Ecological communities are most commonly structured by a mixture of bottom-up processes such as habitat or prey, competition within the same trophic level, and top-down forces from higher trophic levels. Carnivore guilds play a vital role in the broader ecological community by stabilizing or destabilizing food webs. Consequently, factors influencing the structure of carnivore guilds can be critical to patterns in ecosystems. Coyotes (Canis latrans), bobcats (Lynx rufus), gray foxes (Urocyon cinereoargenteus), raccoons (Procyon lotor), red foxes (Vulpes vulpes), and striped skunks (Mephitis mephitis) occur sympatrically throughout much of their geographic ranges in North America and overlap in resource use, indicating potential for interspecific interactions. Although much is known about space use, habitat relationships, and activity patterns of the individual species separately, little is known about factors that facilitate coexistence and how interactions within this guild influence distribution, activity, and survival of the smaller carnivores. For example, gray fox populations appear to have declined in Illinois since the early 1990s and it is unknown if the increase in bobcat and coyote populations during the same time period is the cause. I conducted a large-scale non-invasive carnivore survey using an occupancy modeling framework to quantify factors affecting the structure of this widely-occurring carnivore guild. I used baited remote cameras during 3-week surveys to detect carnivores at 1,118 camera-points in 357 2.6-km2 sections (clusters of 3-4 cameras/section) in the 16 southernmost counties of Illinois (16,058 km2) during January-April, 2008-2010. I collected microhabitat data at each camera-point and landscape-level habitat data for each camera-cluster. In a multi-stage approach, I used information-theoretic methods to develop and evaluate models for detection, species-specific habitat occupancy, multi-species co-occupancy, and multi-season (colonization and extinction) occupancy dynamics. I developed hypotheses for each species regarding the occupancy of areas based on anthropogenic features, prey availability, landscape complexity, and vegetative landcover. I used photographic data, Poisson regression, and mixed-model logistic regression to quantify temporal activity of carnivores in the study area and how interspecific factors influence temporal patterns of activity. Of the 102,711 photographs of endothermic animals I recorded photographs of bobcats (n = 412 photographs), coyotes (n = 1,397), gray foxes (n = 546), raccoons (n = 40,029), red foxes (n = 149) and striped skunks (n = 2,467). Bobcats were active primarily during crepuscular periods, and their activity was reduced with precipitation and higher temperatures. The probability of detecting bobcats at a camera point decreased after a bobcat photograph was recorded, suggesting avoidance of remote cameras. Across southern Illinois, bobcat occupancy at the camera-point and camera-cluster scale (point = 0.24 ± 0.04, cluster = 0.75 ± 0.06) was negatively influenced by anthropogenic features and infrastructure. Bobcats had high rates of colonization (0.86) and low rates of extinction (0.07) during the study, suggesting an expanding population, but agricultural land was less likely to be colonized. The number of coyote photographs decreased with increased temperature, but increased with previous coyote photographs, suggesting an attraction to bait in cold weather. Nearly all camera clusters were occupied by coyotes (cluster = 0.95 ± 0.03) during the entire study. At the camera-point scale, coyote occupancy (overall point = 0.58 ± 0.03) was higher in hardwood forest stands with open understories than in other habitats. Similar to coyotes, gray foxes were more likely to be photographed in cold weather and after a previous detection had occurred. However, gray fox occupancy was much lower (point = 0.13 ± 0.01, cluster = 0.29 ± 0.03) at all scales. At the camera-cluster scale, with a buffer-area size that represented 20% of the estimated home-range size of gray foxes, the species selected spatially-complex areas with high proportions of forest, and low proportions of grassland and agriculture land cover. Gray fox occupancy of camera clusters was positively related to anthropogenic features within 100% estimated home-range buffers. Collectively, the results suggest gray fox occupancy was greatest near, but not in, anthropogenic developments. Red foxes occupied a similar proportion of the study area as gray foxes (point = 0.12 ± 0.02, cluster = 0.26 ± 0.04), but were more closely associated with anthropogenic features. Indeed, at all three scales of red fox occupancy analysis, anthropogenic feature models received more support than other hypotheses. Camera-cluster extinction probabilities were higher for both gray foxes (0.57) and red foxes (0.35) than their colonization rates (gray fox = 0.16, red fox = 0.06), suggesting both species may be declining in southern Illinois. I recorded more striped skunk photographs in January and February (i.e., during the breeding period) than in March and April. Striped skunks occupied a large portion of the study area (point = 0.47 ± 0.01, cluster = 0.79 ± 0.03) and were associated primarily with anthropogenic features, especially if the features were surrounded by agricultural land and not forest. Raccoons were essentially ubiquitous within the study area, being photographed in 99% of camera clusters. In some instances, the presence of other carnivores appeared to be an important factor in the occupancy of the 4 smaller species, but in general, habitat models were more supported than co-occurrence models. Habitat had a stronger influence on the occupancy of gray foxes and red foxes than did the presence of bobcats. However, the level of red fox activity, represented by the number of photographs recorded in a camera cluster, was negatively correlated with bobcat activity. Gray fox occupancy and level of activity were reduced in camera-clusters occupied by coyotes, but were not related to bobcat occupancy. When not considering the presence of coyotes, gray foxes appeared to use camera points with fewer hardwood and more conifer trees, which was counter to previous findings. However, when adding the effect of coyote presence, gray fox point models indicated a positive relationship with hardwood stands. Therefore, gray foxes were more likely to occupy camera points in hardwood stands than conifer stands if coyotes were also present; suggesting that hardwood stands may enhance gray fox-coyote coexistence. The 2 fox species appeared to co-occur with each other at the camera-point scale more frequently than expected on the basis of their individual selection of habitat. Similarly, camera-point occupancy of red foxes was higher when coyotes were present. These apparent canid associations may be a response to locally-high prey abundance or an unmeasured habitat variable. Activity levels of raccoons, bobcats, and coyotes were all positively correlated. Collectively, my results suggest that although gray foxes and red foxes currently coexist with bobcats and coyotes, the foxes have reduced activity in the areas occupied by larger carnivores, especially when bobcats and coyotes are highly active. Further, hardwood stands may contain trees with structure that enhances tree-climbing by gray foxes, a behavior that probably facilitates coexistence with coyotes. Therefore, efforts to manage gray foxes should focus on maintaining and increasing the amount of mature oak-hickory forest, which presumably provides a suitable prey base and refugia from intraguild predation. Additionally, the varying results from different scales of analyses underscore the importance of considering multiple spatial scales in carnivore community studies.

A robust ecosystem requires a functionally heterogeneous community of organisms with a wide range of traits that permits broad resource partitioning. Understanding community diversity patterns can help investigate drivers of community assembly and how different metrics reflect the success of restoration in grassland or weed control in cropland. The objectives of my study were to identify assembly drivers influencing community taxonomic, phylogenetic, and functional diversity. The first study examined the effect of different ecotypes of dominant species on grassland community diversity along a spatial aridity gradient during restoration. This study showed that ecotype significantly affected species richness and shaped taxonomic, phylogenetic, and functional diversity. Accordingly, restorations should consider ecotypic variation as a critical biological filter to community assembly in grassland ecosystems. Given the community response across the tallgrass prairie, restoration practitioners should draw attention to regional sources of dominant species because ideal ecotypic sources can affect species richness and even sustain the phylogenetic and functional patterns. The restoration efficacy of existing ecosystems should be evaluated to large-scale diversity patterns to detect gaps and limitations that will reveal which diversity components to highlight for further restoration investment. The second study investigated temporal variations in diversity metrics among dominant species ecotypes and a drought treatment on the importance of external and internal filters in shaping the assembly of grassland communities. In this study, species richness decreased significantly during the early stages of restoration while phylogenetic and functional diversity was maintained over eight years. I also found no significant effect of experimental drought treatment on community biodiversity. Moreover, ecotypic variation as an internal filter played a key role in grassland assembly but the external filter was less strong because of high trait overlap among species within a community. In general, this study highlighted the consequence of integrating both interspecific and intraspecific trait variabilities and the value of concentrating on functional traits to comprehend better how trait variability is coupled with species coexistence. Future investigations are necessary to examine the distinctive origins of variability in plant traits and how they contribute to grassland community assembly. The third study focused on whether weed management tactics such as a glyphosate-resistant (GR) cropping system were beneficial to control weed diversity in the soil seedbank of the agroecosystem. Both phylogenetic and functional diversity of the soil seedbank was relatively stable with different GR cropping systems across six years. The neutral assembly of the soil seedbank may imply that the belowground weed community could be restrained by stochastic mechanisms, such as dispersal and demographic stochasticity of seeds, during agricultural activities. Therefore, I recommend integrated weed management with a sustainable perspective to fight against the evolutionary feedback due to weed herbicide resistance. While the GR cropping system still seems beneficial, future weed control cannot overlook the extensive impact of GR systems on biodiversity variations, the shifts in weed composition, and the resistance evolution of weed species to herbicides in the agroecosystem.

As the largest and most poorly environment on Earth, the deep-sea is facing global threats from climate change and anthropogenic disturbance further compounded by the lack of critical baseline data on seafloor species composition and community structure. Many data-deficient regions include those in geographically-isolated offshore environments, like low-latitude seamounts, where sampling and surveys have been limited, resulting in critical knowledge gaps that do not allow for effective conservation measures to be realized. This work seeks to characterize the coral fauna of tropical seamount environments greater than 150 m depth and understand the environmental controls on species distribution and community assembly for long-lived, ecologically-important species, primarily from the Octocorallia, Antipatharia, Stylasteridae, and Scleractinia. Methodologies for accomplishing this research have included analysis of remotely operated vehicle (ROV) video surveys and identification of collected voucher specimens to understand biogeographic patterns within coral communities on seamounts and other rugged seafloor features in 3 different regions: the tropical western Atlantic (Anegada Passage), the equatorial central Pacific (Phoenix Islands), and the tropical eastern Pacific (Costa Rica). These regions represent vastly different oceanographic regimes in terms of biological productivity and water column structure resulting in differential effects on deep-sea coral communities. Evidence from these three regions has shown significant effects of the role that oceanic water masses have on structuring deep-water coral biodiversity and suggests that these features, along with other abiotic environmental variables, are important indicators for understanding species distribution patterns, community structure, and global biogeographic patterns. More broadly, the results of this work have demonstrated the capabilities of exploratory ROV surveys, across multiple platforms, to add practical knowledge to coral species inventories and identify bathyal biogeographic patterns in remote regions of the deep sea. The results of this work, serving as baseline coral biodiversity surveys for each area, are also germane to evaluating the effects of human-mediated disturbance and global climate change in the deep ocean. These disturbances also include ocean acidification, ocean deoxygenation, deep-sea mining, and bottom-contact fishing, all of which have been identified as threats to the seamount benthos. / Biology

Many real life complex networks consists of a tremendous amount of nodes and edges which make them difficult to extract and analyze. This thesis aims to examine what network prop- erties that can be deduced when considering small samples of a complex network and how well they correspond to the characteristics of the complete network. This is of importance as sampling will most likely be the de facto method when analyzing complex networks in the future. The study examine the scale-free property, the small-world property and the com- munity structure of the network spanned by the KTH domain. The method consisted of gathering data about the network through sampling it in a breadth-first manner using a web crawler. The samples was then compared with respect to each property. The results was that good approximations of the scale-free property could be made from small samples of the KTH network. However, no good approximation could be made about the small-world property using the sampling technique. Good approximations about a node’s community affiliation could be observed. However, general conclusions of the com- plete network’s community structures could not be made. To summarize, the result indi- cate that small samples can be used to approximate some properties of the complete KTH network. However, to determine if the result is true for the general case more research is necessary. / Komplexa nätverk i vår omvärld består av ett stort antal hörn och kanter vilket gör dem svå- ra att extrahera och analysera. Denna rapport undersöker vilka nätverksegenskaper som kan härledas vid undersökningen av små stickprov av ett nätverk och hur bra dessa representerar egenskaperna hos det fullständiga nätverket. Detta är av betydelse eftersom användandet av små stickprov kommer troligtvis att vara standarden vid undersökningar av nätverk i framtiden. Denna studie undersökte scale-free egenskapen, small-world egenskapen och community strukturen för nätverket som omfattas av KTH domaänen. Metoden innefattade att samla in data om nätverket genom stickprov baserat på en bredden-först sökning. Detta realiserades genom att använda en sökrobot. Sedan jämfördes de olika stickproven med avseende på de olika nätverksegenskaperna. Resultetat visade att nätverkets scale-free egenskap kunde approximaeras med små stickprov. Däremot var det inte möjligt att approximera nätverkets small-world egenskap genom användet av den givna stickprovsmetoden. Goda approximationer observerades för att avgöra ett hörns community tillhörighet men den allmäna community strukturen kunde inte approximeras. Sammanfattningsvis visade resultatet att stickprov kan användas för att approximera vissa egenskaper hos det fullständiga KTH nätverket men att mer forskning krävs för att avgöra om resultaten kan generaliseras.

Floral visitation alone has been typically used to characterize plant-pollinator interaction networks even though it ignores differences in the quality of floral visits (e.g. transport of pollen) and thus may overestimate the number and functional importance of pollinating interactions. However, how network structural properties differ between floral visitation and pollen transport networks is not well understood. Furthermore, the strength and frequency of plant-pollinator interactions may vary across fine temporal scales (within a single season) further limiting our predictive understanding of the drivers and consequences of plant-pollinator network structure. Thus, evaluating the structure of pollen transport networks and how they change within a flowering season may help increase our predictive understanding of the ecological consequences of plant-pollinator network structure. Here we compare plant-pollinator network structure using floral visitation and pollen transport data and evaluate within-season variation in pollen transport network structure in a diverse plant-pollinator community. Our results show that pollen transport networks provide a more accurate representation of the diversity of plant-pollinator interactions in a community but that floral visitation and pollen transport networks do not differ in overall network structure. Pollen transport network structure was relatively stable throughout the flowering season despite changes in plant and pollinator species composition. Overall, our study highlights the need to improve our understanding of the drivers of plant-pollinator network structure in order to more fully understand the process that govern the assembly of these interactions in nature.

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