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Item Effects of de-snaring on the demography and population dynamics of African lions(Montana State University - Bozeman, College of Letters & Science, 2023) Banda, Kambwiri; Chairperson, Graduate Committee: Scott CreelLions and other African large carnivores are in decline, due in part to effects of illegal hunting with snares, which can reduce prey availability and directly kill or injure carnivores. It is difficult to effectively remove snares from large ecosystems by patrolling, but an additional approach to reduce effects on large carnivores is to monitor the population closely and de-snare individuals who are found in a snare or have broken free but still carry the wire (often with serious injury). The effectiveness of de-snaring programs to reduce impacts on large carnivores has not been directly tested. Here, we used long-term demographic data from 386 individually identified lions in the Luangwa Valley Ecosystem to test the effects on population growth (lambda) and population size (N) of a program to remove snares from injured lions and treat their wounds. Stochastic Leslie matrix projections for a period of five years showed that the population grew with the benefits of de-snaring but was expected to decline without de-snaring. Mean annual growth (lambda) was 1.037 (growth in 70% of years), closely matching observed changes in population size. Mean annual growth was 0.99 (with growth in 47% of years) for a model that assumed snared animals would have died if not treated, and 0.95 (with growth in 37% of years) for models that also accounted for super-additive effects via the death of dependent cubs and increased infanticide with increased male mortality. De-snaring requires intensive effort, but it can appreciably reduce the effect of snaring on lion population dynamics.Item Reproductive and juvenile ecology of mountain whitefish in the upper Green River, Wyoming(Montana State University - Bozeman, College of Letters & Science, 2022) Brown, Colter Davis; Chairperson, Graduate Committee: Christopher S. GuyMountain Whitefish Prosopium williamsoni are a salmonid native to the northern Rocky Mountains that has experienced declines in population abundance in rivers throughout Idaho, Colorado, Wyoming, and Montana. Problems with recruitment are suspected, but often the specific mechanisms causing population declines are unknown. Our approach to better understand the mechanisms that influence Mountain Whitefish population dynamics was to compare population characteristics between the Green River, Wyoming and the Madison River, Montana populations. Boyer et al. (2017a) conducted an extensive study on the movement and reproductive ecology of Mountain Whitefish in the Madison River, and we used this study as a template to make direct comparisons between the populations. Our primary research questions were 1) what is the age and length at first maturity, spawning periodicity, fecundity, and age structure of Mountain Whitefish, 2) what is the spatial and temporal distribution of Mountain Whitefish through their spawning period, and what influence do abiotic factors have on spawning and movement, and 3) what is the spatial distribution and habitat use of age-0 Mountain Whitefish? We collected otoliths and gonadal samples from 127 Mountain Whitefish in the Green River, implanted 100 fish with radio transmitters and tracked them from September 1 to early November in 2019 and 2020, determined spawning period and locations using egg mats, kick netting, and angling, and sampled age-0 Mountain Whitefish using a beach seine in slow-water habitats. The geographic separation and difference in hydrogeomorphic conditions between the systems allowed us to form generalizations about Mountain Whitefish in the Intermountain West. We found Mountain Whitefish in both systems mature between ages 2 and 4, primarily spawn annually, have a similar relative fecundity, spawning movements vary, males begin movement prior to females, and age-0 fish drift downstream of spawning locations and use slow-water silt-laden habitats after hatching. The main disparities between systems were that in the Green River water temperature was more suitable for embryo development, and age structure was more uniform and older. This research enhanced our understanding of Mountain Whitefish reproductive and juvenile ecology and provided evidence for factors that may influence recruitment of Mountain Whitefish.Item African wild dog demography in an ecosystem with reduced prey and dominant competitors(Montana State University - Bozeman, College of Letters & Science, 2021) Goodheart, Benjamin Michael; Chairperson, Graduate Committee: Scott Creel; Scott Creel, Matthew S. Becker, Milan Vinks, Kambwiri Banda, Carolyn Sanguinetti, Paul Schuette, Elias Rosenblatt, Chase Dart, Anna Kusler, Kim Young-Overton, Xia Stevens, Alstone Mwanza and Chuma Simukonda were co-authors of the article, 'Low apex carnivore density does not release a subordinate competitor when driven by prey depletion' in the journal 'Biological conservation' which is contained within this thesis.Conservation of competitively subordinate carnivores presents a difficult challenge because they are limited by dominant competitors. Prey depletion is one of the leading causes of large carnivore decline worldwide, but little is known about the net effect of prey depletion on subordinate carnivores when their dominant competitors are also reduced. African wild dogs are often limited by high densities of dominant competitors, particularly lions. We measured African wild dog density and survival, using mark-recapture models fit to 8 years of data from 425 known individuals in the Greater Kafue Ecosystem, Zambia. The GKE is affected by prey depletion, particularly of large herbivores, and thus the density of lions is significantly lower than ecologically comparable ecosystems. Counter to expectations from mesopredator release theory, wild dog density in GKE was far lower than comparable ecosystems with higher lion and prey density, though annual survival rates were comparable to large and stable populations. Average pack size was small and home range size was among the largest recorded. Our results show that low lion density did not competitively release the GKE wild dog population and we infer that the low density of wild dogs was a product of low prey density. Our results suggest that there is an optimal ratio of prey and competitors at which wild dogs achieve their highest densities. This finding has immediate implications for the conservation of the endangered African wild dog, and broad implications for the conservation of subordinate species affected by resource depletion and intraguild competition.Item Population structure, gene flow, and genetic diversity of Rocky Mountain bighorn sheep informed by genomic analysis(Montana State University - Bozeman, College of Agriculture, 2020) Flesch, Elizabeth Pearl; Chairperson, Graduate Committee: Jennifer Thomson; Jay J. Rotella, Jennifer M. Thomson, Tabitha A. Graves and Robert A. Garrott were co-authors of the article, 'Evaluating sample size to estimate genetic management metrics in the genomics era' in the journal 'Molecular ecology resources ' which is contained within this dissertation.; Tabitha A. Graves, Jennifer M. Thomson, Kelly M. Proffitt, P.J. White, Thomas R. Stephenson and Robert A. Garrott were co-authors of the article, 'Evaluating wildlife translocations using genomics: a bighorn sheep case study' in the journal 'Ecology and evolution' which is contained within this dissertation.; Tabitha A. Graves, Jennifer M. Thomson, Kelly M. Proffitt and Robert A. Garrott were co-authors of the article, 'Genetic diversity of bighorn sheep population is associated with dispersal, augmentation, and bottlenecks' submitted to the journal 'Biological conservation' which is contained within this dissertation.This dissertation evaluated the genomics of bighorn sheep (Ovis canadensis) herds across the Rocky Mountain West to determine optimal sample size for estimating kinship within and between populations (Chapter Two), to detect gene flow due to natural dispersal and translocations (Chapter Three), and to evaluate the correlation between genetic diversity and influences on population size (Chapter Four). To date, wildlife managers have moved many bighorn sheep across the Rocky Mountain West in an effort to provide new genetic diversity to isolated herds. However, little is known about the genetics of these herds and the real impacts of translocations. To learn how populations have been impacted by these management actions, we genotyped 511 bighorn sheep from multiple populations using a new cutting-edge genomic research technique, the Illumina Ovine High Density array, which contained about 24,000 to 30,000 single nucleotide polymorphisms informative for Rocky Mountain bighorn sheep. First, we determined that a sample size of 20 to 25 bighorn sheep was adequate for assessment of intra- and interpopulation kinship. In addition, we concluded that a universal sample size rule for all wild populations or genetic marker types may not be able to sufficiently address the complexities that impact genomic kinship estimates. Secondly, we synthesized genomic evidence across multiple analyses to evaluate 24 different translocation events; we detected eight successful reintroductions and five successful augmentations. One native population founded most of the examined reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Finally, we determined that influences on population size over time were correlated with genetic diversity. Gene flow variables, including unassisted connectivity and animals contributed in augmentations, were more important predictors than historic minimum population size and origin (i.e. native vs. reintroduced). This hypothesis-based research approach will give wildlife managers additional biological insight to help inform various management options for bighorn sheep restoration and conservation.Item Vital rates, annual abundance, and movement of white sharks in the northeastern Pacific(Montana State University - Bozeman, College of Letters & Science, 2020) Kanive, Paul Edward; Chairperson, Graduate Committee: Jay J. Rotella; Jay J. Rotella, Salvador J. Jorgensen, Taylor K. Chapple, James E. Hines, Scot D. Anderson, Barbara A. Block were co-authors of the article, 'Size-specific apparent survival rate estimates of white sharks using mark-recapture models' in the journal 'Canadian journal of fisheries and aquatic sciences' which is contained within this dissertation.; Jay J. Rotella, Taylor K. Chapple, Scot D. Anderson, Timothy White, Barbara A. Block and Salvador J. Jorgensen were co-authors of the article, 'Estimation of regional annual abundance and evidence for increasing numbers of white sharks off California' which is contained within this dissertation.; Jay J. Rotella, Taylor K. Chapple, Scot D. Anderson, Mauricio Hoyos-Padilla, Barbara A. Block, Salvador J. Jorgensen were co-authors of the article, 'Connectivity between the central California and Guadalupe Island white shark populations' which is contained within this dissertation.Reliable estimates of populations' vital rates and abundance are fundamental requirements for making assessments and informed management decisions regarding any species. For large marine fish species whose movements are extensive throughout ocean basins, data for individuals are difficult to acquire. Without empirical data, large assumptions must be made about a species' vital rates (i.e. survival and fecundity) to make population assessments, which can potentially lead to erroneous results. Using mark-recapture and acoustic-telemetry data, I conducted analyses estimating vital rates, annual abundance, and coastal movement for white sharks (Carcharodon carcharias) off California, US. First, I used a novel approach to estimate size-specific annual apparent survival rates and to test for differences in survival between sexes after accounting for imperfect sex assignment. Our results provide little evidence for differences in sex-specific survival rates. However, I estimated the first size-specific annual apparent survival rates for sub-adult and adult white sharks. Second, I estimated annual abundance for four white shark demographic groups off the coast of California over an eight-year study period. The estimated total annual population of sub-adult and adult white sharks increased from 180 to 266 individuals during the study. Additionally, group-specific population growth rate point estimates were all > 1.00, which indicates that all groups had positive annual positive growth during the study period, although, uncertainty around those estimates were greater for sub-adults than adults and does not rule out other possibilities for population trajectories. Finally, through collaboration between Mexico and the US, I was able to analyze a comprehensive acoustic telemetry dataset that explored connectivity between two main aggregation sites that form the northeastern Pacific population of white sharks. I found that movement between the two regions was rare and more probable to be sub-adult sharks. These analyses underscore the value of collecting and analyzing empirical data to develop reliable estimates of vital rates for a top marine predator. The work also illustrates the ongoing need to cultivate international research collaboration to include data from both the US and Mexico to make accurate population inferences for the northeastern Pacific population of white sharks.Item Assessment of variation in the detection and prevalence of blood parasites among sympatrically breeding geese in western Alaska(Montana State University - Bozeman, College of Letters & Science, 2021) Buchheit, Raymond Matthew; Chairperson, Graduate Committee: Jay J. Rotella; Joel A. Schmutz, Brian Uher-Koch and Andrew M. Ramey were co-authors of the article, 'Assessment of variation in the detection and prevalence of blood parasites among sympatrically breeding geese in western Alaska' submitted to the journal 'Journal of wildlife diseases' which is contained within this thesis.Haemosporidian parasites may impact avian health and are subject to shifts in distribution and abundance with changing ecological conditions. Therefore, understanding variation in parasite prevalence is important for evaluating biologically meaningful changes in infection patterns and associated population level impacts. Previous research in western Alaska indicated a possible increase in Leucocytozoon infection between emperor geese (Anser canagicus) sampled in 1996 (<1%, n=134), and during 2011-2012 (19.9%, 95% CI: 3.0-36.8%, n=77); however, different detection methods were used for these estimates. Prior research in this same region identified a lack of Leucocytozoon parasites (0%, n=117) in sympatrically breeding cackling geese (Branta hutchinsii minima) in 2011. In this study, we molecularly screened blood samples collected from sympatrically breeding emperor and cackling geese in western Alaska during additional breeding seasons to better assess temporal and species-specific variation in the prevalence of blood parasites. We found similar prevalence estimates for Leucocytozoon parasites in emperor goose blood samples collected in 1998 and 2014, suggesting consistent infection of emperor geese with blood parasites at these time points. Using samples from sympatric geese sampled during 2014, we found evidence for higher incidence of Leucocytozoon parasites among emperor geese (20.3%, 95% CI: 11.8-32.7%) as compared to cackling geese (3.6%, 95% CI: 1.1-11.0%) reinforcing the previous finding of species-specific differences in infection. Furthermore, we detected Leucocytozoon, Haemoproteus, and Plasmodium blood parasites in unflighted goslings of both species, supporting the possible transmission of these parasites at western Alaska breeding grounds. Our results help to clarify that prevalence of Leucocytozoon parasites have likely remained consistent among emperor geese breeding in western Alaska since the late 1990s and that this species may disproportionally harbor Leucocytozoon parasites as compared to sympatrically breeding cackling geese.Item Inbreeding and inbreeding depression in linebred beef cattle(Montana State University - Bozeman, College of Agriculture, 2020) Hieber, Jordan Kelley; Chairperson, Graduate Committee: Jennifer ThomsonThis research applied genomics and phenotypic information in three different beef cattle populations. The methods applied were association analyses, runs of homozygosity, and genetic correlations. This incorporated both genomic and phenotypic approaches to identify the results of linebreeding in two closed Hereford populations. Further work evaluated carcass and maternal traits from the American Simmental Association Carcass Merit Program using genomic and phenotypic information to identify how carcass-based selection decisions impact maternal performance of Simmental-based cattle. Line 4 pedigree inbreeding, genomic inbreeding, and genomic pedigree inbreeding ranges were 0 - 36%, 0 - 49%, and 0 - 29%, respectively, and average inbreeding was 12.6%, 12.3%, and 17.7%, respectively. Line 1 pedigree inbreeding, genomic inbreeding, and genomic pedigree inbreeding ranges were 0 - 71%, 0 - 46%, and 0 - 63%, respectively, and average inbreeding was 42.1%, 14.4%, and 31.0%, respectively. Average rate of change in inbreeding per year was 0.03% over 55 years for Line 4 and -0.03% over 83 years for Line 1. Identified for Line 4 were 45 ROH regions, 35 strongly significant single nucleotide polymorphisms, three strongly significant SNP within ROH, and some significant SNP within 12 previously identified genes. Identified for Line 1 were 50 ROH regions, 93 strongly significant SNP, three strongly significant SNP within ROH, and some significant SNP within 11 previously identified genes. Within the Simmental dataset, nine chromosomes had genome-wide significance, explaining 0.2142 percent of total phenotypic information. The single-locus model identified 365 novel regions and 251 novel positional candidate genes. The multi-locus model identified 393 novel regions and 283 novel positional candidate genes. Also, detrimental genetic correlations between carcass characteristics and maternal traits were less than previously reported. Analyses utilized in this study indicate ROH and significant SNP can be used to identify regions of the genome affected by inbreeding. Also, simultaneous selection for carcass and maternal traits reduced the negative impact seen with single-trait selection for carcass traits.Item Associations of broad scale vegetation characteristics and abundances, nest densities, and nest survival of mixed-grass prairie songbirds in northern Montana(Montana State University - Bozeman, College of Agriculture, 2019) Pulliam, John Patrick; Chairperson, Graduate Committee: Lance McNewGrassland bird populations are declining faster than any other avian guild. In northern Montana, four species are experiencing severe population declines: Baird's sparrow (Centronyx bairdii), chestnut-collared longspur (Calcarius ornatus), McCown's longspur (Rynchophanes mccownii), and Sprague's pipit (Anthus spragueii). In 2017 and 2018, I evaluated abundance, nest density and nest survival of these species in relation to local vegetative conditions with the goal of identifying important breeding season vegetation conditions to inform management. I conducted fixed-radius point-counts at 100 sites to estimate local abundance, rope drag surveys to estimate nest density, nest monitoring to estimate nest survival, and vegetation surveys to estimate vegetation structure and composition across grassland habitats in Phillips County, MT. Point-counts and rope drag surveys were carried out with replicated visits to allow estimation of species-specific detection probabilities. Vegetation conditions were measured at the plot level (9-ha) to provide information at scales relevant for land managers. The abundance of Baird's sparrows was positively associated with residual grass cover and litter cover. Chestnut-collared longspur abundance was negatively associated with residual grass, exotic grass, and shrub cover and had a quadratic relationship with biomass. Plot-level abundance of McCown's longspurs was negatively associated with both shrub cover and biomass. Sprague's pipit abundance declined with exotic grass cover and exhibited a quadratic relationship with biomass. Limited sample size only allowed inference of nest density and nest survival for chestnut-collared longspurs. Nest density was negatively associated with plot scale exotic grass cover, biomass, and slope. I did not find support for any vegetation covariates on nest survival for chestnut-collared longspurs. These results provide some guidance for landscape managers interested in improving habitat for these species. The contrasting results among species, however, emphasize the need for heterogeneity in vegetation structure and composition. The disconnect between relevant covariates for nest density and nest survival suggest possible maladaptation for chestnut-collared longspurs. This result suggests that an index of productivity for this species that does not include both nest density and nest survival may produce erroneous results.Item Impacts of weather, habitat, and reproduction on the survival and productivity of wild turkeys in the northern Black Hills, South Dakota(Montana State University - Bozeman, College of Letters & Science, 2019) Yarnall, Michael James; Chairperson, Graduate Committee: Andrea Litt; Andrea R. Litt, Chad P. Lehman and Jay J. Rotella were co-authors of the article, 'Precipitation and reproductive effort combine to alter survival of wild turkey hens in the northern Black Hills, SD' submitted to the journal 'Journal of wildlife management' which is contained within this thesis.; Andrea R. Litt, Chad P. Lehman and Jay J. Rotella were co-authors of the article, 'Impacts of weather on reproductive productivity of wild turkeys in the northern Black Hills, SD' submitted to the journal 'Journal of wildlife management' which is contained within this thesis.The study of population ecology is motivated by a desire to understand variation in the factors that drive wildlife population dynamics. Robust vital rate estimates are crucial for effective wildlife conservation and management, particularly for at-risk or harvested species. In avian populations, the survival of females, nests, and young are important drivers of population growth, although the relative importance of each rate can differ among species. Annual and regional variation in vital rates within species is common; further, local climatic and habitat conditions may influence population dynamics. During 2016 - 2018, we used radio telemetry to study the impacts of weather and habitat conditions on the survival and productivity of Merriam's wild turkeys (Meleagris gallopavo merriami) in the northern Black Hills of South Dakota. Specifically, we quantified the impacts of 1) precipitation and reproductive effort on hen survival, 2) precipitation and habitat conditions on nest survival, and 3) precipitation and temperature on early poult survival. Precipitation reduced the survival of hens and nests, although the magnitude depended on the hen's incubation status or the vegetation characteristics at the nest site. Based on precipitation data from 2017, the estimated annual survival rate for a hen that did not incubate was 0.535 (SE = 0.038), whereas that and for a hen that incubated for 26 days was 0.436 (SE = 0.054). The probability that a nest would survive from initiation to hatching for a nest initiated by an adult hen on the median date of nest incubation in 2017 was estimated to be 0.432 (SE = 0.084). The estimated probability that a poult would survive from hatching to 4 weeks of age was 0.387 (SE = 0.061). Our results clearly demonstrate a negative cost of reproduction, as predicted by life-history theory, and show that hens and nests in this ecosystem are more vulnerable to predation during or immediately following rainfall, as predicted by the moisture-facilitated nest-predation hypothesis. Survival and productivity of turkeys was lower in our study area than in other portions of the Black Hills; we recommend that managers take steps to limit human-induced hen mortality of this important game species.Item Assessing respiratory pathogen communities and demographic performance of bighorn sheep populations: a framework to develop management strategies for respiratory disease(Montana State University - Bozeman, College of Letters & Science, 2017) Butler, Carson Joseph; Chairperson, Graduate Committee: Robert A. GarrottRespiratory disease (pneumonia) is a persistent challenge for bighorn sheep (Ovis canadensis) conservation as sporadic epizootics cause up to 90% mortality in affected populations and are often followed by numerous years of low juvenile recruitment attributed to lamb pneumonia. Domestic sheep (Ovis aries) and domestic goats (Capra aegagrus hircus) are the origin of the disease and asymptomatically carry respiratory pathogens that cause respiratory disease when introduced to bighorn sheep. Pathogens that have been linked to respiratory disease in bighorn sheep include several species of bacteria in the Pasteurellaceae family and another bacterial species, Mycoplasma ovipneumoniae. Despite substantial efforts by management agencies to prevent contact between bighorn sheep and domestic sheep and goats, respiratory disease epizootics continue to affect bighorn sheep populations across much of their distribution with uncertain etiology. This study sought to investigate efficacy of diagnostic protocols in detecting Pasteurellaceae and Mycoplasma ovipneumoniae and generate sampling recommendations for different protocols, assess the distribution of these disease agents among 17 bighorn sheep populations in Montana and Wyoming and evaluate what associations existed between detection of these agents and demographic performance of bighorn sheep populations. Analysis of replicate samples from individual bighorn sheep revealed that detection probability for regularly-used diagnostic protocols was generally low (<50%) for Pasteurellaceae and was high (>70%) for Mycoplasma ovipneumoniae, suggesting that routine pathogen sampling likely mischaracterizes respiratory pathogen communities. Power analyses found that most pathogen species could be detected with 80% confidence at the population-level by conducting regularly-used protocols multiple times per animal. Each pathogen species was detected in over half of the study populations, and consideration of detection probability discerned that there was low confidence in negative test results for populations where the Pasteurellaceae species were not detected. 76% of study populations hosted Mycoplasma ovipneumoniae and Pasteurellaceae pathogens, yet a number of these populations were estimated to have positive population growth rates and recruitment rates greater than 30%. Overall, the results of this work suggest that bighorn sheep respiratory disease may be mitigated by manipulating population characteristics and respiratory disease epizootics could be caused by pathogens already resident in bighorn sheep populations.