Coastal sage scrub (CSS), a lowland plant community native to California, is home to many rare, threatened, or endangered plants and animals. Fire, a natural feature of CSS, is essential for maintaining species diversity. However, the invasion of non-native grasses has altered the fire regime in CSS, increasing fire frequency and fire season length and decreasing fire intensity. Changes in the historical fire regime may in turn cause feedbacks that favor non-native species, resulting in the loss of biodiversity in invaded CSS sites. Numerous studies have examined patterns of post-fire succession in CSS; however, the role that the pre-fire seed bank and the relative abundance of natives to non-natives play in vegetation regrowth and community recovery is unclear. A lack of adequate pre-fire data on community composition makes testing hypotheses about the role of seed banks in post-fire recovery challenging. I propose to study recovery of the plant community in two differentially invaded CSS sites (East and West field) following a fire at the Bernard Field Station in September 2013. Data collected at the two sites from 2009-2013 reveal that non-native grass cover was significantly higher than native cover at both sites, though the West field had slightly higher native forb cover. Furthermore, the invasive grass Bromus diandrus almost entirely dominated the East field. Vegetation cover in the West field was more diverse with the abundance of other non-natives (Bromus hordeaceus, Bromus madritensis, Vulpia myuros) and natives (Amsinckia menziesii, Lupinus spp.) significantly higher than in the East field. To determine the effects of these pre-fire differences on recovery processes, I will carry out a randomized block experiment with four treatments (control, native seed addition, non-native grass removal, and both native seed addition and removal of non-native grasses). Twelve blocks will be evenly divided between the East and West fields. I propose to measure relative seedling abundance for both native and non-native species after each significant rainstorm over a three-year study period. I hypothesize that the composition of seed banks pre-fire will predict vegetation regrowth post-fire. Specifically, I predict that, under control conditions, B. diandrus will dominate the East field post-fire given its high abundance pre-fire. Further, I predict that regrowth in controls plots in the West field will be more variable given its more diverse seed bank pre-fire. Lastly, I predict that native forbs will exhibit the greatest degree of recovery in plots where active restoration methods (seeding and non-native grass removal) are employed; the effects of these restoration methods should be strongest in the East field because the pre-fire vegetation community was more heavily weighed towards non-native species. This study will add crucial knowledge to our understanding of how the pre-fire seed bank in CSS affects its recovery post-fire, which may inform future conservation efforts to ensure the continued health and protection of CSS sites around California.

Bats are ecologically important around the world, partially because they eat insects. They are globally threatened by human activities. The extent of bat populations in South Asia has not been as well-monitored or researched as other parts of the world. Determining the size of a large colonial bat population is difficult, and can be aided through video footage or photographs. This study aimed to determine the population size of Tadarida plicata that inhabit the Gomantong Cave system in Borneo. Images of an evening emergence were used to determine the speed of flight, and then the number of bats to emerge from the cave through particle analysis in ImageJ. The counts, subsequent extrapolation, and comparison to previous estimates of flight speed indicated a population size approximately half the size of previous estimates, emphasizing the importance of continued monitoring. Using ImageJ particle analysis was deemed to be an effective way of estimating the number of bats in large populations.

An organism's body size entails both physiological and ecological costs. Furthermore, as a parameter in analyzing organisms, it represents a fundamental and essential morphometric character. Reductions in size following mass extinction is a commonly observed phenomenon in the fossil record. This study examines the evolutionary significance of this phenomenon termed the: 'Lilliput Effect' by proposing that it represents a rapid evolutionary response to altered selection pressures during a mass extinction. This primary hypothesis is evaluated against two additional hypotheses of size reduction: 1) stunted growth as a response to stressed ecosystems, and/or 2) mass extinctions are size selective. These hypotheses were tested using data from shell size measurements and morphology primarily from molluscs and brachiopods from both North America and Denmark.. Morphological differences were evaluated using Elliptical Fourier Analysis (EFA) of outline shape in conjunction with Principle Components and Canonical Variate Analysis. The first part of this study provides a detailed methodology for data collection and analysis. New methods were developed which display promise in improving the degree to which differences and similarities in shape can be elucidated using EFA. These methods were then employed to test hypotheses of morphological change through minor events of local significance in the Florida Neogene and following the K/Pg mass extinction. Data sources for the K/Pg mass extinction were from high resolution (10 cm intervals) collection of bulk samples from the Brazos River in Texas as well as reposited museum specimens for the Braggs locality in Alabama and Danish samples. Study of size and evolution through more minor local events in the fossil record entailed measurements and shape analysis of left valves of bivalves from the genus Chine. Various environmental changes occurred at variousmpoints during the Neogene in Florida Neogene, most profoundly documented during the Plio-Pleistocene with accompanying faunal turnover. TheChione specimens analyzed were derived from a discontinuous sequence encompassing ~18 Ma and represent material from the Miocene Chipola Formation through to the Recent. The size of Chione increased from the Miocene to the Pliocene and then decreased from the Pliocene into the Pleistocene possibly due to lower primary productivity. The later part of the Pleistocene into the Recent was characterized by increased size relative to the early Pleistocene and size was stable through this interval. Morphologically, Chione changed in shape from the Miocene to the Pliocene, but remained in stasis from the Pliocene to the Recent suggesting that stabilizing selection may work well during periods of rapid, minor, environmental perturbations. There were a number of global changes occurring within the late Maastrichtian pr and the results of size measurements of molluscs demonstrate a decrease in size prior to the K/Pg mass extinction in Texas likely in response to a number of global scale events occurring towards the close of the Cretaceous that was also associated with morphological evolution in the small bivalve Breviarca webbervillensis. Paleocene material from Texas was dominated by smaller, newly evolved allochthonous grazing gastropods. These gastropods are thought to be newly evolved lineages as their first occurrence is marked in the Paleocene. Smaller sized nuculid bivalves were also a prominent feature in the Texas Paleocene and showed a rapid size beginning 40 cm above the boundary clay. At Braggs, Alabama, two groups, gastropods and oysters showed decreases in size across the boundary, and these changes are most likely a product of animpoverished Paleocene ecosystem. The pectinids were the only group of bivalve mollusc to xii reduce in size following extinction in Denmark most likely in response to a reduction in bryozoan substrate which resulted in a very soft coccolith-derived mud substrate in the mass extinction's aftermath. Size measurements from the Danish brachiopods showed reductions in size across the boundary in all genera except Rugia. There was a marked size reduction in specimens from the upper Maastrichtian at Stevns Klint as compared to the lower Maastrichtian at Mons Klint. The reasons for this are most likely due to lower temperatures at Stevns based on isotope data as well as lower productivity evidenced by lower δ13C values. There was a change in morphology for Terebratulina chrysalis in the earliest Paleogene due to shifted selective pressures favoring increased surface area as an adaptation to softer substrates. Size reduction within Danish sequences is evolutionary in nature as the Danian is characterized by different species within existing Maastrichtian genera and two new genera. The results of this study demonstrate that changes in body size can be a result of evolution from changing selective pressures as well as ecological perturbations. Distinguishing evolutionary forcings from ecological requires the collection and understanding of morphological data. Changes in size for Terebratulina chrysalis could have easily been interpreted as ecological were it not for morphological results showing the changes in surface area resulting from changing selective pressure. Late Cretaceous changes in climate and sea level produced observable changes in size and morphology in Breviarca webbervillensis. Potential size selectivity of the K/Pg mass extinction failed to account for any of the patterns observed in the data. Gryphaeid oysters in Denmark would have been a perfect candidate to support conclusions of size selectivity as they were the largest molluscs measured in this study and survived mass extinction.

Because nitrogen isotopes are fractionated along the soil-plant-insect-bat-guano pathway, it may be possible to reconstruct environmental and climatic changes reflected in the nitrogen isotopic composition of guano. A 1.5-m core of bat guano from Zidită Cave (western Romania) provides a record of climatic and anthropogenic influence on the regional nitrogen cycle and paleoenvironmental controls on nitrogen transforming processes. Increasing and decreasing trends of nitrogen isotopic composition (δ15N values) correspond well with changes in the influence of farming practices, deforestation, and forest expansion. These influences likely had a significant effect on the openness of the nitrogen cycle, resulting in changes in δ15N values of soil, plants, and ultimately guano. While δ15N values have gradually decreased since AD 1700, decadal trends towards more positive values at AD 1840 and 1920 coincide with increases in tree pollen (forest recovery). Additionally, the accumulation of relatively15N-depleted guano coincides with periods of increased fire frequency, deforestation, and crop/herbaceous pollen (agricultural practices). δ13C record of bulk guano indicates that carbon isotopic variation results from changes in water availability. Comparison of δ13C to δ15N indicates that there is a significant correlation between nitrogen and carbon isotopic composition of guano. When water availability was high (low δ13C values), δ15N values of bulk guano trend towards higher values. Although this connection to climate is the opposite of the findings from previous work correlating δ15N values of plant foliage and precipitation amount, the relationship between nitrogen isotopic values and water availability still appears to have merit. Based on these findings, δ15N of guano appears to be a signal for changes in N cycling of the Mada region that occurs, primarily in response to the precipitation received, further modified by intense changes in anthropogenic activity.

Mollusk shells contain proteins within and between the crystals of calcium carbonate. These organic molecules play an important role in biomineralization and shell function, and their stable isotope ratios of carbon and nitrogen are also thought to record important ecological information about the animal's diet and nutrient sources. These proteins can be preserved for millions of years, offering potential insight into pre-anthropogenic ecological conditions. However, shell organics in older shells are typically recovered in reduced abundances due to leaching and remaining organics are often converted from insoluble proteins to soluble, free amino acids, making them difficult to detect and recover. Therefore, demineralization and organics-capture methods must be optimized for yield to extract much-needed ecological information from older shells. This project compared insoluble and soluble organic yields of modern gastropod Strombus alatus shells demineralized with acids of varying concentrations and temperatures. Results suggested that demineralizing shell fragments with 0.1 M HCl at a ratio of 0.9 L HCl/g of shell was optimal. Average percent organic yields ~0.2% for modern and ~0.06% for fossil Strombus spp. Future applications of this work include using this refined method to reconstruct food webs across broad temporal scales.

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.

Torrecillas Lagoon in the North Coast of Puerto Rico has experienced extensive anthropogenic influence over the past 400 years. Elevated concentrations of Potential Toxic Elements (PTEs) have been reported in surficial sediments. The main goal of this dissertation was to implement in Puerto Rico the use of benthic foraminifers as a bioindicators of PTEs and to compare the impact of Cu(II) on field samples with results of experimental work using cultures. Analyses included geochemical assessment for bulk and carbonate- soluble bioavailable concentrations of PTEs in surface, core and pore-water samples, as well as analyses of grain-size, Percent Total Organic Carbon (%TOC), Percent Carbonate (%CO3), foraminiferal assemblages and distribution, and ecological indices. PTEs of concern (Cu, Zn, Ni, Pb, Cr, As, Li, Se, Fe, Mn, V, Se) have relatively uniform spatial distributions. Areas with higher concentrations are associated with higher %TOC and %mud, as well as with anoxic conditions. Temporal distributions show limited variability although an overall decrease in enrichment indicates improvement of environmental conditions in the 20th century. Ammonia beccarii, Quinquloculina rhodiensis, Q. seminulum, and Ammobaculites agglutinans are the dominant foraminifers in the lagoon and are characteristic of stressed coastal environments. Several PTEs, including bioavailable Cu and Zn are negatively correlated with the dominant foraminiferal taxa and with diversity indices, indicating that these pollutants are influencing the spatial and temporal distributions of foraminiferal assemblages. Ammonia beccarii abundance negatively correlates with bulk concentration of Cu(II) and exhibits no correlation with its bioavailable fraction. These observations suggest that fractionation and bioavailability of PTEs need to be considered more in depth as influences on ecological indices and foraminiferal behavior. Exchangeable and oxidizable fractions are considered the most likely to influence the ecology of foraminifers under most circumstances. Ammonia aomoriensi was exposed to Cu(II) concentrations (0–0.32 µmol/L) under controlled conditions (25ºC, 35PSU and pH= 7.8). After a 23-day treatment, foraminifers exposed to 0.22 and 0.32 µmol/L concentrations exhibited reduced growth and morphological deformities in which the long axis of the chamber extended ventrally, increasing the height of the trochospire. The waters in Torrecillas lagoon show strong stratification, with hypoxic/anoxic (DO/L) and corrosive (pH< 7.4) conditions below 4 m depth. The presence of such strong gradients in very shallow water represents a dynamic chemical environment, with changes occurring on day-night cycles, tidal cycles, and especially with storm activity that induces mixing of otherwise highly stratified, very localized waters. Recognizing the potential for sequestered PTEs to be mobilized is essential insight for coastal management agencies that must assess the risks of existing PTEs during coastal engineering activities (e.g., dredge and fill activities) and major storm events.

The regular occurrence of hurricane-associated winds has been an important factor in shaping the structure and composition of the forest ecosystems of the Florida Everglades. Forest communities in the Everglades are adapted to hurricane disturbances, but increased frequency and/or intensity of hurricanes may lead to decline or even collapse of these communities. The overall objective of this project is to understand the patterns, pace, and mechanisms of the recovery process to Hurricane Andrew damage in four Everglade forest communities: pinelands, hardwood hammocks, bayhead tree islands, and cypress domes. This study combines long- and short-term field measurements and experimental garden studies to determine how the four woody plant community types recover from hurricane impacts. Most of the community types were adversely affected by storm damage in the short-term (3 years post-hurricane) through altered growth rates and canopy defoliation, however these effects were relatively short lived and were not visible in shifts in species composition after the long-term (20 year) recovery period. Only in the most diverse communities over the long-term there was a delayed mortality in damaged individuals that drove a diversity loss. This loss was not present over the short-term recovery time period. Using individual damage extent and short-term recovery growth rates, I developed a simplified model that accurately predicted surviving individual stem size over long-term recovery periods of Taxodium distichum within cypress domes and select hardwood hammock species. The shadehouse experiments demonstrated the importance of nutrient availability to growth of seedlings of canopy dominants. Recruits of these species responded to changing environmental conditions associated with storm impact through a variety of strategies in accordance with their adaptive traits. Synergistically, the combined parts of this dissertation demonstrate directional community and species-specific shifts that vary over time scales. Storm impacts have the potential to alter community composition and diversity within impacted systems, and in particular the Everglades ecosystem.

Invasive species have caused billions of dollars in damages to their introduced environment through direct effects on wildlife and by altering their introduced habitats. For a species to be considered invasive, it must successfully navigate the stages of invasion: it must be introduced, become established, spread, and have a quantifiable impact on its introduced environment. The numbers of introductions and individuals released affects the genetic diversity of nonnative populations which, in turn, can affect their invasion success. The Mayan Cichlid (Cichlasoma urophthalmus) is endemic to the Atlantic coast of Mexico and Central America. It was first detected in the United States in 1983 in Everglades National Park. Since then, it has spread across more than 70,000 hectares throughout southern and central Florida. I have established the Mayan Cichlid to be a successful invader in Florida by quantifying per capita negative impacts of Mayan Cichlids on densities of Sheepshead Minnow (Cyprinodon variegatus), Marsh Killifish (Fundulus confluentus), and Eastern Mosquitofish (Gambusia holbrooki) over a 15-year period. I also analyzed the role of genetics in the invasion success of the Mayan Cichlid. I used a mitochondrial gene, cytochrome b, and 17 microsatellite loci to identify the sources for the Mayan Cichlid introduction into Florida. Cytochrome b data supported an introduction from Guatemala; microsatellite data suggested movement of Mayan Cichlids from the upper Yucatán Peninsula to Guatemala and introductions from Guatemala and Belize to Florida. I also found evidence of cytonuclear disequilibrium together with low genetic diversity within the Florida population which indicate a population bottleneck and admixture between two distinct lineages upon introduction, followed by rapid spread resulting in a panmictic population genetically distinct from the native range populations. I found much less genetic structure and a weaker correlation between genetic diversity and geographic distance within Florida compared with Mexico and Central America. Low number of effective alleles, heterozygosities, and FST values and the genetic similarity of Florida sites also indicate an admixed population or one that has rapidly expanded from a small initial group.

With the ever-increasing human population, more people reside in urban areas than ever before; this is having marked effects on the landscape and in turn, wildlife. This study uses automatically triggered wildlife cameras to assess the distribution of three carnivore species (coyotes, Canis latrans; red foxes, Vulpes vulpes; and gray foxes, Urocyon cinereoargenteus) around the Pioneer Valley of Massachusetts in relation to a gradient of human development. Cameras were placed at 141 locations within the 320-km2 study area over the course of three field seasons (3,052 trap nights). Relative abundances for fourteen other species and site characteristics (e.g., elevation, forest cover type, distance to urban edge) for each camera location were determined to develop a generalized linear model for the distribution of each species across the study area. Coyote distribution was most affected by the relative abundances of their prey species and not by landscape characteristics or sympatric carnivore species. Coyotes are the top predator in the area and therefore their distribution is correlated with the relative abundances of their prey species, unlike other parts of their range where they are controlled by larger carnivores. Red and gray foxes both had negative relationships with the relative abundance of coyotes as coyotes have been shown to adversely impact fox distributions and access to resources. Both red and gray foxes were also negatively or uncorrelated with increased levels of urbanization, which is both supported and refuted by published literature and is likely system specific.