Biology

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Flow as a Mediator of Ecosystem Engineering: Hydrodynamics Shape Chemical Modification by Kelp and Mussel Beds
(2026-02-05) Murie, Kindall; Carrington, Emily
Ecosystem engineers are organisms that modify their physical and chemical surroundings in ways that shape the structure and function of ecological communities. Physically, they build biogenic structures that modify flow, light, and habitat complexity. Chemically, they change oxygen and pH levels through metabolic processes such as photosynthesis and respiration. These modifications can either facilitate the presence of associated species by creating favorable microhabitats or inhibit them by amplifying environmental stress. Understanding the circumstances under which and how these shifts occur has become increasingly important as climate change intensifies environmental variability in coastal ecosystems. Advancing our understanding of how ecosystem engineers shape their communities requires considering how external factors, particularly flow, mediate their influence on the surrounding environment. Driven by tides, waves, and currents, flow regulates water residence time and thus the accumulation or dispersion of biologically modified water. Yet despite its central importance, the role of flow in controlling the strength and direction of ecosystem engineering remains poorly understood.This dissertation examines how local hydrodynamics influences the capacity of marine ecosystem engineers to modify their surrounding chemical environments. It focuses on two contrasting but complementary systems: an autotroph, bull kelp (Nereocystis luetkeana), and a heterotroph, mussels (Mytilus spp.). Looking across these systems provides a broader view of how different types of engineers—those that produce oxygen through photosynthesis and those that consume it through respiration—shape their local chemical environments. By studying both systems, this work links two aspects of ecosystem engineering: 1) oxygen production and depletion, and 2) explores how flow determines when these species have the potential to act as facilitators or inhibitors within their communities. I combined field observations with laboratory and field experiments to explore how flow dynamics interact with biological traits, such as canopy structure, density, and behavior, to determine when these engineers act as facilitators or inhibitors within their communities. Across chapters, the work progresses from identifying environmental controls on kelp-driven chemical modification (Chapter 1) to isolating mechanistic feedbacks between flow, mussel behavior, and chemistry (Chapter 2), and then investigating density effects on chemistry and behavior by out-planting manipulated mussel aggregations in natural conditions (Chapter 3). Chapter 1 addresses a fundamental gap in understanding how hydrodynamic variability constrains the ability of kelp forests to alter seawater chemistry. Using high-frequency, long-term measurements of flow, light, dissolved oxygen (DO), and pH, this chapter quantifies how diel and tidal cycles interact to control the timing, magnitude, and spatial pattern of kelp-driven chemical change within a tidally dominated bull kelp forest in the Salish Sea. The results show that kelp effects on local seawater chemistry are not static “hotspots” but dynamic, flow-dependent features that shift predictably across space and time. Kelp-driven increases in DO occur primarily during daytime slack tides, when reduced flow allows oxygen-enriched water to remain within the canopy before being rapidly replaced by the next tidal exchange. These findings demonstrate that even in a highly productive kelp forest, strong and variable tidal currents limit the persistence of chemical modification to only a few hours per tidal cycle. As a result, the capacity for kelp forests to function as chemical refugia depends less on their metabolic potential and more on the hydrodynamic context that influences water retention and exchange. By explicitly linking diel and tidal processes, this chapter reframes kelp-driven buffering from a static to a dynamic process and provides a framework for predicting when and where macrophyte canopies can locally ameliorate chemical stress. Chapter 2 builds on this framework by examining how flow and organismal behavior mediate chemical modification in a heterotrophic engineer, the mussel. Valve gaping in mussels regulates the flow generated by their pumping activity, which drives water exchange between the ambient environment and the interstitial spaces within aggregations. This chapter presents an experimental approach that couples behavioral measurements from high-frequency gape sensors with real-time oxygen data to evaluate how valve activity and flow together shape interstitial water chemistry across three Mytilus species. Two consistent patterns emerged: oxygen depletion within mussel beds decreased exponentially with increasing flow speed, and gaping behavior remained largely static across flow and low-oxygen conditions. The absence of compensatory gaping under low-flow conditions indicates limited behavioral feedbacks between gaping, chemistry, and flow, underscoring the dominant role of physical flow in driving oxygen dynamics within mussel aggregations. Variation in oxygen depletion among species was best explained by differences in biomass density, suggesting that morphometric traits, rather than behavior, primarily govern their capacity for chemical modification. These findings refine our understanding of ecosystem engineering by identifying the conditions under which structural and hydrodynamic factors outweigh behavioral influences. Chapter 3 builds on insights from Chapter 2 by extending the work into the field, where mussel aggregations experience natural tidal flow and greater variation in density. The first goal was to determine whether higher mussel densities lead to stronger oxygen depletion under natural flow conditions. A second goal was to test whether the relationship between flow speed and dissolved oxygen follows the same exponential pattern observed in the steady-flow flume (Chapter 2), and whether mussel gaping remains insensitive to flow and oxygen variation across different aggregation positions in a more dynamic environment. The field experiment showed that oxygen concentrations declined sharply with increasing aggregation density, with the highest-density aggregations exhibiting the lowest mean DO levels, the largest diel fluctuations, and frequent short-lived hypoxic events. Gaping behavior varied with density and position within an aggregation, as interior mussels gaped wider and spent more time open than edge mussels, but showed little response to short-term changes in flow or oxygen availability. These results demonstrate that structural traits of an aggregation, such as density, amplify chemical modification, while flow regulates its magnitude and persistence. Moreover, there was no evidence that behavior provides any buffering capacity once physical exchange is constrained. Across systems, this dissertation highlights a unifying principle: the capacity of marine engineers to alter their environment depends primarily on how their biological traits, such as metabolism, structure, and abundance, interact with hydrodynamic forces. By quantifying how flow controls oxygen variability across autotrophic and heterotrophic systems, this work advances a better understanding of when and where ecosystem engineers function as facilitators or inhibitors, emphasizing the central role of local physical dynamics in shaping their ecological influence.
Reconstructing the evolution of gene function for a master regulator of flowering: LEAFY in the fern Ceratopteris richardii
(2026-02-05) McConnell, Hannah Elizabeth; Di Stilio, Verónica
All land plants have a life cycle with alternation of generations that includes both a haploid, gamete-producing gametophyte and a diploid spore-producing sporophyte. Over evolutionary time, land plants have gone from having independent, longer-living gametophytes with ephemeral, dependent sporophytes, as in the bryophytes, to large, independent sporophytes which support small, dependent, short-lived gametophytes in the seed plants. A critical angiosperm innovation is the production of flowers, which enclose unisexual gametophytes within the sporophyte. The evolution of the flower has been hypothesized to have occurred through a combination of cooption of genes present in the seed plant common ancestor, and expansion of gene families involved in flower development. A common approach to learning about the evolution of flowering genes is to investigate their homologs in representatives of earlier diverging lineages of non-flowering plants. For instance, ferns represent a lineage in a key phylogenetic placement representative of early-diverging vascular plants and sister to all seed plants, with independent and photosynthetic gametophytes and sporophytes. In more derived lineages, where gametophytes are small and dependent, studying the dependent stage is more challenging and less informative, leaving open questions about the role of genes of interest across both life stages. In this dissertation, I focus on the homosporous fern Ceratopteris richardii (C. richardii), to investigate gene function across the plant life cycle. This research aims to broadly inform understanding of the functional evolution of key reproductive genes in land plants. The goal of Chapters 1 and 2 is to investigate the role of the floral meristem identity gene LEAFY (LFY) in C. richardii gametophytes and sporophytes. My work uncovered new roles for the two C. richardii LFY paralogs, CrLFY1/2, in gametophyte reproduction, particularly in sperm cells and in the lateral meristem that generates gametangia. In the sporophyte, I found a conserved function in early embryogenesis, in the first division of the fern zygote, a role previously described for a moss species but not in any vascular plant. Together, these findings highlight a novel haploid reproductive function for LFY homologs, suggesting that this may have been an ancestral role that was coopted by sporophytes as they became the dominant stage of the plant life cycle. In Chapter 3, I investigate the developmental genetics of the fern gametophyte. C. richardii gametophytes develop as either hermaphrodites, with a multicellular meristem that produces both egg (in archegonia) and sperm (in antheridia), or as ameristic males (developing from a transient apical cell), which produce only sperm. The first spores to germinate develop into hermaphrodites, which secrete the hormone antheridiogen, inducing surrounding gametophytes to develop as males. By comparing transcriptomes of mature male and hermaphrodite gametophytes via RNA-seq, I find a total of 22,719 expressed genes, over half of which (12,424) are differentially expressed between the two sexes, 47.8% upregulated in males and 52.2% upregulated in hermaphrodites. Gene ontology analysis indicated that microtubule genes have high mutual correlation to CrLFY1, suggesting a potential novel role of CrLFY1 in regulating aspects of sperm development.
Echoes in the Chambers: Exploring the Ecology and Evolution of Mesophotic Zone Scavengers in Chambered Cephalopods
(2026-02-05) Veloso, Job Lukas; Ward, Peter D
Cephalopods are ecologically and evolutionarily significant marine invertebrates, yet major gaps remain in our understanding of their trophic ecology and physiological adaptations, particularly among deep-living and morphologically conserved lineages such as nautiloids. This dissertation investigates the ecological and metabolic dimensions of phragmocone-bearing cephalopods through a multi-scalar isotopic approach. In Chapter 1, stable isotope analyses (δ¹³C and δ¹⁵N) of multiple Nautilus and Allonautilus populations across the Pacific reveal strong geographic structuring of isotopic niches, with region-specific variations in baseline carbon sources and trophic levels. Chapter 2 focuses on mesophotic scavengers, including nautiloids and other reef slope taxa, and applies nitrogen-based trophic level estimates to show convergence in foraging roles across distinct geographic locales in Fiji and Papua New Guinea. Chapter 3 compares metabolic signatures of extant nautiloids, sepiids, and extinct ammonoids using Cₘₑₜₐ, a carbon-isotope-based proxy for metabolic rate. Results show that modern nautiloids exhibit lower metabolic signals than both extinct ammonites and extant cuttlefish, consistent with their slow-growing, low-energy lifestyles. Together, these findings illuminate the trophic ecology, niche dynamics, and physiological diversity of chambered cephalopods across evolutionary time, enhancing our understanding of how environmental constraints shape deep-sea and mesophotic life.
Try Everything: Coupling Phytolith and Isotope Records to Reconstruct South American Landscapes During Global Warming and Cooling Events of the Cenozoic
(2025-10-02) Stiles, Elena; Strömberg, Caroline A.E.
The Intergovernmental Panel on Climate Change (IPCC, 2024) predicts that, regardless of policy changes, atmospheric CO₂ levels, and consequently, global temperatures, will rise over the next century to levels unprecedented in human history. However, these levels are not unprecedented in Earth's geologic past. Over the Cenozoic (the last 66 million years), global climate has undergone repeated warming and cooling episodes driven by fluctuations in atmospheric CO₂, superimposed on a long-term trend of cooling and declining pCO₂. To better predict how future climate change may affect global ecosystems, we can turn to the fossil record to examine how climate and biospheres responded to similar variability in the past.In this dissertation, I combine phytolith (opaline silica particles deposited in or around plant cells) and isotope records to reconstruct landscape evolution in South America during periods of global climate warming and cooling in the early and late Cenozoic. I also conduct a modern reference study to test and compare the spatial resolution of phytolith assemblages and isotope signatures across a spatially complex landscape.In Chapter 1, I explore the evolutionary history of lowland vegetation in southern South America during the Paleocene and Eocene using phytolith records. Previous reconstructions, including some paleobotanical data, proposed that grass-dominated ecosystems may have existed in the region at this time, contradicting global patterns of grassland evolution and other fossil evidence. I present a basin-wide phytolith analysis of Paleocene and Eocene terrestrial deposits from the San Jorge Basin, Argentine Patagonia. This expands on earlier phytolith studies and integrates new radiometric dates to provide a temporally resolved reconstruction of early Cenozoic vegetation. My results show that forests dominated lowland ecosystems from the Paleocene through the middle Eocene. Palm abundance increased from the middle to late Eocene as these forests began transitioning to cooler, drier, and more open vegetation types. These findings are supported by paleobotanical, geochemical, and faunal records. Grasses remained rare and were likely restricted to forest understories until at least the Early or Middle Miocene, challenging hypotheses that propose extensive early Cenozoic grassy habitats in South America. In Chapter 2, I test the spatial resolution of phytolith assemblages across a heterogeneous landscape and compare them to the carbon isotope composition of the soil organic matter from which they were extracted. This study addresses a key uncertainty in fossil phytolith interpretation: to what extent do phytoliths reflect local versus regional vegetation? This is especially important for fossil reconstructions, where sample coverage is often sparse. Can we detect vegetation heterogeneity from just a few assemblages? How do phytolith signals compare to carbon isotopes, a widely used proxy for vegetation structure? To explore this, I analyzed samples from three transects in the piedmont of the Eastern Colombian Andes, a region that includes grasslands, forests, and palm swamps, each sharply demarcated. My results show that phytolith assemblages reflect both the vegetation at the collection site and surrounding plant communities. Phytoliths and carbon isotopes capture overlapping but distinct aspects of vegetation structure and are most powerful when used together. Additionally, phytoliths can offer insight into fire regimes, potentially indicating where and what kinds of vegetation were burning. These results underscore the value of phytoliths for reconstructing vegetation heterogeneity and fire history in both modern and ancient ecosystems. In Chapter 3, I focus on a cooling period that followed the last major Cenozoic warming event, the Miocene Climatic Optimum (17 to 15 million years ago). This subsequent cooling, is recorded in the fossil-rich deposits of La Venta, a semi-arid region in Colombia. Despite its significance as one of the most important vertebrate fossil sites in the Neotropics, little is known about the vegetation that supported its fauna or how tropical climate changed during this time. To address these gaps, I use phytoliths and clumped isotope paleothermometry to reconstruct vegetation and climate between 14 and 7 million years ago. The results suggest that the region remained forested throughout the interval and that vegetation density increased as local temperatures cooled and seasonal rainfall may have intensified, creating more humid conditions overall. These findings contrast sharply with climate models that predict drying across the tropics during the Miocene Climatic Transition and provide the first terrestrial temperature record for tropical South America during this time. This discrepancy highlights the importance of regional proxy records in validating and improving global climate models.
From the cell surface to the field: Receptor-mediated herbivore induced defenses in legume crops
(2025-10-02) Guayazan Palacios, Natalia; Steinbrenner, Adam D
The recognition of herbivore-associated molecular patterns (HAMPs) via pattern recognition receptors (PRRs) initiates signaling cascades that lead to the accumulation of direct and indirect defenses against herbivorous pests. Inceptin 11 (In11) is a peptide HAMP present in the oral secretions of Lepidoptera caterpillars that triggers these defense responses in legume crops. In11 is recognized by the Inceptin Receptor (INR), which induces changes in gene expression preceding the accumulation of antiherbivore defenses. However, the molecular mechanisms regulating In11-induced defenses via INR remain largely unexplored.This dissertation proposes a molecular mechanism by which In11-induced genes encoding gut-stable direct defenses are transcriptionally regulated by the plant circadian clock. Furthermore, this work demonstrates that INR is required in legumes for the In11-induced attraction of predators, which act as indirect defenses against herbivores in the field. These findings provide the first evidence of a time-dependent response to a specific HAMP and directly link core circadian clock transcription factors to plant immunity against herbivores. Lastly, this study presents the first conclusive molecular and ecological evidence that a specific plant immune receptor directly controls ecologically relevant tritrophic interactions.
The Logic of Change: Contextual Adaptation of a Mobile Gene
(2025-10-02) Grassi, Nathan; Kerr, Benjamin
Understanding how genotypes map to fitness is fundamental to the description and prediction of adaptive evolution. Through differential reproductive fitness of heritable variation, populations enhance survival and reproduction within the selective environment. In this dissertation, I employ experimental evolution of cefotaxime resistance in the plasmid-encoded blaTEM with selection occurring in two bacterial species that host this gene. I measure resistance phenotype during the evolution experiment and utilize monoculture barcoded fitness assays to evaluate the competitive ability of numerous plasmid genotypes hosted by the same species in a range of antibiotic environments. I introduce the concept of an adaptive window to delineate the region of concentration space where each sampled mutation would be selectively accessible in each species. We observe that resistance effects of mutations often correlate between species, but the window of selective accessibility is shifted between species due to differences in intrinsic resistance level. In Chapter 2, I perform side-by-side monoculture and coculture barcoded fitness assays to evaluate the competitive ability of plasmid-host pairings across distinct host communities. We observe that both plasmid genotypic fitness and the fitness effect of mutations can depend strongly on host community structure. Together, these chapters demonstrate that the ecology and evolution of mobile genetic elements can be shaped by host genomic and host community contexts. More generally, this dissertation highlights the dynamic nature of the genotype-to-fitness mapping which is modulated by contextual factors ranging from within the gene, cell, or ecosystem.
Uncovering the molecular mechanism of flowering in a marine angiosperm, Zostera marina, and evaluating the effects of warming on flowering processes
(2025-08-01) Nolan, Christine T; Imaizumi, Takato
Florigen and antiflorigen genes within the phosphatidylethanolamine-binding protein (PEBP) gene family regulate flowering in angiosperms. In eelgrass (Zostera marina), an estuarine foundation species, flowering and seed production are crucial for population resilience, especially in the face of rising seawater temperatures, more frequent extreme weather events, and anthropogenic disturbances. Yet, the molecular mechanism underpinning flowering remains unknown. In Chapters 1 and 2, we investigate the role of florigen and antiflorigen genes in Zostera marina in the regulation and onset of flowering. We identified thirteen PEPB genes in in Z. marina (ZmaPEBP); ten FT (florigen) homologs, two TFL1 homologs, and one MFT homolog. Among these thirteen ZmaPEBP genes, when over-expressed in Arabidopsis, two genes (ZmaFT2 and ZmaFT4) cause an early flowering phenotype, and two genes (ZmaFT9, and ZmaTFL1a) caused a late flowering phenotype. To gain insight into the function of these four genes in eelgrass, we analyzed gene expression in different plant tissue from adult perennial shoots in either vegetative or flowering reproductive phases at three sites (Willapa Bay, WA USA). ZmaFT2, ZmaFT4, and ZmaTFL1a expression was higher in flowering rhizome and shoot tissues, while ZmaFT9 was solely expressed in leaves of vegetative shoots. We also analyzed gene expression in annual eelgrass shoots over the growth season from three sites across two bays (Willapa Bay, WA and Yaquina Bay, OR USA). ZmaFT2, ZmaFT4, expression increased at the time of flowering and ZmaTFL1a expression increased after flowering onset occurred. ZmaFT9 expression was high in leaves of early vegetative seedlings but decreased shortly before flowering onset. Our results suggest that ZmaFT2 and ZmaFT4 may promote flowering and ZmaTFL1a may be involved with flowering-related developmental processes, such as shoot architecture, while ZmaFT9 may inhibit flowering in eelgrass. In Chapter 3, using Z. marina, we applied a common garden approach to experimentally test how flowering and its underlying molecular mechanisms responded to elevated water temperature (+3Â°C). We focused on developmental and reproductive traits paired with ZmaPEBP gene expression to gain insight to the molecular mechanism underpinning differences in flowering responses. We compared annual shoots from two source populations (Willapa Bay and Padilla Bay, WA, USA) to understand natural variation not only in morphological and reproductive traits, but also in ZmaPEBP gene expression governing flowering onset. At the individual and population levels, annual seedlings in the +3Â°C heated treatment produced more spathes and accelerated development of inflorescences so seeds dispersed sooner. Also, seedlings from Padilla Bay flowered at greater rates and earlier than Willapa Bay, and these differences were exaggerated by the +3Â°C heated treatment. Two predicted floral activators, ZmaFT2 and ZmaFT4 had increasing expression throughout the summer regardless of population and showed no response to the temperature treatment. ZmaFT9 expression, a predicted repressor of flowering onset, was expressed at lower levels in the shoots grown in the +3Â°C heated treatment, and even more so in the Padilla Bay population which flowered earlier than the Willapa Bay population. ZmaTFL1a, a gene predicted to be involved with downstream flowering processes, showed no significant response to the temperature treatment. These results highlight the contribution of ZmaFT9 expression to the temperature-based response of timing of flowering onset. Elevated seawater temperature impacted flowering timing and spathe production, with potential consequences for seed yield and meadow resilience. Combined, these studies support the key role of antiflorigen (ZmaFT9) in the molecular control of flowering in Z. marina, not only as the main determinant of flowering onset, but also as an integrator of temperature into the flowering response. Florigen genes that contribute to the activation of flowering (ZmaFT2 and ZmaFT4) and genes that are responsible for flowering related developmental processes (ZmaTFL1a) are also important components of the flowering mechanism.
From the ground to the skies: Ecomorphological predictors of diet and trophic diversification in small Neotropical mammals
(2025-08-01) Villalobos Chaves, David; Santana, Sharlene E.
During the evolution and dietary diversification of vertebrates, astounding morphological, physiological and behavioral adaptations evolved to procure and efficiently process their preferred food resources. These adaptations affect how well each species obtains energy, survives and reproduces in their environment, and are directly related to resource partitioning and diversification patterns. This dissertation seeks to elucidate patterns of morphological and functional adaptations on small Neotropical mammals related to selective pressures exerted by their dietary ecology. I used myomorph rodents and bats as model taxa to develop my research, as these animals show exceptionally high taxonomic and ecological diversity, which makes them ideal for understanding ecomorphological trends in the evolution of feeding structures. Through my three chapters, I tested the hypothesis that evolved differences in size and shape of morphological structures are directly associated with differences in the feeding ecology of the species. Moreover, by linking these adaptations to variations in performance among tasks of vital importance for energy acquisition during feeding (e.g., biting, chewing), I also explored how functional adaptations might have allowed subsequent functional dietary specialization on some taxa and, ultimately, trophic segregation among Neotropical mammal communities. In chapter 1, I coupled data on functional mandibular measurements and dental topography metrics with dietary information under a phylogenetic framework to investigate the functional correlates of mandibular and molar diversity among Akodontine rodents. Here, both mandibular and dental morphologies seem to have evolved to facilitate the efficient processing of specific food items with unique mechanical properties (e.g., arthropod exoskeleton vs plant materials). Both mandibular and dental traits show strong dietary signals towards processing specific food resources, with herbivory and insectivory dietary regimes shaping the most extreme morphologies. Altogether, our study gives insight into the strong relationship between rodent’s feeding structures and dietary ecology, highlighting the traits that are, potentially, under stronger selective forces and that might have facilitated the trophic diversification and specialization in the Akodontine tribe. In chapter 2, I used morphological and performance traits to investigate the influence of feeding ecology on the form-function relationships of feeding structures in rodents, and explored the potential implications of these differences on morphological specialization and resource partitioning among sympatric members of a community in Costa Rica. I found a strong dietary signal on multiple external, mandibular and dental traits, with shape differences being more extreme in specialized feeding ecologies. I also found multiple trade-offs between the morphology and performance of the feeding apparatus of these rodents, highlighting the compromise that usually is detected when extreme morphologies evolve. Our data give insight into form-function-performance relationships of rodent feeding structures and provide clues on potential mechanisms that have allowed trophic diversification among sympatric species. In chapter 3, I investigated the functional relationship among size, shape and feeding performance in a community of Neotropical Free-tailed bats in Costa Rica. Specifically, we evaluated how the size of cranial structures and the shape of molar teeth correlate and influence food processing. We found strong connections of morphological and functional specialization with performance outcomes, highlighting mechanisms of trophic resource partitioning among members of the community. These, in turn, might be influenced by adaptations to the mechanical properties of different food resources. Altogether, our study successfully connected morphology and performance with dietary ecology, setting an example on how to couple these data to better understand ecological patterns and trade-offs of trophic specialization.
Investigating the convergent evolution of nectar-feeding birds through the lens of biomechanics
(2025-08-01) Cuban, David Roby; Rico-Guevara, Alejandro
Nectar-feeding birds employ highly specialized mechanisms to collect minute liquid rewards hidden within floral structures. There are over 20 independent evolutionary origins of nectarivory amongst birds, but little is known about how most of these lineages ingest nectar. In this dissertation, I examine the feeding mechanics of two distantly related nectarivorous bird groups and investigate the effects of nectar concentration on energy intake rates. In Chapter 1, I review what is known about avian nectar-drinking mechanics and define the knowledge gaps that should be addressed to understand how the multitude of nectar-feeding birds are able to consume their liquid food. In Chapter 2, I investigate if convergent morphologies underlie convergent biomechanics of nectar-feeding in two distantly related bird clades: sunbirds (family Nectariniidae) and hummingbirds (family Trochilidae). In Chapter 3, I describe the drinking mechanics of a morphologically unique group of nectar-feeding birds, the hanging parrots (genus Loriculus), and compare them with the mechanics of birds with more “typical nectarivore” feeding apparatus morphologies. In Chapter 4, I use the liquid-ingestion mechanics that I described for sunbirds to predict the nectar consumption rate and energy intake rate of multiple species feeding from a range of nectar concentrations. Using biomechanics to examine the variety of nectar-feeding mechanisms in birds unveils unique biological solutions to complex physical challenges. In turn, these mechanisms can be used to predict and test how different nectar-feeding birds interact with the variety of plant species they encounter in nature and what environmental factors shape their ecological interactions and evolutionary trajectories.
Evolutionary ecology of interactions between plants and nectar-feeding birds across scales
(2025-08-01) Hewes, Amanda E; Rico-Guevara, Alejandro
University of Washington Abstract Evolutionary ecology of interactions between plants and nectar-feeding birds across scales Amanda E. Hewes Chair of the Supervisory Committee: Alejandro Rico-Guevara Department of Biology Plant-pollinator interactions constitute a fantastic system to investigate how ecological and evolutionary processes influence each other. In this dissertation I use honeyeaters (Aves, Meliphagidae), the second-most speciose clade of vertebrate pollinators and an avian family native to Australasia, as a study system to investigate (1) how bird and plant phenotypes interact to determine the outcomes of plant-pollinator interactions and (2) how these interactions can lead to evolutionary consequences such as adaptation, specialization, and coevolution. Chapter 1 begins with a survey of the evidence for convergence in morphology and function across roughly twenty lineages of specialized avian nectarivores. By reviewing the literature on morphological and functional adaptations for nectarivory in these taxa, I found that the feeding apparatus (bill, tongue, hyoid) exhibits the most convergent morphology, and is more commonly modified than the locomotor apparatus (wings and legs) or the digestive and renal systems. This work also illuminated the knowledge gaps that exist in our basic understanding of how birds adapt to nectarivory and provided suggestions for future research.Chapter 2 focuses on the process of nectar feeding in honeyeaters, as one of the primary biophysical challenges faced by nectar-feeding birds is efficient extraction of small nectar volumes from flowers. This chapter uses a biomechanics approach, including high-speed videography and kinematic analyses, across five species to answer the question of how honeyeaters use their brush-tipped tongues to capture nectar. I found that nectar is primarily captured via surface tension between the bristles at the tip of the tongue, a mechanism called fluid trapping, rather that via fluid flow through the grooved body of the tongue. Using fluid trapping as the primary mechanism of nectar capture could be what allows honeyeaters to visit flowers with a wide range of nectar presentations (i.e., nectar volume, sugar concentration). Chapter 3 follows by examining the degree to which hyolingual morphology (the size and shape of the tongue and the bony support called the hyoid) varies across honeyeater species, and whether that morphology correlates with the degree of dietary dependance on nectar. This work employs diverse techniques such as linear morphometrics, anatomical characterization, histology, and computer tomography (CT scans) to provide the most comprehensive survey of this type performed in any bird family. I found that there are six distinct tongue types across honeyeaters, some of which are restricted to particular genera that warrant their own biomechanical analysis of feeding due to their seeming morphological incompatibility with nectar feeding via fluid trapping. Additionally, two aspects of tongue morphology – tongue length and the proportion of the tongue that is bristled – were positively correlated with increased reliance on nectar. These macroevolutionary patterns make sense in light of the biomechanical analysis from Chapter 2, as a longer tongue can access a wider range of flowers in the environment and probe deeper into flowers, while a larger bristled portion of the tongue allows more surface area for nectar collection via fluid trapping. Chapter 4 zooms out beyond the tongue-nectar interface to examine the outcomes of honeyeater-plant interactions in the field. This chapter asks how morphological matching between a honeyeater’s bill and a flower determines pollen transfer between flowers (pollen load acquired from anthers and pollen deposited at floral stigmas) and the feeding efficiency of birds (microliters of nectar consumed per second). In this work I found that honeyeater species differ in their pollination and feeding efficiency at flowers, but that a worse bill-flower match was only correlated with less pollen deposition, not with pollen load or feeding efficiency. The finding that increased morphological matching does not facilitate greater feeding and pollination efficiency of honeyeaters is a surprising insight that pushes us to reevaluate the coevolutionary mechanistic rationale of bird pollination systems. Finally, Chapter 5 uses a community ecology framework to consider how plant traits and interspecific interactions between honeyeater species could influence patterns of bird visitation to plants. This work quantified the honeyeater community composition and nectar resources (as kilojoules of energy per flower and number of flowers produced) at two sympatric species of Australian flowering plants. I found that the two plant species supported significantly different honeyeater communities. The lower-reward plant species (i.e., fewer kilojoules produced per flower and fewer flowers produced) attracted a higher number of small-bodied honeyeater species and was almost never visited by larger species. There were also fewer birds visiting and fewer aggressive interactions at this low-reward plant. These differences in community composition of honeyeater visitors is likely because smaller birds, having lower energetic demands than large species, get relatively more caloric gain from the low-reward plant while avoiding the risk of competition and aggression presented by the high-reward plant species. In summary, this dissertation studies honeyeater-plant interactions across spatial and temporal scales using an integrative approach. This work has filled several knowledge gaps about honeyeater-plant interactions, such as the fact that honeyeaters drink nectar via fluid trapping and have evolved longer, more bristled tongues as an adaptation to increased nectarivory. Broadly, this dissertation illustrates that interdisciplinary research is necessary to holistically investigate the evolutionary ecology of any animal pollination system and provides methods and a conceptual framework with which to do so.
Antagonistic ecosystem engineering influences habitat mosaics: The role of burrowing shrimp in shaping estuarine foundation species
(2025-05-12) hull, wesley w; Ruesink, Jennifer L
Understanding the extent to which ecosystem engineers modify the physical environment is challenging, particularly in dynamic and heterogeneous systems like estuaries, where both organism distributions and abiotic conditions vary spatially and temporally. While bioturbating shrimp can influence sediment properties through reworking, disentangling their pathways of effects on foundational species such as seagrass and bivalves remains complex. Shrimp density-driven changes in sediment composition and penetrability may not fully explain their negative impacts on structure forming species, highlighting the difficulty of linking biotic and abiotic interactions in variable environments. Furthermore, the emerging issue of antagonistic ecosystem engineering—where one engineer's activity prevents another from persisting at functionally relevant densities—compounds this uncertainty. This insight is crucial for predicting ecosystem resilience, guiding restoration efforts, and managing species interactions in dynamic coastal environments.In Chapter 1, I explore the effects of bioturbating shrimp on seagrass. Because ecosystem engineers shape environmental conditions, interactions between ecosystem engineers can depend not only on the external environment but on "which species arrives when" within habitats. Yet, while endpoint outcomes for adults at high density have often been investigated, few studies have examined how these interactions change across density and life history stages. We tested for antagonistic engineering effects of the burrowing shrimp Neotrypaea californiensis (Dana, 1852) at a range of densities on eelgrass Zostera marina L., 1753, including seedlings as well as vegetative shoots. In an observational study, abrupt borders of eelgrass beds were not mirrored by shrimp, and shrimp were never excluded across the full range of observed eelgrass densities, patterns that are inconsistent with alternative stable states. However, eelgrass density declined with increasing shrimp density, and no eelgrass occurred at >336 shrimp m-2. Survival of eelgrass transplants also declined with increasing shrimp density, and in a manipulative experiment, seedlings declined more rapidly than vegetative shoots within a shrimp bed. Thus, shrimp have strong antagonistic engineering effects on eelgrass that increase with shrimp density and can preclude successful seedling establishment and persistence of vegetative shoots. In Chapter 2, I explore the effects of bioturbating shrimp on oysters. Epibenthic organisms on intertidal flats can be affected by underlying sediments and by the activities of bioturbating species that live there. Therefore, bioturbating shrimp have two potential pathways to affect small clusters of juvenile oysters (seeded cultch): directly by moving sediment to the surface, or indirectly by affecting sediment properties (grain size, organic content, penetrability). We examined how oyster (Magallana gigas) survival and size responded to a) shrimp (Neotrypaea californiensis) density, b) mud content and penetrability of sediment, and c) shrimp density due to their effects on sediment properties (indirect pathway). Seeded cultch were deployed from spring through summer at 31 intertidal sites varying in both shrimp density and sediment properties within Willapa Bay, Washington (USA). Shrimp density was negatively associated with mud and organic content but positively with sediment penetrability, as expected from known ecosystem engineering effects of shrimp. However, neither mud content nor penetrability contributed statistically to the negative impact of shrimp density on oyster survival and size. No oysters survived the summer above 50 – 100 shrimp m-2, and remaining oysters were smaller with increasing shrimp density. Overall, negative effects of shrimp on benthic oysters likely occur through the deposition of sediment (28.9 ml burrow-1 day-1) rather than alteration of sediment properties. Our study highlights how the antagonistic ecosystem engineering effect of shrimp on oysters occurs independently of sediment responses to bioturbation and deposit-feeding and quantifies the conditions ensuring the persistence of ecologically- and commercially important foundation species. In Chapter 3, I explore how transplants of seagrass into an area where it was previously excluded by burrowing shrimp can inform seagrass restoration strategies. Seagrass restoration has shown mixed results, even in environments that appear suitable, indicating on-going needs for improved restoration techniques. This study tracked eelgrass (Zostera marina) dynamics at two donor sites and one transplant site over multiple years, using resilience at donor sites and transplant establishment and expansion as key success measures. Despite finer sediments, higher shoot densities, and lower flowering frequencies at lower elevations, eelgrass morphology was similar at both high- and low-elevation donor sites. Recovery times increased with collection intensity, taking up to two years when large plots were completely cleared. Collected shoots were transplanted into plots of four sizes (0.0625–4 m²) and three densities (25–125 m²). Although larger, denser plots were expected to aid establishment in bioturbated areas, the highest initial establishment occurred in small, sparse plots. Over time, sparse and medium-density plots filled in, eventually converging with denser plots within a year. After two years, proportional shoot count changes were inversely related to plot size and density: small, sparse plots saw an 83-fold increase in shoot counts, while large, dense plots saw only a two-fold increase. Large, dense plots initially accumulated fine sediment and organic matter but lagged behind unvegetated areas after one year, likely due to bioturbator loss. Neither donor nor transplant sites showed facilitative effects, potentially due to intraspecific competition. Hydrodynamics around eelgrass shoots may have temporarily delayed sediment accumulation, a key ecosystem function. These findings contribute to improved eelgrass restoration strategies for fringe and upper margin intertidal areas. Overall, I have addressed key interactions that shape the structure and function of intertidal soft sediments, showing how the outcomes among engineering species can become more predictable through incorporating factors such as density and per capita impacts. Borders between engineered habitats provide insight into species interactions, revealing how antagonistic ecosystem engineering shapes community structure. Our findings demonstrate that the effects of these interactions can vary across life history stages, with seedlings often more vulnerable than established individuals. For oysters, burrowing shrimp density serves as a strong predictor of performance, with sediment burial acting as the primary mechanism driving declines in survival and size. In eelgrass restoration, lower shoot collection intensity promotes faster donor site recovery, particularly in fringe and upper boundary habitats, ensuring resilience of natural beds. However, little evidence of self-facilitation in transplanted eelgrass suggests that intraspecific competition, rather than effects of positive density-dependence, constrains expansion, underscoring the complexity of habitat formation in bioturbated environments. Together, this research advances the understanding of ecosystem engineer interactions by demonstrating how antagonistic engineering can disrupt habitat formation and species persistence, emphasizing the importance of considering engineer density, life stage vulnerability, and sediment dynamics in conservation and restoration efforts.
Penguins in the Coal Mine: Unraveling Sentinel Species Responses to Human-Caused Stressors
(2025-05-12) Holt, Katie; Boersma, P Dee
Given the urgent need to understand the rapid changes in marine systems, seabirds can serve as effective sentinel species, offering valuable insights into marine conditions and food webs across a range of spatiotemporal scales. I explore the use of seabirds—specifically Magellanic penguins (Spheniscus magellanicus) at the large, but declining breeding colony of Punta Tombo, Argentina—as sentinel species in multiple contexts. First, I examined the effects of extreme heat on Magellanic penguin adults and chicks. Due to climate change, extreme weather events are becoming more frequent and severe, leading to an increase in direct, adverse thermoregulatory impacts on wildlife. I document the magnitude of an unprecedented, single-day, heat-related mortality event of Magellanic penguin adults and chicks. Mortality rates of adults were unevenly distributed across the colony, suggesting that the presence of microclimates or easier beach access were important factors to penguin survival. Next, I examined how intrinsic traits, specifically sex and body size, affect the foraging success of adult Magellanic penguins, before examining how extrinsic factors, like commercial fishing impact their foraging success. Many seabird species are sexually size dimorphic, with males and females often displaying different foraging behaviors. Sex-specific differences in foraging are often attributed to sexual size dimorphism, yet few have quantified the foraging success of males and females and/or of large and small conspecifics. We found males brought back 38% more food than females and males were more efficient foragers than females, bringing back 69% more food per day. Size did not influence foraging success or foraging efficiency suggesting sex-specific foraging behaviors or roles during breeding are driving differences in foraging success and efficiency. Understanding competition between fisheries and seabirds is critical for developing ecosystem-based management strategies that balance fisheries harvest and conservation goals. I assessed the effect of commercial fishing hours on the foraging success and foraging efficiency of chick-provisioning Magellanic penguins. We found that (1) as the average number of fishing hours increased within the penguins' foraging area, adult foraging efficiency decreased, and (2) both adult sex and the timing of fishing effort relative to chick age influenced this effect. When adults were feeding small chicks, an increase in the number of fishing hours within the foraging range was associated with reduced foraging efficiency, especially for males. When adults were raising large chicks, however, foraging metrics had no relationship to fishing hours, likely because adults can leave larger chicks for longer and are thus less spatially and temporally constrained in their foraging efforts. These results indicate fishing may not be affecting the amount of food breeding adults acquire on a foraging trip, but the rate at which they acquire it.
Plant community and climatic response to Miocene environmental change in the Pacific Northwest (USA): paleoecological tools and applications
(2025-01-23) Lowe, Alexander; StrÃ¶mberg, Caroline
The Miocene epoch (~23-5 Ma) offers important examples of past ecosystem response to global climatic changes in a relatively modern world and critical perspective to current and future climatic change, and as such, has been referred to as “the future of the past”. The Miocene is marked by two major climatic events: warming of the Miocene Climatic Optimum (MCO; 16.9-14.7 Ma) and cooling of the Middle Miocene Climatic Transition (MMCT; 14.7-13.8 Ma). The U.S. Pacific Northwest (PNW) offers a regional record of plant community and climatic response by hosting a suite of well-preserved fossil floras that span the MCO and MMCT in time. Although a rich history of work exists for these floras, an integrated paleoclimate and paleoecological study utilizing plant macrofossils, palynomorphs, and phytoliths, applying updated methodology, and constrained within a high-resolution radiometrically dated temporal framework is currently lacking. In addition, inferring plant ecological strategy, and its relationship to climate and disturbance, in these fossil plant records is hindered by limitations in current paleoecological tools. To refine the use of paleoecological tools, this dissertation presents two “modern analog” studies. In the first (Chapter 1), we refine the reconstruction of leaf economic spectrum (LES) strategies at the community- (i.e., site-) level through a global study of woody non-monocot angiosperm leaf mass per area (LMA) and its morphological correlate, the petiole metric (PM). We find LMA and PM correlate for community mean and variance, but not kurtosis, and provide the necessary equations to reconstruct these community-scale measures and associated uncertainty. This study also highlights the importance of increased temperature seasonality and decreased prevalence of evergreen species in driving low LMA and “fast” LES strategies in temperate climates. However, matching ‘absolute’ LMA distributions between fossil and modern sites does not allow reliable inference of analogous climate types. In the second modern analog study (Chapter 2), we test for links between leaf economic strategies and leaf morphology across succession in North Carolina. We find, among trees, “faster” leaf economic occur in early succession, as predicted, and highlight the utility of PM, leaf margin, and leaf morphological richness in interpreting successional dynamics and associated ecological strategies from fossil leaf assemblages sourced from temperate deciduous forests. The last study of this dissertation (Chapter 3) generates a record of plant communities and climate during the MCO and across the MMCT in the PNW. We find the MCO drove warmer-than-modern annual lowland temperatures, and precipitation like the wetter western PNW today but likely lacking summer drought, hosting mixed mesophytic closed canopy forests. Across the MMCT, the interior PNW cooled in annual and winter temperatures, and likely dried, but this climatic change was tempered closer to the coast. Plant community composition also changed across this interval, with a greater prevalence of deciduous species, and a considerable loss of exotic taxa (those no longer native to the US west coast) and a greater prevalence of open habitats in the PNW interior, which again, was tempered near the coast.
Decoding the Information Content of Fish Sounds and How Fishes Extract Information from Sounds: Insights from the Plainfin Midshipman and Beyond
(2024-10-16) Balebail, Sujay; Sisneros, Joseph A.
Many species have evolved the ability to produce sound for communication. One of the most common types of sounds produced by animals is advertisement calls made by males to attract females for mating. These calls often contain information about morphometric parameters that indicate the quality or reproductive potential of the male. Acoustic communication is commonly observed in ray-finned fishes. While most sonic fish species produce short-duration advertisement calls (~1s or less), the plainfin midshipman fish (Porichthys notatus) produces calls averaging ~10 minutes and up to 2 hours, making them some of the longest vocalizations in the animal kingdom. Despite its long-standing role as a model organism for neuroethology research on acoustic communication and social behaviors, it was unclear if the long-duration hums produced by type I (singing) males contain information about male quality. In Chapter 1, I demonstrate that the acoustic features of the hums produced by type I males are correlated with morphometric parameters indicative of quality, such as body size and condition. This suggests that these hums contain information that females could potentially use in mate-choice decisions. Female midshipman are effective at localizing these hums, following local particle motion cues to find the source. However, there is a 180-degree ambiguity in determining sound direction from particle motion. It has been proposed that gas-filled swim bladders, which detect acoustic pressure, help resolve this ambiguity. Yet, how the swim bladder affects the motion of the fish's inner ears remains unclear. In Chapter 2, I used the finite element method to predict how the swim bladder affects the motion of the otoliths in the inner ear of the midshipman for sounds incident from various directions. I showed that the swim bladder likely resolves the 180-degree ambiguity in directional hearing at behaviorally relevant frequencies for the plainfin midshipman. These predictions can be tested using advanced experimental methods. Many fish do not actively produce sounds but can hear, suggesting that fish hearing may have originally evolved to extract information useful for survival and reproduction from ambient environmental sounds. However, most bioacoustic studies on fishes have focused on communication sounds. In Chapter 3, I review cases where natural ambient sounds serve as sources of information for fishes. I highlight various sources of ambient sound in aquatic environments and hypothesize how they could act as beneficial cues. I also found evidence of natural sounds functioning as noise, disrupting the detection of important signals. This review aims to encourage more studies on ambient sounds and their impact on fish, which is crucial for understanding the effects of underwater noise pollution. Fishes are attracted to sounds such as conspecific advertisement calls. In Chapter 4, I developed Sound-bait, an acoustic trapping method to selectively capture fish species using species-specific attractive sounds. This low-cost method has implications for reducing bycatch in fishing and determining the biological function of fish sounds. In summary, my dissertation provides insights into fundamental questions about fish hearing and acoustic communication, and offers practical applications of this knowledge to aid wildlife conservation.
Exploration of the patterns and processes driving lineage diversification
(2024-09-09) Davis, Hayden R.; Leaché, Adam D
Lineages are constantly evolving, leading to the formation of distinct populations, and in some cases, species. In this dissertation, I explore three independent study systems that are at different stages of the speciation continuum, ranging from very recently diverged subpopulations to species-level diversity. This approach enables me to explore the genomic and life history characteristics driving diversification on multiple evolutionary levels. In Chapter 1, I focus on the genetic, morphological, and life history traits of a population of the Western Fence Lizard occurring at the northernmost extent of the distribution for the species. In Chapter 2, I focus on how interpopulation gene flow patterns correlate with distinct ecoregions in the southwestern United States and northern Mexico for the Western Banded Gecko. Lastly, in Chapter 3, I focus on the efficacy of current methodologies used for species delimitation in Southeast Asian geckos by testing these methods on three distinct species of bent-toed geckos occurring in Borneo. Exploring these three distinct study systems adds valuable insight into the evolution of natural organisms with unique evolutionary pressures across multiple time scales.
Data-Driven Stories Stemming From Public Participation in Science
(2024-09-09) Waugh, Jazzmine Kalila; Parrish, Julia
Seabirds are facing increasing anthropogenic stress in the current era of climate change. Anthropogenic stressors can be direct, such as oil spills increasing seabird mortality via intake of toxins, or indirect, such as marine heat waves decreasing seabird prey quality and quantity. I present research exploring the impacts of anthropogenic stressors on seabird populations, using data from a long-term, fine-grained citizen science dataset. Citizen science, where members of the public help collect data for scientific research, is a method of obtaining vast quantities of rigorous data. It also acts as a potential path for people who have historically been underrepresented in science to be included in science. In this work, I first explore the impacts of direct and indirect anthropogenic stressors on seabirds. In my first chapter, I identify seabird species that are relatively more susceptible to the direct stressor of oil spills, which can be used to help prioritize species for protection. The second chapter uses the natural history stressor of flight feather molt to explore how natural history and a variety of environmental stressors can combine to influence mortality of common murres (Uria aalge) and find that timing is key to determining how these stressors affect mortality. I then turn to consider the diversity of the citizen science participants who collect data like that used in my ecological research. In the third chapter, I quantify how the demographics of citizen science participants have changed over time and differ across types of projects, highlighting opportunities for increased diversity in citizen science. Taken together, my work underscores the use of citizen science both as a means of monitoring changes in populations of marine organisms and as a method of increasing representation for groups that have historically been underrepresented in science.
Oyster aquaculture shapes intertidal communities: from foundation species to higher trophic levels
(2024-09-09) Boardman, Fiona; Ruesink, Jennifer
The work presented in this dissertation sits at the intersection of two major global issues, rapidly increasing stressors on marine systems, and simultaneously, a need for sustainable food solutions. Thus, a wicked problem presents itself: how can we support ecosystem function in marine systems, while also leveraging these systems for food production? The first step to addressing this question is to better understand how aquaculture, in this case oyster aquaculture, shapes intertidal communities. Our work was conducted in Willapa Bay and Grays Harbor, Washington, a globally important region for production of the introduced Pacific oyster (Crassostrea gigas, now Magallana gigas), where we investigated the effects of oyster aquaculture across multiple trophic levels, considering different methods of culture as well as the impacts of associated disturbances. We evaluated the use of oyster culture as habitat to a wide variety of intertidal taxa, focusing first on waterbirds (Chapter 1) and then on nekton (Chapter 2), investigating how organisms respond to culture habitats versus seagrass and mudflat habitats (Chapters 1 & 2). Taxa responses to habitat type were species-specific for birds and nekton generally, with some taxa utilizing oyster culture while others preferred seagrass or mudflat habitats. Some nekton taxa were found to be structure-generalists, meaning they used seagrass and culture habitats similarly. There were very few instances of negative effects of oyster culture on birds or nekton habitat-use, and we concluded that maintaining a mosaic of habitat types best supports the diverse organisms in the estuary. While structures associated with oyster culture provide habitat to a variety of taxa, disturbance events from mechanical shellfish harvest can cause substantial damage to seagrass (Zostera marina, i.e. eelgrass) beds, another habitat-forming foundation species. We investigated how timing of large-scale dredge disturbance interacts with eelgrass phenology and determined that disturbance during the slow-growing overwintering phase or early spring provides the best outcome for eelgrass recovery, with a major contribution from seedlings if the seedbank is given the opportunity to regenerate. Estuaries serve as a resource oasis that link the land to the sea with many organisms spending part of, or the entirety of, their lives as inhabitants. While many estuaries worldwide have been heavily modified anthropogenically and restoration to a “pristine” pre-industrial condition may not be possible, research-based management decisions can conserve or restore function of the ecosystem to better serve native wildlife, commercial fisheries, and aquaculture. Overall, findings from this work can be applied to co-management of estuaries and shellfish aquaculture, with the goal of maintaining ecosystem functioning.
Social Determinants of Sleep
(2024-02-12) Rice, Alicia; de la Iglesia, Horacio
Humans typically sleep in highly built settings that isolate them from environmental regulators of sleep. In postindustrial, highly urbanized environments, these conditions are combined with social schedules that include long commuting times to meet strict school and work times. Together, these conditions have created a “social time” that represents a major determinant of sleep timing and quality.My studies consist of sleep data from two human study populations living in the highly urbanized city of Seattle (Washington, USA) that represent unique contexts in which social time and the built environment have distinct effects on sleep. University students have a late chronotype, or natural inclination to sleep and wake at later times of the day. Students are severely affected by their social obligations because their early school and work times conflict with their late chronotypes. The misalignment between their circadian and social times is described as social jetlag and leads to inadequate sleep duration and quality. Social jetlag and insufficient sleep duration are linked to many health conditions, such as obesity and heart disease. The Covid-19 pandemic shutdown caused workplaces and universities to become remote, which led to little to no commute and more flexibility to choose betimes. We recorded actimetry and light data in students before-Covid (2019), during-Covid (2020), and after-Covid (2021). Compared to before- and after-Covid, during-Covid there was a decrease in the discrepancy between school day and weekend sleep timing, and a longer sleep duration during school days. Light exposure timing also showed higher coherence between school days and weekends during-Covid. Importantly, while interindividual variance in sleep parameters increased during-Covid intraindividual variation did not change, suggesting that increased freedom to choose bedtimes allowed university students to default to their own circadian time and align it better with their social time. People experiencing homelessness are typically not attending school or are unemployed, and unlike students their circadian and social times are more aligned. In contrast, the main challenge they face is the lack of an appropriate environment for optimal sleep. The homeless population in Seattle also has a variety of sleeping environments. We recorded actimetry and light exposure in homeless adults living in tents, tiny houses, permanent or overnight indoor shelters during the winter and summer. We also recorded this data in adults living in stable housing conditions to compare to the unhoused communities. Our results show that both the timing of sleep and its quality is affected by the homelessness conditions and seasons. We also see a drastic difference in light exposure timing and duration due to the differences in Seattle photoperiod in summer versus winter. Both of these studies show the impact of the social environment on a persons’ sleep timing and quality.
Biotic and Abiotic Drivers of Plant-Pollinator Interaction Rewiring
(2023-09-27) Arrowsmith, Kathleen Caroline; Brosi, Berry J.
In this dissertation, I examine variation in plant-pollinator interaction patterns. I present two observational studies exploring drivers of interaction variation, followed by an experiment in which I demonstrate the effect of changing plant-pollinator interactions. First, I use a structural equation modeling framework to demonstrate that temperature variation and plant community dissimilarity directly drive variation in plant-pollinator interaction patterns. Both variables also provide pathways for geographic distance to indirectly impact rewiring. Second, I use a multinomial logistic regression to show that pollinators prefer different flowers at different temperatures, even within a constant plant community. Third, I present an experimental manipulation that connects the removal of the most abundant bumble bee in a community to the production of fertilized seeds in a focal plant. In this experiment, I find that the composition of the plant and pollinator communities as well as the distribution of morphological traits both guilds influences the way in which pollinator removal influences pollination function. As a whole, this dissertation demonstrates that interspecific interactions cannot be considered static components of plant-pollinator communities. Rather, ecologists must consider how changes to biotic and abiotic conditions are likely to affect not only the organisms present in a community but also the interactions between them.
Persistence under pressure: exploring the impact of conjugation rate evolution on the stability of plasmids
(2023-09-27) Muñiz Tirado, Adamaris; Kerr, Benjamin
Plasmids are small, extrachromosomal DNA elements commonly found in bacteria, often carrying accessory genes such as antibiotic resistance genes. They play a pivotal role in disseminating antibiotic resistance within bacterial populations through the process of conjugation, enabling transfer between different bacterial strains or species horizontally, rather than vertically through cellular division. In the absence of selection for the plasmid, its presence in the population tends to decrease due to associated fitness costs. However, coevolution between hosts and plasmids can lead to enhanced plasmid persistence, allowing them to persist even after the selective pressure is removed. There are a variety of ways that plasmids become more persistent, including acquiring compensatory mutations to reduce the cost of carriage, minimizing segregational loss, and increasing conjugation rates. In this study, we specifically investigated the impact of increased conjugation rates, a less explored yet significant factor contributing to plasmid persistence. We employed the Luria-DelbrÃ¼ck Method (LDM) to estimate the conjugation rate of an ancestral and descendant plasmid-host pair consisting of an Escherichia coli host and an IncP- plasmid that coevolved under antibiotic selection favoring plasmid maintenance. Remarkably, we observed a significant increase in conjugation rates, which suggests that the increase in plasmid persistence in a population can be partially explained by an increase in the transfer rate after plasmid-host coevolution. To understand the drivers behind this increase, we formulated two hypotheses: (i) a pleiotropic effect of cost reduction and (ii) direct selection for heightened conjugation rates. While the pleiotropy hypothesis is attractive, our findings lacked robust evidence for it, as there was no significant change in growth rate that would indicate a reduction in plasmid cost. Consequently, we explored the direct selection hypothesis. Although we did not find any conjugation-related mutations in the plasmid, our theoretical model suggested that mutations impacting conjugation rates could potentially drive the mutant plasmid's invasion into the population under certain conditions. Our results shed light on the complexities of plasmid persistence and conjugation rates, indicating that selection under antibiotic pressure not only favors retaining antibiotic resistance genes and alleviating associated plasmid costs, but in some cases, may also promote an increase in horizontal transmission of the plasmid. Thus, selective antibiotic conditions may enhance the spread of antibiotic resistance through horizontal gene transfer.

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