A changing climate has been identified as a major driver of changes in marine species’ distribution, phenology, and habitat selection in recent decades and is expected to continue to influence these traits. These changes are not only happening in our oceans, but within coastal habitats as well, where waters are susceptible to sudden changes in temperature and oxygen levels are influenced by nutrient inputs. These changes which will likely impact fish species that utilize these areas as nurseries, spawning habitat, or foraging grounds. In this dissertation I consider climate impacts on two important predators, the sandbar shark (Carcharhinus plumbeus) and cobia (Rachycentron canadum), both of which rely on coastal habitats like Chesapeake Bay for their survival. I used a series of physiological, survey, tagging, and modeling studies to estimate the current and future impacts of climate change on these two species. Sandbar sharks are unable to handle temperatures as warm as 32°C physiology, but in the wild prefer temperatures between 22-26°C. As a result, I estimate bottom habitat losses in Chesapeake Bay by end-of-century for juvenile sandbar sharks. Although they are relatively intolerant of hypoxia (critical oxygen concentration = 3.5 mg l-1), juvenile sandbar shark appear to prefer areas on the fringes of hypoxic zones to avoid larger sharks and find more abundant prey. Therefore, the continued reduction in oxygen levels throughout the entire water column actually improves juvenile sandbar shark suitable habitat. Being a bottom dwelling species, sandbar shark in Chesapeake Bay may be forced to remain in non-preferred bottom habitat, move up in the water column, or shift to shallower habitats. Cobia are tolerant of high temperatures (32°C) and low oxygen (1.7-2.4 mg/l) which should allow them to withstand the detrimental effects of climate change in Chesapeake Bay, at least through mid-century. Hypoxia and elevated temperatures reduce survival of cobia that are exercised to exhaustion. Although the physiology experiments and habitat models suggest cobia will withstand climate change through mid-century, declines in their suitable habitat in Chesapeake Bay are expected by end-of-century. I project arrival time to occur earlier and departure time to occur later when temperatures are warmer and that by mid- and end-of-century cobia may spend on average up to 30 and 65 more days, respectively, in Chesapeake Bay. As conditions worsen in more southern estuaries, cobia may shift spawning habitat in estuaries and bays further north, such as Delaware Bay, New York/New Jersey Bight, and Long Island Sound, where conditions are more thermally suitable. Over the next 60-80 years, suitable cobia habitat is projected to shift northward from spring to fall and to decrease over the U.S. continental shelf. As cobia shift into new areas, the development of regulations in more northern states will become necessary to promote a sustainable cobia fishery. As species shift their distributions as a result of climate change, it is imperative that we understand why and how these shifts are occurring so that both managers and fishers can ensure important resources continue to be fished sustainably.

Blue catfish Ictalurus furcatus is an invasive species of great concern in coastal habitats throughout the eastern United States, inclulding the Chesapeake Bay and its tributaries. In this dissertation, I use field surveys, laboratory experiments and quantitative modeling to provide insights into several aspects of blue catfish biology at the individual level. In chapter 1, I characterize and compare patterns in growth and body condition in blue catfish populations in the James and York river subestuaries during two stages of invasion. Both the mean growth rate and mean body condition of blue catfish declined in the recent period in response to increases in population abundance. In chapter 2, I uncover life-history plasticity in the reproductive biology of the species: blue catfish in the James River mature at a smaller mean size but provision a greater amount of energy into reproduction than York River fish, which exhibit lower densities than James River fish. In chapter 3, I assess the food demands of blue catfish in a laboratory experiment. I demonstrate that blue catfish have low metabolic demands, as expected for a relatively sedentary benthic fish. Importantly, blue catfish had high survival and significant growth at food levels as low as one third of the maximum, suggesting that the species has a high tolerance of starvation and that individuals may be able to invade and establish in low food habitats in coastal waters. In chapters 4 and 5, I report the results of two laboratory experiments studying the effects of increased salinity on survival, growth and body condition of blue catfish. Blue catfish, typically considered a freshwater species, was found to have a higher salinity tolerance (72-hour LC50 = 15.7 psu) than many freshwater fishes, suggesting the potential of the species to expand its range into most subestuaries of the Chesapeake Bay particularly during wet seasons. Habitats with salinities around 4 psu seemed particularly suitable for blue catfish as growth and body condition were maximized at this salinity despite the lower mean ingestion rates than fish maintained in freshwater. Finally, in chapter 6, I parameterize a full life-cycle bioenergetics model for female blue catfish using data from the literature and from the other chapters of this dissertation. The model supported the implications from other chapters that blue catfish have low maintenance costs, relatively high resistance to starvation and a plastic ability to fuel reproduction even in environments with low food availability. The model, together with results from other chapters, also opened up avenues for further research on characterization of the energetic basis for the observed phenotypic plasticity, identification of physiological modes of action by which salinity might limit survival, growth and reproduction of blue catfish, and ultimately the identification of coastal habitats that might support self-sustaining populations of this invasive fish. This research highlights the need for management efforts to control blue catfish populations in subestuaries where they are already established and to limit the range expansion into novel habitats. Towards this end, this dissertation provides important information on vital rates of blue catfish needed for population models that can be used for management strategy evaluations.

To protect and manage ecosystems over large spatial scales, repeated mapping with remote sensing, such as aerial photography, is valuable, but several potential problems need to be overcome to generate accurate maps. For instance, to monitor submerged aquatic vegetation (SAV), such as seagrass, satellite imagery must often capture seasonal and interannual variation as well as disturbances. We used a model system, SAV and the blue crab Callinectes sapidus in the lower Chesapeake Bay, to examine (i) if Planet Lab (PL) satellite imagery can be used to accurately estimate SAV coverage by comparing PL images coincident with those of the VIMS SAV survey; (ii) if PL imagery can capture seasonal and episodic changes in SAV accurately; and (iii) if PL and VIMS SAV survey imagery can be integrated to assess the relationship between SAV nursery habitat and recruitment of young juvenile blue crabs in mid-summer through early fall. To do so, we analyzed data from six selected sites with high salinity in lower Chesapeake Bay. Our findings were (i) PL satellite imagery was a suitable surrogate for VIMS aerial surveys of SAV conducted annually at the selected sites, with the caveat that PL imagery is at a lower resolution (3 m) than the VIMS SAV survey (24 cm), which could affect the utility of PL imagery for some goals; (ii) PL imagery was able to capture seasonal and episodic changes in SAV cover in the Bay; and (iii) remote sensing imagery taken in late spring and early summer was not representative of SAV cover available to the blue crab during the recruitment period in mid-summer through fall. Consequently, PL imagery can be used to estimate SAV bed area over time scales that are relevant to recruitment of the blue crab in lower Chesapeake Bay. Understanding SAV dynamics and future effects of climate change on SAV can be improved with broad-scale data from remote sensing techniques, such as aerial photography and satellite imagery. However, new platforms such as Planet Lab can provide accurate spatial and temporal distribution patterns for SAV beds relative to abundance of the blue crab during critical phases in its life history. At two locations in the York River, lower Chesapeake Bay, we conducted a mensurative field experiment by sampling percent cover of SAV (eelgrass Zostera marina, widgeon grass Ruppia maritima) and algae (mostly Gracilaria vermiculophylla), density of blue crab juveniles, bed area by Planet Lab, and select independent variables bimonthly over two years. The main findings were: (i) juvenile blue crab density was inversely related to SAV bed area, but reductions in crab density as bed area increased were more than offset by higher total abundance of crabs as bed area enlarged; (ii) crab density was positively related to percent cover of algae (Gracilaria), Ruppia and Zostera; (iii) location, year, season and water depth were not significant predictors of crab density in SAV beds after accounting for the effects of bed area and SAV percent cover; and (iv) potential loss of Zostera in the lower Chesapeake Bay due to global warming was projected to cause either only a modest reduction in crab density if other SAV species do not compensate and bed area remains constant, or crab density could even increase if algae and Ruppia were to compensate for the loss of Zostera.

Eukaryotic organisms that cannot be classified as animals, land plants, or fungi are termed protists. Despite the fact that protists represent the majority of eukaryotic diversity, these organisms have received relatively little attention from biological researchers beyond morphological characterization. Reasons that likely contributed to their neglect include their mostly microscopic nature, that only a few lineages are the causative agents of human disease, that laboratory cultivation can be challenging, and that species concepts for the majority of protists was vague in many lineages. Initial attempts to resolve relationships among eukaryotes produced the five kingdoms model. This model suggested protists were an evolutionary assemblage separate from the animals, plants, and fungi. Molecular systematics provided a more accurate view of relationships amongst eukaryotic taxa. Results from molecular phylogenetic studies demonstrated that protists were a polyphyletic group made of many assemblages, and that more complex lineages such as plants and animals were nested within these assemblages. This new evolutionary framework brought increased attention to protists. The application of molecular biology, especially genomic and transcriptomic sequencing to protists has allowed researchers to generate meaningful data on poorly understood lineages rapidly. Applying these techniques to understudied amoeboid protists, I demonstrated the presence of a complex life cycle in a well-studied group of opportunistic pathogens and their close relatives that was not previously known, as well as characterized new diversity within the group. I made methodological advances in the field of molecular systematics through development of a novel ortholog collection algorithm that I have included in a phylogenomic package capable of resolving ancient (>100 million years) divergences in the tree of eukaryotes. I used the algorithm to build the packages accompanying manually curated database of 240 homologs from 304 eukaryotic taxa. Using the newly developed software and manually curated gene set has yielded the most complete and highly resolved tree of eukaryotes to date. Finally, I used developmental transcriptomics to demonstrate the amoeba Copromyxa protea evolved a means of simple cooperative multicellularity independently from other more well studied multicellular lineages.

Sensory environments are rapidly changing due to increased human activity in urban and non-urban areas alike. For instance, background sounds can interfere with parent-offspring communication and mask cues reflective of predation risk, resulting in elevated vigilance at the cost of provisioning. In chapter 1, we studied nestling provisioning behavior among Western Bluebirds (Sialia mexicana) in response to short-term (1 hr) and long-term (continuous exposure throughout nesting period) noise exposure. Provisioning rates were lower at nests exposed to short-term experimental traffic noise compared to exposure to ambient background sounds. Trial order strongly influenced provisioning behavior, with the decline in provisioning during noise playback occurring only during the second broadcast period of sounds. In contrast, provisioning rates increased with sound levels among nests exposed to long-term noise. Additionally, birds nesting in areas with high levels of noise returned to the nest more quickly than those in quiet areas following a simulated predation attempt. This study suggests that behavioral responses to short-term, experimental exposure to noise may not always be reflective of responses to longer-term noise exposure in real-world settings. It is essential to be cognizant of potential differences between experiments and real-world conditions as urbanization and sensory pollutants increase. The pervasive spread of artificial light at night has been documented to disrupt natural rhythms with varying consequences on wildlife. Disruption to the night sky can alter nestling development either through indirect exposure to light or due to changes in adults’ behavior, both having potential physiological costs or benefits. In chapter 2, we experimentally manipulated light outside of Western Bluebird nesting cavities and investigated whether exposure to light at night affects nestling development and adult behavior. Our results found no evidence of light at night affecting the onset or cessation of adult daily activity. However, we found that nestlings exposed to light have smaller wing chords and lower mass, but better overall body condition than those in the control. The number of chicks in the nest also strongly influenced the effect of the light at night: nests exposed to light with brood sizes of three nestlings had smaller wing chords and better body condition than nests without lights, but there were no strong differences between light exposed and dark nests with five chicks. Although light exposure appears to improve chick body condition, the chicks were smaller overall. These findings suggest that indirect artificial light outside the nesting cavity is enough to have consequences on the development of nesting birds, and ecologically relevant light exposure appears to alter chick condition without a temporal shift in parental behavior.

Elucidating the mechanisms responsible for driving individual variation in behavior is a foundational question in organismal biology. Answering these types of questions is necessary for understanding how tradeoffs are mediated as well as potential constraints on evolutionary responses to selection. In Chapter I, I synthesize the evidence suggesting that testosterone plays a central role in driving individual variation in cooperative reproductive behaviors and mediating the tradeoff between cooperation and competition. The subsequent chapters of my dissertation then focus on understanding the mechanistic sources of individual variation in the cooperative courtship behaviors of male wire-tailed manakins (Pipra filicauda), a Neotropical lekking songbird. Wire-tailed manakins exhibit cooperative courtship display behaviors wherein both floater and territory-holding males perform coordinated courtship displays. Territory-holding males sire essentially all offspring and, among territory-holders, those that are more cooperative exhibit higher reproductive success. Cooperation also benefits floater males in that more cooperative floater males have a higher probability of becoming a territory-holder. In Chapter II, I detail the difficulties associated with measuring circulating testosterone in free-living animals and develop a new field technique that can improve our ability to accurately account for the effects that the stress of capture has on circulating testosterone levels in birds. In Chapter III, I quantify individual variation in the cooperative courtship behaviors of territory-holding male wire-tailed manakins using video cameras. I then use both observational and experimental approaches to show that among territory holders, high testosterone has antagonistic effects on a male's cooperative behavior. Chapter IV focuses on quantifying how an individual's cooperative behavior relates to their telomere length. Telomeres are the segments of repetitive DNA found at the end of chromosomes. Telomeres shorten in response to both physiological and environmental perturbations, are predictive of an individual's mortality risk and, because of these characteristics, are thought to reflect an individual's biological age (as opposed to chronological age). My results show that short telomeres are associated with increased cooperative behaviors and, given that a male's cooperative behavior is reflective of their reproductive investment, suggest that males with lower future reproductive potential (i.e., shorter telomeres) invest more in reproduction. My last chapter (Chapter V) focuses on synthesizing these results and suggests that future research on cooperative behaviors will need to integrate biomarkers of an individual's condition with mechanisms that reflect an individual's social competence to further understand the sources of individual variation in cooperation. / Doctor of Philosophy / Cooperative reproductive behaviors occur when multiple individuals coordinate their reproductive efforts to gain an advantage over other individuals or those individuals that attempt to reproduce in the absence of cooperation. In this context, some individuals have been found to consistently act more or less cooperative, and outstanding questions regarding the evolution of cooperative reproductive behaviors focus on attempting to understand the intrinsic differences among individuals that consistently vary in their cooperative tendencies. In this dissertation, I focus on measuring individual variation in the cooperative reproductive behavior of male wire-tailed manakins, a passerine found in the Amazon Rainforest, as well as the sources of this individual variation. Male wire-tailed manakins perform acrobatic courtship displays for females. Wire-tailed manakins are especially interesting in that multiple males will perform coordinated courtship displays, but only one male within the group typically reproduces. Individual variation in this cooperative behavior also influences how likely an individual is to reproduce. Chapter I synthesizes the evidence across species to suggest that testosterone, a hormone known for influencing competitive reproductive behaviors, influences an individual’s likelihood of acting in a cooperative or competitive manner. Chapter II describes the difficulties associated with measuring circulating testosterone in wild animals and describes techniques that can be used to overcome some of the difficulties associated with measuring circulating testosterone in free-living birds. Chapter III focuses on understanding the relationship between testosterone and individual differences in the cooperative reproductive behaviors of the wire-tailed manakin. I find that those males with higher testosterone or those with experimentally increased testosterone are less cooperative. I discuss my results in the context of understanding how this relationship could influence the evolution of circulating testosterone levels more broadly. Chapter IV examines the relationship between the cooperative reproductive behavior of male wire-tailed manakins and the repetitive segments of DNA found at the end of chromosomes called telomeres. Telomeres shorten as individuals age and the length of an individual’s telomeres has been found to be predictive of their lifespan and mortality risk. My research shows that those individuals with shorter telomeres (or a higher mortality risk) are more cooperative. Given that an individual’s cooperative behavior is predictive of their probability of successfully reproducing, my research suggests that those individuals that are more likely to perish invest more time and energy in attempting to reproduce. In Chapter V, I conclude by summarizing my results and suggesting future research that can further our understanding of the sources of consistent individual differences in cooperative behavior and the evolution of cooperation more broadly.

Dinosaurs are the largest animals to ever walk on the continents and some reached body sizes of up to 70 tons. Observation of their closest living relatives, birds and crocodylians, could never allow for prediction of gigantic dinosaurian forms. Therefore, the fossil record is crucial to understanding the evolutionary changes of these animals through time, including body size trends. The reptile group Archosauria encompasses living and extinct birds and crocodylians as well as non-avian dinosaurs and crocodile relatives called pseudosuchians. My research focuses on studying fossils of extinct archosaurs to determine how the morphology of their skeletons allowed for growth to large body sizes. I am specifically interested in how the vertebral column fits together and how the structures that articulate vertebrae change throughout the phylogeny (i.e. family tree) of Archosauria. Although major body size trends are well known for archosaurs, less research has focused on skeletal features that are associated with the evolution of large body size in that group. I hypothesize that the vertebral column will have these features. To answer the question of how vertebrae morphology is related to body size, I first described eight vertebrae from a large pseudosuchian archosaur Poposaurus langstoni. This animal possesses an accessory articulation between the vertebrae in its trunk region (i.e. between the neck and hips) called the hyposphene-hypantrum articulation. I then surveyed vertebrae from across Archosauria and found a close fit of presence of the articulation with large sizes and that it evolves independently in several archosaur groups. / Master of Science / Dinosaurs are the largest animals to ever live on land and some weighed up to 70 tons. Today, the living relatives of dinosaurs are birds and crocodylians, and observation of these animals could never allow for prediction of gigantic dinosaurian forms. Therefore, paleontologists must study the fossil record to understand the evolutionary changes of these animals through time, including body size trends. Fossils can provide information about the evolution of dinosaurs to enormous sizes and their subsequent shrinking to the small sizes we see today in their living relatives. The reptile group Archosauria encompasses living and extinct birds and crocodylians as well as non-avian dinosaurs and crocodile relatives called pseudosuchians. My research focuses on studying fossils of extinct members of Archosauria, or archosaurs, to determine how changes in their skeletons over millions of years allowed for many species to grow to extremely large body sizes. I am specifically interested in how their vertebrae fit together and how the structures that link together their backbone change throughout the family tree of Archosauria.

In a 1982 paper, Gould and Vrba argue that a conflation of the two components of adaptation of a feature, historical development of the feature and present utility, has caused evolutionists to overlook a missing term in the science of form, which they call 'exaptation'. In the present project, I show that evolutionary biology still contains a confusion in the use of 'adaptation' due to an inappropriate perception of the interaction between the two components of adaptation. Because of the confusion, evolutionists have missed another term in the science of form. Evolutionary theory, specifically the treatment of adaptation, would profit from the introduction of a term referring to features that have a selective history which causes them to appear overly well adapted to their present function. I suggest we refer to these features as hyperadaptations, since they appear to be hyperbolized adaptations. By introducing hyperadaptation into the conceptual framework of adaptation, we can sharpen our understanding of related concepts (adaptation to function, exaptation, maladaptation, etc.) and remove or reduce some confusion regarding the interplay between analysis of historical pathways and ascriptions of (current) function in the diagnosis of adaptation. Furthermore, the improved framework should allow evolutionists to more adequately explain biological phenomena. / Master of Arts

In recent times, the genetic analysis of ancient human remains has contributed significantly to the study of the human past, especially in the subjects of admixture, migrations and social organisation. By utilising distinct methods and source materials, genomic research is adding considerable value to conclusions reached by other disciplines, such as archaeology and history. However, the geographical region of the Levant has only very recently been the subject of genomic research, and the region of Jordan rarely at all, due to poor environmental conditions that hinder DNA preservation and limited access to archaeological excavations and therefore sampling of ancient remains. My Master’s thesis project aimed at generating genome-wide data for 16 Bronze and Iron Age skeletal human remains excavated in the archaeological site of Pella, a multi-period site located in the North Jordan Valley that hasn’t yet been sampled for DNA studies. I also aimed at analysing the resulting data in context with genomic data from the wider region of the Levant, by means of several standard population genetics tests. Additionally, genomic results were interpreted making use of historical and bio-archaeological records specific to the site of Pella. Through an initial assessment of the sequencing data, only six libraries were selected to be included in genome-wide analyses. Surprisingly, the performed tests show two very distinct genomic profiles among the six libraries: four of them have the expected Neolithic-to-Iron Age Levantine profile, while the other two show affinity with ancient and present-day East Asian populations. These results suggest that human mobility in Bronze-to-Iron Age Eurasia could have happened over distances much longer than previously thought. Further target enrichment will provide more power to either reinforce of reject these preliminary results.

The increasing demand for and limited supply of fresh water necessitates an understanding of how human actions affect aquatic ecosystems. Anthropogenic impacts to these ecosystems occur in many forms including eutrophication, invasive species removals, and hydrologic alterations. Ground water extraction is one such action that can dramatically impact wetland hydrology and is increasing in occurrence globally as clean surface water resources are exhausted. Despite the importance of ground water extraction to meet human demand, little information is available concerning the response of vegetation communities to chronic ground water extraction. Over extraction is known to result in reduced water levels and duration, resulting in a shift towards more upland tolerant species; however, detailed information concerning the response of the individual species comprising these communities and how wetlands shift along with pumping regime remains unavailable. The following dissertation combines historical hydrology and ground cover vegetation data with recent monitoring to describe how ground cover (herbaceous species) and canopy (tree species) vegetation respond to fluctuations in hydrology and ground water extraction. Ground cover communities were extremely diverse with a total of 103 species being sampled in the historical ground cover vegetation dataset. Juncus repens was the most widely distributed species and was observed in 36% of all samples. The 29 species most widely observed in the ground cover strata (height) displayed relatively narrow ranges of preferred water depth and duration with Amphicarpum muhlenbergianum being found in the driest areas and Pontederia cordata and Ludwigia repens the wettest. In general species found in shallower water depths also tended to be found in locations with shorter hydroperiods, although woody species tended to found in areas with relatively shallow water depths with extended hydroperiod. Ground cover vegetation is extremely useful as an indicator of recent hydrology, although the hydrologic preference of the species in the current study does not reflect the assumed ecology of the species utilized by Florida Administrative Code 62-340.450. Additional research to validate and improve the accuracy of this classification system is required. When ground water extraction volumes in well fields was significantly reduced, ground cover communities were responsive, as was indicated by Permanova results (Before After Control Impact). All ground cover at wetlands located within well fields became more indicative of wetter conditions while control wetlands responding only to climate and weather all became drier. In contrast, several well fields displayed reductions in water levels and hydroperiod following extraction reductions. The shift in ground cover community indicates that ground water extraction has not produced an alternative stable state and restoration of these ecosystems is possible through alterations in ground water extraction volumes alone. As ground water extraction volumes were increased, tree communities responded by displaying increased occurrance of non-Taxodium sp. trees, mortality of wetland tree species, and light availability. All wetlands remained dominated by mature Taxodium sp. regardless of the amount of ground water impact indicating that each wetland has not yet shifted into a new community type as a result of non-Taxodium tree encroachment; however, recruitment and mortality patterns of both Taxodium and non-Taxodium species indicate this may occur in the future. Changes in light availability at the wetland floor associated with tree species is likely providing an additional feedback mechanism on ground cover communities. Results from this dissertation indicate that vegetation communities are extremely responsive to changes in hydrology and have shown significant changes associated with ground water extraction. These changes may not be permanent; however, and alterations in extraction volumes and timing can provide changes in vegetation communities even after decades. Routine long term monitoring should be conducted, in addition to critical assessments of current extraction volumes, to assess the current status of vegetation ecosystems and allow for individuals to best manage aquatic resources for all uses.