Browsing by Subject "population genetics"
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Item Data from: The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference(2018-07-25) Flagel, Lex; Brandvain, Yaniv; Schrider, Daniel; flag0010@gmail.com; Flagel, Lex; Department of Plant and Microbial BiologyLarge neural network training data sets. The corresponding code for training can be found here: https://github.com/flag0010/pop_gen_cnn Both the data sets and code are associated with this paper: https://www.biorxiv.org/content/early/2018/05/31/336073Item Genetic analysis of moose populations from Minnesota and Yellowstone National Park(2015-12) Tjepkes, TessaBy assessing the amount and geographic distribution of genetic variation in moose we can better understand how microevolutionary processes and landscape features have influenced that variation. How the distribution of moose changes in the future will be partially dictated by the amount and content of genetic variation moose populations possess. Therefore, it will be useful to acquire more moose population genetic data and to study declining populations. My thesis had two primary objectives: (1) to compare the efficacy of DNA extraction from different biological samples and (2) to genotype a subset of Minnesota moose at a locus known to be associated with chronic wasting disease in other cervid populations. DNA for genetic analyses was extracted from blood, tissue, and pellets. Extracted DNA from all source types was sufficient for genotyping using 15 microsatellites and Sanger sequencing. However, DNA extracted from pellets was of both lower quality and quantity than DNA extracted from blood and tissue. Minnesota moose contain polymorphisms that have been correlated with increased susceptibility to chronic wasting disease in cervids in other areas. These results provide valuable comparisons of efficiency and effectiveness of DNA extraction protocols for tissue, blood, and fecal pellets as well as baseline population genetic data that can be used to detect future genetic changes in these populations.Item Genetic and Horticultural Characterization of Hydrangea quercifolia Bartr. (Oakleaf Hydrangea) Throughout its Natural Range of Occurrence(2020-06) Sherwood, AndrewOakleaf hydrangea (Hydrangea quercifolia Bartr.) is an understory shrub native to the southeastern United States. The species occupies a small native range, and little is known about its genetic diversity, needs for conservation or range of phenotypic variation for horticultural traits. This study had two primary objectives. 1) To characterize the structure of the genetic diversity throughout the species range and begin to understand what factors contribute to this structure. 2) To characterize variation for horticulturally important traits. Samples were collected from 188 plants in 73 locations throughout the species range and were genotyped using genotyping by sequencing. A Structure analysis identified 6 genetic clusters which are geographically structured. Although these clusters are weakly differentiated, each has unique alleles. An environmental association analysis determined that environmental variables explain 11.3% of genetic diversity while population structure explains 13.5%. Further, 231 putative adaptive alleles were identified, the majority of which are correlated with precipitation related variables, indicating that precipitation has an impact on genetic diversity in H. quercifolia. Many historically documented populations were found to be either extirpated or at risk of extirpation. The genetic clusters on the southern extent of the species range are relatively small and contain putative adaptive alleles at relatively high allele frequencies. This highlights the importance of preserving representative germplasm from throughout the species range. Seed was collected from 55 populations throughout the species range for the horticultural characterization. Seed germination percentage was characterized in a greenhouse and growth chamber. Plant architecture was characterized as plant height, number of nodes, internode length, number of branches and plant width. Plant architecture was measured in potted and field grown plants in two locations. Tolerance to leaf spot (Xanthomonas campestris L.) was characterized in wild collected seedlings and cultivars by measuring disease severity under natural exposure to inoculum. Cold hardiness was characterized in two winters with a controlled freezing experiment. The first winter, seedlings were tested in January only and the second winter seedlings and cultivars were tested monthly throughout winter. Significant variation among wild populations and cultivars was found for all traits measured in all environments. Mean population seed germination percent ranged from 11% to 93% (mean=61% in greenhouse, 74% in growth chamber). Plant architecture varied by environment, with plants growing larger in Tennessee than in Minnesota. Plant height was correlated with collection site latitude (r=-0.66) with populations from the northeastern extent of the species range being the most compact and populations from Florida being the largest. Leaf spot severity varied significantly among populations and cultivars and was also correlated with latitude in the wild seedlings (r=0.70). Two populations in Florida were identified as sources of resistance to leaf spot while ‘Flemygea’ and ‘Alice’ were identified as having moderate tolerance to leaf spot. Cold hardiness varied among populations and cultivars and among months of the winter. Overall maximum cold hardiness was observed in February (mean LT50=-33.7°C), and several populations maintained an extreme level of cold hardiness into late winter. Midwinter cold hardiness also varied by latitude (r=-0.65). These results indicate that certain wild oakleaf hydrangea populations will be useful for introgressing novel variation into breeding programs.Item How Salamander Species Can Hybridize Extensively Yet Remain Distinct: Insights from Habitat Data, Molecules, and Behavior(2016-07) Lowe, BenjaminThis project explores a situation where two distinctive species hybridize extensively at zones of contact yet appear not to be collapsing into a single species. Lack of impending merger is inferred when regions made up of organisms of mixed ancestry (‘hybrid zones’) are not increasing in extent but instead are stable. There is growing recognition that this phenomenon is common nature. Several forces have been proposed to function in preventing lineage merger in these situations. Selection for different ecological conditions (‘exogenous selection’) is widely acknowledged to maintain species limits, especially when the contacting lineages are associated with different habitats. Genome incompatibilities (when hybridization leads to the breakdown of co-adapted gene complexes, or ‘endogenous selection’) have also been cited as contributing to hybrid zone stability. Positive assortative mating, where individuals preferentially mate with similar individuals, has also been put forward as a process that could prevent the merger of species. Two species of lungless salamanders, Plethodon shermani and P. teyahalee, have parapatric distributions in the southern Appalachian Mountains and form hybrid zones where their distributions meet. I investigated hybrid zone stability and potential factors maintaining species limits between these salamanders. In Chapter 1, I use coalescent simulations to identify a lower bound on the timing of secondary contact, which in turn leads to an expected hybrid zone extent under a model of neutral diffusion. By comparing observed and expected hybrid zone extent, I show that the two species are not in the process of freely merging despite extensive introgression of molecular markers. In Chapter 2, I evaluate predictions of ex- and endogenous selection using ground-level temperature data and character clines fitted to molecular and morphological data. I find evidence for exogenous selection but not for endogenous selection. In Chapter 3 I present data from courtship trials performed in the laboratory that reveal that despite frequent interspecific hybridization, these two species show a preference for conspecifics. These findings shed light on Plethodon hybrid zone dynamics and the maintenance of species limits for hybridizing species.Item Population Genetic Structure Of The Freshwater Mussel Potamilus Alatus In The State Of Minnesota(2020-05) Smith, AshleyFreshwater mussels (family Unionidae) have been declining across North America at an alarming rate. Numerous conservation strategies have been invoked to slow or reverse this decline, with hatcheries and transport of individuals from healthy populations to ailing ones being a common technique. However, moving individuals from one population to another can have unintended consequences if the individuals from the source population are genetically distinct, so it is imperative that conservationists understand the underlying patterns of genetic diversity of the species they are trying to save. This study examines populations of the mussel Potamilus alatus across the state of Minnesota in order to determine the extent of genetic connectivity among different geographic populations are. Analyses of seven different microsatellite loci found that populations within the Mississippi River watershed are genetically similar; however, a population along the Red Lake River is isolated and unique. Any future conservation efforts with Potamilus alatus should take these differences in to account when taking broodstock for hatcheries or transporting individuals between populations, in order to avoid outbreeding depression, or transplanting individuals into environments for which not be genetically suited.Item The spatial scale of adaptation in common ragweed (Ambrosia artemisiifolia)(2019-09) Gorton, AmandaEnvironmental variation at both large and small spatial scales can influence the ecological and evolutionary trajectory of plant populations. Decades of common garden and reciprocal transplant experiments have demonstrated that local adaptation is widespread. However, most experiments examining local adaptation compare populations at a single spatial scale. For my dissertation, I combined field experiments and population genetics to examine how environmental variation at three spatial scales—small (i.e., among populations), regional (i.e., urban vs. rural), and continental (i.e., across latitudes)—shapes local adaptation in common ragweed (Ambrosia artemisiifolia L.). I found evidence for adaptation to urban environments and latitudinal gradients in climate. More specifically, I found evidence that phenotypic divergence at small spatial scales (e.g. within a city) can be greater than divergence found at larger spatial scales. Across latitudes, I found that photoperiod influences the fitness of common ragweed populations, and the relevant spatial scale for adaptation varies across life history stages. In addition, for northern populations of ragweed, I found that climate change is already causing maladaptation. Lastly, my population genomic work with RNA-seq identified new traits of interest that may be involved in local adaptation, including stomatal opening and closing and seed dormancy. I discuss these results with regard to how they can help us understand local adaptation more broadly and in turn predict how plants may respond to climate change.