Browsing by Department "Ecology"

This study seeks to investigate the dynamics of dead plant carbon over fifty years of old-field forest development at the Calhoun Long Term Soil-Ecosystem Experiment (LTSE) in South Carolina, USA. Emphasis is on the transition phase of the forest, which is less well studied than the establishment and early thinning phase or the steady state phase. At the Calhoun LTSE, the biogeochemical and ecosystem changes associated with old field forest development have been documented through repeated tree measurements and deep soil sampling, and archiving of those soils, which now allow us to examine changes that have occurred over the course of forest development to date.

In this dissertation, I first quantify the accumulation of woody detritus on the surface of the soil as well as in the soil profile over fifty years, and estimate the mean residence times of that detrital carbon storage. Knowing that large accumulations of C-rich organic matter have piled onto the soil surface, the latter chapters of my dissertation investigate how that forest-derived organic carbon has been incorporated into mineral soils. I do this first by examining concentrations of dissolved organic carbon and other constituents in soil solutions throughout the ecosystem profile and then by quantifying changes in solid state soil carbon quantity and quality, both in bulk soils and in soil fractions that are thought to have different C sources, stabilities, and residence times. To conclude this dissertation, I present the 50-year C budget of the Calhoun LTSE, including live and dead plant carbon pools, to quantify the increasing importance of detrital C to the ecosystem over time.

This exceptional long term soil ecosystem study shows that 50 years of pine forest development on a former cotton field have not increased mineral soil carbon storage. Tree biomass accumulated rapidly from the time seedlings were planted through the establishment phase, followed by accumulations of leaf litter and woody detritus. Large quantities of dissolved organic carbon leached from the O-horizons into mineral soils. The response of mineral soil C stocks to this flood of C inputs varied by depth. The most surficial soil (0-7.5cm), saw a large, but lagged, increase in soil organic carbon (SOC) concentration over time, an accumulation almost entirely due to an increase of light fraction, particulate organic matter. Yet in the deepest soils sampled, soil carbon content declined over time, and in fact the loss of SOC in deep soils was sufficient to negate all of the C gains in shallower soils. This deep soil organic matter was apparently lost from a poorly understood, exchangeable pool of SOM. This loss of deep SOC, and lack of change in total SOC, flies in the face of the general understanding of field to forest conversions resulting in net increases in soil carbon. These long term observations provide evidence that the loss of soil carbon was due to priming of SOM decomposition by enhanced transpiration, C inputs, and N demand by the growing trees. These results suggest that large accumulations of carbon aboveground do not guarantee similar changes below.

Infusing models for animal movement with more behavioral realism has been a goal of movement ecologists for several years. As ecologists have begun to collect more and more data on animal distribution and abundance, a clear need has arisen for more sophisticated analysis. Such analysis could include more realistic movement behavior, more information on the organism-environment interaction, and more ways to separate observation error from process error. Because landscape ecologists and behavioral ecologists typically study these same themes at very different scales, it has been proposed that their union could be productive for all (Lima and Zollner, 1996).

By understanding how animals interact with their land- and seascapes, we can better understand how species partition up resources are large spatial scales. Accordingly I begin this dissertation with a large spatial scale analysis of distribution data for marine mammals from Nova Scotia through the Gulf of Mexico. I analyzed these data in three separate regions, and in the two data-rich regions, find compelling separation between the different communities. In the northernmost region, this separation is broadly along diet based partitions. This research provides a baseline for future study of marine mammal systems, and more importantly highlights several gaps in current data collections.

In the last 6 years several movement ecologists have begun to imbue sophisticated statistical analyses with increasing amounts of movement behavior. This has changed the way movement ecologists think about movement data and movement processes. In this dissertation I focus my research on continuing this trend. I reviewed the state of movement modeling and then proposed a new Bayesian movement model that builds on three questions of: behavior; organism-environment interaction; and process-based inference with noisy data.

Application of this model to two different datasets, migrating right whales in the NW Atlantic, and foraging monk seals in the Northwest Hawaiian Islands, provides for the first time estimates of how moving animals make choices about the suitability of patches within their perceptual range. By estimating parameters governing this suitability I provide right whale managers a clear depiction of the gaps in their protection in this vulnerable and understudied migratory corridor. For monk seals I provide a behaviorally based view into how animals in different colonies and age and sex groups move throughout their range. This information is crucial for managers who translocate individuals to new habitat as it provides them a quantitative glimpse of how members of certain groups perceive their landscape.

This model provides critical information about the behaviorally based movement choices animals make. Results can be used to understand the ecology of these patterns, and can be used to help inform conservation actions. Finally this modeling framework provides a way to unite fields of movement ecology and graph theory.

Manatees (Mammalia: Sirenia), along with the closely related dugongs, are the only herbivorous marine mammals. Manatees consume a wide variety of vascular plants and algae in both marine and freshwater habitats. However, little is known about what characteristics influence diet and food selectivity, especially in freshwater habitats, which represent a large portion of the available habitat for the endangered Antillean manatee, Trichechus manatus manatus, in Central and South America. Understanding foraging ecology is an important element of effective conservation strategies.

This dissertation investigated various aspects of the foraging ecology of the Antillean manatee in a freshwater habitat, specifically: 1) how plant availability (i.e. species richness, diversity, and abundance) varied seasonally with changes in water depths, 2) manatee food selectivity from a representative set of plant species from that freshwater habitat, and 3) the relationship of plant nutritive compounds and availability with manatee food selectivity. In addition, this dissertation describes the multiple uses of sonar technology for studying manatees and habitat characteristics in freshwater.

Plant availability to manatees was evaluated by conducting monthly plant surveys from July 2010-July 2011 in four contact lakes in the wetlands of Tabasco, Mexico. Manatee food selectivity was examined by conducting food selection experiments on a wild adult manatee during the low water season with 54 plant species representing 25+ genera. The nutritive components (i.e. crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HC), and ash) and plant availability values for selected and non-selected plants species were evaluated to determine their relationship with manatee food selectivity. The applicability of using side-scan sonar for manatee research was tested in various freshwater and estuarine habitats in Honduras, Costa Rica, Panama, and the wetlands of Tabasco, Mexico between 2006-2011.

The major findings of this dissertation are as follows. Plant species richness, diversity, and abundance were greatest during the rising water season (July-August) and lowest during the low water season (March-June). No plants were available in April-June, which represented the majority of the low water season. The wild manatee

selected 27 (11+ genera) of the 54 species examined during the feeding experiments. Of the plant characteristics tested (i.e. nutritive components and plant availability), only digestible fiber (HC) was significantly related to manatee food selection, with manatees

selecting plants with higher HC content. Four unique applications were identified for the use of side-scan sonar to facilitate manatee research in freshwater habitats: 1) confirmation of visual sightings and determination of group size, 2) determination of mother-calf pairs, 3) habitat characterization, and 4) assisting manatee captures.

Results from this study reveal that manatees living in the freshwater wetlands of Tabasco, Mexico have to cope with a highly seasonal availability of plants and that while manatees consume plants from a wide variety of genera, they are highly selective. Unlike other herbivorous mammals, manatee food selectivity was not influenced by CP, NDF, or ADF, but rather by digestible fiber. A unique suit of anatomical and physiological characteristics suggests that manatees may be fiber digestion specialists. Both seasonal plant availability and the manatee's large dietary breadth must be considered when developing 1) conservation strategies for wild manatees in freshwater habitats and 2) protocols for captive rehabilitation of orphaned and stranded manatees that will be reintroduced into the wild.

This dissertation consists of four chapters. The first three chapters examine protected areas (or parks) from multiple perspectives. Parks are the first, and often only, line of defense in efforts to conserve biodiversity. Understanding of their promise and problems is necessary to achieve conservation outcomes. Chapter One determines vegetation patterns in and around parks of differing management categories across the Amazon, Congo, South American Atlantic Coast, and West African forests. Within these forests, protected areas are the principle defense against forest loss and species extinctions. In the Amazon and Congo, parks are generally large and retain high levels of forest cover, as do their surroundings. In contrast, parks in the Atlantic Coast forest and West Africa show sharp boundaries in forest cover at their edges. This effective protection of forest cover is partially offset by their very small size: little area is deep inside park boundaries. Compared to West Africa, areas outside parks in the Atlantic Coast forest are unusually fragmented.

Chapter Two addresses a human dimension of protected areas. Given certain characteristics, parks areas may either attract or repel human settlement. Disproportionate increases in population growth near park boundaries may threaten their ability to conserve biodiversity. Using decadal population datasets, we analyze population growth across 45 countries and 304 parks. We find no evidence for population growth near parks to be greater than growth of rural areas in the same country. Furthermore, we argue that what growth does occur near parks likely results from a general expansion of nearby population centers. Parks may experience unusual population pressures near their edges; indeed, individual case studies provide examples. There is no evidence, however, of a general pattern of disproportionate population growth near their boundaries.

Chapter Three provides a review of common approaches to evaluating protection's impact on deforestation, identifies three hurdles to empirical evaluation, and notes that matching techniques from economic impact evaluation address those hurdles. The central hurdle derives from the fact that protected areas are distributed non-randomly across landscapes. Matching controls for landscape characteristics when inferring the impact of protection. Applications of matching have revealed considerably lower impact estimates of forest protection than produced by other methods. These results indicate the importance of variation across locations in how much impact protection could possibly have on rates of deforestation.

Chapter Four departs from the focus of protected areas and instead addresses a more theoretical aspect of community ecology. Ecological theories suggest that food webs might consist of groups of species forming blocks, compartments or guilds. Chapter Four considers ecological networks (subsets of complete food webs) involving species at adjacent trophic levels. Reciprocal specializations occur when (say) a pollinator (or group of pollinators) specializes on a particular flower species (or group of such species) and vice versa. We characterize the level of reciprocal specialization for various classes of networks. Our analyses include both antagonistic interactions (particularly parasitoids and their hosts), and mutualistic ones (such as insects and the flowers that they pollinate). We also examine whether trophic patterns might be palimpsests. That is, there might be reciprocal specialization within taxonomically related species within a network, but these might be obscured when these relationships are combined. Reciprocal specializations are rare in all these systems even when tested using the most conservative null model.

Phenology, the timing of biological events across the year, is shifting in response to climate change. Not all species within a community are responding to the same environmental cues by shifting their phenology to the same degree. As a consequence, the strength and direction of species’ interactions are also undergoing rapid changes. In this dissertation, I used observations, experiments, and demographic modeling to explore the relationship between climate, phenology, and species interactions in one terrestrial and one aquatic field system. With these two systems, I attempted to answer the central question, “What are the environmental drivers and ecological consequences of phenological shifts?”

In chapter two, I examined how co-flowering subalpine spring ephemerals (Claytonia lanceolata, Mertensia brevistyla, and Mertensia fusiformis) in the Colorado Rocky Mountains, USA compete with and facilitate one another for biotic and abiotic resources. These flowering species were the first to emerge and flower shortly after snowmelt. As a result of phenological shifts, these species showed greater temporal overlap under early snowmelt conditions. Using field experiments, I found that these species did not facilitate one another or compete for pollinator resources, but they did affect each other’s vital rates in two years.

In chapter three, I simulated how the presence of neighbors, including all heterospecific neighbors, affected population growth of Claytonia and Mertensia under future predictions of spring snowmelt date. I used data from field experiments to parameterize integral projection models and forecast population growth into the future. I found that neighbors significantly influenced population growth rate under average snowmelt conditions, but not under early snowmelt conditions. Under future predictions of early snowmelt, populations declined rapidly regardless of neighbor presence.

In chapter four, I worked with the Northeast Climate Adaptation Science Center to determine the environmental drivers of alewife (Alosa pseudoharengus) migration in Massachusetts. First, I used field-collected daily fish counts to assess how the timing of migration has changed. I found that some of the streams showed significant advances in run timing, while others did not. Second, I combined migration timing metrics with publicly available climate data. I found that shorter, wetter winters and mild spring temperatures were correlated with earlier run initiation dates.

Collectively, my research from subalpine meadows and coastal streams revealed three significant conclusions. First, the temporal variability in the strength and direction of species interactions may be important for predicting future coexistence. Second, unequal phenological shifts between members of a community may not only impede coexistence, but could facilitate coexistence in the future through positive effects on population growth. Finally, experiments mechanistically linking phenology and species interactions are necessary for understanding implications of phenology on coexistence.

Unprecedented rates of warming and an inability to curtail greenhouse gas production

has fueled the discussion of how to mitigate climatic impacts. Climate impacts

on forests are coarsely understood. A large number of interacting environmental

variables affect every aspect of forest life cycles, and studies incorporating local

factors are scarce. For this study, a large manipulative climate experiment in both

northern(Massachusetts) and southern(North Carolina) sites was used to examine the

effect of climate change on demographic and physiological rates of 11 tree species

representative of the Eastern Deciduous Forest.

First, to clarify how environmental conditions of the next century will alter

seedling carbon assimilation, a hierarchical multivariate model that synthesizes over

16,000 instantaneous carbon exchange measurements from 285 trees of four species

was developed. Estimates of species-level light response curve parameters were used

to predict individual-level seasonal carbon budgets. This model revealed how the

balance between respiration and photosynthesis shifts with temperature, moisture,

and overstory canopy status. Furthermore, it showed that elevated temperatures

(3C and 5C) shift the seasonal species carbon budget allowing some Lirodendron

tulipifera to grow as much a 5.5 times more massive in elevated temperatures.

In addition, for certain species, demographic rates of seedlings can be scaled to

above-ground growth using short-term physiological responses.

Second, the relationship between seedling size and water-use was examined.

Trees grow from environmentally sensitive seedlings to large canopy individuals

capable of buffering environmental stress. At some intermediate size, a threshold is reached

where greater resilience results when increased resource gain overcomes the added

costs of size. For two seasons of this manipulative warming experiment, 123 external

heat pulse sapflow sensors were applied to 4 species (Acer rubrum, Lirodendron tulipifera,

Quercus alba, and Quercus rubra). The experimental seedlings, which vary in

mass from less than a tenth of a gram to 41 grams, were included to demonstrate

that both size and species influence water use. While larger size leads to increased

transpiration, reduced soil moisture paired with larger size leads to unpredictable

reductions in sapflow. Small seedlings were predictably reactive, but large seedlings

were both the least and most reactive to soil moisture reductions. When soil moisture

improved, after periods of moisture limitations, small individuals quickly recovered

and large individuals to a lesser extent. These results suggest that the seedlings of

this experiment were not consistently big enough to gain an advantage in water-use

like their larger canopy counter parts.

Lastly, this climate-warming experiment was expanded to include 4000 seedlings

of 11 total species across both the northern and southern sites. High-resolution subannual

growth measurements and a hierarchal Bayesian state-space model provided

a more accurate picture of seedling growth responses to sub-annual climatic variation,

by focusing on determinate vs. indeterminate growers and the interactions

between growth phenology, temperature tolerances, and climatic shifts. Determinate

species enhanced annual growth by shifting growth earlier in the season when

temperatures were more suitable, avoiding hot and dry conditions of summer. Indeterminate

species annual growth, which is focused within the summer, is dependent

on their ability to maintain growth during increasingly warmer and dryer summers.

Co-occurring species may respond differently and competitive regimes are shifted by

how growth phenology aligns with the seasonal patterns of climate change.

Questions of forest responses to climate change are multi-scaled. Responses depend

on local conditions, life-stage, natural history, and the scale of inference. Climate

change does not occur in isolation all factors must be weighed when evaluating

a response. For this study a manipulative climate experiment was used to address

these questions and investigate the effect of climate change on trees of the Eastern

Deciduous Forest.

Coastal plain ponds are an understudied and threatened wetland ecosystem with many unique environmental attributes. Research in these ponds can investigate species-environment relationships, while simultaneously providing ecosystem-specific information crucial to their continued conservation and management. This dissertation explores patterns in coastal plain pond vegetation composition and species-environment relationships across space, through time, and in the seed bank and standing vegetation.

In a two-year field study at 18 coastal plain ponds across the island of Martha's Vineyard, Massachusetts, I investigated species-environment relationships within and among ponds. I identified vegetation species presences and abundances within 1 m2 quadrats, which ran continuously along transects established perpendicular to the water's edge. Species data were analyzed against local and landscape-scale environmental data. I also conducted a one-year seed bank study in which sediments from four coastal plain ponds were incubated in growth chambers and composition was compared to the standing vegetation. One hundred and thirty-four plant species were identified during vegetation sampling and 38 species were identified from incubated sediments.

I found significant compositional change across space in response to environmental gradients, with patterns in species composition occurring at both local and landscape scales. Elevation was the only local factor strongly correlated with species composition. Significant landscape-scale environmental factors included surficial geology and pond water salinity. Species composition was significantly correlated with hydrologic regime in 2005 but not in 2006. Overall patterns in vegetation species composition and abundance were more closely related to landscape-scale environmental variables than to local environmental variables.

I also found that coastal plain ponds undergo significant compositional change from one year to the next. Interannual variability disproportionately affected certain ponds and quadrats more than others, highlighting patterns in the relationships between compositional change and environmental attributes. Specifically, ephemeral ponds, ponds located on the moraine, ponds with high specific conductance values, and quadrats located closer to the waterline exhibited greater compositional change from 2005 to 2006 than permanent ponds, ponds located on the outwash plain, ponds with low specific conductance values, and quadrats located further from the waterline.

Finally, I found that coastal plain ponds exhibit a low degree of similarity between composition in sediments and standing vegetation. More species were identified in the standing vegetation than in the seed bank, and in most cases average species richness per quadrat was higher in the standing vegetation than in the seed bank. Seed bank and standing vegetation samples from ponds with different surficial geology were compositionally distinct. Seed bank samples from permanent and ephemeral ponds were compositionally distinct whereas standing vegetation samples were not.

Rivers interact with their valleys from headwaters to mouth, but nowhere as dynamically as in their floodplains. Rivers deliver water, sediments, and solutes onto the floodplain land surface, and the land in turn supplies solutes, leaves, and woody debris to the channel. These reciprocal exchanges maintain both aquatic and terrestrial biodiversity and productivity. In this dissertation I examine river-floodplain exchanges on the well-studied Nyack Floodplain, a dynamic, gravel-bedded floodplain along the Middle Fork Flathead River in the mountains of northwest Montana. I quantify exchanges at multiple timescales, from moments to centuries, to better understand how connectivity between aquatic and terrestrial habitats shapes their ecology.

I first address connectivity in the context of a long-standing question in ecosystem ecology: What determines the rate of ecosystem development during primary succession? Rivers have an immediate effect on floodplains when scouring floods remove vegetation and nutrients such as nitrogen (N) and leave only barren soils, but they might also affect the ensuing primary succession through the gradual delivery of N and other materials to floodplain soils. I quantify N inputs to successional floodplain forest soils of the Nyack Floodplain and find that sediment deposition by river flood water is the dominant source of N to soils, with lesser contributions from dissolved N in the river, biological N fixation, and atmospheric deposition. I also synthesize published rates of soil N accumulation in floodplain and non-floodplain primary-successional systems around the world, and I find that western floodplains often accumulate soil N faster than non-floodplain primary successional systems. My results collectively point to the importance of riverine N inputs in accelerating ecosystem development during floodplain primary succession.

I next investigate the role of river-floodplain exchanges in shaping the spatial distribution of a suite of soil properties. Even after flood waters have receded, dissolved N, carbon (C), and moisture could be delivered from the river to floodplain soils via belowground water flow. Alternatively, C inputs and N withdrawals by floodplain vegetation might be a dominant influence on soil properties. To test these hypotheses, I excavated and sampled soil pits from the soil surface to the water table (50-270 cm) under forests, meadows, and gravel bars of the Nyack Floodplain. Near-surface soils had C and N pools and N flux rates that varied predictably with vegetation cover, but soil properties below ~50 cm reflected influence by neither vegetation cover nor aquifer delivery. Instead, soil properties at these depths appear to relate to soil texture, which in turn is structured by the river's erosional and depositional activities. This finding suggests the revised hypothesis that soil properties in gravel-bedded alluvial floodplains may depend more on the decadal-scale geomorphic influences of floods than on short-term vertical interactions with floodplain vegetation or aquifer water.

Lastly, I explore the potential sources of organic C to the diverse and active community of aquatic organisms in the floodplain aquifer, where the lack of light prohibits in-situ organic C production by photosynthesis. I quantify floodplain carbon pools and the fluxes of organic carbon connecting the aquifer, river, and overlying forest. Spring flood waters infiltrating the soil are responsible for the largest dissolved carbon flux into the aquifer, while very large floods are essential for the other major C input, the burial of woody carbon in the aquifer. These findings emphasize the importance of a dynamic river hydrograph - in particular, annual floods and extreme annual floods - in delivering organic C to the aquifer community.

Overall, this dissertation draws our attention not just to the current exchanges of C, N, water, and sediment but to the episodic nature of those exchanges. To fully understand floodplain ecosystems, we have to consider not just present-day interactions but also the legacies of past floods and their roles in delivering solutes, eroding forests, depositing sediments, and physically shaping the floodplain environment.

Climate change is expected to increase climate variability over much of the world, including the timing and magnitude of weather events such as droughts and heat waves. Although ecologists have made great strides in quantifying how climate conditions at annual or longer timescales regulate populations and communities, the role of individual weather events and intra-annual variability is still relatively unknown. In this dissertation I seek to quantify how the Chihuahuan desert summer annual plant community responds to intra-annual variability, and in doing so better understand how biodiversity is maintained in this community and how this community may respond to climate change.

In chapter one, I present a general approach to quantify how plants respond to short-term variability. Using this approach, I find that species in this community show an environmentally dependent life history tradeoff between growth in wet conditions and survival in dry conditions. This tradeoff could have important implications for both species coexistence and responses to climate change, as I show in chapters two and three.

In chapter two, I seek to understand how a diverse community of annual plants is maintained in an environment with a single primary limiting resource, water. I show that the tradeoffs found in chapter one and environmental variability lead to conditions in which each life history is favored. The differences in life history are explained in part by tradeoffs in balancing carbon uptake and water use.

In chapter three I forecast how this community of annual plants may respond to climate change. I find that while increasing variability is likely to lead to reduced growth, survival, and reproduction in almost all species, it favors species with slower growth in wet conditions but and high survival in dry condition which do comparatively better in increasingly variable conditions.

Few areas of the planet are untouched by human actions, be they marine or terrestrial. Marine habitats face disturbance from overexploitation of fisheries and pollution while terrestrial habitats face significant threat from land cover conversion and degradation. To address these threats, conservationists utilize a variety of population viability analyses to both assess and manage species’ health. The results of these analyses often play a key role in determining when intervention is necessary and which actions will be the most successful. Within this dissertation, I used several population modeling approaches to advance our understanding of changes in the landscape on the persistence of populations and by extension, species.

This dissertation may be broadly divided into two halves, the first assessing a single, local population and the second evaluating metapopulations. In Chapter 2, I combined telemetry data on sooty terns (Onychoprion fuscatus) with a long-term capture-mark-recapture dataset from the Dry Tortugas National Park to map the movements at sea for this species, calculate estimates of mortality, and investigate the impact of hurricanes on a migratory seabird. Included in the latter analysis is information on the locations of recovered bands from deceased individuals wrecked by tropical storms. I present the first known map of sooty tern migration in the Atlantic Ocean. The results indicate that the birds had minor overlaps with areas affected by the major 2010 oil spill and a major shrimp fishery. Indices of hurricane strength and occurrence are positively correlated with annual mortality and indices of numbers of wrecked birds. As climate change may lead to an increase in severity and frequency of major hurricanes, this may pose a long-term problem for this colony.

In the latter half of this dissertation, I utilized a variety of metapopulation analyses for conservation at multiple scales. As a landscape becomes increasingly fragmented through habitat loss, the individual patches become smaller and more isolated and thus less likely to sustain a local population. Metapopulation theory is appropriate for analyzing fragmented landscapes because it combines empirical landscapes features with species-specific information to produce direct information on population extinction risks. Combining a spatially explicit metapopulation model with empirical data on endemic species’ ranges and maps of habitat cover, I could calculate the metapopulation capacity— a measure of a landscape’s ability to sustain a metapopulation.

Mangroves provide an ideal, model landscape for my analysis in Chapter 3. Of conservation concern, one can easily delineate their patch boundaries. I calculated metapopulation capacity for 99 metapopulations from 32 different mangrove-endemic bird species globally in the years 2000 and 2015. Northern Australia and South East Asia have the highest richness of mangrove-endemic birds, with some hotspots also occurring in Guyana and French Guiana. The areas with the highest metapopulation loss are the Caribbean, the Pacific coast of Central America, Madagascar, Borneo, and isolated patches in Southeast Asia in Burma and Malaysia. Regions with the highest loss of habitat area are not necessarily those with the highest loss of metapopulation capacity. Often it is not a matter of how much, but how the habitat is lost since fragmentation of patches has a complicated relationship with extinction risk.

After analyzing the effects of habitat loss and fragmentation on a species’ risk of extinction, it is natural to examine the reverse, the restoration of habitat. In Chapter 4, I used metapopulation models to prioritize locations for potential habitat corridors. I compared these results to standard connectivity models that have grown in popularity to illustrate how together they provide a more complete set of recommendations for the recovery of species. For this chapter, I use the golden lion tamarin (Leontopithecus rosalia) as the focal species. Endemic to the highly fragmented Atlantic coastal forest of Brazil, the golden lion tamarins are a highly studied species of top conservation concern. I identified the best locations for habitat restoration to increase metapopulation capacity and how they compare with movement of individuals in the current landscape. I also evaluated how a previous corridor restoration ranked according to these methods and how it effects future conservation planning. While large, occupied patches are significant for both sets of models, metapopulation models also indicate the importance of nearby, medium-sized empty patches that if connected by a corridor would facilitate the growth and recovery of tamarin populations.

In summary, I applied a suite of population modeling techniques to an assortment of landscapes and species for conserving biodiversity. Despite the variety of models used, I illustrate the flexibility and utility of population ecology to conservation management.

Uptake and storage of carbon by forest ecosystems continues to be a major research topic needed for the quantification of global budgets in an increasing atmospheric carbon dioxide environment. However, there are considerable challenges in quantifying carbon budgets of forest across a wide range of spatial and temporal scales. Although general trends in the components of carbon budgets emerge when analyzed over large spatial or temporal scales, these relationships tend to weaken, or even reverse, at smaller spatial (e.g. stand level) and temporal scales. On the other hand, continuous measuring and monitoring is not a feasible or sensible approach for the range of global forests. There is growing need to identify the key variables that drive variability in these localized budgets at multiple time scales. These results will assist in upscaling stand-level observations into large-scale modeling approaches.

Forest carbon dynamics are closely-coupled with the hydrologic cycle, so an approach that attempts to bridge these dynamics must incorporate water availability and use. Water is necessary for trees to transport nutrients, maintain cellular function, and regulate stomatal conductance; however, water is also related to other biological processes, including microbial decomposition of soil carbon, and physiologically-important abiotic factors, such as atmospheric vapor pressure deficit. Thus, much of the key to understanding the variability in forest carbon cycles is identifying the sensitivity of the processes of the carbon cycle to water availability.

Therefore, my research takes the following approach: I begin by using sap flux sensors to measure tree-level transpiration over a four-year period and combine these values with other estimates of stand-level evaporation to generate an accurate estimate of total evapotranspiration, partitioned by component and tree species (Chapter 2). To assess the sensitivity of the water fluxes in the forest, I next establish a complete hydrologic budget for the forest stand over four years, including one severe and one mild drought (Chapter 3). I then focus on the flux of carbon from the soil and its variability over space and time. Using automated, high-frequency measurements of soil CO₂ flux over a 10-year period and including 3 forest stands, I assess inter- and intra-stand variability as well as inter- and intra-annual variability in soil flux in relation to climatic factors and stand characteristics representing productivity (Chapter 4). In order to assess how soil CO₂ flux may change over longer periods of time within the context of global change, I analyze how enrichment of [CO₂] independent of and combined with soil nitrogen availability alter the balance of carbon in a stand (Chapter 5). Finally, building off these previous chapters, I examine the relationship between carbon uptake, allocation, and turnover in a mixed-species forest experiencing interannual variability in water availability (Chapter 6).

I conclude that (Chapter 2) sap flux sensors can successfully be used to estimate tree- to stand-level transpiration if one accounts for both nocturnal water movement through the tree stem and spatial variability of species composition and demography within a stand. (Chapter 3) Despite reductions in transpiration by some species during water-limited (i.e. drought) periods, the magnitude and duration of these reductions results in annual water use that is similar to a non-drought year. The consequence of this invariability in transpiration and evapotranspiration for the hydrologic cycle is that changes in annual precipitation translate directly to changes in water supplied to rivers and streams. (Chapter 4) Diurnal to seasonal variability in soil CO2 flux is driven by temperature, whereas interannual variability is most-strongly influenced by soil moisture. Furthermore, spatial variability of soil CO₂ flux is directly related to forest productivity, and by proxy, leaf production, across biomes and, to a lesser extent, across stands within a region. However, within-stand variability may be inversely related to leaf production as a result of differential allocation of carbon between aboveground and belowground uses based on local resource availability. (Chapter 5) Although elevated atmospheric [CO₂] enhances productivity, it may only result in a small increase in the flux of CO₂ from soils. Instead, nitrogen availability explains much of the variability within a forest stand, regardless of [CO₂], with increasing nitrogen availability resulting in lower allocation of carbon belowground and greater aboveground productivity. (Chapter 6) Interannual variability in water availability can affect gross primary productivity in mature forests but these effects may primarily affect the following growing season. The proportionate changes in gross primary productivity appears to show greater reductions with previous year's soil moisture than net primary productivity, leading to increased carbon use efficiency following drought. Variability in leaf biomass in this relatively stable, mature stand appears to drive the interannual variability in photosynthesis as well as the demand for carbon used for biomass production and metabolic activity.

How genetic variation is maintained in the face of persistent natural selection is a central question in evolutionary biology. Here, I leverage a focal polymorphism, leaf chemical profile in a perennial wildflower (Boechera stricta, Brassicaceae) to investigate the ecological and genetic mechanisms that may influence the maintenance of variation in this trait.

In the first chapter, I present data from a suite of common garden and greenhouse experiments showing that the alleles underlying variation in chemical profile have contrasting fitness effects across environments. I identify two putative selective drivers on chemical profiles, and utilize phenotype-environment associations and molecular genetic analyses to test for additional evidence of past selection by these drivers. Together, these data are consistent with balancing selection on chemical profile, likely caused by pleiotropic effects of genes that influence secondary chemical biosynthesis on herbivore defense and drought response.

In the second chapter, I utilize a multi-year, manipulative field experiment to test for the effects of variation in selective drivers on genotypes conferring contrasting chemical profiles. I integrate variable effects of the environment on fitness components across life history and across environments to assess patterns of lifetime fitness. These data suggest that environmental conditions in which contrasting genotypes can both persist may be widespread.

Together, these chapters provide complementary perspectives on the question of persistent natural variation, suggesting that variation in secondary metabolic profiles in B. stricta may persist at present due to balancing selection, and may continue to persist in the future under variable environmental scenarios.

Microbes are the foundation of all ecosystems and crucial players in major ecosystem processes. However, most of our ecological theory was developed for plants and animals and thus may not help us understand these important communities. Previous syntheses have found mixed evidence for ecological patterns in observational data of microbes. In my dissertation, I combine observation and experiments to identify forces structuring microbial communities and how these are similar or different from those at play in systems of macroorganisms. In two chapters, I test new ecological hypotheses in soil microbial communities. In later chapters, I draw on similar ecological theory to explore the relative importance of host and microbial control for the gut microbiota.

In chapter one, I analyze insect, fungal, and bacterial responses to urbanization and habitat fragmentation. This study is the first of its kind to compare scaling relationships between macro- and micro-organisms in the same habitats. I find that microbial communities were vastly more immune than even the smallest of animals to human perturbation.

In chapter two, I seek to identify the drivers responsible for microbial community assembly during secondary succession. I use a fully factorial microcosm experiment that manipulates both biotic and abiotic factors in microcosms emulating old-fields. I find that both plant community and soil conditions are important for determining microbial community composition but that unique taxa respond to each driver.

In chapter three, I aim to quantify and document the impact of gut nitrogen availability on the microbiota. I find that stoichiometric mismatch between microbes and gut resources is pervasive for mammals, indicating that nitrogen may be limiting. Furthermore, I show that nitrogen availability in the gut is under host control, with host secreted nitrogen serving as a dynamic means for the host to manipulate microbial composition.

In chapter four, I use both in and ex vivo approaches to document shifts in composition and changes in the environment in the gut following antibiotic treatment. I find that the most significant abiotic shift is an increase in redox potential, which is due primarily to changes in microbial metabolism rather than a host response. Feedbacks between the environment and the microbial community, as well as dispersal limitation, then contribute to compositional change during post-antibiotic succession.

Much of our knowledge of the mammalian immune system comes from laboratory studies of model organisms in highly controlled settings; however, in nature, organisms experience myriad biotic and abiotic pressures that can influence the immune response. Understanding how the immune system operates in natural systems therefore requires studies of animals living in socially and ecologically relevant environments. Here, I investigated the drivers of individual variation in immunocompetence in a wild population of meerkats (Suricata suricatta) living in the Kalahari Desert. The meerkat is characterised by aggressively mediated female social dominance, and although hormonal masculinization is present to varying degrees in all adult, female meerkats, the dominant female in each clan has greater concentrations of total androgens than does any other clan member. I therefore tested if the immunocompetence handicap hypothesis (ICHH), which posits that androgens in males mediate a trade off between reproductive success and immunocompetence, could apply to females and perhaps extend to their offspring. From 2012-2015, I followed and sampled approximately 300 meerkats living in 24 social clans. I related measures of immunocompetence (i.e., gastrointestinal parasite burdens and innate immune function) to environmental, demographic, social, and endocrine variables. I tested for transgenerational effects of maternally derived androgens on offspring immunocompetence by administering an antiandrogen to pregnant dominant dams. For adult meerkats, I found that there is a cost to dominance, in terms of reduced immunocompetence and that those with greater androgen concentrations (either inferred from fecal androgen metabolites or measured directly from blood as androstenedione, A4) had greater parasite burdens and weaker immune responses. Because, in female meerkats, A4 appears to exert the dual effects of promoting reproductive success and compromising immunity, I propose that the ICHH can apply to females. Moreover, the immunosuppressive consequences of female hormonal masculinization extend beyond the dams to their offspring, via prenatal exposure to raised androgens, and therefore may represent a transgenerational consequence of sexual selection operating in females. By studying immune function in natural systems, we can gain a broader perspective on immune function from an ecological and evolutionary context.

Beaked whales (family Ziphiidae) and sperm whales (Physeter macrocephalus) are apex marine predators found throughout the world’s deep oceans. These species are challenging to observe, and little is known about fundamental aspects of their ecology, including their spatiotemporal distributions and habitat use. Passive acoustic monitoring (PAM), can be used to detect their echolocation clicks during foraging dives, thereby providing an indication of species presence. My dissertation investigates the distribution, seasonal occurrence, and diel variability in acoustic detections of beaked whales and sperm whales in the western North Atlantic Ocean, using multi-year passive acoustic recordings collected along the continental slope between Florida and Nova Scotia. First, I describe spatiotemporal patterns in detections of beaked whale echolocation clicks from five beaked whale species and one signal type of unknown origin. At least two beaked whale click types were detected at each recording site, and detections occurred year-round, with site-specific variation in relative species occurrence. Notably, Cuvier’s beaked whales (Ziphius cavirostris) were regularly detected in a region where they have not been commonly observed, and potential habitat partitioning among Cuvier’s and Gervais’ (Mesoplodon europaeus) beaked whales was apparent within their overlapping ranges. To examine the potential effects of using duty-cycled recording schedules on the detection of beaked whale clicks, I performed a subsampling experiment, and found that short, frequent listening periods were most effective for assessing daily presence of beaked whales. Furthermore, subsampling at low duty cycles led to consistently greater underestimation of Mesoplodon species than either Cuvier’s beaked whales or northern bottlenose whales (Hyperoodon ampullatus), leading to a potential bias in estimation of relative species occurrence. Next, I examine the occurrence of sperm whale echolocation clicks, which were recorded commonly between southern New England and North Carolina, but infrequently off the coast of Florida. In the northern half of the study region, I observed distinct seasonal patterns in the daily prevalence of sperm whale clicks, with a winter peak in occurrence off Cape Hatteras, North Carolina, followed by an increase later in the spring at sites further north, suggesting a shift in sperm whale concentrations which may relate to enhanced productivity occurring at higher latitudes in the spring. Finally, I explore the variability in daily detection rates of beaked whales and sperm whales in relation to dynamic oceanographic conditions off the Mid-Atlantic coast. Detection rates did not appear to correlate with temporal environmental variability, and persistent habitat features may be more important in predicting the occurrence of these species. Together, my dissertation provides substantial baseline information on the spatiotemporal occurrence of beaked and sperm whales in the western North Atlantic Ocean, highlighting the diversity within this guild of deep-diving odontocetes and demonstrating the use of PAM to provide species-specific insight into their ecology.

Climate change is driving vegetation community shifts in coastal regions of the world, where low topographic relief makes ecosystems particularly vulnerable to sea level rise, salinization, storm surge, and other effects of global climate change. Salinization has clear effects on vegetation, as few plant species can survive in brackish water, and these shifts in vegetation lead to declines in biomass carbon stocks, as well as significant changes in habitat structure and biodiversity. The rate and extent of these impacts on other wetland ecosystem properties and function is far less certain. This dissertation investigates the ecosystem consequences of saltwater intrusion in coastal wetlands, from shifting vegetation at the landscape scale, to soil biogeochemistry and wetland carbon cycling.Coastal plant communities globally are highly vulnerable to future sea-level rise and storm damage, but the extent to which these habitats are affected by the various environmental perturbations associated with chronic salinization remains unclear. In 2016, a series of vegetation plots across the Albemarle-Pamlico Peninsula that had been surveyed 7-13 years earlier were revisited in order to measure changes in tree basal area and community composition over time. I found reduced tree basal area in plots at lower elevations and with higher current soil salt content, while these factors explained only a small fraction of the measured changes in tree community composition. While tree basal area increased in the majority of plots, I measured declines in basal area in multiple sites with high soil salt content or low elevation. This decadal comparison provides convincing evidence that increases in soil salinity and saturation can explain recent changes in tree biomass, and potential shifts in community composition in low-elevation sites along the North Carolina coast. In Chapter 3, I quantified land and land cover change in the Alligator River National Wildlife Refuge (ARNWR), North Carolina’s largest coastal wildlife preserve, from 1985 to 2019 using classification algorithms applied to a long-term record of satellite imagery. Despite ARNWR’s protected status, and in the absence of any active forest management, 32 % (31,600 hectares) of the refuge area has changed land cover classification during the study period. A total of 1151 hectares of land was lost to the sea and ~19,300 hectares of coastal forest habitat were converted to shrubland or marsh habitat. As much as 11 % of all forested cover in the refuge transitioned to ghost forest, a unique land cover class that is characterized by standing dead trees and fallen tree trunks. This is the first attempt to map and quantity coastal ghost forests using remote sensing. These unprecedented rates of deforestation and land cover change due to climate change may become the status quo for coastal regions worldwide, with implications for wetland function, wildlife habitat and global carbon cycling. Salinization of freshwater wetlands is a symptom of climate change induced sea level rise. The ecosystem consequences of increasing salinity are poorly constrained and highly variable within prior observational and experimental studies. Chapter 4 presents the results of the first attempt to conduct a salinization experiment in a coastal forested wetland. Over four years, marine salts were applied to experimental plots several times annually with the goal of raising soil salinity to brackish levels while soil porewater in control plots remained fresh. Each year I measured aboveground and belowground vegetation biomass along with soil carbon stocks and fluxes. Despite adding more than 1.5 kg of salt per m2 to our experimental plots over four years, the ecosystem responses to salt treatments were subtle and varied over the multi-year experiment. In the final year of the experiment, soil respiration was suppressed, and bulk and aromatic soil carbon became less soluble as a result of salt treatments. The more stable carbon pools—soil organic carbon and vegetation associated carbon—remained unaffected by the salt treatment. This experiment demonstrates substantial ecosystem resistance to low dose salinity manipulations. The inconsistent soil carbon responses to experimental salinization I observed in the field led me to question how differences in soil pH and base saturation might alter the impacts of salinity of soil microbial activity. To test this, I performed a salt addition experiment on two series of wetland soils with independently manipulated salt concentrations and solution pH to tease apart the effect of these seawater components on soil carbon cycling (Chapter 5). Microbial respiration and dissolved organic carbon solubility were depressed by marine salts in both soils, while pH manipulation alone had no effect. Salinity treatments had a far greater effect on soil pH than did our intentional pH manipulation and there was a strong interaction between salt treatments and soil type that affected the magnitude of soil carbon responses. Site soils varied significantly in pH and base saturation, suggesting that the interaction between salinity and edaphic factors is mediating soil carbon processes. The degree of salinization and the effective pH shift following seawater exposure may vary widely based on initial soil conditions and may explain much of the variation in reports of salt effects on soil carbon dynamics. I suggest that these edaphic factors may help explain the heretofore inconsistent reports of carbon cycle responses to experimental salinization reported in the literature to date.

In this work, I explore the impacts of anthropogenic climate change on the krill-reliant marine ecosystem of the western Antarctic Peninsula. I use long-term ecological monitoring data to examine the impact of highly variable krill recruitment on a krill predator population, and I use archived backscatter data from an Acoustic Doppler Current Profiler (ADCP) to investigate biotic and abiotic drivers of summer krill distribution along the mid-to-coastal shelf region of the western Antarctic Peninsula.In Chapter 1, my coauthors and I examine the impact of cyclical krill recruitment on Adélie penguins. Between 1992 and 2018, the breeding population of Adélie penguins around Anvers Island, Antarctica declined by 98%. In this region, natural climate variability drives five-year cycling in marine phytoplankton productivity, leading to phase-offset five-year cycling in the size of the krill population. We demonstrate that the rate of change of the Adélie breeding population also shows five-year cycling. We link this population response to cyclical krill scarcity, a phenomenon which appears to have arisen from the interaction between climate variability and climate change trends. Modeling suggests that, since at least 1980, natural climate variability has driven cycling in this marine system. However, anthropogenic climate change has shifted conditions so that fewer years in each cycle now prompt strong krill recruitment, triggering intervals of krill scarcity that result in drastic declines in Adélie penguins. Our results imply that climate change can amplify the impacts of natural climate oscillations across trophic levels, driving cycling across species and disrupting food webs. The findings indicate that climate variability plays an integral role in driving ecosystem dynamics under climate change. In Chapter 2, I explore the viability of using archived Acoustic Doppler Current Profiler (ADCP) backscatter data to examine krill distribution on the WAP. During the Palmer LTER’s oceanographic cruises, the ship runs an ADCP the entire time it is at sea. An ADCP is a sonar instrument designed to measure water velocity across the water column, but the collected data can also be repurposed to provide information on the distribution and density of sound-scattering objects. Therefore, in regions where the primary sound-scattering objects are zooplankton, the ADCP can be used to map zooplankton distribution. I explore whether archived data (2005-2018) from an ADCP on Palmer LTER sampling cruises can be retroactively analyzed to provide information about the amount and distribution of krill in the water column along the western Antarctic Peninsula. I found that, given the uncertainty on several key instrument parameters, the ADCP’s estimates of krill biovolume are likely to have uncertainty spanning at least an order of magnitude and therefore the ADCP cannot on its own be used to estimate absolute biovolume. However, available evidence suggested that variability in seawater properties and ADCP system parameters is either low and/or can be accounted for using available measurements, and therefore meaningful relative biovolume estimates can theoretically be achieved. Several challenges – including the mismatch between depths sampled by the ADCP and those sampled by net tows, as well as the fact that krill are not the only species present in the sampled region – add uncertainty to comparisons between ADCP data and ground-truthing data available from tows. However, I found highly significant though noisy empirical relationships between the biovolume of krill in tows and the backscatter coefficient calculated from the ADCP, indicating that the ADCP does give useful information about the amount of krill and can be used to map krill distribution along the ship track. In Chapter 3, I use the ADCP backscatter data from Palmer LTER cruises to explore the effect of abiotic and biotic factors on krill distribution along the mid-to-coastal shelf region of the WAP. I find that krill recruitment around Palmer Station is more closely linked to krill density 600km south than to krill density on the sampling line next to Palmer Station, suggesting that krill density further south along the Peninsula is more dependent on recent recruitment than krill density further north. Net tows support this idea, indicating that a larger proportion of recruits are found in the south of the grid than in the north. I also determine that the distance between patches of high biomass becomes exponentially greater with increasing time since a high krill recruitment event, indicating that the foraging conditions become much more difficult as time elapses since a high krill recruitment event. I find evidence that krill are spatially correlated with areas of high primary productivity, suggesting that krill may move to aggregate in these areas and that changing distributions of primary productivity under climate change are likely to change krill distributions. I examine whether krill show avoidance behaviors, such as retreating to colder water at depth, in response to high summer temperatures, but I find no evidence of this and even find a spatial correlation between krill and areas of higher temperature. I conclude that krill are likely not yet temperature-stressed in this region of the WAP. Overall, lowered primary productivity and krill recruitment – and perhaps temperature as it becomes even warmer – will likely have major impacts on the distribution of krill, and therefore on their accessibility to predators and fisheries.