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The prevalence of hypoxia in aquatic systems has increased in recent decades and climate change is expected to worsen the extent and severity of hypoxic phenomena worldwide. Moreover, aquatic hypoxia has produced adverse ecological consequences and stimulated research interest within the Laurentian Great Lakes. The physiological stress imposed by hypoxia reduces habitat quality for most aquatic biota and causes changes in patterns of resource use and food web dynamics. We conducted a review of the primary literature to identify trends in prevalence of Great Lakes hypoxia research and broadly classify the unique hypoxic conditions afflicting Great Lakes ecosystems. We found that the majority of research effort toward Great Lakes hypoxia is focused on the Lake Erie central basin. Our review further revealed that this does not characterize the breadth of hypoxic phenomena that occur throughout the Great Lakes region. We then utilized a long-term monitoring dataset provided by the U.S. Environmental Protection Agency Great Lakes National Program Office to quantify the impact of Lake Erie central basin hypoxia on habitat quality of several fish species. We found that bioenergetics-based growth-rate potential models have a potential application as the framework for the development of biological endpoints that measure the effects of hypoxia on aquatic biota. Finally, we utilized stable isotope analysis to look for broad spatial and temporal trends in resource utilization within distinct regions of the Lake Erie central basin, with hypoxia and large-scale hydrodynamic patterns serving as potential driving patterns for spatial differences.

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Krynickillus melanocephalus was first seen in Sweden 2015. It is now labeled as an invasive species and it potentially poses a threat to the ecosystem, but the slug has not yet shown to have great negative impact in gardens and agricultural fields. There is limited ecological knowledge about the species. This study aims to increase the knowledge about habitat preference of the species during oviposition. Fifty slugs were placed in experimental arenas containing four compartments, each containing a different substrate: birch leaves, gravel, potting soil and sphagnum moss. The position of the slugs were recorded daily for three consecutive days. Further, position of laid eggs were recorded at two different times. Slugs showed a preference for leaves at oviposition, and 88 % of the eggs were laid in this substrate, and the fewest eggs were laid in moss (0,6 %). The slugs were found the most in contact with the leaves. The result has expanded our knowledge about the species, which is important to develop ways to hinder and slow down its invasion. Future research about substrate preference in this species should focus on how humidity and temperature may affect the substrate preference, as well as on movement behaviour during oviposition, perhaps by means of PIT telemetry. The study provides practical advice regarding how to deal with garden waste in areas that are inhabited by the species, where, in particular birch leaf compost should not be moved around. / Den svarthuvade snigeln upptäcktes i Sverige först 2015. Nu är den klassad som eninvasiv art och blir ännu ett hot mot våra ekosystem. Den kan även utgöra ett hot motträdgårdsägare, men än så länge har snigeln inte observerats ha åstadkommit störreskada. Arten är relativt okänd och därav är litteraturen väldigt begränsad. Min studiesyftar därför till att öka den ekologiska kunskapen om arten. Preferens föräggläggningssubstrat undersöktes samt föredraget habitat underäggläggningsperioden. Femtio sniglar användes i studien och dessa placerades iexperimentarenor innehållande mindre plastkorgar med fyra olika substrat; björklöv,grus, blomjord och vitmossa. Sniglarnas position observerades vid tre tillfällen undertre dagar och i vilket substrat äggen placerats noterades vid två tillfällen. Sniglarvisade en tydlig preferens för löv som äggläggningssubstrat där proportionen lagdaägg var 0,88. Minst antal ägg fanns i mossan (0,6%). Sniglarna befann sig ocksåoftare i kontakt med lövsubstratet än de andra substraten. Resultatet har berikat vårkunskap om arten, kunskap som är viktig för att utveckla metoder för att bekämpadess spridning. Framtida viktiga studier om artens äggläggning kan inkluderabeskrivning av dess rörelsebeteende med hjälp PIT-telemetri, samt undersökningarom hur olika temperaturer och fukthalter påverkar substratpreferens. Min studie hargett insikt i praktiska implikationer om hur trädgårdsavfall bör hanteras i områdendär arten existerar, specifikt att komposter med björklöv inte bör flyttas runt.

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.