Assembly is a process that shapes the abundance and identity of species in a community. Niche and neutral theory explain assembly processes with mechanisms driven by either species differences, or functional equivalence and stochastic dispersal. In 2017 I sampled vegetation and environmental variables at 59 sites in the Noxubee National Wildlife Refuge and Tombigbee National Forest of Mississippi to explore forest understory community assembly. I developed and assessed a framework of predictions concerning general patterns and underlying mechanism. Evidence of dispersal limitation and functional equivalence were expected under neutral theory. Local environmental characteristics, surrounding landscape variables, and fire were significant determinants of beta diversity. Dispersal was not a strong predictor of beta diversity. I found evidence of both niche complementarity and functional equivalence, as well as niche differences among common vines and an introduced vine (Lonicera japonica). Overall, the results were more congruent with predictions expected under niche theory.

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<p> Invasive species have developed long-term relationships with humans, especially since the start of the Industrial Revolution, and they have caused immense damage to native environments, ecosystems, and economies. An emerging invasive insect that has recently gained considerable attention is the spotted lanternfly (SLF). Early detection of SLF infestations in new areas or at low densities can lead to a more efficacious management and reduce costs associated with control them. Developing approaches to detect the presence of invasive species, favorable habitats for their establishment, and predicting potential spread will be crucial for effective management strategies to protect native environments and the economy. The goal of my thesis is to improve the understanding of how spotted lanternfly changes the spectral profile and chemical composition of host tree species. I found that spotted lanternfly feeding influences host canopy chemical and spectral properties. Specifically, I was able to use leaf-level hyperspectral measurements to differentiate SLF infestations levels in silver maple and red maple, shown by my first chapter, along with black walnut in my second chapter. Further, I was able to find differences in phenolic compounds in response to SLF infestations in red maple. The results of my study have the potential to be scaled up from leaf-level to landscape-level measurements. I have identified spectral signatures in red maple, silver maple, and black walnut that can be used to identify infestations from spectral data collected from UAVs or satellites. This potentially provides a new method for detection that is easier than traditional ones (like manual scouting and trapping). </p>

Molecular dating (or molecular clock) is a powerful technique that uses the mutation rate of biomolecules to estimate divergence times among organisms. In the last two decades, the theory behind the molecular clock has been intensively developed, and it is now possible to employ sophisticated evolutionary models on genome-scaled datasets in a Bayesian framework. The molecular clock has been successfully applied to virtually all types of organisms and molecules to estimate timing of speciation, timing of gene duplications, and generation times: this knowledge allows contextualizing past and present events in the light of (paleo)ecological scenarios. Molecular clock studies are routinely used in evolutionary and ecological studies, but their use in applied fields such as agricultural and medical entomology is still scarce in particular because of a paucity of genome data. Genome-scaled clocks have been successfully applied, for example, to various model organisms such as Anopheles and Drosophila, as well as to invasive mosquitoes Aedes aegypti and Aedes albopictus. Many other invasive pests are emerging worldwide aided by global trade, increased connectivity among countries, lack of prevention, and flawed invasive species management. Among them, there is Aedes koreicus and Aedes japonicus, two invasive mosquito species which are monitored for public health concerns because of their harboured human pathogenic viruses. For these, as well as for other insects of societal relevance, such as the parasitoid Trissolcus japonicus, there is a paucity of gene markers and no genome data for large scale molecular clock studies. Invasive pests are typically studied using microevolutionary approaches that tackle events at an intraspecific level: these approaches provide important information for the pest management, for example, by revealing invasion routes and insecticide resistances. Approaches that tackle the deep-time evolution of the pest, such as the molecular clock, are instead less used in pest science. Many important traits associated with invasiveness have evolved by speciation over a long time frame: the molecular clock can reveal the paleo-ecological conditions that favoured these traits helping a better understanding of pest biology. Molecular clock, when coupled with phylogenomics, can further identify genes and patterns that characterize the pest: this knowledge can be used to enhance management practices. Although this is a data-driven thesis, its major aim is to provide new results to demonstrate the utility of the molecular clock in pest science. This has been done by systematically apply the molecular clock to various neglected organisms of medical and agricultural relevance. To this aim, I generated new genome data and/or assembled the largest genome-scaled data to date. I studied the molecular clock in mosquitoes, focusing on the Aedini radiation (Chapter 2) and identified a strong incongruence between the mitochondrial and nuclear phylogeny for what concerns their molecular clock. This result highlighted the importance of employing genome scaled data for these species to exclude stochastic effects due to poor/inaccurate sampling in clock studies. To tackle the absence of data, I further assembled the whole mitogenome of emerging invasive species Aedes koreicus and Aedes japonicus with the aim of producing useful data for molecular typing and of inferring divergence estimates using whole mitogenomes (Chapter 3). Dated phylogenies point toward more recent diversification of Aedini and Culicini compared to estimates from previous works, addressing the issue of taxon sampling sensitivity in dated phylogeny. Although it is possible to perform molecular clock studies on single/few gene markers, the current trend is to couple this methodology with genome-scaled datasets to reduce the stochastic effect of using few genes. For this reason, I sequenced the draft genome of A. koreicus and A. japonicus (Chapter 4). The assemblies were extremely fragmented, highlighting the problem of sequencing large genomes using short reads. The assemblies provided, however enough information for genome skimming allowing extraction of BUSCO genes for downstream analyses, whole mitogenome assemblies (used in Chapter 3), and characterisation of the associated metagenome. These data need to be integrated by long reads; it provides, however a first framework to investigate the genome evolution of these species. I further sequenced and assembled the genome of Trissolcus japonicus, the parasitoid wasp of the invasive pest Halyomorpha halys. To elucidate its divergence, estimate and define an intraspecific typing system to differentiate strains for biocontrol strategies, I reconstructed the mitochondrial genomes of two populations: the mitogenomes were surprisingly identical, suggesting that they belong to the same de facto population. I further provide a detailed clock investigation of Zika, a virus harboured and transmitted by some Aedes species (Chapter 5). Using the largest set of genomes to date, I could set the origin of ZIKV in the middle age and its first diversification in the mid-19th century. From a methodological point of view, the clocking of this virus highlighted the importance of checking for recombination and for cell-passages to obtain correct divergence estimates. I finally show my contributions to molecular clock studies of three other invasive species (Chapter 6): I helped disentangle the divergence times of Bactrocera, a genus of invasive fruit files pest of agriculture; I contributed in performing a phylogenomics study of opsin genes in Diptera; I used chloroplast and nuclear genome data to reconstruct the divergences of the invasive reed Arundo. In the various Chapters of my thesis, I highlighted the limits and the problems of current molecular clock methodologies and identified the best practices for different types of organisms in order to develop a cross-discipline understanding of the molecular clock techniques. The various results presented in this thesis further demonstrate the utility of the molecular clock approach in pest studies.

<p>  </p> <p>Spotted-wing Drosophila (SWD), <em>Drosophila suzukii</em> (Matsumura), is an economically-important pest of small fruits worldwide. Currently, timing of management is based on morphological identification of adult flies captured in baited monitoring traps; however, distinguishing SWD from other native drosophilids in traps is a time-consuming process that requires magnification. And a degree-day model that could help small fruit growers understand and predict the seasonal activity of this pest has not been developed for Indiana. Due to the low tolerance for maggots in fruit market, most small fruit growers rely on intensive, insecticide applications on a calendar-based schedule without guidance on the activity levels of SWD. </p> <p>A total of 6,051 SWD adults were monitored weekly using commercial Scentry traps at three highbush blueberry orchards during May to August. I applied the published SWD developmental thresholds of 7.2 °C (lower) and 31.5 °C (upper) and the single-sine method to calculate accumulated degree days in the year of 2021 and 2022. A predictive model from two years of data at three locations exhibited an S-shaped curve, with 5%, 25%, and 50% of adults detected at ~907, 1,293, and 1,523 CDD, respectively. By examining infestations in three varieties, ‘Bluecrop’, ‘Blueray’, and ‘Elliot’, I found that blueberry infestation rate increased as the trap captures increased. The use of early-ripening highbush blueberry varieties can reduce infestation and regardless of variety, as berries became softer, the number of SWD egg scars in berries increased.</p> <p>DNA-based diagnostic methods, like loop-mediated isothermal amplification (LAMP), have the potential to improve SWD detection by replacing morphological identification with DNA-based identification. Positive results of the LAMP assay are based on a visible color change from pink to yellow when focal DNA is present. I tested the reliability of LAMP results using SWD DNA and then evaluated the sensitivity of LAMP in discriminating between SWD and two native drosophilids common captured in monitoring traps in Indiana, <em>Drosophila affinis</em> and <em>D. simulans</em>. I found the LAMP assay can quickly and accurately identify SWD with as little as 0.1 ng/μl of DNA. Following optimization, the assay also suggested success in discriminating between SWD and these two native species: it only requires an individual fly, DNA extraction is not necessary. </p> <p>By better predicting seasonal SWD activity and optimizing DNA-based diagnostics for this pest, this study can help improve the timely detection of SWD and the management in small fruit systems. </p>

Sleeper populations are established populations of a non-native species whose population growth is limited by one or more abiotic or biotic conditions, such as climate change. While the northeastern US is predicted to be a hotspot for future invasions, identifying potential sleeper populations before they become invasive can inform proactive, climate-smart invasive species management. I focused on 169 introduced species that are established in one or more northeastern states. I used the Environmental Impact Classification for Alien Taxa (EICAT) framework to systematically identify and review the peer-reviewed literature for these candidate species to quantify their negative ecological and socioeconomic impacts. I identified 49 plants with ‘major’ impacts linked to the decline of multiple native species or loss of community diversity. Using high negative ecological impact, habitat suitability, and climate suitability as selection criteria, I highlight 37 species as high priority for management in the North Atlantic –Appalachian Region.

Two prominent factors posing a major threat to biodiversity in marine ecosystems are climate change and the establishment of invasive species, and the interaction between these two. Because of the upwelling of cold, nutrient-rich water, the coast of Portugal is a thermal refuge and distribution edge for cold-adapted species, making it a particularly important study area from a biodiversity point of view. In this study I investigated the physiological tolerance to heat stress of six different native and co-occurring non-native marine species, red algae; C. crispus and G. turuturu, brown algae; S.polyschides  and U. pinnatifida,  and mussels ; X.securis and M.galloprovincialis,  in the intertidal  rocky coast of Portugal. Dynamic ramping assays with four different durations and intensity of thermal stress was conducted for each specie to determine a so-called thermal death time (TDT) curve and the thermal tolerance parameters CTmax (the temperature that will cause death within one min) and z (the decrease in thermal decay over time) for each specie. To compare the thermal tolerance between the native vs non-native species a linear mixed effects model was applied. This study found a significantly higher thermal tolerance to extreme temperatures expressed as the upper critical temperature CTmax in the invasive red algae G. turuturu and mussel X.securis compared to its native counterparts C.crispus and M.galloprovincialis. The study found no significant difference in the thermal tolerance expressed for the kelp species S. polyschides and U.pinnatifida which had a similar response to the heat challenge. The implication from these the findings for the coast of Portugal, could be that the invasive algae and mussel might better survive an extreme event such as a heatwave then the co-occurring native, while the invasive kelp species would respond in a similar way to the heat challenge. Hence the invasive capacity might depend more on the invasion window after a stressful event and on how well the native species recover from a heat stress. The findings from this study call for further conservation, restoration and monitoring efforts in this area given the biodiversity supported by the important intertidal marine native species. Furthermore, management to avoid spread of the invasive mussel into the Portuguese. coast and limit further increase in abundance of the invasive algae species. These results are highly relevant for projections on how further climate changes might affect the invasive and native species at the coast of Portugal.

<p dir="ltr">North American beaver are ecosystem and habitat altering mammals with a wide distribution in North America. Beaver are associated with bodies of fresh water while utilizing riparian habitat by foraging on woody and herbaceous, terrestrial and aquatic vegetation, as well as creating lodges, dams, dens, and scent mounds. Chain O’Lakes State Park was chosen as a study area for surveying beaver activity and woody species communities. The aim of the study was to better understand the relationship between beaver, and specifically, the woody vegetation in their foraging and home range. There is a large swath of habitat that beaver can utilize and alter within Chain O’Lakes State Park including the lakes, streams, and forests that attract visitors. The factors that have been found to influence beaver utilization in Chain O’Lakes State Park (and North America at large) are woody species community composition, abundance of heavily preferred woody species, as well as a combination of both an absence of predators and an abundance of aquatic vegetation. Based on the distribution of heavily, occasionally, and rarely preferred woody species across the understory (new individuals) and overstory (mature individuals) stratum an inference can be made that most of the riparian habitat around the lakes will continue to and/or shift into a higher proportion of species that beaver heavily select. A minority of the habitat shall shift away from those species and towards rarely and/or occasionally selected species. I will provide USDA APHIS Wildlife Services that play a wildlife management role in Chain O’Lakes State Park with the survey information detailing how beaver and their structures interact with the ecosystem, hypothesized methods for preserving the woody species that are targeted by beaver foraging within the park, and supplementary information that may aid in maintaining the riparian habitats for the benefit of park’s biodiversity and wildlife persistence while continuing to provide an enriched experience within Northwest Indiana with the potential to inform the greater collection of parks and maintained land at large.</p>