<p dir="ltr">Sepidiini is a large and morphologically diverse tribe of darkling beetles (Tenebrionidae) in the subfamily Pimeliinae, containing ~1,000 species and subspecies. Despite the presence of many large and charismatic species and the cultural significance of some of its members, the toktokkie beetles, this tribe has been lacking revision at all taxonomic levels. To develop a framework for taxonomic revisionary work, in Chapter 1, I reconstructed a phylogeny of the tribe using targeted enrichment sequencing data. I also scored a comprehensive suite of diagnostic characters for the tribe to test in a phylogenetic context. Based on the results of the study, I proposed revising the subtribe Oxurina Koch, 1955, <b>sens. nov. </b>(now containing the genera <i>Oxura </i>Kirby, 1918, and <i>Miripronotum </i>Louw, 1979) and moving the genera <i>Decoriplus </i>Louw, 1979, <i>Pterostichula </i>Koch, 1952, <i>Stenethmus </i>Gebien, 1937b, and <i>Synhimba </i>Koch, 1952 to a new subtribe Stenethina <b>subtr. nov. </b>The tree topology also supports revising or synonymizing the genera <i>Dichtha </i>Haag Rutenberg, 1871, and <i>Amiantus </i>Fåhraeus, 1870,<i> </i>and revising the genus <i>Somaticus </i>Hope, 1840.</p><p dir="ltr">In Chapter 2, I performed a partial revision of the subtribe Hypomelina Koch 1955. A new genus <i>Bufoniopsis </i><b>gen. nov. </b>is erected containing one newly described species <i>Bufoniopsis hypnosis</i> <b>sp. nov. </b>The genus <i>Hypomelus </i>Solier, 1843, and all of its species are redescribed, and three new species are described: <i>Hypomelus johnprinei</i> <b>sp. nov</b>., <i>Hypomelus lorettalynnae</i> <b>sp. nov.</b>, and <i>Hypomelus tomhalli</i> <b>sp. nov</b>. One species was moved from <i>Hypomelus </i>to <i>Triangulipenna</i><i> </i>Louw 1979<i> </i>and redescribed, <i>Triangulipenna vulipnus </i>(Haag Rutenberg, 1873)<i> </i><b>comb. nov. </b><i>Triangulipenna </i>was redescribed and three new species were described, <i>Triangulipenna tylerchildersi </i><b>sp. nov.</b>, <i>Triangulipenna dollypartonae</i> <b>sp. nov</b>., and <i>Triangulipenna ralphstanleyi</i> <b>sp. nov</b>. A revised key to the genera of Hypomelina is provided as well as keys to the species of <i>Hypomelus </i>and <i>Triangulipenna</i>.</p><p dir="ltr">Toktokkie beetles—members of the subtribe Molurina Solier, 1843—are known for their substrate tapping behavior which is a form of sexual communication in which beetles tap their abdomens on the ground to locate mates. Despite the fact that this behavior is well-known among people in southern Africa, very little research has been done on the topic. In Chapter 3, I document variation in tapping patterns across the subtribe Molurina. Three characters of tap trains were found to vary: length of tap trains, tapping rate, and tapping pattern. Ancestral state reconstruction was performed for each of the characters. Characters were found to be only partially linked to ancestry. Additionally, in any given locality sampled, no two species had the same “song”. This suggests that signal partitioning could be influencing species “songs”.</p>

<p>The tribe Edrotini is the largest component group of the largest tenebrionid subfamily, Pimeliinae, in the Americas, with 427 described species/subspecies in 55 genera. However, the group is taxonomically impeded, with the last comprehensive revision published nearly 115 years ago. This is particularly regrettable since members of this tribe are ubiquitous in arid regions throughout the Americas and are exceptionally diverse in their morphology and behaviors. To provide phylogenetic context and a foundation for taxonomic work, in Chapter 1 I sample a majority of genera and reconstruct the first phylogeny of the Edrotini, using targeted enrichment sequencing. My results indicate major changes are required to both edrotine tribal composition and generic concepts. In combination with a suite of eight morphological characters I use this phylogeny to reconstruct ancestral states and test for characters correlated with stridulation the tribe. I find stridulation is strongly correlated with two morphological characters and propose a defensive function for these structures</p> <p>In Chapter 2, I use the molecular phylogeny in combination with 100 morphological characters to evaluate all Edrotini genera and members of five related tribes with constrained parsimony analyses. Based on the results thirteen genera are transferred from the Edrotini and the tribal classification is revised, with 35 genera recognized and description of a further five recommended. One neotype and seven lectotypes are designated for type species. A dichotomous key to genera is provided. Thirty-one current genera are redescribed; two species described; and four genera described, including four species. One subgenus is elevated to genus and three genera are placed as subgenera pending a species-level revision of the clade. Six genera, four subgenera, and one species are synonymized. Eleven species are transferred to the correct genus and one replacement name proposed. </p> <p>And in Chapter 3, I revise the genus <em>Edrotes</em> LeConte to include eight species distributed across arid southwestern North America. All species are redescribed, of which three are brought out of synonymy. A neotype for <em>E. rotundus</em> (Say) is designated. The synonymic position of five species is amended. An illustrated key to <em>Edrotes</em> species is included. A molecular phylogeny of all species is generated and used to infer divergences dates and historical biogeography for the genus. The most recent common ancestor of <em>Edrotes</em> is dated to the late Miocene or early Pliocene and inferred to have inhabited the Sonoran Desert. </p>

<p><br></p> <p>Thrips, Thysanoptera, represent an ancient (~407 m.y.a.) order of ~6000 tiny insects from 9 families. Despite the small size of the order, thrips have a diversity of life histories, diets, and survival strategies. Thrips represent a challenge to fieldworkers and axonomists alike due to the morphological similarity between species and the lack of homologies between families. Recent </p> <p>molecular evidence has reopened debate over the phylogenetic relationships of the families of Thysanoptera.</p> <p>In this thesis we use genomic approaches to elucidate and clarify the early nodes in order to answer evolutionary questions about the Thysanoptera, their mitochondrion symbiotes, and their </p> <p>coevolutionary interactions with a group of economically important viruses; tospoviruses. Our results support previous ordinal hypotheses and show families in both sub-orders radiating </p> <p>around the emergence of the angiosperms ~120 m.y.a. We show that all thrips lineages likely have highly rearranged mitochondrial genomes, even on an intraspecies level, and that this rearrangement phenomena occurs very quickly in evolutionary time. We provide comment on the caution that must be taken with mitochondrial loci in any phylogenetic analysis with this new </p> <p>evidence and argue for the impact of among-site-rate-heterogeneity to be further investigated within thrips hylogenetics. We show that much more data is needed before thrips and tospovirus relationships can be fully elucidated but that two dueling hypotheses are emergent from our studies: either 5 very new separate vector/virus relationships, or one very old relationship that has been lost by the vast amount of thrips. We call for targeted taxa selection and show how new genomic methods can target certain taxa based upon the identification of </p> <p>assembled proteins from illumine shotgun read data.</p>

<p dir="ltr">The lichen-feeding tiger moth tribe Lithosiini (Erebidae: Arctiinae) represent the largest radiation of invertebrate lichenivory. Caterpillars feed on lichen and as they feed, also sequester lichen polyphenolics, a behavior unique to these insects. The role of these compounds is believed to defend lithosiines against predators as larvae have been found to be protected against predators such as ants and moths to predators such as birds and bats. Experimental testing with controlled diets is necessary to fully make this connection, however little is known about host specifics for lithosiines. Furthermore, although lithosiines are monophyletic, the lack of a fully resolved phylogeny hampers investigation into many of the shallower level relationships, e.g. those among genera and species, within the group.</p><p dir="ltr">I addressed these knowledge gaps using the subtribe Cisthenina. Members of this group have been used to investigate predator-prey interactions and been included in morphological and molecular studies. Thus, while the group still needs attention, there is an ample amount of legacy loci data available for its members. I used these data to investigate the evolutionary relationships at the genus level, but to increase resolution in my analyses I additionally sampled taxa throughout the group with a recently developed anchored hybrid enrichment (AHE) probe set. I combined it with the legacy loci to both increase taxon sampling and resolution. I confirmed that trees made strictly from the legacy loci were unsuccessful and resulted in poorly supported relationships that made little sense. The addition of the AHE data greatly helped resolve relationships, however, there remained areas that were poorly supported and they appear to be genera with only a few loci. Thus, there is still room for improvement, but this offers a way for moving forward in lithosiine research, particularly to involve others who may have limited funding, equipment, and/or personnel and may only be able to afford legacy loci in diverse collaborations.</p><p dir="ltr">As the AHE probe set worked well with genus-level relationships I further attempted to use it in species delimitation of the notorious <i>Hypoprepia fucosa</i>-<i>miniata </i>species complex. Members of this group are varying shades of yellows, oranges and reds and have a convoluted taxonomic history. I gathered and organized over 4,000 specimens and using the AHE probe set found support for five distinct species. Interestingly, I used other morphological characters such as genitalia, but found no differences between species and a large amount of intraspecific variation. This suggests other courtship behaviors may be present and external morphology, i.e., color patterns, remain the best way to identify species. As part of this I am describing a new species and raising one from subspecies and as species are now readily distinguishable, they can be used for further investigations into lithosiines.</p><p dir="ltr">I used a member of this complex, <i>H</i>. <i>fucosa</i> to then evaluate the use of species distribution models (SDMs) to better understand their niche and how it relates to plausible lichen hosts. I evaluated 17 lichen species from two lichen genera, <i>Physcia </i>(13 species) and <i>Myelochro</i><i>a </i>(4 species)<i>. </i>These genera were selected based on previous feeding assays and the metabolites found in them have also been found in <i>H</i>. <i>fucosa </i>further suggesting caterpillars may feed on them. SDMs typically only use environmental factors to define and predict species niches. I compared the niches described by traditional SDMs to assess how similar they were, but I also investigated the use of lichens as biotic factors in the models. I assessed the influence each lichen had on the moth’s distribution found the niche of every lichen to be significantly different than that of the moth and their inclusion in SDMs of <i>H</i>. <i>fucosa </i>to improve model performance. This suggests <i>H</i>. <i>fucosa </i>caterpillars to be polyphagous, but to have some connection with these lichens. Further investigation with live specimens is needed, but these results support this as an effective way to describe lithosiine niches to better understand lichen feeding.</p>

<p dir="ltr">In a rapidly changing world, human actions and natural events are reshaping ecosystems and presenting new challenges for conservation efforts. Within this context, unraveling the recent ecosystem transformations and their implications on a fine scale is required. The impacts of such changes are not always sudden but often gradual and sometimes as a result of historical events. With the recent advancement in technologies, the resolution of information by genome sequences spans from millions of years ago (hindcasting) to future generations (forecasting). Aquatic ecosystems pose their own challenges when it comes to ecosystem changes and the types of data required to assess impact and help inform conservation efforts. My dissertation comprises three chapters focused on using genomic techniques to generate data valuable for the conservation and management of aquatic ecosystems. Each of the three chapters is a distinct manuscript in terms of scientific publications, where Chapter 1 has already been published, Chapter 2 has been submitted to a journal, revised, and is now awaiting publication, and Chapter 3 is in preparation for submission to a peer-reviewed journal. In Chapter 1, dietary DNA from harvested North American river otter (<i>Lontra canadensis</i>)<i> </i>was used to determine whether metabarcoding of stomach content could be used to identify fish prey species consumed. In Chapter 2, DNA sequencing of endangered pupfish species in the Tularosa Basin of New Mexico was studied; before my work, it was nominally comprised of a single species, the White Sands pupfish (<i>Cyprinodon tularosa</i>). The results indicate a rapid speciation event occurred within about the last ~5000 years, driven primarily by genetic drift. Chapter 3 extends Chapter 2 by assessing the dynamics of genomic diversity over space and time while evaluating the short-term evolutionary dynamics (~18 generations) of the two native pupfish populations. This temporal study aimed to determine if the extraordinarily rapid evolution over the last ~5000 years (observed in Chapter 2) could be detected over timescales more relevant to conservation and management efforts. Overall, this dissertation used genomic sequence data from metabarcoding of the COI gene region in the otter stomach content as well as pool sequencing and whole genome resequencing of pupfish to provide key biological insights into the conservation of these aquatic species. This dissertation also provides insights into avenues for further study and highlights the significant role that conservation genomics can play in the future. The findings presented in the three chapters are discussed within the context of species’ conservation and management.</p>

<div>Chromosomal mechanisms of sex determination vary greatly in phylogenetically closely related species, indicative of rapid evolutionary rates. Sex chromosome karyotypes are generally conserved within families; however, many species have derived sex chromosome configurations. Insects display a plethora of sex chromosome systems due to rapid diversification caused by changes in evolutionary processes within and between species. A good example of such a system are insects in the blow fly family Calliphoridae. While cytogenetic studies observe that the karyotype in blow flies is highly conserved (five pairs of autosomal chromosomes and one pair sex chromosome), there is variation in sex determining mechanisms and sex chromosome structure within closely related species in blow flies. The evolutionary history of sex chromosomes in blow fly species have not been fully explored. Therefore, the objective of this research was to characterize the sex chromosome structures in four species of blow flies and investigate the selective forces which have played a role in shaping the diverse sex chromosome system observed in blow flies. The blow fly species used in this study are Phormia regina, Lucilia cuprina, Chrysomya rufifacies and Chrysomya albiceps. Phormia regina,and Lucilia cuprina have a heteromorphic sex chromosome system and are amphogenic (females produce both male and female offspring in equal ratio). In contrast, Chrysomya rufifacies and Chrysomya albiceps, have a homomorphic sex chromosome system, are monogenic (females produce unisexual progeny), have two types of females (arrhenogenic females – male producers and thelygenic females – female producers), and sex of the offspring is determined by the maternal genotype. </div><div>To accomplish these tasks, a total of nine male and female individual draft genomes for each of the four species (including three individual draft genomes of Chrysomya rufifacies – male, and the two females) were sequenced and assembled providing genomic data to explore sex chromosome evolution in blow flies. Whole genome analysis was utilized to characterize and identify putative sex chromosomal sequences of the four blow fly species. Genomic evidence confirmed the presence of genetically differentiated sex chromosomes in P. regina and L. cuprina; and genetically undifferentiated sex chromosomes in C. rufifacies and C. albiceps. Furthermore, comparative analysis of the ancestral Dipteran sex chromosome (Muller element F in Drosophila) was determined to be X-linked in P. regina and L. cuprina contributing to sex chromosome differentiation but not sex-linked in C. rufifacies and C. albiceps. Evolutionary pressures are often quantified by the ratio of substitution rates at non-synonymous (dN) and synonymous (dS) sites. Substitution rate ratio analysis (dN/dS) of homologous genes indicated a weaker purifying selection may have contributed to the loss of sex-linked genes in Muller element F genes of the undifferentiated sex chromosome as compared to the differentiated sex chromosome system. Overall, the results presented herein greatly expands our knowledge in sex chromosome evolution within blow flies and will reinforce the study of sex chromosome evolution in other species with diverse sex chromosome systems.</div><div><br></div>

<p dir="ltr">Infectious diseases are caused by a multitude of organisms, ranging from viruses to bacteria, from parasites to fungi, and can be passed directly or indirectly from one person to another. Further, they continue to be a leading cause of death, especially in low-resource countries, thereby emphasizing the need for continued investigation. Understanding transmission of such diseases is vital as management or prevention of outbreaks through detection, reporting, isolation, and case management are ever-evolving. One way by which scientists can study infectious diseases is through a combination of epidemiological, genomic, and evolutionary biology approaches. This doctoral research occurred precisely at this interface, spanning across the fields of genomics, molecular biology, and epidemiology, as applied to the study of infectious disease dynamics of two separate pathogen systems (protozoan and virus).</p><p dir="ltr">The first half of this research (Chapters 1 + 2) involved the implementation of SARS-CoV-2 genomic sequencing and surveillance at Purdue University. Through this investigation in a university setting (Chapter 1), this work identified relevant variants of concern in hundreds of newly sequenced viral genomes and compared variant temporal trends with other similar university settings using publicly available data. Further phylodynamic analysis of Gamma (P.1) genomes from campus revealed multiple introductions into the Purdue community, predominantly from states within the United States. A second study (Chapter 2) assessed the transmission of variants over the course of an entire academic year from 2021-2022 in Purdue’s highly vaccinated community. This research described the rapid transition from Delta to Omicron variants and investigated variant introduction events into the campus. This comprehensive analysis showed that robust surveillance programs coupled with viral genomic sequencing and phylogenetic analysis can provide critical insights into SARS-CoV-2 spread and can help inform mitigation strategies for future pandemics.</p><p dir="ltr">The latter half of this body of research (Chapters 3 + 4) focused on malaria, which is a disease caused by <i>Plasmodium </i>species<i> </i>parasites and transmitted to humans through the bites of infected mosquitoes. The first investigation explored diagnostic accuracy metrics across a malaria transmission gradient in Zambia through a comparison of the diagnostic performance of Rapid Diagnostic Tests (RDT) and Light Microscopy (LM) with photo-induced electron transfer polymerase chain reaction (PET-PCR) as the gold standard using 2018 Malaria Indicator Survey (MIS) data. Results suggested that RDTs and LM both performed well across a range of transmission intensities, but low parasitaemia infections can affect accuracy. This suggests that more sensitive tools should be utilized to identify the last cases as Zambia moves towards malaria elimination. In addition to diagnostic metrics, preventing disease is also crucial for infectious diseases, and vaccines present one mechanism by which this can be done. Research to develop a malaria vaccine with sustained high efficacy has spanned decade. However, the process has proven to be challenging, with several vaccine candidates having advanced to early-stage trials, but only a few demonstrating sustained efficacy in clinical testing. The goal of the last investigation (Chapter 4) was to shed light on the diversity of <i>Plasmodium falciparum </i>antigens which could be considered when developing future malaria vaccines. Results of evolutionary and genomic analyses of Whole-Genome-Sequences from Zambia and other countries in Africa suggest that conserved merozoite antigens and/or transmission-blocking antigens should be prioritized when developing future malaria vaccines.</p>

<p> Chapter 1 is the first revision of the New World species of the genus <em>Rhipidandrus</em> LeConte, 1862 (Coleoptera: Tenebrionidae). All previously described species except <em>R. fungicola</em> Friedenreich, 1883 are redescribed, including a diagnosis and distribution information. <em>Rhipidandrus punctatus</em> <strong>n. sp.</strong> is described from Peru, Panama, and Chiapas, Mexico. New synonymies (junior synonyms first) include: <em>R. mexicanus</em> Sharp, 1905 = <em>R. paradoxus</em> (Palisot de Beauvois, 1818); <em>R. cornutus</em> (Arrow, 1904) = <em>R. panamaensis </em>(Barber, 1914) = <em>R. peruvianus</em> (Laporte, 1840); <em>R. peninsularis</em> Horn, 1894 = <em>R. micrographus</em> (Lacordiare, 1865). <em>Eledona peruviana </em>Laporte, 1840 is recognized as <em>nomen nudum</em> according to ICZN 1999: Article 12. A revised species checklist, a dichotomous key, an interactive key, and distribution maps are also presented.  </p> <p>Chapter 2 represents the first phylogenetic insight into the relationships within Bolitophagini in relation to Toxicini with more than three taxa sampled. For analyses, 34 taxa were sampled, with representatives from nine bolitophagine genera and seven toxicine genera with 3 outgroup taxa. Six gene regions from nuclear, ribosomal, and mitochondrial DNA were amplified using polymerase chain reactions and sequenced. Bayesian and maximum likelihood analyses were run on the 4049 bp concatenated dataset via the CIPRES Science Gateway. In both resulting trees, the monophyly of Bolitophagini is recovered with high support (BS = 100, PP = 100). The monophyly of Toxicini was recovered, but with poor support (BS = 60, PP = 70). The monophyletic clade containing both Bolitophagini and Toxicini was also recovered with high support (BS = 100, PP = 100).  </p> <p><br></p>