UMD Theses and Dissertations
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Item ECOLOGICAL APPLICATIONS OF MACHINE LEARNING TO DIGITIZED NATURAL HISTORY DATA(2022) Robillard, Alexander John; Rowe, Christopher; Bailey, Helen; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Natural history collections are a valuable resource for assessment of biodiversity and species decline. Over the past few decades, digitization of specimens has increased the accessibility and value of these collections. As such the number and size of these digitized data sets have outpaced the tools needed to evaluate them. To address this, researchers have turned to machine learning to automate data-driven decisions. Specifically, applications of deep learning to complex ecological problems is becoming more common. As such, this dissertation aims to contribute to this trend by addressing, in three distinct chapters, conservation, evolutionary and ecological questions using deep learning models. For example, in the first chapter we focus on current regulations prohibiting the sale and distribution of hawksbill sea turtle derived products, which continues internationally in physical and online marketplaces. To curb the sale of illegal tortoiseshell, application of new technologies like convolutional neural networks (CNNs) is needed. Therein we describe a curated data set (n = 4,428) which was used to develop a CNN application we are calling “SEE Shell”, which can identify real and faux hawksbill derived products from image data. Developed on a MobileNetV2 using TensorFlow, SEE Shell was tested against a validation (n = 665) and test (n = 649) set where it achieved an accuracy between 82.6-92.2% correctness depending on the certainty threshold used. We expect SEE Shell will give potential buyers more agency in their purchasing decision, in addition to enabling retailers to rapidly filter their online marketplaces. In the second chapter we focus on recent research which utilized geometric morphometrics, associated genetic data, and Principal Component Analysis to successfully delineate Chelonia mydas (green sea turtle) morphotypes from carapace measurements. Therein we demonstrate a similar, yet more rapid approach to this analysis using computer vision models. We applied a U-Net to isolate carapace pixels of (n = 204) of juvenile C. mydas from multiple foraging grounds across the Eastern Pacific, Western Pacific, and Western Atlantic. These images were then sorted based on general alignment (shape) and coloration of the pixels within the image using a pre-trained computer vision model (MobileNetV2). The dimensions of these data were then reduced and projected using Universal Manifold Approximation and Projection. Associated vectors were then compared to simple genetic distance using a Mantel test. Data points were then labeled post-hoc for exploratory analysis. We found clear congruence between carapace morphology and genetic distance between haplotypes, suggesting that our image data have biological relevance. Our findings also suggest that carapace morphotype is associated with specific haplotypes within C. mydas. Our cluster analysis (k = 3) corroborates past research which suggests there are at least three morphotypes from across the Eastern Pacific, Western Pacific, and Western Atlantic. Finally, within the third chapter we discuss the sharp increase in agricultural and infrastructure development and the paucity of widespread data available to support conservation management decisions around the Amazon. To address these issues, we outline a more rapid and accurate tool for identifying fish fauna in the world's largest freshwater ecosystem, the Amazon. Current strategies for identification of freshwater fishes require high levels of training and taxonomic expertise for morphological identification or genetic testing for species recognition at a molecular level. To overcome these challenges, we built an image masking model (U-Net) and a CNN to mask and classify Amazonian fish in photographs. Fish used to generate training data were collected and photographed in tributaries in seasonally flooded forests of the upper Morona River valley in Loreto, Peru in 2018 and 2019. Species identifications in the training images (n = 3,068) were verified by expert ichthyologists. These images were supplemented with photographs taken of additional Amazonian fish specimens housed in the ichthyological collection of the Smithsonian’s National Museum of Natural History. We generated a CNN model that identified 33 genera of fishes with a mean accuracy of 97.9%. Wider availability of accurate freshwater fish image recognition tools, such as the one described here, will enable fishermen, local communities, and citizen scientists to more effectively participate in collecting and sharing data from their territories to inform policy and management decisions that impact them directly.Item Multi-locus phylogenetic analysis of Amphipoda indicates a single origin of the pelagic suborder Hyperiidea(2019) Biancani, Leann M; Cummings, Michael P; Osborn, Karen J; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Hyperiidea is an exclusively pelagic suborder of amphipod crustaceans, exhibiting a wide array of unique adaptations to life in the dark, open expanse of the oceanic midwater. No common morphological synapomorphy unites approximately 350 described species. Instead, hyperiid amphipods are defined only by their pelagic existence. Hyperiidea exhibits many of the characteristics of an adaptive radiation and could represent a midwater example of this phenomenon. Previous morphological and molecular analyses have led to uncertainty in the shared ancestry of Hyperiidea. The evolutionary history of their diverse adaptations, as well as their relationship to other amphipods, remains unknown. Here we present results of a multi-locus phylogenetic analysis of publicly available amphipod sequences for three nuclear loci (18S, 28S, and H3) and two mitochondrial loci (COI and 16S) from over 300 amphipod genera, 40 of which are hyperiids. We recover strong support for a monophyletic Hyperiidea as well as reciprocally monophyletic hyperiid infraorders Physocephalata and Physosomata (with enigmatic genera Cystisoma and Paraphronima more closely related to Physosomata). We also identify several benthic, commensal amphipods representing potential sister groups for Hyperiidea. These taxa have not previously been considered close hyperiid relatives and include the genera Amphilochus, Colomastix, Anamixis, Paranamixis, and Leucothoe. Our results support the current definition of Hyperiidea and inform the phylogenetic placement of the suborder within Amphipoda.Item The Diversity of Sex Chromosomes within African Cichlids(2018) Gammerdinger, William Jacob; Kocher, Thomas; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Genetic sex-determination is one of the most prevalent systems by which the sex of an organism can be established. The genes that determine sex reside on chromosomes that experience a unique pattern of evolutionarily processes, which often leads to the degradation of genes surrounding these sex-determination loci. The widespread degradation of sex chromosomes has been noted in the relatively old and heteromorphic sex chromosomes of therian mammals and birds. However, with the advent of next-generation sequencing, it is now possible to study the earliest stages of sex chromosome evolution in relatively homomorphic sex chromosomes. African cichlid fishes are a powerful model system for studying the early stages of sex chromosome evolution because of the diversity and young age of their sex chromosomes. This dissertation develops methods for studying young sex chromosomes and employs these approaches to evaluate the sex chromosomes within tilapia and Lake Tanganyika cichlid fishes. Furthermore, this research demonstrates a method for identifying the ancestral state for species sharing a common sex chromosome system and a process for evaluating the functional significance of these shared mutations. Lastly, this dissertation proposes a mechanism for the diversity of sex chromosome systems observed within African cichlid fishes. This analysis not only characterizes the decay of several known young sex chromosomes, but also reveals multiple previously undiscovered sex chromosome systems within the African cichlid fishes. These novel sex chromosome systems likely represent only a fraction of the true variety of sex chromosome systems within this group, and therefore push forward the argument for characterizing the sex chromosome systems of more cichlid species in order to better understand the early stages of sex chromosome evolution.Item UNRAVELING THE EVOLUTIONARY HISTORY OF NOCTURNALITY IN THE STRISORES(2017) White, Noor; Carleton, Karen L; Braun, Michael J; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Tracing the processes of adaptation is a fundamental practice in the study of evolutionary biology. By combining multiple lines of evidence, we can elucidate the processes of diversification, speciation, and ultimately, evolution. For my doctoral dissertation, I studied the evolutionary history of a superorder of birds (Strisores) that have undergone a dramatic life history transition, the shift from a day-living (diurnal) to a night-living (nocturnal) lifestyle. Previous study found that the diurnal Apodiformes (swifts and hummingbirds) are nested deep within the clade of nocturnal or crepuscular Caprimulgiformes (nightbirds). However, resolution of the other major lineages eluded previous efforts, precluding analysis of the evolution of nocturnality in this group. To resolve the phylogeny of Strisores, I utilized a novel class of genome-scale markers, ultraconserved elements (UCEs). UCEs are operationally defined regions of extreme conservation between two or more genomes. I collected and sequenced ~4,000 UCEs from each of 191 species of birds representing every major extant lineage, plus two crocodilian outgroups—a greater number of elements than had ever been collected or studied before. With this data, I have resolved the phylogeny of the largest and oldest (Caprimulgidae and Nyctibiidae, respectively) lineages of nightbirds, as well as the superorder Strisores, and have shed light on best practices for the use of UCEs in phylogenomics. With a phylogeny representing the evolutionary history of Strisores I then ask when, and where, potential adaptations to nocturnality occurred. To this end, I have developed a molecular tool to efficiently enrich 47 genes comprising the phototransduction cascade, a network of genes that converts the absorption of a photon by an opsin into a neural signal. I demonstrated that this tool is effective in 33 bird species chosen to cover extant avian diversity. The data captured using this array will facilitate the identification of potential molecular adaptations to nocturnality, enable the improvement of models predicting opsin sensitivity from sequence data, and allow strong inference about the perception of color across birds and other vertebrates.Item The Ecology of Urbanization: A Study of Soil Microbial Community Rosponse(2016) Epp Schmidt, Dietrich Jonathan; Yarwood, Stephanie A; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Urbanization is associated with global biodiversity loss of macrophauna and flora through direct and indirect mechanisms, but to date few studies have examined urban soil microbes. Although there are numerous studies on the influence of agricultural management on soil microbial community composition, there has been no global-scale study of human control over urban soil microbial communities. This thesis extends the literature of urban ecology to include soil microbial communities by analyzing soils that are part of the Global Urban Soil Ecology and Education Network (GLUSEEN). Chapter 1 sets the context for urban ecology; Chapters 2 addresses patterns of community assembly, biodiversity loss, and the phylogenetic relationships among community members; Chapter 3 addresses the metabolic pathways that characterize microbial communities existing under different land-uses across varying geographic scales; and Chapter 4 relates Chapter 2 and 3 to one another and to evolutionary theory, tackling assumptions that are particular to microbial ecology.Item Evolution of Pair-rule genes(2015) Lu, Yong; Pick, Leslie; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)All insects have a segmented body. The genes controlling segment development have been well characterized in the fruit fly, Drosophila melanogaster. These genes were divided into three categories: gap genes specify several continuous segments over a broad region of the embryo; Pair-Rule Genes (PRG) are responsible for segment formation and are the first set of genes to be expressed in repetitive patterns in the embryo; Segment polarity genes define anterior and posterior polarities within each segment.To understand how PRGs evolve, I took a comparative approach in this thesis. First, I compared the function of the Drosophila PRG ftz-f1 to that of its mammalian orthologs by expressing them all in Drosophila embryos. I found that the molecular function of this family of nuclear receptors has been highly conserved during evolution. Next, I set out to establish new insect model systems to study PRG function. While, some PRGs have been studied in other insects, most of these studies focused on holometabolous insects. My work focused on the sister group to the holometabolous insects, the Hemipteroid Assemblage. I participated in the genome annotation of a hemipteras insect, Oncopeltus fasciatus. I annotated nuclear receptor super family, Hox and PRGs in Oncopeltus. I further studied the expression and function of four PRGs in Oncopeltus. Using in situ hybridization and RNAi, I found that, Of-ftz and Of-hairy do not have segmentation function, while Of-ftz-f1 has function in oogenesis and segmentation. Of-runt was found to induce cell death in oocytes, but its function in segmentation needs further analysis. Using the knowledge and expertise I gained from Oncopeltus, I successfully set up in situ hybridization, antibody staining and parental RNAi in an invasive hemipteran insect pest, the Brown Marmorated Stink Bug (BMSB) Halyomorpha halys. These studies show that the expression and function of PRGs varies extensively in diverse insects, despite the overall conservation of a segmented body plan.Item Epidemiology and population structure of Xylella fastidiosa, the causal agent of bacterial leaf scorch, among urban trees in the District of Columbia(2014) Harris, Jordan Lee; Balci, Yilmaz; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)A survey of urban trees affected by bacterial leaf scorch caused by Xylella fastidiosa was conducted in the District of Columbia during 2012 and 2013. Disease occurred most frequently with Quercus palustris, Q. rubra, Ulmus americana, and Platanus occidentalis. Eight other symptomatic and five asymptomatic tree species were found infected. The bacterium was also detected on asymptomatic portion of seven tree species. The occurrence of crown dieback was found significantly associated with X. fastidiosa-infection on Q. palustris, Q. rubra, U. americana, and P. occidentalis. A multi-locus sequence typing analysis using 10 housekeeping loci for X. fastidiosa revealed five clonal strains among the urban trees. These strains were host specific, with only one clone being associated with members of the red oak family, American elm, American sycamore, and two clones being associated with mulberry. Long-term management strategies aimed at mitigating the occurrence of bacterial leaf scorch disease are discussed.Item The Ecology of Early Cretaceous Angiosperms: Insights from the Fossil Record(2014) Jud, Nathan A.; Neel, Maile C.; Wing, Scott L.; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The Early Cretaceous diversification of flowering plants was not preceded by a mass extinction event. This suggests that biotic factors intrinsic to flowering plants played an important role promoting diversification, but the rarity of fossils of early flowering plants makes identifying the important features difficult. Here, I present the results of my specimen-based analysis of plant megafossil collections from Lower Cretaceous deposits of the United States. First, I describe previously unrecognized eudicot leaf fossils from a historically important Aptian (Lower Cretaceous) plant fossil site in the Potomac Group, and I provide a set of characters for recognizing the fossil leaves of these plants. Then, I present a morphotype catalog for the fossil plants from and Aptian-early Albian (Lower Cretaceous) site in the Potomac Group. This collection includes one angiosperm morphotype. Next I describe the angiosperm morphotype identified in the previous chapter. I show that it is widely distributed among coeval collections of the Potomac Group and some specimens were previously described as ferns. The preservation of attached stems leaves and root provides direct evidence of weedy, fast-growing, herbaceous angiosperms in the Aptian-early Albian. In the following chapter, I use megafossil data from the literature and museum collections to test the hypothesis that the diversification of flowering plants is associated with an increase in alpha diversity during the Early Cretaceous. Despite the evidence for a high diversification rate among early flowering plants, I found no relationship between collection age and collection richness, but I found strong evidence that angiosperms were consistently rare during the Aptan-middle Albian, and that locally abundant angiosperms became common during the late Albian, long after the initial diversification. Finally, I use new plant megafossil collections that I made from the Cloverly and Sykes Mountain Formations in Wyoming, USA, for a more high-resolution study of early angiosperm diversity, distribution, and abundance. I show that the Cloverly Formation records the appeareance of flowering plants in North America, and that by the Albian angiosperms were widely distributed among available habitats. I test the hypothesis that variation in community composition (beta diversity) increased with the appearance of angiosperms. I did not find strong support for the hypothesis that angiosperms increased beta diversity; however, rarefaction analysis shows that the rate of morphotype discovery in both the pre-angiosperm and the angiosperm interval is high, which means that additional sampling may reveal a difference in beta diversity between the two intervals. Together my findings indicate that flowering plants diversified during the Early Cretaceous not because they had features that allowed them to displace other plant groups, but because they were uniquely able to maintain high diversification rates in the face of rarity and dispersed populations.Item Molecular evolutionary studies on Trypanosoma cruzi, the agent of Chagas disease(2013) Flores Lopez, Carlos Alberto; Machado, Carlos A; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The use of DNA sequences to address diverse evolutionary questions has increased steadily with the growing availability of genome sequence data. In this study, I make use of DNA sequence data to describe several evolutionary aspects of the protozoan parasite responsible for Chagas disease, Trypanosoma cruzi. Chagas is estimated to infect 7.7 million people and cause the deaths of approximately ten thousand people every year in Latin America. Just like many other parasitic diseases, Chagas does not have a vaccine or an effective drug treatment. In this body of work, I specifically: (1) describe the evolutionary history of the major strains of the parasite through the use of phylogenetic analyses of 32 loci and demonstrate that the parasite's original classification into two major evolutionary lineages does not reflect the evolutionary history of the parasite, (2) demonstrate that there is strong evidence for just one major recent hybridization event during the history of T. cruzi divergence and not two as previously suggested, (3) show that all major extant T. cruzi lineages diverged recently (less than 3 million years ago), well before the arrival of humans in the Americas, (4) describe a new T. cruzi lineage that appears to have diverged in North America ("TcNA"), (5) show that a significantly larger fraction of protein-coding genes have experienced positive selection in T. cruzi than in Leishmania spp., a pattern likely due to the greater versatility of T. cruzi in its host range, cell tropism and cell invasion mechanisms, and (6) illustrate a recent major expansion of a few surface protein families in T. cruzi that seem to be linked to the evolution of the parasite's ability to invade multiple cell tissues and multiple host species. These results demonstrate the applicability and power of molecular evolutionary analyses for understanding parasitic diseases.Item Molecular phylogenetics, biodiversity and life history evolution of Yponomeutoidea (Lepidoptera: Ditrysia), with a catalog and an overview of the lepidopteran fossils(2013) Sohn, Jae-Cheon; Mitter, Charles; Entomology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Yponomeutoidea, one of the earliest-branching superfamilies of advanced (ditrysian) Lepidoptera, comprise about 1,800 species worldwide, including notable pests and models of insect-plant interaction. Yponomeutoids were one of the earliest lepidopteran clades to evolve external feeding and to colonize extensively herbaceous angiosperms. Despite the group's economic importance, and its value for tracing early lepidopteran evolution, the biodiversity and phylogeny of Yponomeutoidea have been relatively little studied. Even the monophyly and composition of the superfamily have been in doubt. In this dissertation, the most detailed molecular phylogeny to date for Yponomeutoidea is presented (Chapter 1). The resulting phylogeny is compared to previous morphological evidence, and its implications for evolutionary trends in yponomeutoid host association and biogeography are explored. As a prerequisite to divergence dating in the Yponomeutoidea, which is necessarily based on outgroup fossils as none are known for yponomeutoids, a general summary and overview of the lepidopteran fossil record (Chapter 2) is provided, based a recent, comprehensive catalog of known fossils. For chapter 2, all known lepidopteran fossils have been catalogued with annotations of their preservation, specimen deposition, fossil localities and ages (Chapter 3). As a contribution toward better characterization of yponomeutoid biodiversity, taxonomic reviews are provided for the New World genera Eucalantica and Atemelia (Chapter 4). The molecular phylogeny estimate (Chapter 1) is based on 8-27 protein coding nuclear genes sequenced in 86 Yponomeutoidea and 53 outgroups. Monophyly for Yponomeutoidea is corroborated. Results from different analyses are highly congruent and relationships within Yponomeutoidea are well supported overall. There is strong support overall for monophyly of families (or major parts thereof) previously recognized on morphological grounds, including Yponomeutidae, Ypsolophidae, Plutellidae, Glyphipterigidae, Argyresthiidae, Attevidae, Praydidae, Heliodinidae, and Bedelliidae. The formerly yponomeutid subfamily Scythropiinae are elevated to family rank (Scythropiidae stat. rev.). Host plant family associations of yponomeutoid subfamilies and families are non-random, but show no trends suggesting parallel phylogenesis, and are less conserved than is mode of feeding (e.g. internal versus external). My analyses reveal previously unrecognized tropical clades in several families, and suggest that previous characterization of yponomeutoids as predominantly Palearctic/ Holarctic was based on insufficient sampling.