Browsing by Subject "Phylogenetics"

Now showing 1 - 7 of 7
  • Thumbnail Image
    Item
    Molecular phylogenetics of the New World blackbirds (Icteridae)
    (2012-12) Powell, Alexis Frederick Leo Alvey
    The New World blackbirds (Icteridae) are among the best known songbirds, both through exemplar species, such as the Red-winged Blackbird (Agelaius phoeniceus), and collectively, as a model clade in studies of morphological, ecological, and behavioral trait evolution. Knowledge of phylogeny is a prerequisite for comparative studies and the basis for systematic classification, yet there has been no comprehensive analysis of blackbird phylogeny. In Chapter 1, I present the phylogeny of the grackles (Quiscalus spp.) inferred from cytochrome b and ND2 gene sequences. A primary concern was determining the relationships of the extinct Slender-billed Grackle (Q. palustris) and Q. nicaraguensis, which is unusual among grackles for its restricted geographic range. I found the Slender-billed Grackle to be most closely related to one of two major haplotype clades of Q. mexicanus, the other being sister to Q. major. Q. nicaraguensis appears sister to Q. lugubris. I also found that Q. mexicanus, niger, and lugubris contain deeply-divergent lineages. In Chapter 2, I present a method for partitioning whole mitochondrial genome sequences to optimize model-fitting during phylogenetic analyses. Because standards for rigorous phylogenetic analyses of mitogenomes were lacking, developing such a method was a prerequisite for analyzing the mitogenomes of a clade of South American endemic blackbirds. I found that the most useful categories for partitioning were codon position, RNA secondary structure pairing, and the coding/noncoding distinction, and that a scheme with nine data groups outperformed all of the more complex alternatives (up to 44 data groups) that I tested. In Chapter 3, I present the first comprehensive species-level phylogeny of the Icteridae. By using mitochondrial gene sequences from all ~108 currently-recognized species, together with strategic sampling of 4 nuclear loci and whole mitochondrial genomes at the generic level, I was able to resolve most relationships with high confidence. The best-resolved phylogeny is consistent with strongly-supported results of past studies, but it also contains many novel robustly-resolved inferences of relationship, including some unexpected placements of taxa that had not been included in previous molecular phylogenies, resolution of the relationships among major subclades within Icteridae. I suggest taxonomic revisions based on those results.
  • Thumbnail Image
    Item
    Molecules & morphology reveal ‘new’ divergent, widespread Lampsiline species (Bivalvia: Unionidae)
    (2018-06) Keogh, Sean
    The recognition of biodiversity in imperiled groups of organisms is fundamental to their conservation. In the Family Unionidae, the greatest radiation of freshwater mussels, species descriptions have been misled by extreme intraspecific shell variation and conversely interspecific conchological stasis. Lampsilis teres (Rafinesque, 1820) a polymorphic, widespread species has historically been split into as many as three subspecies that correlate to phenotypic variants. Recently, one subspecies was elevated to species level based on unique morphology and molecular differences. However, other subspecies designations are no longer recognized and no study has investigated these phenotypes with molecular characters. In this study I characterize the morphology of two phenotypes of L. teres using geometric and traditional morphometrics and use molecular phylogenetics to test the hypothesis that phenotypes represent separate species. Results from my molecular analyses unanimously indicate that L. teres as it is currently recognized is made up of two divergent, non-sister species. Herein I redescribe Lampsilis anodontoides (Lea, 1831) and use morphometrics and machine-learning algorithms to characterize shell morphology variation in each taxon.
  • Thumbnail Image
    Item
    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).
  • Thumbnail Image
    Item
    Spatial and Molecular Epidemiological Approaches for Evaluating Dynamics of Foot-and-Mouth Disease Virus in India and Vietnam
    (2021-10) Wijewickramalage Gunasekara, Umanga
    Foot and mouth disease virus (FMDV) is still endemic in many regions worldwide. Many widespread FMDV lineages have emerged from South Asia, and subsequently spread to other regions, including Southeast Asia, making these two regions important epicenters for FMDV evolution and transboundary transmission. The progressive control pathway (PCP) proposed by the World Animal Health Organization and the Food and Agriculture Organization (OIE/FAO) provides a framework for countries to reduce the incidence of the disease, with the ultimate goal of achieving zonal or country-wide freedom from disease. The PCP pathway is outcome-oriented and relies on a self-evaluation process before being accredited by the OIE and obtaining the official status for a given stage. Different epidemiological methods are acceptable for evaluation of the progress at each stage, yet OIE/FAO does not provide specific guidelines in regard to methods for epidemiological evaluation. In this dissertation, the objective was to demonstrate how recent and newly developed epidemiological approaches can be applied to support progression through PCP stages in South and Southeast Asia. Two countries in those two regions, India and Vietnam, both countries in stage 3, were used as case studies to examine how commonly available types of epidemiological data, such as reported outbreaks and sequence data, can be analyzed to understand the spatial dynamics of FMDV circulation, assess the effectiveness of vaccination programs, and delineate high-and low-risk areas. Ultimately, this work will serve as a proof-of-concept for novel methods for genomic surveillance, which could be used as a cost-effective means to generate sequence data needed for surveillance and epidemiological analysis and help the countries to move towards stage 4 of the PCP. The first chapter provides an overview of the PCP with a focus on stages 1-3, epidemiological approaches typically used to support PCP activities, and the FMD situation in India and Vietnam. The second chapter specifically explores FMD situation in India and applies Bayesian space-time regressions to investigate factors underlying the spatial heterogeneity in risk of reported outbreaks, including an assessment of how mass vaccination impacted the spatial and temporal distribution of disease. However, such spatial models account for population connectivity by incorporating spatial autocorrelation amongst contiguous spatial units, which is likely a poor representation of population connectivity for highly mobile hosts such as livestock. The third chapter explores the ways to improve Bayesian space-time regression models using the phylogeography to account for patterns of population connectivity. Finally, monitoring circulating virus strains and rapid detection of novel strains is a necessary component of FMD control as part of the PCP, and sequence data also enables a number of other epidemiological approaches to understand virus circulation in a country. Conventional methods to acquire sequence data in the field are not efficient as a means for routing genomic surveillance, and it may be more effective to identify sentinel surveillance points to detect emerging outbreaks, such as slaughterhouses. Genomic surveillance at slaughterhouses was explored in the fourth chapter using FMDV sequence data from Vietnam. The final chapter is an overview of demonstrated methods to improve FMD control measures and support progression in PCP stages in FMD endemic countries in endemic regions of South and Southeast Asia.
  • Thumbnail Image
    Item
    Studies on Puccinia coronata var. coronata and other recently observed rust fungi in Minnesota
    (2023-07) Greatens, Nicholas
    In the spring of 2017, a prolific crown rust fungus was observed on the highly invasive glossy buckthorn (Frangula alnus) around Central Park, Roseville, MN. Field observation and greenhouse studies established the grass host as another invasive species, reed canarygrass (Phalaris arundinacea), and sequencing identified the rust fungus as Puccinia coronata var. coronata sensu stricto (Pcc), a taxon of likely Eurasian origin not previously known in Minnesota. Curiously, this new pathogen appeared to have a desirable effect locally, strongly affecting only two invasive plant species. In a research project that began in 2019 and was funded in 2020 by the Minnesota Invasive Terrestrial Plants and Pests Center, we pursued three goals, which correspond to the first three chapters of this dissertation: 1) to determine the distribution of Pcc in Minnesota and North America; 2) to assess its host specificity on potential buckthorn and grass hosts; and 3) to evaluate its potential as an augmentative biological control agent of one or both of its invasive hosts. We report Pcc across the range of glossy buckthorn in the Midwest and Northeastern U.S. but find that it is absent on susceptible reed canarygrass outside the range of glossy buckthorn within Minnesota. Cereal crop and turfgrass species were highly resistant to Pcc, but other grass and buckthorn species were susceptible, including some native North American species. In greenhouse trials, Pcc significantly reduced the height and biomass of both reed canarygrass and glossy buckthorn, supporting its use as a possible biological control agent of one or both of its hosts, although non-target effects and deployment strategies would require further consideration. Chapter four describes a similarly designed study around another crown rust fungus, Puccinia digitaticoronata, which we confirm for the first time in North America. We investigate its relation to other crown rust fungi and its pathogenicity on grass and buckthorn species. In greenhouse studies, the popular turfgrass species Kentucky bluegrass (Poa pratensis) is broadly susceptible, along with numerous other native and weedy Poa spp. Common buckthorn (Rhamnus cathartica), another widespread invasive species, is an aecial host of the rust fungus and likely facilitates its sexual cycle locally. Chapter five combines the results of two small projects published as plant disease notes: first reports of Puccinia glechomatis, a rust of creeping Charlie (Glechoma hederacea) in Minnesota and of a Puccinia sp. causing rust of lemongrass in Minnesota.
  • Thumbnail Image
    Item
    Systematics, Gill Raker Morphology, and Pharyngeal Arch Development of Suckers (Cypriniformes: Catostomidae)
    (2015-06) Hirt, Michael
    Morphological diversity is shaped by past evolutionary history, function, and ontogeny. Evolutionary history plays an important role in shaping morphological diversity and morphology itself can affect the future evolutionary trajectory of taxa. Morphology is shaped by function through selection and function can be constrained by morphology. Differences among taxa in their morphology arise due to changes in the pattern of development in those taxa. Therefore, a full understanding of morphological diversity requires knowledge about evolutionary history, morphological function, and ontogeny. Suckers, family Catostomidae, are a group of freshwater fish with interesting trophic morphology and feeding habits. I used molecular sequence data and fossil calibrations to reconstruct the phylogeny and divergence times of the families of Cypriniformes, including Catostomidae. I found evidence that gene choice, base compositional heterogeneity, and rate heterogeneity provide challenges to reconstructing the evolutionary history of the order and I found that body size is correlated with the rate of molecular evolution not only in Cypriniformes but in many groups of fishes. Suckers, like most fish, have gill rakers which are complex, repetitive, finger-like projections in the interior of the branchial arches that are important in feeding and vary among species. I quantified and compared gill raker morphology among sucker species and found that multiple aspects of gill raker morphology interact to predict function. Gill rakers are just one component of the complex trophic apparatus of suckers. I described and compared the sequence of chondrification and ossification of the paired elements of the pharyngeal arches and the histological development of the palatal organ, chewing pad, and pharyngeal teeth in five species of suckers and found several examples where heterochrony has shaped the trophic morphology of suckers.
  • Thumbnail Image
    Item
    Three keys to the radiation of angiosperms into freezing environments
    (Nature Publishing Group, 2014) Zanne, Amy E; Tank, David C; Cornwell, William K; Eastman, Jonathan M; Smith, Stephen A; FitzJohn, Richard G; McGlinn, Daniel J; O’Meara, Brian C; Moles, Angela T; Reich, Peter B; Royer, Dana L; Soltis, Douglas E; Stevens, Peter F; Westoby, Mark; Wright, Ian J; Aarssen, Lonnie; Bertin, Robert I; Calaminus, Andre; Govaerts, Rafaël; Hemmings, Frank; Leishman, Michelle R; Oleksyn, Jacek; Soltis, Pamela S; Swenson, Nathan G; Warman, Laura; Beaulieu, Jeremy M
    Early flowering plants are thought to have been woody species restricted to warm habitats1, 2, 3. This lineage has since radiated into almost every climate, with manifold growth forms4. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species’ traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits5 and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile6, but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold.