<p dir="ltr">Metabolic pathways are shaped by dynamic biotic interactions. My research delves into coevolution exemplified through two distinct projects that investigate the specialized metabolism of organisms as a consequence of biotic interactions. The first project focused on the remarkable metabolic adaptations of <i>Elysia crispata</i> morphotype clarki. This sea slug possesses the extraordinary ability to sequester and maintain functional chloroplasts (kleptoplasts) from the algae it consumes, allowing it to sustain photosynthetically active kleptoplasts for several months without feeding. To better understand the underlying molecular mechanism of this phenomenon, I generated a comprehensive 786 Mbp draft genome of <i>E. crispata</i> using a combination of ONT long reads and Illumina short reads. The resulting assembly provided a foundational resource for phylogenetic, gene family and gene expression analyses. This work advanced our understanding of the genetic underpinnings of kleptoplasty, shedding light on the evolution and maintenance of this unique metabolic strategy in sacoglossan sea slugs. I next investigated the transcriptional impacts of herbivory on maize (<i>Zea mays</i>) and green foxtail (<i>Setaria viridis</i>), induced by fall armyworm (<i>Spodoptera frugiperda</i>) and beet armyworm (<i>Spodoptera exigua</i>) feeding. This study aimed to contrast the defensive mechanisms of these grasses in response to each herbivore, and determined that green foxtail transcriptionally differentiates its responses to fall armyworm and beet armyworm herbivory. The fall armyworm has evolved a counter adaptation to lessen plant secondary metabolite production by producing a salivary protein (SFRP1) that suppresses jasmonate signaling. Investigation of the combinatorial effects of SFRP1 and beet armyworm herbivory determined the addition of endogenous SFRP1 during beet armyworm feeding is sufficient to reduce green foxtail defense responses. Results of this research shed light on host-pest reciprocal adaptations and the role of SFRP1 as an oral secretory protein. Coexpression analysis of maize and green foxtail transcriptomic responses to herbivory also identified putative genes involved in specialized metabolic pathways in green foxtail, providing insights into plant-insect interactions and potential solutions to herbivory in wild plant species. These findings highlight how gene diversification can contribute to pest resistance in grasses. Together, these seemingly unconnected projects underscore how biotic interactions influence metabolic processes across diverse organisms and reveal the fascinating intricacies of their adaptations to environmental challenges.</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>

<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>