As sea-level rise converts coastal forest to salt marsh, marsh invertebrates may migrate inland; however, the resulting changes in forest and marsh invertebrate communities, including the stage of forest retreat that first supports saltmarsh species, remain unknown. Additionally, the ghost forest that forms in the wake of rapid forest retreat offers unknown quality of habitat to marsh invertebrates. In a migrating marsh on the Eastern Shore of Virginia, USA, ground-dwelling arthropod communities were assessed across the forest-to-marsh gradient, and the ecological equivalency of ghost forest and high marsh habitats was evaluated to determine if marsh invertebrates utilized expanded marsh in the same way as existing marsh. Composition and diversity patterns were evaluated across the gradient for entire arthropod communities captured by pitfall and leaf litter samples, as well as springtail, ant, and beetle communities. Ecological equivalency was assessed by comparing community structure (composition and diversity) for epifauna and infauna as well as functional metrics (diet and body condition) for two marsh species found in both high marsh and ghost forest (the detritivore amphipod, Orchestia grillus, and the hunting spider, Pardosa littoralis). Community composition differed between zones, driven largely by retreating forest taxa (e.g., Collembola), marsh taxa migrating into the forest (e.g., the saltmarsh amphipod O. grillus), and unique taxa (e.g., Hydrophilinae beetles) at the ecotone. The overlap of these groups likely contributed to an observed peak in rarefied species diversity at the ecotone for pitfall samples. The composition and diversity patterns of springtails, ants, and beetles differed from entire arthropod community patterns, with springtails showing highest diversity in the high forest, and ants exhibiting peaks in diversity in high forest and ecotone. The low forest was the most inland zone to accommodate O. grillus, a saltmarsh species that may serve as an early indicator of marsh migration into forests. Ghost forest habitat offered expanded variation in both community composition and O. grillus diet. Both forest and marsh species were present in the ghost forest, and O. grillus occupied a larger trophic niche width in the ghost forest from consuming both marsh and terrestrial material. Despite these differences, ghost forest habitat supported the majority of marsh species, and observed marsh species present in both habitats primarily consumed from the marsh grass food web with no lasting difference in body condition. Because of its capacity to support saltmarsh species, the ghost forest can be considered largely ecologically equivalent to high marsh at this site, which may inform evaluations of marsh spatial extent. Forest retreat and marsh migration thus provide an important opportunity for generalist saltmarsh invertebrates to maintain their habitat extent in the face of marsh loss due to sea-level rise.

Plants can alter their chemical, structural (‘resistance strategy’), or morphological traits (‘tolerance strategy’) to deter or mitigate herbivore damage. Developed in terrestrial ecosystems, plant defense theory provides a testable framework for evaluating drivers of plant trait variation and defense strategy selection. Yet, it has rarely been tested in coastal vegetated ecosystems, where intense grazing can denude large spatial areas and disrupt ecosystem services and functioning. Through the lens of plant defense theory, this dissertation examines abiotic and biotic control on traits and defense in the tidal marsh plant, Spartina alterniflora, and assesses their influence on further grazing and herbivore distribution. As a foundation species, Spartina regulates how marshes keep pace with sea-level rise, thus herbivore removal of Spartina directly affects marsh resilience. In mesocosms, I manipulated salinity and simulated herbivory on brackish and freshwater Spartina to evaluate the growth-rate hypothesis and the optimal defense theory (Chapter II). Simulated herbivory reduced tolerance traits and brackish Spartina was better defended than freshwater Spartina, supporting these hypotheses. Elevated salinity caused greater variation in freshwater Spartina traits, suggesting climate-driven saltwater intrusion may not affect brackish marshes, but could mediate freshwater Spartina response to herbivory. In mesocosms, I assessed how nutrient enrichment affected Spartina defense against grazing from the marsh periwinkle, Littoraria irrorata (‘resource-availability hypothesis’ or RAH) (Chapter III). Trait variation was assessed across plant age (original versus clonal new stems), which can influence traits in terrestrial plants. Nutrients promoted tolerance traits while decreasing constitutive resistance, supporting the RAH. Newer stems had higher tolerance and resistance traits, implying they are better defended than older stems. Neither nutrient availability nor plant age stimulated Littoraria consumption in feeding assays, suggesting nutrient loading will not intensify top-down control, and may increase vertical accretion through enhanced tolerance traits. Lastly, I examined if Spartina traits influenced consumer fronts created by the purple marsh crab, Sesarma reticulatum (Chapter IV). Despite causing marsh die-off in New England, in southern marshes, including Virginia, the Sesarma front is moving inland, allowing tall-form Spartina to revegetate and prevent marsh loss. Others hypothesized that sediment characteristics, abiotic conditions, and predation pressure drive this movement inland. Here, I tested if Spartina palatability, nutritional quality, and accessibility also act as a driver, as plant traits can determine herbivore distribution in terrestrial ecosystems. A caging study then evaluated if Sesarma grazing directly shapes Spartina traits. Intense predation pressure in the low marsh and enhanced Spartina forage quality in the high marsh were the only significant predictors of Sesarma front movement. Grazing from Sesarma affected short- and tall-form Spartina differently. Herbivory increased palatability and reduced short-form Spartina’s ability to mitigate damage, while having little effect on tall-form Spartina. Thus, higher constitutive defense in tall-form and increased palatability of short-form Spartina further propagate the Sesarma front inland. Overall, this dissertation demonstrates that plant traits can influence ecosystem resilience, directly through biomass production, and indirectly by shaping herbivore distribution, and should be considered when assessing how coastal vegetated ecosystems are affected by climate change and anthropogenic disturbance.

Harmful algal bloom (HAB) events are generally marked by the over-abundance of one particular HAB species. Co-occurrence of multiple HAB species or HAB toxins, especially at low cell or toxin concentrations, is common. While much research has been dedicated to understanding the detrimental effects of individual HAB species and toxins on human health and the environment, implications of HAB co-occurrence for seafood safety and shellfish health are poorly understood.Oysters support economically-valuable fisheries and aquaculture worldwide, however, oysters encounter co-occurring HAB species and toxins in their environment. Some HAB species and toxins are harmful to oyster health, harming the immune system, reducing feeding rates, or causing mortalities. Additionally, oysters co-accumulate HAB toxins; some associated with human health syndromes, such as diarrhetic shellfish poisoning. To support productive and safe oyster industries, the effects of co-occurring HAB species and toxins on larval oyster health, and the bioaccumulation of multiple toxins in adult oysters in the Chesapeake Bay, were investigated. The health and survival of larval oysters is paramount to shellfish productivity. Individual and combined effects of co-occurring HAB species and toxins were assessed using multiple series of 96-h bioassays with larval oysters; larval inactivity and mortality were measured throughout. Karlodinium veneficum and Prorocentrum cordatum are co-occurring HAB species associated with shellfish health issues. Independently, low cell concentrations of either species caused larval inactivity. Additionally, K. veneficum swarmed larvae and caused significant larval mortalities. The co-occurrence of P. cordatum did not alter the larval effects of K. veneficum. Separate bioassays examined co-occurring Alexandrium catenella and Dinophysis acuminata, and associated toxins: saxitoxin (STX), okadaic acid (OA), and pectenotoxin-2 (PTX2). Exposure to live A. catenella caused larval inactivity, while exposure to either species caused larval mortalities. Exposure to D. acuminata lysate or PTX2 also caused larval mortalities, with A. catenella lysate, STX, and OA exhibiting no significant larval inactivity or mortalities. Larval effects during lysate or toxin co-exposure were driven by D. acuminata lysate or PTX2, respectively. In both bioassays, the observed larval effects of co-exposure were driven by one HAB species or toxin. To inform seafood safety management, baseline HAB toxin data from Chesapeake Bay adult oysters were collected over two years. Azaspiracids (AZA1, AZA2), domoic acid (DA), OA, dinophysistoxin-1 (DTX1), PTX2, karlotoxins (KmTx1-1, KmTx1-3), goniodomin A (GDA), and microcystins (MC-RR, MC-YR) were detected in oysters. Regulated toxins were well below seafood safety limits, however, the presence of hepatotoxic, freshwater MCs in estuarine oysters reflects an urgent need for regulation of these toxins in seafood. Co-accumulation of toxins was common. Furthermore, solid phase adsorption toxin tracking devices (SPATTs) were co-deployed with oysters to assess additional methods of toxin monitoring. SPATTs provided additional toxin data that complemented, but could not replace oyster toxin data. As HAB species ranges shift and the need for sustainable shellfish aquaculture increases, so too does the need for understanding combined effects of HABs on shellfish, and the potential for toxin co-accumulation within shellfish. Regional and species-specific studies like these can inform and enhance HAB monitoring, mitigation, and management strategies.

Climate change is one of the greatest challenges the natural world currently faces, particularly in marine ecosystems, as many marine organisms are sensitive to warming water temperatures and other aspects of climate change. The Mid Atlantic Bight region is warming rapidly in comparison to the rest of the world’s oceans. In the face of climate change, organisms must either adapt to altered environmental conditions or shift their distribution to avoid extinction. One such example of the latter is the Atlantic Surfclam (Spisula solidissima), whose range has exhibited a shift over the past 4 decades, recorded in both stock assessments and fishing industry activity. This organism supports a substantial fishery, worth approximately $30 million annually. The surfclam’s optimal temperature range is relatively narrow, with thermal stress occurring around 20oC and death occurring with sustained temperatures beyond 24oC. This organism’s sensitivity and exposure to climate change make it likely that this species will exhibit a climate-driven range shift, which may be incorrectly interpreted as a response to fishing pressure in an otherwise well managed stock. This study used growth data stored in archived Atlantic Surfclam shell hinges to investigate the relationship between climate drivers and the historic range shift of this species. Shells used in this analysis came from federal survey collections performed by the Northeast Fisheries Science Center in the years of 1986, 2008, and 2011-2016. A random 10% sample was imaged and aged to fit von Bertalanffy growth curves to individual clams. Parameters from the von Bertalanffy growth model (maximum size and the growth coefficient, k, used as a proxy for growth rate) were used to summarize clam growth. Linear models were constructed to use individual and environmental variables (location, station depth, temperature, time, and age at collection) to predict indices of clam growth. Results found that depth had a negative effect on maximum size; clams grew smaller in deeper water and larger in shallower water. The most useful temperature metric was number of extreme warm days (days above 20oC). Temperature had a negative effect on maximum size, but a positive effect on growth rate; clams grew faster but to smaller maximum sizes with higher occurrence of extreme warm events, likely reflective of respiratory and physiological demands not being met by feeding ability at high temperatures in large clams. Over time, clams in the south decreased in size while clams in the north increased in size, suggesting a northward movement of optimal range, potentially explained by increased food abundance in northern areas of this region. Over time, growth rate in deeper depths increased, but did not match the earlier reversed pattern in magnitude of higher growth rates in shallower waters, suggesting that an offshore movement is occurring but may be limited by decreased light penetration, benthic primary production, and food availability at increasing depths. These results describe a relationship between environmental variables and surfclam growth, supporting the occurrence of a historical range shift driven by climate change. These results may be useful in future studies predicting continued effects of climate change on this species growth and distribution.

The organic, methylated form of mercury (Hg), methylmercury (MeHg), is a highly toxic global pollutant that affects humans, wildlife, and ecosystem health. While exposure to high dosages of MeHg is often fatal, much less is known about the physiological effects of exposure to lower, sub-lethal dosages. Further understanding of how MeHg exposure alters organ performance at a cellular level is critical to understanding the health effects on both humans and wildlife impacted by environmental contamination. To assess the impact of MeHg on eukaryotic organisms, we tested how lifetime, dietary exposure impacts telomere length shortening in various tissues of the zebra finch (Taeniopygia guttata) at four early ages post-hatch. Telomere length is a recently popularized biomarker of biological aging and individual quality, influenced by both genetics and the environment. We used real time PCR to measure relative telomere length (T/S ratio) of brain, liver, kidney, heart, and red blood cells and explored interactions between ages and dietary treatment. We predicted that birds exposed to an environmentally relevant level of Hg would have reduced telomere lengths than compared to controls due to increased oxidative stress and subsequent cellular damage. Rather, in all tissues and virtually all ages, Hg exposed birds had longer telomere lengths, suggesting alterations in telomere maintenance pathways, inhibited cellular proliferation, and/or MeHg-induced rapid selection.

Human population history and the social composition of human groups during the Middle Neolithic (MN) in Scandinavia is still to be fully understood. The possibility of obtaining genomic data from ancient tissues has opened a new horizon for understanding ancient human populations. Using cutting-edge technology for molecular ancient genetics, I screened the genomes of 14 individuals from the farming Trichterbecher kultur from the Megalithic passage grave Frälsegården in Gökhem parish in Västergötland, Sweden, and aimed to understand their genetic makeup and elucidate their kin relationships and population affinities to surrounding groups. I found strong kinship relationships inside of the passage grave, suggesting that their burial traditions reflected social structure. Mitochondrial and Y chromosome haplogroups show higher female-inherited genomic diversity and suggest a putative male-lineage preservation across megalithic populations of the time. A clear pattern of differentiation between MN farmers and hunter-gatherers (HGs) is accompanied by signals of admixture based on shared uniparental haplogroups and a tendency for Gökhem to resemble other TRB populations. Further analyses, higher coverage and more published ancient genomes will allow to provide more detailed proof of the social and genetic structuring of populations cohabitating Scandinavia during the Neolithic transition.

Studies of certain ecological, chemical, and physical factors as they affect ascospore formation in bakers' yeast. Especial attention ls given to the effect of carbon dioxide, oxygen, temperature, and cell concentration. The ability of 43 yeast cultures of differing types and geographical sources to form ascospores on three sporulation media is compared. Variations in the numbers of ascospores formed by isolates from a commercial yeast package as well as in the progeny of a single isolate were observed. A practical hybridization method is described. Based on the findings of these studies a technique for the preservation of yeast cultures is suggested. With 20 tables and 5 figures. / Doctor of Philosophy (PhD)

Native oyster populations have largely collapsed worldwide, with extensive losses of habitat and ecological function. Efforts to restore oysters have been initiated in Europe, Australia, China and North America. In 2004, the first large-scale oyster restoration project was constructed in Chesapeake Bay, employing novel methods including increasing reef height to mimic pre-exploitation reefs, enlarged reef area to address spatial scale, and augmenting recruitment. High-relief reefs (HRR) were built from 25-40 cm in height to better mimic pre-exploitation reefs, while low-relief reefs (LRR) were built at 6-8 cm off existing bottom, mimicking repletion methods by state fishery management agencies used for almost a century. Results documented in 2009 for the HRR were very promising but questions remained regarding longevity of these reefs, as no restoration construction at the time showed evidence of long-term persistence nor gain in function, declining significantly within five years post-construction. We document here the ongoing high performance and long-term persistence of this restored oyster reef network, located in the Great Wicomico River, Virginia. Chapter 1 is an introduction to the topic. Chapter 2 is a thorough description and analysis of the history of the oyster fishery in Virginia from colonial times to the present. To properly restore oysters, an understanding of what happened to them and their habitat since European colonization was deemed necessary to avoid the mistake of shifting the baseline. Such a shift would lead to a lowering of standards, necessary research, and development of restoration methods such that restoration failure would likely continue. Chapter 3 assesses the efficiency of the fishing gear, an oyster patent tong, to measure the number of oysters precisely and accurately in a given sample. As it is our chosen gear for monitoring throughout the study period, it was essential to ensure the monitoring gear chosen was sufficient to produce reliable results. Chapter 4 investigated the recruitment signal in the Great Wicomico River, compared it to pre-construction data and determined that the recruitment signal in the river was enhanced, beginning several years post-construction of the sanctuary reefs. The assessment also provided information that suggests the stock-recruitment signal for oysters is strongly influenced by regional weather patterns, with drought conditions significantly enhancing the recruitment signal, even when stock levels are too low to see any distinct pattern between stock and recruitment. Chapter 5 documents the results of all monitoring data from 2006-2019 and, due to this, also serves as my ending discussion. Oyster densities, biomass and shell volume were examined. Results suggest the restored reef network has successfully transitioned to a self-sustaining reef system, with high density and biomass/m2 on the HRR, along with a positive shell budget. LRR lags far behind regarding density and biomass/m2 and does not demonstrate a positive shell budget over time. The HRR is also demonstrating a positive rate of reef height gain relative to local sea level rise. Overall, our data suggest that native oyster restoration can be successful, though novel methods were required to do so.

A growing human population, shifting human dietary habits, and climate change are negatively affecting global ecosystems on a massive scale. Expanding agricultural areas to feed a growing population drives extensive habitat loss, and climate change compounds stresses on both food security and ecosystems. Understanding the negative effects of human diet and climate change on agricultural and natural ecosystems provides a context within which potential technological and behavioral solutions can be proposed to help maximize conservation. The purpose of this research was to (1) examine the potential effects of climate change on the suitability of areas for commercial banana plantations in Latin America in the 2050s and how shifts in growing areas could affect protected areas; (2) test the ability of small unmanned aerial vehicles (UAVs) to map productivity of banana plantations as a potential tool for increasing yields and decreasing future plantation expansions; (3) project the effects on biodiversity of increasing rates of animal product consumption in developing megadiverse countries; and (4) estimate the capacity of global pasture biomass production and Fischer-Tropsch hydrocarbon synthesis (IGCC-FT) processing to meet electricity, gasoline and diesel needs. The results indicate that (1) the overall extent of areas suitable for conventional banana cultivation is predicted to decrease by 19% by 2050 because of a hotter and drier climate, but all current banana exporting countries are predicted to maintain some suitable areas with no effects on protected areas; (2) Spatial patterns of NDVI and ENDVI were significantly positively correlated with several metrics of fruit yield and quality, indicating that UAV systems can be used in banana plantations to map spatial patterns of fruit yield; (3) Livestock production is the single largest driver of habitat loss, and both livestock and feedstock production are increasing in developing biodiverse tropical countries. Reducing global animal product consumption should therefore be at the forefront of strategies aimed at reducing biodiversity loss; (4) Removing livestock from global pasture lands and instead utilizing the biomass production could produce enough energy to meet 100% of the electricity, gasoline, and diesel needs of over 40 countries with extensive grassland ecosystems, primarily in tropical developing countries.

Southern African populations harbour great genetic diversity enhanced by  population migration to the area in the last two millennia. Africa is perhaps the least studied continent in regards to population genetics and is often underrepresented in global studies. Studying sex-biased admixture in admixed populations is a great tool to understand population demographic history as well as sex-biased admixture from past events. Various studies on sex-biased admixture in Southern Africa have shown male sex-biased admixture from the incoming Bantu-speaking populations. One study by Hollfelder (2018) shows female Bantu-speaking sex-biased admixture. Here I will try to determine if ascertainment bias is the cause of the unexpected results in Hollfelder (2018). I will do this by comparing the original results, genotyped using the Illumina Omni 2.5M Array, to overlapping SNPs in two different arrays, the Affymetrix Human Origin Array and the Infinium H3Africa Consortium Array. Additionally, I will use whole genome data containing same individuals and individuals from similar populations to form a hypothesis on how the sex-biased admixture should look like without ascertainment. Then extracting variants from the whole genome data to two array SNP panels, the Illumina 2.5M Array and the Infinium H3Africa Consortium Array. For both parts in my project a method by Goldberg and Rosenberg (2015) will be used to calculate female and male contribution from admixture proportions of the X-chromosome and the autosomes estimated using the software ADMIXTURE. The results obtained could not determine if ascertainment bias was the sole factor skewing the results. The overlap with the Affymetrix Human Origin Array showed results closest to expected results based on previous studies, suggesting that ascertainment bias likely affects the results. The results attained using the whole genome indicated that the genotype calls of individuals present in both parts of the study did not fully match and that was confirmed using a principal component analysis. Unfortunatly the data used and analytical limitations in this project did not yield answers to how ascertainment bias affects calculations on sex-biased admixture. The X-chromosome is difficult to work with, especially when using data from multiple publications, as there is no standard common best-practice pipeline available on how to process the data leading to different data sets having been treated differently, which possibly affects downstream analysis when combining data sets.