoing suppression beyond only predator-prey dynamics. Diet data for cutthroat trout and lake trout were evaluated at varying densities to determine the effects of density on diet composition and diet plasticity. During the lake trout high-density state, lake trout consumed fewer native cutthroat trout and switched to amphipods, which were also consumed by cutthroat trout, resulting in high diet overlap between the species. As suppression reduced invasive lake trout densities, lake trout returned to consuming cutthroat trout and diet overlap was released. A shift in lake trout delta 13C signatures from the high-density state to the moderate-density state also corroborates higher consumption of cutthroat trout and invasive lake trout diet plasticity. Beyond predator-prey dynamics of lake trout and cutthroat trout, the invasion of lake trout caused > or = 25% change in energy flux for all organisms in Yellowstone Lake except for copepods. Food-web functional state did not change among food webs, but percentage of functional state contributing to total flux did vary. Herbivory was the dominant food-web functional state for all years, with the greatest percentage of flux from herbivory in 2011. In addition, by using a whole-ecosystem model that accounted for whirling disease and historical (natural) lake-level variation, I show that suppression of the lake trout population is necessary for cutthroat trout recovery, but the amount of suppression effort needed for cutthroat trout to reach recovery benchmarks is linked to severity of climate change. Additionally, if climate change increases the frequency and severity of reduced lake levels in the future, cutthroat trout recovery benchmarks may need to be adapted. With this research, I demonstrate how the feedbacks among predator-prey dynamics, disease, and climate change can complicate the suppression of invasive species and the conservation of invaded ecosystems and must be considered for establishing realistic conservation benchmarks.Item Combination of acoustic telemetry and side-scan sonar provides insight for lake trout Salvelinus namaycush suppression in a submontane lake(Montana State University - Bozeman, College of Letters & Science, 2021) Siemiantkowski, Michael James; Chairperson, Graduate Committee: Christopher S. GuyExpansion of an invasive Lake Trout Salvelinus namaycush population in Swan Lake, Montana threatens a core area population of Bull Trout Salvelinus confluentus in Montana. Given the increased efficacy of suppression using novel embryo suppression methods, there is renewed interest in Lake Trout suppression in Swan Lake. The specific questions of this study were: 1) where are Lake Trout spawning, 2) where are the most used spawning sites, 3) what is the amount of spawning habitat, 4) does the estimated spawning area differ between estimates from telemetry locations and side-scan sonar imagery of suitable spawning substrate, and 5) how much phosphorous and nitrogen would be added to Swan Lake if carcass-analog pellet treatments were implemented? Acoustic tags were implanted in 85 Lake Trout in July and August of 2018 and 2019. Nightly tracking efforts during September, October, and November of 2018 and 2019 resulted in 1,744 relocations for 49 individual Lake Trout. Kernel-density analysis was used to evaluate Lake Trout aggregation locations identifying 10 distinct spawning sites -- corroborating previous studies. Visual observation of Lake Trout embryos confirmed spawning at three sites with the remaining seven sites considered to be unconfirmed spawning sites. All confirmed spawning sites were located in the littoral zone along areas of steep bathymetric relief and were the most used across both spawning seasons. In 2019, side-scan sonar imaging was used to classify and quantify the total area of suitable spawning substrate, which comprised 12.8% of the total surface area estimated for confirmed sites and 11.4% for unconfirmed spawning sites. Simultaneous treatment of all confirmed and unconfirmed spawning sites would require 205,709 + or - 86 kg of carcass-analog pellet material, resulting in 370.4 + or - 0.2 kg of phosphorous and 7,487.9 + or - 3.1 kg of nitrogen inputs to Swan Lake. Thus, pellet treatment would increase the Carlson's trophic state index (TSI) values from 20.8 to 27.7 for total phosphorous, and from 22.1 to 26.2 for total nitrogen. Based on a TSI threshold value of < 40 for an oligotrophic lake, the use of carcass-analog pellets could be a feasible addition to renewed Lake Trout suppression efforts in Swan Lake.Item Impacts of a non-native forb, Alyssum desertorum Stapf., and non-target effects of Indaziflam in the sagebrush steppe of Yellowstone National Park(Montana State University - Bozeman, College of Agriculture, 2021) Meyer-Morey, Jordan; Chairperson, Graduate Committee: Lisa J. RewNon-native plants can reduce biodiversity and disrupt essential ecosystem services and functions. For most non-native plant species however, quantitative evidence of negative effects is lacking, as are fundamental demographic details; such information can inform whether and at what growth stage to implement control. Control strategies can also negatively impact non-target native plant communities; therefore, evaluating the tradeoffs of management and understanding the actual impacts of the invader is essential. I sought to understand the life history, and evaluate the competitiveness and impacts of the non-native annual forb, Alyssum desertorum Stapf., as well as non-target effects of management, across an elevation gradient in a cool, mountain sagebrush (Artemisia tridentata ssp. vaseyana (Rydb.) Beetle) steppe plant community. Seed viability, fecundity, overwintering success, and likelihood of reaching reproductive maturity of A. desertorum all declined as elevation increased; all life stage transition rates were high, suggesting that targeting seed production or fall germination would be the most effective means for control of this species. Replacement series experiments revealed that A. desertorum is a weak competitor with functionally similar species. Additionally, in the field, the presence of A. desertorum did not affect species richness nor Shannon's diversity aboveground or in the soil seedbank, and functionally similar native annual forbs were not displaced in invaded areas. I evaluated the efficacy and non-target effects of the pre-emergent herbicide, indaziflam, in diverse sagebrush steppe with localized infestations of A. desertorum across an elevational gradient. While indaziflam effectively controlled A. desertorum for two years, the richness and diversity of the surrounding community was reduced. Indaziflam inhibited recruitment of forbs, both in the field and in the seedbank. As indaziflam provides residual control of the soil seedbank for up to three years, my results suggest the future community composition may be altered, particularly native annual forb populations. Considering the weak competitive ability of A. desertorum, the species' minimal impacts to richness and diversity, and the negative effects of indaziflam to annual native forb species, I conclude that the non-target effects of indaziflam would outweigh any benefits to controlling A. desertorum in intact sagebrush steppe.Item Use of eDNA to estimate abundances of spawning Yellowstone cutthroat trout in Yellowstone National Part, Wyoming, USA(Montana State University - Bozeman, College of Letters & Science, 2020) Detjens, Colleen Rachel; Chairperson, Graduate Committee: Alexander V. ZaleInvasive Lake Trout Salvelinus namaycush and whirling disease have reduced the abundance of native Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri (YCT) in Yellowstone Lake, Yellowstone National Park, thereby disrupting the Yellowstone Lake ecosystem. One indication of the YCT population decline is the decrease in the number of adults returning to tributaries to spawn each spring. Yellowstone National Park implemented a gillnetting program to remove Lake Trout starting in 1995 to restore YCT abundance and size structure and thereby conserve the Yellowstone Lake ecosystem. An important metric for evaluating the success of the program is the number of YCT ascending spawning tributaries each year. Annually, 9 to 11 of these tributaries are visually surveyed on a weekly basis from May through July for the presence of spawners, but these surveys are time consuming. The use of environmental DNA (eDNA) has become increasingly common for determining presence of aquatic species and may provide managers with a more efficient tool for estimating abundances of YCT spawners. The primary objective of my study was to evaluate the efficacy and accuracy of using eDNA to detect the presence and estimate abundance of YCT spawners by collecting eDNA samples from spawning tributaries to Yellowstone Lake in conjunction with visual surveys of YCT spawners. A secondary objective was to evaluate whether terrestrial or semi-terrestrial species such as grizzly bear Ursus arctos horribilis and North American river otter Lontra canadensis could be detected in a water sample from YCT spawning tributaries. Environmental DNA quantities were more effective for determining presence of YCT spawners than for predicting their abundances, but eDNA quantities were positively related to spawner abundances. The difference between eDNA rates when spawners are present versus absent may provide managers with an efficient method for monitoring YCT in tributaries throughout Yellowstone Lake basin. I also demonstrated that DNA from a terrestrial species, grizzly bear, can be detected in water samples. Incorporation of eDNA sampling with existing methods for monitoring YCT spawners in Yellowstone Lake tributaries would facilitate an increased scale of assessment and allow for detection and quantification of multiple species of current and future interest from single samples.Item Non-target effects of a novel invasive species management strategy: benthic invertebrate responses to lake trout embryo suppression in Yellowstone Lake, Wyoming(Montana State University - Bozeman, College of Letters & Science, 2020) Briggs, Michelle Anne; Chairperson, Graduate Committee: Lindsey Albertson; Lindsey K. Albertson, Dominique R. Lujan, Lusha M. Tronstad, Hayley C. Glassic, Christopher S. Guy and Todd M. Koel were co-authors of the article, 'Carcassd deposition to suppress invasive lake trout causes differential mortality of two common benthic invertebrates in Yellowstone Lake, Wyoming' in the journal 'Fundamental and applied limnology' which is contained within this thesis.; Lindsey K. Albertson, Dominique R. Lujan, Lusha M. Tronstad, Hayley C. Glassic, Christopher S. Guy and Todd M. Koel were co-authors of the article, 'Non-target effects of a novel suppression technique for invasive fishes: responses of benthic invertebrate communities' submitted to the journal 'Ecological applications' which is contained within this thesis.Invasive species threaten native biodiversity and ecosystem function, and suppression is often required to reduce these effects. However, invasive species management actions can cause harmful, unintended consequences for non-target taxa. In Yellowstone Lake, Wyoming, invasive lake trout (Salvelinus namaycush) have reduced abundance of the native Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri), decreasing availability of an important food source for aquatic and terrestrial predators. Gillnets are used to suppress adult lake trout, and the lake trout carcasses are then deposited onto spawning sites in the littoral zone to cause embryo mortality by reducing dissolved oxygen concentrations as they decay. However, this management action may have non-target effects on organisms in the lake, including benthic invertebrates, which comprise a large portion of native trout diets. Some taxa of invertebrates may benefit from the addition of nutrients to the littoral zone, while other taxa may experience mortality in response to low dissolved oxygen conditions caused by carcass decay. We conducted two field experiments to understand how carcass treatment affects benthic invertebrates in Yellowstone Lake. First, we conducted an in situ experiment with individual invertebrates housed in small chambers covered by carcasses to determine if carcass treatment causes mortality of hypoxia-tolerant amphipods and hypoxia-sensitive caddisflies. We found that carcass treatment caused increased mortality in caddisflies but not amphipods. Second, we conducted a field experiment to investigate how carcass treatment affects invertebrate communities when applied at entire spawning sites. We also compared invertebrate communities at cobble-dominated lake trout spawning sites to macrophyte-dominated sites to determine if carcass treatment could alter food web dynamics at a lake-wide scale. We found that carcass treatment causes non-target effects on benthic invertebrates, specifically reducing immobile taxa, hypoxia-sensitive taxa, and Chironomidae, and altering community structure. Areas dominated by macrophytes had more abundant and larger invertebrates than spawning sites. Due to the small spatial extent of spawning sites and the higher abundance of invertebrates at other habitats in the lake, we conclude carcass treatment can have localized non-target effects at a local scale but is unlikely to alter food-web dynamics at a lake-wide scale.Item Feasibility of walleye population suppression in Buffalo Bill Reservoir, Wyoming(Montana State University - Bozeman, College of Letters & Science, 2019) Kaus, Daniel Joseph; Chairperson, Graduate Committee: Christopher S. GuyBuffalo Bill Reservoir, Wyoming is managed as a wild Rainbow Trout Oncorhynchus mykiss and Cutthroat Trout Oncorhynchus clarkii fishery. Nonnative Walleyes Sander vitreus were discovered in 2008, and spring sampling of Walleye indicate natural recruitment and a rapidly expanding population. Walleyes pose a predation threat to the wild trout populations in Buffalo Bill Reservoir. The Wyoming Game and Fish Department (WGFD) is interested in suppressing the Walleye population using mechanical removal with electrofishing and gillnetting during the Walleye spawning period. The purpose of this study was to evaluate the population demographics of Walleyes in Buffalo Bill Reservoir. Age-structured population models were used to estimate the Walleye population growth rate for scenarios with and without Walleye removal. To inform the population models, age-specific fecundity, probability of maturity, natural mortality, and fishing mortality were estimated. Mean asymptotic population growth rate for the five scenarios were estimated as 1.22 (95% CI of 1.05 to 1.37) for no suppression, 1.18 (95% CI of 1.04 to 1.32) for electrofish exploitation, 1.04 (95% CI of 0.88 to 1.19) for gill-net exploitation, 0.91 (95% CI of 0.61 to 1.36) for angler exploitation, and 0.81 (95% CI of 0.66 to 0.96) for angler and gill-net exploitation combined. Results from the age-structured population models suggest that long-term population suppression is a viable goal, and additional gill-net effort and angler harvest incentives should be pursued. During this study the density of mature Walleyes was low, indicating that the population had not yet reached carrying capacity. Analysis of population inertia indicates that the projected abundance of the initial population vector results in a lower population size compared to projected abundance of a population with stable-age distribution. Results from this study will be used to inform cost-effective management decisions regarding the future of the recreational fishery in Buffalo Bill Reservoir. The cost per mature female removed in 2017 was $490.91 and $80.08 for electrofish and gill net removal, respectively. Future suppression efforts should be monitored using population indices of age diversity for female Walleyes.Item Dynamics of Yellowstone cutthroat trout and lake trout in the Yellowstone Lake ecosystem : a case study for the ecology and management of non-native fishes(Montana State University - Bozeman, College of Letters & Science, 2015) Syslo, John Michael; Chairperson, Graduate Committee: Christopher S. Guy; Christopher S. Guy and Todd M. Koel were co-authors of the article, 'Trophic overlap and temporal diet shifts for a nonnative and a native salmonid in Yellowstone Lake, Yellowstone National Park' submitted to the journal 'Transactions of the American Fisheries Society' which is contained within this thesis.; Christopher S. Guy, Todd M. Koel, Patricia E. Bigelow, Philip D. Doepke, Brian D. Ertel and Jeffrey L. Arnold were co-authors of the article, 'Response of Yellowstone cutthroat trout to suppression of non-native lake trout in the Yellowstone Lake ecosystem' submitted to the journal 'Canadian journal of fisheries and aquatic sciences' which is contained within this thesis.The introduction of lake trout Salvelinus namaycush into Yellowstone Lake preceded the collapse of the native Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri population. As a system with a simple fish assemblage and several long-term data sets, Yellowstone Lake provided a unique opportunity to evaluate the ecology of a native salmonid in the presence of a non-native salmonid population undergoing suppression in a large natural lake. Diet data for Yellowstone cutthroat trout and lake trout were evaluated at varying densities to determine the effects of density on diet composition. Temporal diet shifts from 1996-1999 to 2011-2013 were likely caused by limitation of prey fish for lake trout. Diets, stable isotopes, and depth-related patterns in CPUE indicated lake trout > 300 mm consumed primarily amphipods, making them trophically similar to Yellowstone cutthroat trout from during 2011-2013. A lake trout removal program was initiated during 1995 to reduce predation on Yellowstone cutthroat trout. Abundance and fishing mortality were estimated for lake trout from 1998 through 2013 and Yellowstone cutthroat trout from 1986 through 2013. Density-dependence was evaluated by examining individual growth, weight, maturity, and pre-recruit survival as a function of abundance. In addition, a simulation model was developed for the lake trout- Yellowstone cutthroat trout system to determine the probability of Yellowstone cutthroat trout abundance persisting at performance metrics given potential reductions in lake trout abundance. Estimates of Yellowstone cutthroat trout abundance varied 5-fold and lake trout abundance varied 6-fold. Yellowstone cutthroat trout weight and pre-recruit survival decreased with increasing Yellowstone cutthroat trout abundance; however, individual growth and maturity were not related to abundance. Lake trout population metrics did not vary with lake trout abundance. Simulation model results were variable because of uncertainty in lake trout pre-recruit survival. Conservative estimates for required lake trout reductions were > 97% of 2013 abundance for a > 70% probability of Yellowstone cutthroat trout persistence at the performance metrics outlined in the Native Fish Conservation Plan. Lake trout removal will likely reduce lake trout abundance and result in Yellowstone cutthroat trout recovery if the amount of fishing effort exerted in 2013 is maintained for at least 15 years.Item Efficacy of suppressing non-native lake trout in an isolated backcountry lake in Glacier National Park(Montana State University - Bozeman, College of Letters & Science, 2014) Fredenberg, Carter Roger; Chairperson, Graduate Committee: Christopher S. GuyPrior to the recent invasion of non-native lake trout Salvelinus namaycush, Glacier National Park (GNP) supported approximately one-third of the remaining natural lake habitat supporting threatened bull trout Salvelinus confluentus. However, bull trout populations have recently declined and are at high risk of extirpation in several lakes in western GNP due to the establishment of lake trout. In 2009, the U.S. Geological Survey and the National Park Service began suppressing lake trout in Quartz Lake (352 ha) to reduce impacts to native bull trout. The objectives of this study were to: (1) describe the demography of the lake trout population during the suppression program (2009-2013); (2) identify the timing and location of lake trout spawning; (3) determine the most efficient combination of gill net mesh color and twine diameter to capture juvenile lake trout (age 2 to age 4); (4) assess the effects of suppression on the growth rate of the lake trout population and use this information to model harvest scenarios; and (5) determine whether suppression negatively impacted bull trout. Lake trout exhibited slower growth, lower condition, and lower fecundity relative to other populations. Spawning locations were identified on cobble and boulder substrates (depths 2-20 m) near the base of two avalanche chutes where adults began aggregating between 1 and 9 October prior to thermal destratification (11-12 C°). Catch rates of spawning (ripe) adults were highest 12-25 October when temperatures declined to below 10 C°. Gill nets with 0.1 mm twine thickness and green color increased catchability of juvenile lake trout. Although density dependent parameters were not included, population simulation models indicated the population was growing exponentially and would likely reach carrying capacity within ten years without suppression. Suppression resulted in declining population growth rates (lambda) from 1.23 prior to suppression to 0.61-0.79 during suppression. Bull trout redd abundances remained stable throughout the suppression period. My results indicate targeted suppression successfully reduced lake trout abundance and that continued suppression at or above observed exploitation levels is needed to ensure continued population declines and to avoid impacts to the bull trout population.