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Publication Identifying Predictive Patterns in the Native and Introduced Ranges of Invasive Plant Species(2024-09) Pfadenhauer, WilliamGlobally, invasive plant species have severe environmental, economic, and cultural impacts. The extent and permanence of these impacts increases rapidly with time, and as such, the most effective way to prevent impacts of invasive plants is to prevent their introductions to susceptible environments. However, not all non-native plants species become invasive. Indeed, many non-native plants are desirable for their agricultural, economic, and cultural benefits, meaning that indiscriminate bans on the introduction of all non-native plants would be unnecessary and unrealistic. Therefore, accurate predictions of which species will invade and which environments will be most susceptible to invasion can help inform proactive management policies. Ideally, these policies prevent the introduction of harmful species and subsequently preclude these species’ negative impacts, while simultaneously maximizing the benefits of harmless non-native plants. In Chapter 1, I focus on species that are native to the continental United States to differentiate established (non-native but non-harmful) plant species from invasive (non-native and harmful) plant species using characteristics of their native ranges. My results indicate that generally, species with larger tolerances of abiotic conditions in their native ranges are more likely to be invasive outside their native ranges. In Chapter 2, I evaluate susceptibility of different countries and land masses to plant invasion at a global scale. I find that worldwide, the percent of established plant species that have become invasive is approximately twice as high as previously estimated, and that islands and tropical ecosystems are particularly vulnerable to plant invasion. In Chapter 3, I determine which traits of islands are most closely associated with increased rates of establishment and invasion. This analysis indicates that, for plants, both establishment and invasion are strongly associated with habitat heterogeneity, but only establishment is associated with anthropogenic disturbance. The results from all three chapters have strong implications for future management strategies, especially weed risk assessments. First, non-native plant species that are proposed for introduction to a new location should be considered as having a higher risk of invasion if they have larger, more abiotically complex native habitats. Secondly, weed risk assessments should be calibrated to reflect the overall risk of invasion for each location in which they are applied. Since islands and tropical environments generally have higher invasion risks, weed risk assessments used in those environments should reject a larger percent of the non-native species that are proposed for introduction. Lastly, islands and archipelagos with heterogenous environments should be assumed to have higher risks of plant invasion than continents, regardless of the degree of anthropogenic disturbance present. Taken together, these recommendations could improve the overall accuracy of weed risk assessments, and therefore, also reduce the negative impacts of invasive plant species.Publication NESTLINGS AND NEURONS: EARLY LEARNING, AUDITORY PERCEPTION, AND SIGNAL EVOLUTION IN SONGBIRDS(2024-05) Schroeder, Katie M.Social decisions of animals are guided by innate predispositions, sensory biases, and experiences related to communication signals. In many taxa, early life experiences are especially formative in later signal discrimination, signal production, and mate preference. Missing from our understanding is how sensory circuits are innately primed, then shaped by experiences to ultimately result in behavioral decisions. My dissertation addresses this gap by seeking evidence for natal learning and population-specific sexual signal structure in songbirds. I first experimentally exposed wild nestling swamp sparrows to songs from either their local subspecies or a foreign subspecies. I found that only nestlings that heard both local and foreign song types were able to discriminate between the two. With nestling learning ability tenable in the wild, I then performed electrophysiological recordings in the auditory forebrain of zebra finches across ages and showed that auditory processing is already adultlike and able to distinguish species song types within the first 10 days. I next explored how auditory forebrain responses change in concordance with early social and auditory experiences by raising zebra finches in different social environments. Units from cross-fostered and isolated individuals showed increased firing rates and decreased selectivity and responsiveness relative to normally-reared units. Specifically, cross-fostered units were less selective and responsive to conspecific song, mirroring an observed reduction in attentiveness to conspecific songs during behavioral trials. These first three experiments, in combination, establish evidence of neural plasticity and song type learning ability in young altricial songbird nestlings, and fill in some of the steps linking sensory experience to behavioral output. My last project returned to wild swamp sparrows to explore the effect of subspecies differences in beak morphology on fine scale song structure. I show that songs of the larger-beaked subspecies contain more low-performance notes and note transitions than the smaller-beaked subspecies, and that consistency of a given acoustic metric was highest for features that each subspecies sang with lower performance. Taken together, my dissertation broadly connects signalers with receiver behaviors through signal production and sensory processing, as well as suggests implications of these processes in the context of population divergence in swamp sparrows.Publication Population- and Community-level Investigation of Human Milk Oligosaccharide Structure on Bifidobacterium longum subsp. infantis Phenotype(2024-05) Hilliard, Margaret A.Human milk oligosaccharides (HMOs) are the third most abundant component in human milk without a direct nutritive value to the infant. Instead, HMOs arrive intact to the gastrointestinal tract (GIT) available for utilization by the gut microbiota. Bifidobacterium longum subsp. infantis (B. infantis) is a high G+C gram-positive anaerobic bacterium that colonizes the GIT of infants, with a genome encoding proteins arrayed in co-linear loci dedicated to the binding, import, and intra-cellular degradation of HMOs as a carbohydrate source. Utilization of HMOs by B. infantis results in metabolic end products such as lactic acid, acetic acid, and potentially formic acid that lower the infant gut pH, protect against pathogen colonization and may serve as cross-feeding metabolites for other taxa. In addition, B. infantis colonization normalizes intestinal barrier function and thus may play a protective role in the development of inflammatory and metabolic disorders. A major line of scientific inquiry is dedicated to characterizing the physiological role of B. infantis dominance within the infant gut, as some host benefits are species- and strain-specific. Thus, to better understand physiological variation in B. infantis, this study characterizes the genomic and phenotypic variation of novel B. infantis strains isolated from a rural population of infants located in upstate New York, and the impact of human milk oligosaccharide structural variation on community interactions between B. infantis, heterologous microbiota, and their secreted metabolites in a modeled infant gut microbiome. B. infantis strains isolated in this study were phylogenetically distinct from publicly available reference strains and stratified based on host population. Strains isolated from the Old Order Mennonite (OOM) host population were genetically more like each other compared to reference strains, which extended to the genomic variation observed in HMO utilization loci related to binding and transport. Phenotypes were carbohydrate-dependent and expectedly, like the type strain (ATCC 15697), B. infantis strains secrete formic acid during LNnT fermentation at the expense of lactic acid. Unexpectedly though, the growth rate and biomass of B. infantis had a negative relationship with 1,2-PD production when grown on 2’FL. Finally, strains isolated from the OOM host population produced greater concentrations of metabolites such as lactic and acetic acids after HMO fermentation despite metabolic ratios remaining the same between the two populations. HMO structure impacted the bifidobacterial population within an in vitro microbial community, but function was largely dependent on the initial microbial composition. Formic acid utilization and propionic acid production were observed, regardless of HMO structure or supplementation of B. infantis to the derived fecal communities. One community exhibited hallmarks of lactic acid utilization, likely by Eubacterium or Clostridium, which were potentially converted to butyrate via the acetyl-CoA pathway. B. infantis lactic and formic acid production likely contributes to syntrophy in this model, whereas B. infantis HMO utilization is the likely rate-limiting state in cooperative networks with microbial partners that secrete propionate and butyrate from bifidobacterial metabolic end-product utilization. In summary, this study characterizes the impact of HMO structural variation on the metabolic phenotype of B. infantis in vitro using axenic and heterogenous fecal-derived cultures that model syntrophic interactions in the infant gut microbiome.Publication The Impacts of Environment and Host Evolutionary Relationships on Lemur Microbiota(2024-02) Burten, Rachel BRecent studies have shown that the mammal microbiome is modified by environmental conditions, and that reduced microbiome functionality is associated with host health issues. Microbiome data in wild and captive primate populations can therefore be used to assess their health as they encounter a variety of environments. Comparative studies of the microbiome can also inform disease ecology, conservation, and captive management strategies tailored to different primate species. Therefore, this study examines how the hair, oral, and gut microbiota of nine wild and captive lemur species are determined by host phylogenetic relationships and host environment. I found that host species identity appeared to explain most of the variation in microbiome composition: lemurs in the same genus had similar microbiomes, even across different environments. Surprisingly, lemurs living in both low and high disturbance areas in the wild had less diverse microbiomes than captive lemurs, adding to the growing body of evidence that microbiome diversity may not be a consistent indicator of microbiome health. Instead, microbiome composition and differential abundance of microbes across samples may reveal more about meaningful shifts in the microbiome. Wild lemur microbiomes varied more in composition than captive lemur microbiomes, which were all similar and less variable even across different captive institutions. This suggests that captivity has a Westernizing and homogenizing effect on the microbiome. This effect was more strongly observed in the gut and hair microbiome than the oral microbiome. Based on the results of this study, the oral microbiome appears to be a conserved and highly filtered microbial community. Conversely, the hair microbiome is most subject to external effects and can serve as an indicator of the environmental microbes to which the host is exposed. The effect of host environment on the microbiome was also more strongly observed in folivorous lemurs (Propithecus spp.) compared to the other generalist and frugivorous lemurs in the study, which aligns with previous research which found that folivore microbiomes are more strongly affected by captivity and habitat disturbance. This project is the most comprehensive comparative full-body analysis of the lemur microbiome to date.Publication THE WILD TOMATO CLADE OFFERS INSIGHTS INTO FLESHY FRUIT TRAIT EVOLUTION AT THE PHENOTYPIC AND MOLECULAR LEVELS(2024-02) Barnett, Jacob RBiologists have long been fascinated by the diversity of fleshy fruits, yet questions remain as to how this variety has evolved. According to the dispersal syndrome hypothesis, flowering plants improved their reproductive success by producing fleshy fruits with appealing combinations of traits that attract animal dispersers. However, animal preferences may not be the only selective pressure driving fruit trait diversity—conflicting forces include damage-inflicting seed predators and pathogens, abiotic habitat conditions, or constraints stemming from non-adaptive mechanical, developmental, or phylogenetic limitations. Few studies have examined the early stages of fleshy fruit evolution across an entire clade of recently diverged plant species. The tomato clade, a group of 14 congeneric species (Solanum sect. Lycopersicon) that includes the cultivated tomato and 13 species of wild relatives, presents an exciting opportunity to fill this gap in our understanding of fruit trait divergence. The system is well studied as a model of fruit development and genetics, providing a stronger knowledge of the molecular underpinnings of traits than is possible with most other fruit systems. Wild tomato species adapted to a range of environments and are known to display multiple fruit colors, sugar profiles, and aromas. However, the extent of fruit trait and genetic diversity across all 13 wild species and the phylogenetic patterns in this variation have not previously been assessed. This dissertation project presents a novel approach and scale to fruit evolution studies using the tomato clade. Specific aims are to: 1) examine the extent and pattern of variation in disperser-relevant ripe fruit phenotypes across wild tomato species and assess whether these traits vary together in syndromes, 2) quantify variation in ripe fruit volatile aroma compounds and their biochemical pathways across the clade as well as whether scent could communicate an honest signal of nutrient content to animal dispersers, and 3) explore patterns of molecular evolution in a set of five genes known to affect different aspects of ripe fruit sugar content and composition in wild tomatoes. In addition to further developing the wild tomato system as a model for fleshy-fruited plant evolution, this research is applicable to plant breeders working on crop improvement.Publication CLIMATE CHANGE EFFECTS ON MARINE SPECIES PHYSIOLOGY AND BIOGEOGRAPHY(2024-02) Barley, Jordanna MClimate change is causing large changes to our species and ecosystems on physiological, evolutionary, and ecological levels. In addition, there is considerable spatial variability in global temperature changes, meaning that species, and populations of the same species, are experiencing vastly different rates of warming. Therefore, it is important to include population-level perspectives when researching the effects of climate change so that we can more precisely predict how species are going to respond in the future. In chapter 1, I use meta-analytic techniques to quantify the difference in thermal tolerance plasticity across populations of the same species. I provide evidence that populations with higher average thermal tolerances have limited thermal tolerance plasticity, likely because maintaining a high thermal tolerance comes with trade-offs. My results show that one trade-off is likely that populations lose their ability to change their viii thermal tolerance through plasticity. In chapter 2, I use a current range expansion of a salt marsh crab species into the Gulf of Maine to examine the possibility of spatial sorting as a mechanism for range expansion in marine systems. I provide possible evidence for the first observation of spatial sorting in marine systems. In addition, these results suggest that spatial sorting could be an important factor in marine range expansions in many coastal systems. In chapter 3, I examine why a similar crab species in the same system has not expanded its range at the same rate as other species in the Gulf of Maine. My results suggest that both temperature and spatial sorting are unlikely to be important in this species range edge dynamics. Instead, results on the larval behavior in this species provide a possible avenue for future research to determine this species’ range limit mechanisms. Together, these studies show that population level perspectives in research determining the effects of climate change are imperative to predicting how and if species are going to be able to respond and add to a growing body of research investigating the mechanisms that underlie these responses.