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Theses and Dissertations

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Browsing Theses and Dissertations by Author "Ackerfield, Jennifer, committee member"

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    Conservation genetics and phylogeography of a disjunct prairie plant: Clematis fremontii (Ranunculaceae)
    (Colorado State University. Libraries, 2022) Krakowiak, Alaina, author; Simmons, Mark, advisor; Ackerfield, Jennifer, committee member; Hufbauer, Ruth, committee member; McGlaughlin, Mitchell, committee member
    Premise: Clematis fremontii has a unique disjunct distribution with populations found in multiple distinct and widely separated mixed-grass and xeric limestone prairie habitats in the Great Plains, Ozarks, and Southeast. It is considered rare and endangered in much of its range. This study assesses genetic differentiation and diversity of C. fremontii in and among these disjunct areas in order to 1) inform conservation strategies, and 2) better understand the biogeographic processes that shaped its current range. Methods: 116 samples collected from 17 populations across the species' range plus 10 outgroup samples of C. ochroleuca were sequenced using a double digest restriction-site associated DNA (ddRAD) approach. Genetic diversity and structure were analyzed using STRUCTURE, multivariate ordination, and other statistical approaches. hierarchical relationships were estimated with Tetrad, TNT, and a neighbor-net analysis. Results: All populations showed moderate genetic diversity, and geographic regions showed moderate genetic differentiation from one another. Analyses generally demonstrated that initial divergence was between groups occurring east and west of the Mississippi River, but we found further structuring among disjunct regions. We also found evidence for secondary contact between eastern and western groups, particularly in the Georgia population. Conclusions: Small, isolated populations of Clematis fremontii have higher levels of genetic diversity than we expected, but habitat loss still poses a major threat. Current levels of genetic diversity could indicate an extinction lag. Restoration and population augmentation efforts are needed for this species to persist long-term. Additionally, our data supports the hypothesis that separation of eastern and western C. fremontii populations dates to relatively recent Pleistocene events. This could be a vicariance event, such as meltwater mega-flooding of the Mississippi River, or an eastward expansion from a more widespread western group during an interglacial period. Our data did not support the hypotheses of ancient vicariance via the formation of the Mississippi embayment or very recent expansion dating to the Hypsithermal Interval. We also found that C. fremontii accumulated genetic variation upon isolation in xeric limestone prairie habitats, similar to a rapid radiation.
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    ItemOpen Access
    Paralogy or reality? Exploring gene assembly errors in a target enrichment dataset
    (Colorado State University. Libraries, 2022) Rosén, Austin, author; Simmons, Mark P., advisor; Ackerfield, Jennifer, committee member; Richards, Christopher, committee member; Stewart, Jane, committee member
    De novo gene assembly of short read data is inherently difficult – similar to the process of assembling a jigsaw puzzle. I describe three errors that occurred with the assembly of target enrichment data in the genus Cirsium (Asteraceae): inconsistent contig selection, artificial recombination, and inconsistent intron determination leading to over-alignment of non-homologous nucleotides. These errors occurred in 39% of loci in the dataset and were often a by-product of undetected paralogs: assembled loci that likely contained paralogous or homoeologous sequences but did not trigger default paralog warnings by the assembly program, HybPiper. Default HybPiper thresholds for identifying paralogy during the assembly process were insufficient to filter such loci. A custom target file was created in which putative paralogs were separated into independent loci. The custom target file was successful in reducing, but not eliminating, assembly errors in the dataset. A final iteration of quality control was performed to create a dataset largely free of assembly errors. However, phylogenetic inferences applied to this final cleansed dataset were unable to resolve the taxonomic relationships between the sampled specimens. Rather, these results affirm that Cirsium is a taxonomically problematic genus and may require population-level genetic data or integrative taxonomy approaches to delimit species boundaries.