For animals at high altitude, low oxygen (hypoxia) is an unremitting stressor that has the potential to impair metabolism and performance. The hypoxic chemoreflex senses reductions in the partial pressure of O2 in the arterial blood and thus elicits many of the physiological responses to hypoxia, including increases in breathing and activation of the sympathetic nervous system. The hypoxic chemoreflex is vital to surviving acute exposure to severe hypoxia, but the advantage of this reflex during chronic hypoxia is less clear. The goals of my thesis were to examine how control of breathing by the hypoxic chemoreflex has evolved in high-altitude natives to maintain O2 transport in chronic hypoxia, and to elucidate the potential genetic mechanisms that were involved. This was accomplished using deer mice (Peromyscus maniculatus) native to high- and low-altitudes, in addition to a strictly low-altitude species (P. leucopus). I found that high-altitude deer mice breathe with higher total ventilation using preferentially deeper breaths, contributing to higher O2 saturation of arterial blood, but in contrast to lowland mice highlanders do not exhibit ventilatory plasticity in response to chronic hypoxia. These phenotypes appeared to be uniquely evolved in the highland population and arise during the onset of endothermy in early post-natal development. I then used second-generation inter-population hybrids to evaluate the effects of genetic variation (specifically, in the hypoxia-inducible factor 2a gene Epas1 and in haemoglobin genes) on an admixed genomic background. The high-altitude variant of α-globin could completely explain the deep breathing pattern of highland mice, whereas the high-altitude variant of Epas1 and possibly β-globin contributed to their apparent lack of ventilatory plasticity in response to chronic hypoxia. Together, the physiological changes elicited by these mutations contribute to maintaining O2 uptake and metabolism in the cold and hypoxic environment at high altitude. / Thesis / Doctor of Philosophy (PhD) / High-altitude environments are amongst the harshest on earth, with extremely low levels of oxygen, but some animals not only survive but thrive in these conditions. How these animals do so was previously not well understood. My thesis has uncovered how the evolution of respiratory physiology contributes to high-altitude adaptation in the deer mouse, the species with the broadest altitudinal distribution of any North American mammal, and has elucidated the genetic mechanisms involved. My work contributes to understanding nature’s solutions to oxygen deprivation – an all too common problem in many human and animal diseases.

With global climates changing rapidly, animals must adapt to new environmental conditions with altered weather and phenology. Key to adapting to these new conditions is adjusting the timing of reproduction to have offspring when the conditions are best to maximize growth and survival. Using a long-term dataset on a wild population of yellow-bellied marmots (Marmota flaviventer) at the Rocky Mountain Biological Laboratory (RMBL), we investigated how the timing of reproduction changed with changing spring conditions over the past 50 years. Marmots are hibernators with a four-month active season. It is thus crucial to reproduce early enough in the season to have time to prepare for hibernation, but not too early so as snow cover prevents access to food. Importantly, climate change in this area has increased spring temperatures by 5 °C and decreased spring snowpack by 50 cm over the past 50 years. This directional change in climate may have caused adaptation. Given that adaptation to environmental conditions could arise from either microevolution or phenotypic plasticity, we evaluated how female marmots adjust the timing of their reproduction and estimated the importance of both genetic variance and plasticity in the variation in this timing. We show that, within a year, the timing of reproduction is not as tightly linked to the date a female emerges from hibernation as previously thought. We report a positive effect of spring snowpack but not of spring temperature on the timing of reproduction. There is inter-individual variation in the timing of reproduction but not in its response to changing spring conditions. Genetic variance in the timing of reproduction is low, and heritability was 8%. Earlier pup emergence date increases the number and weighted proportion of pups surviving their first winter, indicative of directional selection on this trait. The same pattern is not found for litter size with no effect of pup emergence date on the number of pups born. Further, all three of these traits are not under stabilizing selection. Taken together, it seems that we should expect some changes in this population with changing climatic conditions, but because of plasticity and not due to natural selection. Further, future studies on the marmots should not operate under the assumption that females reproduce immediately following their emergence.

Biofouling is the accumulation of sessile marine organisms, such as algae, tube worms and barnacles on man-made substrata and has negative economic and ecological implications. Ship hulls are readily fouled, which significantly increases drag while decreasing ship fuel efficiency when moving through water. Fouled hulls have also become important vectors of invasive species. These problems are minimized when hulls are painted with a toxic anti-fouling or non-toxic foul-release coating. Due to recent restrictions of anti-fouling paint use, research and development of non-toxic alternatives has increased. Novel hull coating efficiency is often quantified by the critical removal stress value of barnacles from the coating. Barnacle adhesive cement protein content is thought to be responsible for barnacles’ incredible ability to adhere underwater. The expression level and type of adhesive proteins has eluded scientists due to their extreme insolubility within cured barnacle cement. Identification of these proteins may provide insight to the adhesion of fouling species and aid coating development. Barnacles are a cosmopolitan organism, able to withstand a wide range of environmental conditions, yet foul-release coating research had not previously incorporated environmental factors as variables in determining coating performance. Temperature is known to affect protein structure and function and is also a formative factor of barnacle larvae survival and development. Even so, the interaction between temperature and barnacle adhesion to has not previously been explored. We examined the effect of temperature on barnacle adhesion to foul-release coatings. After observing differences in critical removal stress due to temperature, we attempted to attribute these differences to specific proteins within the adhesive using 2D SDS PAGE. Gel image analysis determined that there were significant differences in cement protein expression between barnacles raised within different temperatures. Preliminary protein identification with Mass Spectronomy (MALDI TOF/TOF) was performed, however further research and a larger barnacle genomic database is needed to elucidate barnacle cement protein sequences.

Anthropogenic impacts to the environment are unavoidable currently; however, my research investigates a potential mitigation method for amphibians dealing with poor health outcomes caused by detrimental anthropogenic changes to their wetlands. Environmental stressors such as antibiotics leeching from manure of domesticated farm animals into local wetlands can cause a dysbiosis of the gastrointestinal bacterial flora within tadpoles. Dysbiosis of gastrointestinal bacteria during early tadpole development is associated with a decrease in development rate, decrease in body mass accumulation, and other poor health outcomes. I investigated if increasing the indigestible fiber (prebiotic) content in wood frog tadpole’s alfalfa based diet could return tadpoles with stripped microbiomes (dysbiotic gastrointestinal bacterial community composition) to the same phenotype of healthy control tadpoles. I also did a pilot study to see if diet could help in increasing survival post infection with Ranavirus, and from both studies, I created NGSS aligned curriculum and activities. I found that a 10% corn starch enriched alfalfa diet significantly increased the body mass accumulation and development rate of stripped tadpoles. I found there was an association with metabolism and gut dysbiosis. Unfortunately, the connection in regards to corticosterone release was unclear. There was an association with diet and survival, but it needs to be repeated with a larger sample size.

Small but mighty phytoplankton can be used as excellent model organisms to answer questions that are of importance to marine biologists and researchers in experimental evolution alike. For example, marine biologists are interested in finding out, how, in a changing ocean, the phytoplankton foundation of the ocean ecosystem is going to change - can we use short-term data to extrapolate to longer timescales? What are the physiological consequences of selection in stable and fluctuating high-pCO2 environments? From a more evolutionary perspective, is elevated pCO2 alone enough to drive evolution in marine algae? Can we select organisms to maintain plasticity in fluctuating environments, and how does selection in a fluctuating environment affect their ability to evolve? Can we detect a cost of plasticity? I have used theoretical and practical approaches from both disciplines to answer these questions, as they are ultimately similar questions that are important to address, and the lack of communication between disciplines has lead to conflicting predictions on the fate of populations in changing environments. Using evolutionary theory and applying it to an organism with a known function in the marine environment allows us to make ecologically relevant predictions while also enabling us to disentangle the underlying evolutionary mechanisms. While there have been some studies focusing on evolution of marine algae in climate change scenarios since I started my PhD, my study is the first to test the link between phenotypic plasticity and adaptation empirically, and it is also the first to use 16 rather than single or few genotypes of an algae, thereby creating the statistical power necessary to make any predictions. In a short-term CO2 enrichment study, and a selection experiment, those 16 physiologically and genetically distinct lineages of Ostreococcus, the smallest free living eukaryote, were selected for 400 generations in fluctuating and stable high pCO2 environments. I have shown that short-term plastic responses in phenotype can predict the magnitude of long-term evolutionary ones. Ostreococcus lineages in fluctuating environments evolve to be more plastic with no associated costs, and the adaptive response to selection in a high pCO2 environment is to grow more slowly in monoculture, but to be more successful competitors in mixed culture. High-pCO2 evolved lineages are genetically and physiologically different from their ancestors. Importantly, their quality as a food source for zooplankton will change, with possible repercussions for the ocean ecosystem at a whole. Furthermore, the lineages’ ability to perceive pCO2 levels in the surrounding medium is altered after evolution in fluctuating and high pCO2 environment, allowing them to broaden the window in which they can respond to changes in their environment without suffering metabolic stress.

Unprecedented rates of anthropogenic environmental change have resulted in dramatic decreases in biodiversity worldwide. In order to persist during changes in both the abiotic and biotic environment resulting from anthropogenic stressors such as climate change and habitat degradation, populations must be able to respond or face extirpation. Predicted population-level responses to environmental change include i) range shifts as individuals disperse into more suitable regions, ii) phenotypic plasticity allowing for shifts in the mean phenotype of the population or iii) microevolution resulting from a genetic change within the population. The goal of this thesis is to assess how species within a community respond to a dramatic change in the environment. This study used the sediment record of a Subarctic pond to investigate the impacts of a rapid increase in salinity on two species of the crustacean zooplankton Daphnia. One species, Daphnia tenebrosa, was unable to persist in the high salinity conditions and is believed to have been extirpated from the system. The other species, Daphnia magna, was tolerant of the new environmental conditions and was present throughout the sediment record. To investigate the changes in life history of D. magna, resting eggs from the sediment were hatched to compare iso-female lines from pre- and post-disturbance time periods. No differences were observed between the clone lines, suggesting that phenotypic plasticity allowed D. magna to persist despite the rapidly changing environmental conditions, and that microevolution in salinity tolerance may not have occurred in this population. This study suggests that, in environments with moderate levels of post environmental change, pre-existing phenotypic plasticity may play a greater role than microevolution in species response to environmental changes. However, not all species from a community display the same response to environmental changes, as seen in this study with the extirpation of D. tenebrosa. To better understand how communities will be affected by future environmental change, further investigations need to be made on what factors influence species response. Identifying species response may allow conservation efforts to focus on species that are unlikely to adapt to environmental change, and are most at risk. / Thesis (Master, Biology) -- Queen's University, 2013-09-29 21:54:34.881

In this diploma thesis has been tested potential of maternal influences on body growth at two model groups of geckos with large interspecific body size variability. The effect of egg manipulation to hatchling size was proved to be significant for hatchlings at both model species Paroedura picta and Goniurosaurus lichtenfelderi. However, in adult animals, there were no more significant body size differences caused by egg manipulation. It leads to conclusion that both species of geckos have compensatory growth and its adult size is likely to be primarily genetically determined. Key words: maternal effect, egg manipulation, body growth, allometric engeneering, Paroedura picta, Goniurosaurus lichtenfelderi

Doctor of Philosophy / Division of Biology / Theodore Morgan / Temperature is a critical environmental parameter and thermal variation has significant effects on local adaptation and species distributions in nature. This is especially true for organisms that are isothermal with their environment. Variation in temperature imposes stress and directly influences physiology, behavior, and fitness. Thus, to thrive across a range of thermal environments populations must contain sufficient genetic variation, the capacity to respond plastically, or some combination of both genetic and plastic responses. In this work I first quantified patterns of phenotypic and genetic variation in nature and then dissected the genetic basis of variation in thermal traits. In the first aim I used natural populations of Drosophila melanogaster collected from a latitudinal transect in Argentina to investigate variation in heat stress resistance and cold plasticity within and among populations. I found heat stress resistance was highly variable within populations, but was strongly associated with the monthly maximum average temperature of each site. For cold plasticity I was able to demonstrate significant variation in plasticity within and among populations, however the among population variation was best explained by the altitude of each site. I hypothesized that this was caused by a difference in temperature fluctuations at high altitude sites relative to low altitude sites. To evaluate this hypothesis I paired our study with existing laboratory data that demonstrated significant fitness differences between high and low plasticity (and altitude) sites when these populations were reared in variable thermal environments. Thus, cold plasticity is an adaptive response to environmental variation. The final project focused on understanding the genetic basis of thermal variation. I fine-mapped a single co-localized heat and cold tolerance QTL via deficiency and mutant complementation mapping to identify four novel thermal candidate genes. There was no overlap of the deficiencies or genes associated with cold or heat stress resistance. Sequence analysis of each gene identified the polymorphisms that differentiate the lines. To test for independent associations between these polymorphisms and variation in nature the Drosophila Genome Reference Panel was used to confirm associations between allelic variation and cold tolerance in nature.

Coral reef ecosystems worldwide are facing increasing degradation due to disease, anthropogenic damage, and climate change, particularly in the Tropical Western Atlantic. Mesophotic coral ecosystems (MCEs) have been recently gaining attention through increased characterization as continuations of shallow reefs below traditional SCUBA depths (>30 m). As MCEs appear to be sheltered from many stressors affecting shallow reefs, MCEs may act as a coral refuge and provide larvae to nearby shallow reefs. The Deep Reef Refugia Hypothesis (DRRH) posits that shallow and mesophotic reefs may be genetically connected and that some coral species are equally compatible in both habitats. The research presented here addresses key questions that underlie this theory and advances our knowledge of coral connectivity and MCE ecology using the depth-generalist coral Montastraea cavernosa. Chapter 1 presents an overview of the DRRH, a description of MCEs in the Gulf of Mexico (GOM), and the framework of research questions within existing reef management infrastructure in the GOM. Through microsatellite genotyping, Chapter 2 identifies high connectivity among shallow and mesophotic reefs in the northwest GOM and evidence for relative isolation between depth zones in Belize and the southeast GOM. Historical migration and vertical connectivity models estimate Gulf-wide population panmixia. Chapter 3 focuses on population structure within the northwest GOM, identifying a lack of significant population structure. Dominant migration patterns estimate population panmixia, suggesting mesophotic populations currently considered for National Marine Sanctuary protection benefit the Flower Garden Banks. Chapter 4 quantifies the level of morphological variation between shallow and mesophotic M. cavernosa, revealing two distinct morphotypes possibly representing adaptive tradeoffs. Chapter 5 examines the transcriptomic mechanisms behind coral plasticity between depth zones, discovering a consistent response to mesophotic conditions across regions. Additionally, variable plasticity of mesophotic corals resulting from transplantation to shallow depths and potential differences in bleaching resilience between shallow and mesophotic corals are identified. The dissertation concludes with a synthesis of the results as they pertain to connectivity of shallow and mesophotic corals in the Gulf of Mexico and suggests future research that will aid in further understanding of MCE ecology and connectivity. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

Rapid climate change is a significant threat to the long-term persistence of native tree populations. Concern has been expressed that tree populations might fail to adapt due to rate of change, insufficient adaptive variation in tree populations and limits to dispersal. In contrast, others have contended that most tree species have high phenotypic plasticity, maintain high levels of within-population genetic variation and exhibit effective gene dispersal capability, all characteristics which should enable an adaptive response. To assess the potential adaptability of tree populations we need to understand their genetic diversity and phenotypic plasticity to build on the currently limited evidence base and guide decisions about seed sourcing for establishment of new woodlands desired to meet ambitious planting targets. Currently the seed sourcing system divides the island in four regions of similar size although it is not based on any genetic or ecological information. We discuss the suitability of this system with the insight of the data collected from native tree populations growing in experimental trials. In this thesis we study genetic diversity and phenotypic plasticity patterns in over 30 native tree populations across all Great Britain for three broadleaved species: ash (Fraxinus excelsior), rowan (Sorbus aucuparia), and silver birch (Betula pendula). To obtain these data we assessed the variation in multiple traits in several common garden experiments for each species, which were grown in contrasting environments. There is a tendency in provenance experiments to consider height as a proxy for fitness. We demonstrate that tree height is not enough to understand tree fitness and its adaptability capacity. We assessed our tree populations for growth (survival, tree height, DBH), stem form (number of forks), leaf phenology (leaf flushing and senescence) and leaf anatomical traits (leaf area, stomatal density and stomatal size).Great Britain has very distinct and heterogeneous environments likely to have given rise to adaptive differentiation. Knowing the geographical pattern of the genetic differences we can see the direction selective pressures have had on each of the traits studied, and we compare differences in patterns across the traits and species. Comparing populations growing in different environments we assessed the variation in phenotypic plasticity by trait and the direction of these plasticity. We found that tree populations across Great Britain are highly genetically variable and show genetic differences which have a geographical pattern, and that the patterns and size of the differences vary by species. Phenotypic plasticity varies across traits and interactions between genotype and environment make plasticity in some traits more unpredictable than others. We conclude that tree populations of ash, rowan and birch are well adapted to the diverse and oceanic climate of Great Britain, and that levels of genetic diversity and phenotypic plasticity provide a high capacity to respond to environmental change.