The Wood Thrush (Hylocichla mustelina) is declining throughout its range, yet is capable of persisting in both contiguous forests and small forest patches surrounded by human suburban development. Thus, it is an ideal species for gaining insight into the effects of suburbanization on migrant songbirds. I investigated two aspects of Wood Thrush nesting ecology: nest ectoparasites and nest defense behavior in order to determine if suburbanization influences either aspect. Nests from suburban forests had fewer haematophagous mites, though the abundance of haematophagous blowfly larvae did not differ between suburban and contiguous forests. There was no relationship between the abundance of mites and nest site characteristics, though blowfly abundance may be related to nesting substrate species. Parasites had little effect on nestling condition. In regard to nest defense, suburban Wood Thrushes had shorter flight initiation distances and mounted more active defenses during initial nest visits than birds nesting in contiguous forests, suggesting a previously-established sensitization response to human disturbances in suburban birds. I found no consistent shifts in aggression over subsequent nest visits in either habitat type, suggesting that throughout the breeding season, Wood Thrushes neither habituate nor sensitize further to repeated human disturbances. My results suggest that Wood Thrushes nesting in suburban forest patches are subject to fewer nest ectoparasites and defend their nests more aggressively than conspecifics nesting in contiguous forests. These results draw attention to the fact that although Wood Thrushes persist in both rural and suburban habitats, their nesting ecology may be different between these habitat types.

A large amount of the world’s biodiversity is located in a disproportionately small amount of area, namely the tropics. Many of these areas are experiencing rapid landscape changes, mainly in the form of deforestation for agricultural practices. Current conservation efforts are focused on agricultural areas and their ability to provide habitat. The conservation value of a novel land-sparing agroforestry system, known as Integrated Open Canopy (IOC), was recently demonstrated on the study site when applied to coffee. IOC coffee supports forest species that are uncommon or absent in shade grown coffee. I generated best management practices for IOC farms relative to the conservation of forest-dependent birds by examining what features support the highest richness of species. The goal was to help develop guidelines for the implementation of IOC grown coffee. The Golden-winged warbler (Vermivora chrysoptera) is a Neartic-Neotropical migrant of high conservation priority which has been documented using a range of nonbreeding habitat types, including IOC coffee farms. However, as is the case with many migrant species, little is known about whether survival differs among habitats. Though generally forest dependent, previous work found Golden-winged warblers select for habitat features other than categorical forest types, such as canopy height and microhabitat features. In an attempt to identify quality nonbreeding habitat, I estimated Golden-winged survival rates specific to an array of habitat features.

In North America 72% of freshwater mussel species are endangered, threatened, or of special concern due to factors such as habitat loss and degradation, biological invasion, and land use change. Propagation of freshwater mussels has been considered a necessary conservation strategy for population restoration where threats have been mitigated but small population sizes limit population viability. Yellow lampmussel is a species of freshwater mussel that is endangered, threatened, or imperiled throughout its range; therefore, I evaluated laboratory techniques (probiotic supplements and secondary rearing designs) to improve culture of yellow lampmussel for population restoration. Several aquaculture facilities commonly use probiotics; thus, I used commercial probiotics to determine if 1) probiotic concentration and 2) type of probiotic mixture improved growth or survival of juvenile mussels during primary culture. I further asked whether probiotics affected mussels by reducing ammonia, thereby improving water quality. Some probiotics increased survival (and, in one experiment, increased growth) of juvenile mussels, regardless of concentration, but results were variable by experiment and probiotic type. Probiotics did not significantly reduce ammonia concentrations, so this was unlikely the mechanism of benefit. I also investigated the effect of different secondary rearing systems at two culture facilities on growth and survival of juvenile mussels in two size classes (5.0 mm). I used five different secondary culture systems that were either indoors (dogpans and baskets) or outdoors (trough, airlift upweller, tank upweller, baskets), where water was either recirculating or flow-through. Survival was exceptional in all larger size class rearing systems, and the baskets in the ponds had the greatest growth rates. Smaller mussels had lower survival than the larger mussels, indicating that when deploying juvenile mussels into outdoor culture systems mussels size should be greater than 5.0 mm. Results of this project will inform future rearing yellow lampmussel in New England and more broadly add to the limited literature on probiotic use and secondary rearing designs in freshwater mussel culture.

Controlling influenza A virus (IAV) infections remains a challenge largely due to the high replication and mutation rates of the virus. IAV is a negative-sense RNA virus with two main surface proteins — hemagglutinin (HA) and neuraminidase (NA). HA recognizes and binds sialic acid on host cell receptors to initiate virus entry. NA also recognizes sialic acid on host cell receptors but functions by cleaving sialic acid interactions to release progeny virus. Because both HA and NA interact with sialic acid on the host cell surface with opposing effects, their balance is essential for optimal viral infectivity. However, the evolutionary constraints that maintain HA and NA function, while conserving a functional balance, are not fully understood. I adapted the comprehensive and systematic mutational scanning technology, termed EMPIRIC (Exceedingly Meticulous and Parallel Investigation of Randomized Individual Codons), to investigate the local fitness landscape of regions of HA under standard conditions and under drug pressure. We observed that synonymous substitutions had a higher mean absolute fitness effect in the signal than a neighboring HA region used as a control. Folding ∆G calculations revealed a hairpin loop that appeared to be differentially enriched between human and swine IAV variants in sequences of circulating strains. However, the molecular mechanism resulting in the observed host species-specific constraints remains undefined. Studying the fitness landscape of the receptor binding site of HA revealed the high sensitivity of this region to mutation. However, modulating the levels of NA activity by mutation and by using the NA inhibitor oseltamivir enabled the identification of HA mutations with adaptive potential under selection pressure by oseltamivir. These results highlight the importance of the HA-NA functional balance virus replication and in the development of resistance to oseltamivir inhibitors. These studies provide improved understanding of IAV biology, and can inform the development of improved antiviral agents with reduced likelihood for resistance.

Periodically-harvested fisheries closures (PHCs) are a widespread form of community-based marine spatial management used throughout the Indo-Pacific that also is currently being intensively advocated by conservation organizations for supporting productive fisheries and healthy marine ecosystems. However, local implementation of PHCs has historically been designed to support occasional and efficient exploitation of fish stocks, and not necessarily sustainable fisheries yields and stock conservation. The efficacy of PHCs for achieving their historical cultural objectives of periodicity and efficiency of harvest, simultaneously with achieving contemporary fisheries objectives of fisheries productivity and conservation is undetermined. As a result, the utility of PHCs for supporting contemporary ecosystem-based fisheries management is uncertain given environmental, social and climate change. We developed a biological-economic fisheries model of PHCs to test the value of this form of marine resource management for achieving cultural, fisheries and conservation objectives under sustainable and overfishing scenarios. Our results reveal PHCs to be more effective at achieving the multiple objectives than either non-spatial or fully-protected area management when fisher impact on fish behavior is considered. These results describe the performance of PHCs in general when fish behavior is considered, but does not provide detailed guidance for a particular PHC. Thus, we modified and calibrated our biological-economic fisheries model with empirical data from Nakodu Village on Koro Island in Fiji. The calibrated model allowed us to estimate the effectiveness of Nakodu Village’s current PHC management and predict consequences of future management actions. Results suggest that 5-year PHC closures are optimal for simultaneously achieving fisheries productivity and conservation goals in Nakodu Village. These findings challenge the dogma that PHCs are simply a cultural legacy and warrant further investigation of the utility of PHCs for supporting ecosystem-based management beyond the Indo-Pacific.

Lethal interactions between carnivorans (interspecific killing) may influence their population dynamics, behavior, and other important aspects of their ecology. In this study, I expand upon previous research on the broad-scale patterns of interspecific killing in Carnivora (Palomares & Caro 1999, Donadio & Buskirk 2006) with a greatly expanded dataset (inclusion of scat and stomach data and more intensive sampling of the literature), and suggest avenues for future research. While like previous studies, I found a positive effect of relative body size between killer species and killed species on the likelihood of forming a killing interaction, I failed to find evidence that this effect had a body size ratio threshold above which interactions become less common, suggesting a greater role of non-competitive killing than previously believed. I also found evidence for a positive influence of range overlap and dietary overlap on species interactions, but found mixed effects of phylogeny. This study suggests that our previous understanding of the broad-scale dynamics interspecific killing in Carnivora was, due to limited sampling, incomplete in scope. Incidental killing, whereby killing interactions occur as a byproduct of opportunistic lethal encounters caused by the hyperpredatory behavior of carnivorans, has a number of interesting implications for our understanding of interspecies aggression, including research on intraguild predation and its effects.

Several studies have investigated the ecological factors that affect behavior in Micrathena gracilis, a diurnal orb-weaving spider that forages on flying insects during the day. However, none yet have considered how the temporal distributions of prey and predator occurrences shape their daily behavioral rhythms, especially web construction, which involves a heavy energetic investment well in advance of potential nutritional benefit. Recently, several orb-weaving spider species have been shown to exhibit a variety of abnormal rhythms, suggesting that circadian clock-controlled rhythms may play an unexpected role in behavioral evolution. Despite the appearance of significant insect abundance in the evenings, M. gracilis individuals stop foraging, take down their webs, and retreat before they can capitalize on this opportunity. Is the nutritional benefit of this forfeited prey significant compared to what they collect during the day, and if so, what potential cost might justify opting out of this potential gain? To investigate, sticky traps for prey collection and a camera array for recording predator activity were used at a local field site to survey what risks and rewards these spiders face throughout the 24-hour day. Spider activity and web captures in the field were also used to confirm behavioral patterns and capture success throughout the day. It was found that spiders begin foraging when prey becomes available but cease while prey is still abundant. These observations appear to support a theoretical model of behavioral decisions under predation risk. However, recorded predation events were rare, and predation was not confirmed outside of the foraging timeframe. These results support the notion that the circadian rhythm of Micrathena gracilis is shaped by factors other than prey availability, but the theoretical pressure from predation risk requires further investigation.

Circadian clocks enable coordination of essential biological and metabolic processes in relation to the 24-hour light cycle. However, there are many habitats that are not subject to this light cycle, such as the deep sea, arctic regions, and cave systems. This study analyzes the circadian pattern of isolated populations of a subterranean spider, Meta ovalis from two Tennessee caves and five Indiana caves. Locomotor activity was recorded with TriKinetics LAM50 Locomotor Activity Monitor under a 12-hour light (L), 12-hour dark (D) (LD 12:12) cycle preceding total darkness (DD). Significant differences were found within and among populations found in Tennessee cave systems in average free running period and onset of locomotor activity. Selection, drift, and genetic fixation are explored as the causes of variation in the present study, using M. ovalis as the model organism. All five caves in Indiana show little variation, whereas both Tennessee caves show large interindividual variation.

Poikilothermic organisms experience trade-offs associated with life at different temperatures caused by incompatible physiological and biochemical demands caused by temperature extremes. As the result many such organisms exhibit acclamatory effects, adjusting their metabolism and physiology to recently experiences temperatures. One such acclamatory effect is the metabolic compensation that allows an organism to withstand increases in temperature by decelerating biological rates below Arrhenius expectations, presumably reducing energetic demand and reducing stress. Daphnia magna is resilient across a wide temperature range, and if acclimated to mildly stressful temperatures first, exhibits longer survival in lethal temperatures. Certain genotypes of Daphnia also exhibit higher acute thermal tolerance than others, indicating the presence of genetic variation and local adaptation in heat tolerance. This study examined the effect of ambient temperature (5°C-37°C) and acclimation history (2 generations at 10°C or 25°C) on the oxygen consumption rates of 8 genotypes of Daphnia (4 with high acute temperature tolerance, and 4 low). There are nonlinear decelerations of Daphnia respiratory rates across a temperature gradient when acclimated to 25°C or following short 8-hour acclimation to measurement temperatures. Furthermore, Daphnia exposed to a near-lethal temperature (35°C) with a subsequent 24-hour recovery period at their native 25°C-acclimation temperature shows no indication of respiratory damage. Genotype showed no difference in metabolic compensation, indicating the process is genetically constrained. Regulation of mitochondrial and membrane function are promising areas to further characterize the mechanism of metabolic compensation found in this study.

Poikilothermic organisms experience trade-offs by differential physiological demands generated by temperature extremes. Many such organisms exhibit acclimatory effects, adjusting their metabolism and physiology to recently experienced temperatures. One such acclimatory effect is metabolic compensation, the deceleration of biological rates below Arrhenius expectations. Daphnia magna is eurythermal, and if acclimated to mildly stressful temperatures first, survives longer in lethal temperatures. This study examined the effect of ambient temperature (5°C-37°C) and acclimation history (lifetime at 10°C or 25°C) on the oxygen consumption rates of 8 genotypes of Daphnia with high or low acute temperature tolerance. There were decelerations of respiratory rates across a temperature gradient when acclimated to 25°C or following short 8- hour acclimation to measurement temperatures. Daphnia exposed to a near-lethal temperature (35°C) with a 24-hour recovery period at 25°C-acclimation temperature showed no difference in respiratory control compared to unexposed 25°C-acclimated Daphnia. Genotypes showed no difference in potential compensatory ability.