Browsing by Subject "Population genetics"

Now showing 1 - 5 of 5
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    B-G gene structure, genetic variation and expression in the turkey (Meleagris gallopavo) major histocompatibility complex
    (2013-02) Bauer, Miranda Marie
    The major histocompatibility complex (MHC) is a genomic region encoding for genes with various immune functions in vertebrates. Although this region has been studied extensively in humans, mice and agriculturally important species such as cattle, horses and chickens, the organization and functional significance of the turkey MHC is relatively unknown. One set of loci located in the avian MHC, designated as B-G genes, have been identified and sequenced within the B-locus of the turkey, chicken and quail, with additional B-G loci identified in the extended MHC of the latter two species. These genes are linked to the class I and class II loci of the MHC and also show regions of extreme polymorphism (Miller, 1984). The total number, function and significance of the B-G genes are yet unknown in any bird species. In turkeys, three B-G genes were previously sequenced within the B-locus (Chaves et al., 2009a), with evidence suggesting additional functional B-G genes located past the 5' ends of the sequenced MHC region. Evidence in the chicken shows differential expression of B-G genes in various immune tissues, which suggests potential immune function. This research used 454 FLX Next Generation Sequencing technology (Roche) for sequencing a bacterial artificial chromosome (BAC) and identified two additional B-G genes located past the 5' end of the core B-locus of the turkey. These genes were annotated using in silico analysis and show organization similar to those in the chicken and quail. Using this information, sequence variation of the B-G genes was compared in different stocks of turkeys. Because each of the three groups, (commercial, heritage and wild), have been selected for different characteristics, variation within these loci was expected. This experiment found variation among loci within the three groups of turkeys. Lastly, B-G gene expression was investigated with quantitative real-time PCR using liver tissue of aflatoxin challenged birds. A low level of expression was observed for three of the four BG genes investigated, with BG5 expression invariant in all individuals across treatment groups. BG4 expression levels fluctuated within and between groups and a higher level of expression was measured in the lactobacillus + aflatoxin group. This work extended the turkey B-locus sequence past the homologous region in the chicken and marks the first examination of sequence variation and gene expression of multiple B-G genes in any species. Sequence variation and expression differences among loci support a hypothesis of distinct functions for these molecules.
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    Genetic diversity, structure, and hybridization in a harvested gray wolf (Canis lupus) population in Minnesota
    (2015-12) Rick, Jessica
    The demographic, social, and genetic effects of harvest-based management practices are not fully understood, especially in social carnivore species. Minnesota was one of several states that instituted a public hunting and trapping season to manage gray wolves (Canis lupus) following the delisting of wolves from the Endangered Species Act in 2012. Hunters and trappers harvested 413 wolves in Minnesota in 2012, about three times the average number of wolves removed annually under depredation control in previous years. Using tissue from wolves harvested during the 2012 and 2013 seasons in Minnesota, I assessed the population genetic consequences of this increase in anthropogenic mortality to determine if the harvest led to changes in population genetic structure and diversity in the first post-harvest year. I also sequenced a portion of the mitochondrial DNA (mtDNA) control region to assess the extent of gray wolf-eastern wolf (C. lycaon) and gray wolf-coyote (C. latrans) hybrid ancestry in Minnesota wolves. I found no significant difference in genetic diversity indices or mtDNA haplotype frequencies between years; however, population genetic structure and effective gene flow among the sampled wolves changed from 2012 to 2013. These analyses provide a baseline to determine variation in structure between years is normal for Minnesota wolves and how changes in genetic structure positively or negatively impact wolf populations. Baseline population genetic analysis at the beginning of managed harvest enabled my analysis of initial genetic responses to harvest, and will allow for comparisons with the population genetic structure of historical and future wolf populations in Minnesota.
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    Limits to range expansion in the native annual legume Chamaecrista fasciculata.
    (2011-08) Stanton-Geddes, John Louis
    Species range limits are determined by historical (e.g., range expansion), ecological (e.g., biotic interactions) and genetic (e.g, gene flow) processes, but comprehensively understanding the relative role of these processes in limiting any single species‟ range has been elusive. This research is timely for understanding species‟ responses to climate change. The goal of this research was to examine the processes that limit the range of the native annual legume Chamaecrista fasciculata, by integrating ecological-genetic field studies and population genetic laboratory studies. In Chapter 1, I investigate the extent to which C. fasciculata is in demographic range edge equilibrium at its western and northern range edges, and the effect of biotic interactions at these range edges. I find that C. fasciculata fitness is reduced to zero when planted beyond the western and northern range limits, indicating it is in equilibrium with its range. Neighbors increase early-season survival, but decrease seedpod production. The goal of Chapter 2 was to examine if the mutualism between C. fasciculata and its associated rhizobia was disrupted beyond the range edge, potentially limiting range expansion. The results demonstrate that compatible rhizobia are nearly absent beyond both range edges, which may limit range expansion. In Chapter 3, I ask how the habitat where C. fasciculata establishes may change with range shifts. I conclude that habitat type influences C. fasciculata fitness, but the outcome depends on both the substrate and competitive environments. Finally, in Chapter 4, I use population genetic methods to gain insight into the history of range expansion, population structure and gene flow. Population genetics indicate that the edge populations have reduced genetic diversity compared to the southernmost interior population, and are highly differentiated from each other. However, there is little evidence for contemporary gene flow between populations at the scale investigated. Overall, this work suggests that ecological-genetic or metapopulation dynamics are likely to be involved in setting the northern and western range limits. Further, it highlights the value of integrated approaches to studying species‟ range limits.
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    Minnesota's Red-tailed Hawks: Probabilistic Origins of B.j. abieticola and Dark-morph Migrants
    (2022-08) Pesano, Alexandra
    The Red-tailed Hawk (Buteo jamaicensis) is one of North and Central America’s most common, polymorphic raptor species, with an extensive geographic range divided into 12 putative subspecies ranges. In North America, plumage polymorphism occurs along a clinal gradient with dark-morph individuals becoming less prevalent east of the Rocky Mountains. Polymorphism and other plumage traits can be used to identify individuals to a subspecies, but high levels of intergradation and individual variation can complicate identification. Duluth, Minnesota, USA is a migratory hotspot well known for phenotypically diverse Red-tailed Hawks, including B.j. abieticola and dark-morphs plumages. Due to atypical plumage traits of B.j. abieticola and dark-morphs, subspecific origins of Minnesota’s migratory individuals are not always resolved. Genetic data was collected from Duluth’s migratory Red-tailed Hawk population and known subspecies populations, B.j. calurus and B.j. borealis, to determine the probabilistic subspecific origins of B.j. abieticola and dark-morph migrants. Twelve microsatellite markers were used to analyze and compare genetic diversity and population structure within and among breeding populations and the migratory individuals. Bayesian statistics were also performed to determine probabilistic assignments of migratory individuals to putative subspecies. Supplemental spatial data was also collected from two presumed adult dark-morph B.j. abieticola. Pairwise FST revealed the B.j. abieticola and dark-morph migrants were both more genetically similar to B.j. borealis than B.j. calurus. Population assignment probabilities supported that these migratory individuals were more closely related to B.j. borealis than B.j. calurus. Furthermore, preliminary satellite transmitter data from one presumed adult dark-morph B.j. abieticola migrant revealed the individual spent at least one summer east of the Rocky Mountains. These findings suggest Minnesota’s B.j. abieticola and dark-morph migrants have a higher probability of originating from B.j. borealis, a Red-tailed Hawk subspecies historically known to only present light-morph plumage, than B.j. calurus.
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    Multilocus assessment of population differentiation in Baja California birds: implications for community assembly and conservation
    (2014-08) Vazquez Miranda, Hernan
    This dissertation is an assessment of biological diversification at the community, species, and population levels from large continental scales in the Americas to small regions between Mexico and the U.S. using birds as a study system. In Chapter 1, I calculate when the avian community of the Baja California peninsula diverged from the mainland using mitochondrial and nuclear DNA sequences. I discovered that even though birds fly and could have arrived to the peninsula in independent dispersal waves, genetic estimates correspond to few events of diversification that correspond to historical barriers to gene flow and more recent ecologic scenarios. Additionally, I find evidence for recognizing four peninsular lineages as valid species, doubling the number of endemic birds in Baja California. Chapter 2 is a collaboration with Keith Barker. In it, we explore the continental diversification of wrens in the genus Campylorhynchus solving all evolutionary relationships by sequencing 23 genes and multiple individuals per lineage, developing a new metric for comparing all sorts of phylogenetic trees, and clarifying biogeographic and behavioral evolution aspects in the Neotropics. In Chapter 3, me and collaborators Kelly Barr, Craig Farquhar, and Robert Zink merge historic fire ecology and population genetics to understand how and when the black-capped vireo (Vireo atricapilla), went from being a historically common bird to being considered currently as endangered in its breeding grounds in the oak savannas of Oklahoma, Texas and northern Mexico. Five online supplementary files (OSFs) accompany this dissertation: the first file includes voucher numbers, geographic information, substitution models, used primers, and full likelihood values in Chapter 1 (OSF 1); the second file contains Bayesian trees ivand taxon pair distributions in Chapter 1 (OSF 2); the third file includes voucher numbers, evolutionary models, recombination tests, and primers used in Chapter 2 (OSF 3); the fourth file includes the randomization design in Chapter 2 (OSF 4); and the fifth file includes geographic information for all samples, primers, and multilocus phylogeny of vireos used in Chapter 3 (OSF 5).