Theses and Dissertations at Montana State University (MSU)
Permanent URI for this collectionhttps://scholarworks.montana.edu/handle/1/733
Browse
3 results
Search Results
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 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.