<p>Amur honeysuckle (<i>Lonicera maackii</i>) is a shrub endemic to East Asia which has become invasive and nearly ubiquitous to the forest ecosystems of eastern North America. Through its extended growing season, competitive ability, and potential allelopathy, Amur honeysuckle alters native herbaceous-layer plant communities and inhibits the regeneration of native tree species. As such, it is representative of a range of invasive shrub species imported from East Asia. My thesis contributes to questions fundamental to the understanding this and other invasive shrubs: 1) How do species become invasive? 2) How can the invasions of the species be effectively controlled? 3) How does the ecosystem respond to treatment of the invasive species?</p> <p>First, I examined the role of self-compatibility within Amur honeysuckle. I compared the berry production, seed production, and germination rates between closed-pollinated and open-pollinated flowering branches of Amur honeysuckle individuals across multiple types of invasions (heavy, light, and sprouting). I found that Amur honeysuckle not only possesses the ability to self-pollinate, but that it can produce viable self-pollinated seed sets. This ability may help explain how Amur honeysuckle able to invade isolated forest patches far removed from the main invasion.</p> <p>Second, I evaluated the effectiveness of a novel herbicide adjuvant in reducing the amount of herbicide needed in the ‘cut-stump’ method of controlling Amur honeysuckle. Combining various concentrations of the most common herbicide in the world, glyphosate, with concentrations of cellulases derived from fungi, 2XL, I examined whether the cellulases improved the effectiveness of glyphosate, potentially by increasing glyphosate movement into the vascular tissue of Amur honeysuckle through the degradation of cell walls. While 2XL was not an effective adjuvant, glyphosate concentrations of less than half the recommended dosages were equally effective as higher concentrations in preventing sprouting of treated stumps. The ineffectiveness of 2XL may imply a need for protein-mitigated diffusion of glyphosate across cell walls and into the vascular tissue of the plant, which would be inhibited by the breakdown of cell walls.</p> Finally, I tested how deeper intensities of mulching-head treatments affected the sprouting response of Amur honeysuckle and the response of the herbaceous-layer plant community after treatment. I found a negative relationship between the volume of sprouting Amur honeysuckle and increasing depth of mulching-head treatment. Additionally, increasing mulching-head intensities were correlated with increased herbaceous layer diversity and conservation value as represented by Floristic Quality Index. Mulching-head treatments are a promising tool in controlling heavy invasions of non-native shrubs.

<p>Biological invasion is a major and growing threat to global biodiversity and human well-being, but research on the impacts of invaders on their recipient environments lags behind that on the mechanisms driving invader establishment and spread. The total impact of an invader is defined by its range size, abundance per unit area, and per-capita effect, with both per-capita effects and abundance varying over time and across the invader’s range. These context-dependencies are determined, in part, by functional differentiation between the invader and its recipient system. In this thesis, I investigate how functional differentiation between invaders and their recipient communities regulates the impact of plant invaders on community diversity and/or biomass production.</p> <p>First, I compare the effects of invasive Callery pear (<em>Pyrus calleryana</em> Decne.) to functionally similar native trees in three early-successional meadow environments in Indiana’s eastern corn belt plains. Despite my prediction that <em>P. calleryana</em> would have greater negative effects on the total biomass and diversity of the understory plant community compared to native trees, I found that <em>P. calleryana</em> had no significant impact on total cover, species richness, or Shannon’s or Simpson’s diversity indices for the understory community, compared to native <em>Liriodendron tulipifera</em> L., <em>Platanus occidentalis</em> L., or non-tree control plots. Likewise, <em>P. calleryana</em> had no significant impact on the native, introduced, woody, or native tree subsets of the understory community. These results indicate that the trait differences between <em>P. calleryana</em> and functionally similar native trees – and thus the per-invader effect of <em>P. calleryana</em> on its recipient community – are not of a great enough magnitude to produce changes in the understory community composition of these highly invaded, low diversity meadow environments with relatively new and sparse <em>P. calleryana</em> invasions. </p> <p>I then investigate the role of functional overlap in moderating invader impacts in California serpentine grassland communities through the lens of classic niche theory, which predicts that functional differentiation minimizes competition and therefore allows functionally distinct invaders to achieve higher establishment success but lower per-capita effects on their recipient communities. I tested this prediction by establishing small-scale experimental communities composed of individual or multiple functional groups differentiated by phenology – early-season annuals, nitrogen-fixing early-season annuals, and late-season annuals – and seeding these communities with early- or late-season invaders. I found that as invader density increased, effects on resident community biomass depended on complex patterns of invader and resident functional overlap. Across all resident community functional groups, the high density of early-season invaders enables them to capture a greater portion of total community biomass than late-season invaders, but early-season invaders reduce the ratio of resident:total invader biomass production by less, per-unit-biomass, than late-season invaders. These results highlight the need to consider both niche and fitness differences in predicting invader impacts and the complex nature of resident-invader interactions, which may not be sufficiently captured by coarse functional groups.</p>

Master of Science / Department of Biology / Craig Paukert / The zebra mussel is an invasive bivalve that was first confirmed in Kansas in 2003, and has decreased zooplankton abundance and altered the aquatic community in other areas where it has invaded. However, little is known about its effects on the aquatic communities of warm-water Great Plains reservoirs. We analyzed zooplankton, benthic macroinvertebrate, and juvenile and small-bodied fish abundance in the littoral zone of an Eastern Kansas reservoir with an established zebra mussel population (El Dorado Reservoir) and a control reservoir without zebra mussels (Melvern Reservoir) for two years pre-zebra mussel invasion (2001-2002) and two years post-invasion (2008-2009). We found no difference in littoral zooplankton abundance between reservoirs across time, but abundance of some macroinvertebrate taxa increased, and abundance of juvenile Lepomis spp. and red shiners decreased in the littoral zone of El Dorado Reservoir in August of the post-zebra mussel invasion period in comparison to the control reservoir. We also analyzed abundance and condition of six adult reservoir fishes in El Dorado Reservoir and three control reservoirs in Eastern Kansas for ten years pre-zebra mussel invasion (1993-2002) and five years post-invasion (2004-2008). Adult white crappie abundance remained constant in El Dorado Reservoir but decreased in the control reservoirs during the post-zebra mussel invasion period, and condition of adult bluegill, white bass, and white crappie decreased in El Dorado Reservoir in the post-zebra mussel invasion period compared to the control reservoirs. Our findings suggest that zebra mussel invasion in El Dorado Reservoir may have affected some benthic macroinvertebrates, juvenile and small-bodied fishes, and adult fishes. We did not find evidence that zebra mussels have had substantial effects on the zooplankton community of El Dorado Reservoir. However, July-August zebra mussel veliger densities in El Dorado Reservoir averaged less than 12 veligers/L in four of the six post-zebra mussel invasion years. Additional research and long-term monitoring of zooplankton, macroinvertebrates, and fishes will be necessary to determine the full effects of zebra mussels on the aquatic communities of warm-water reservoirs throughout North America.

BACKGROUND:The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant.RESULTS:We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease.CONCLUSIONS:A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease.

The principle of competitive exclusion holds that the strongest competitor for a single resource can exclude other species. Yet in many systems, more similar species appear to stably coexist than the small number of limiting resources. Understanding how and when similar species can stably coexist has taken on new urgency in managing biological invasions and their ecological impacts. Recent theoretical advances emphasize the importance of predators in determining coexistence. The effects of predators, however, can be mediated by behavioral changes induced in their prey as well as by their lethality. In this dissertation, I ask how considering multiple trophic levels changes our understanding of how a grass invasion (Pennisetum ciliare) affects species diversity and dynamics in southeastern Arizona. In considering interactions with plant consumers, and with the predators of those consumers, this research reveals more general ecological processes that determine species diversity across biological communities. I first present evidence from a grass removal experiment in the field that shows increased emergence and short-term survival of native perennial plants without grass. This is consistent with Pennisetum ciliare causing the observed concurrent decline in native plant abundance following invasion. I then present results from greenhouse and field studies consistent with that suppression of native plants being driven primarily through resource competition rather than increased rodent granivory. Granivorous rodents do not solely function as consumers, however, because they cache their harvested seeds in shallow scatter-hoards, from which seeds can germinate. Rodents thus act also as seed dispersers in a context-dependent mutualism. The primary granivores in areas invaded by Pennisetum ciliare are pocket mice (genus Chaetodipus), which have a well-studied tendency to concentrate their activity under plant cover to avoid predation by owls. Because the dense canopy of the grass may provide safer refuge, I hypothesized the pocket mice may be directly dispersing native seeds closer to the base of the invasive grass. Such a behavior could increase the competitive effect of the grass on native plant species, further driving the impacts of the invasion. By offering experimental seeds dusted in fluorescent powder and tracking where the seeds were cached, I show that rodents do preferentially cache experimental seeds under the grass. This dispersal interaction may be more general to plant interactions with seed-caching rodents across semi-arid regions that are experiencing plant invasions. Finally, I ask how the predator avoidance behavior exhibited by these rodents affects their ability to coexist with one another. Not only could their diversity affect that of the plant community, but the effects of plant invasions can cascade through other trophic levels. Theoretical understanding of how similar predator avoidance strategy alters coexistence had not yet been developed, however. Instead of a field study, therefore, I modified a general consumer-resource model with three trophic levels to ask whether avoidance behavior by the middle trophic level alters the ability of those species to coexist. I found that more effective avoidance behavior, or greater safety for less cost, increased the importance of resource partitioning in determining overall niche overlap. Lowering niche overlap between two species promotes their coexistence in the sense that their average fitness can be more different and still permit coexistence. These results provide novel understanding of behavioral modifications to population dynamics in multi-trophic coexistence theory applicable to this invasion and more broadly.

Coastal Sage Scrub (CSS) is a low scrubland plant community native to the coasts of California, housing many threatened and endangered species. Due to the invasion of non-native plants, many areas of CSS have type converted to annual grasslands and the fire frequency has accelerated; fire in turn, may facilitate further invasion, leading to a loss of biodiversity. While many studies document post-fire succession in these communities, pre-fire data are rarely available for comparison, especially data on seedling emergence. I analyzed post-fire recovery of a type-converted grassland community, comparing seedling emergence data for the first and third year after fire to the three years preceding the fire. Non-native species abundances declined more after the fire than did native abundances. This pattern was still present in 2015, three years post-fire. Two native species, Amsinckia menziesii var. intermedia (Amsinckia) and Phacelia distans (Phacelia), were subjects of seed addition treatments pre-fire, but I found no evidence that past seeding increased their abundances post-fire. Amsincki did recover to its pre-fire density three years after the fire, while the density of Phacelia declined over 75% in both the year immediately post-fire and three years after the fire. However, a third native species, Lupinus bicolor (Lupinus), was both much more abundant and also more spatially widespread both immediately after the fire and two years later. This supports the hypothesis that Lupinus is stored in the soil seed bank and the fire may have given this species the opportunity to recover by lowering abundances of non-native competitors. This analysis will inform future conservation efforts by improving our understanding of how seed banks impact the post-fire recovery of native species.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Human-modified habitats form increasingly large components of landscapes, threatening biodiversity and creating challenges for conservation. In some cases altered habitats form entirely novel ecosystems that may support new combinations of species and species abundances, and create habitat space in otherwise transformed landscapes. In the Western Cape of South Africa, woody invasive species contribute to landscape-level habitat transformation and form novel ecosystems. Invasive Australian Acacia species are especially problematic in lowland areas where they create dense thickets and substantially transform both biotic communities and abiotic processes. Despite the prominence of Acacia thickets across the Western Cape, their ability to support native fauna is not well understood and the objective of this study was to assess the significance of Acacia thickets as habitat for the region’s avifauna. Birds were surveyed in Acacia thickets in the south-western Western Cape in three seasons to examine species richness, abundance and functional abundance. Furthermore, I examined the extent to which differences in patch-level vegetation structure alter bird communities. Between survey sites and seasons, significant variation was observed in assemblage richness, density, median body size and biomass. Variation in vegetation density, stem density, mean vegetation height and total canopy cover best explained variation in bird assemblages. Eighty species were estimated to utilize Acacia thickets and assemblages had a mean density of 7.78 birds per ha. The most abundant feeding guilds were the mixed feeders and insectivores. The median body size observed was 15.2 g and the body size frequency distribution of all species in Acacia spanned a similar range compared to the body size frequency distribution for the species list for the entire Western Cape. The mean biomass of bird communities was 0.224 kg per ha. Using data on bird density and biomass, Acacia thickets across the Fynbos Biome support and estimated average of over 21 million birds with a combined biomass of over 600 thousand kg. This study found that Acacia thickets in the Western Cape support a subset of the region’s birds with the most abundant species being small mixed feeders, which are also frequently urban-adapted. Compared with other habitat types, Acacia support bird assemblages with moderate species richness and density. This study shows that Acacia thickets, as a novel habitat, provide a significant amount of habitat space in a highly transformed landscape and highlights the need for comprehensive evaluation of altered habitats before assumptions are made about their ecological value. / AFRIKAANSE OPSOMMING: Getransformeerde habitatte maak vermeerderend groot deel uit van die omgewing, dit bedreig biodiversiteit en skep groter uitdagings vir bewaring. In sommige gevalle vorm hierdie getransformeerde habitatte geheel nuwe ekosisteme wat moontlik nuwe kombinasies van spesies en spesie volopheid kan onderhou. Verder skep nuwe ekosisteme habitat spasie in anders veranderde landskappe. In die Wes-Kaap van Suid-Afrika dra die Australiese Acacia indringer spesies is veral problematies in laagliggende areas, aangesien dit digte ruigtes vorm, asook beide die biotiese gemeenskappe en die abiotiese prosesse aansienlik transformeer. Ten spyte daarvan dat daar volop Acacia ruigtes in die WesKaap is, word min verstaan van hul vermoë om inheemse fauna te onderhou. Die hoofdoel van hierdie studie was om die belang van Acacia ruigtes as habitat vir die area se voëllewe te bepaal. Voël-opnames in die suidwestelike dele van die Wes-Kaap is gedoen in Acacia ruigtes oor drie seisoene, om spesierykheid, volopheid en funksionele volopheid te ondersoek. Verder is die mate waartoe verskille in die plotte van die plantegroei struktuur, die voëlgemeenskappe verander, geondersoek. Daar was aansienlike variasie waargeneem in die spesiesamestelling rykheid, voorkoms digtheid, mediaan liggaamsgrootte en biomassa van die voëls tussen die onderskeie voëlopnaam plotte en die seisoene. Die variasie in plantegroei digtheid, stam digtheid, mediaan plantegroeihoogte en totale kroonbedekking verduidelik hierdie variasie in spesiesamestelling die beste. Tagtig voëlspesies Acacia ruigtes benut en die populasiesamestelling het ‘n gemiddelde digtheid van 7,78 voëls per ha. Die mees algemene voel-voeding-guldes was die gemengde-voedsel-vreters en insekvreters. Die median liggaamsgrootte waargeneem was 15,2 g en die liggaamsgrootte frekwensieverspreiding van alle spesies in Acacia ruigtes is ooreenkomstig met die liggaamsgrootte frekwensieverspreiding vir die spesielys vir die hele Wes-Kaap. Die gemiddelde biomassa van voel gemeenskappe was 0.224 kg per ha. Acacia ruigtes oor die fynbosbioom wat ‘n geskatte gemiddelde van meer as 21 miljoen voels ondersteun, met ‘n gesamentlike biomassa van meer as 600 duisend kg. Hierdie studie het bevind dat Acacia ruigtes in die Wes-Kaap ‘n onderafdeling van die streek se voels ondersteun, met die mees algemene spesies as die klein gemengde-voedsel-vreters, wat ook dikwels stedelik aangepas is. In vergelyking met ander habitattipes ondersteun Acacia ruigtes voel samestellings met matige spesierykheid en digtheid. Hierdie studie toon dat die Acacia ruigtes, as ‘n nuwe habitat, ‘n beduidende hoeveelheid habitat ruimte in ‘n hoogs getransformeerde omgewing skep en beklemtoon die behoefte aan ‘n omvattende evaluering van veranderde habitatte, voor aannames gemaak word oor hul ekologiese waarde.

Invasive species, a top threat affecting global biodiversity, become invasive through a process including four stages: transport, establishment, spread, impact and integration. Species currently in this process provide opportunities to empirically derive the mechanisms driving each of these stages, make predictions based on these mechanisms and then to test these predictions. This research examines the current invaded distribution, potential invasion and community-level impacts of a popular aquarium trade fish (Hemichromis guttatus Günther, 1862) in an endemic hotspot, Cuatro Ciénegas, in Coahuila, México and discusses the policy and conservation management implications of these findings. In Chapter 1, the problem of invasive species, the study site and the focal species of this work are introduced. In Chapter 2, the critical thermal minimum and maximum temperature limits and temperature preference of H. guttatus are identified because temperature is hypothesized to be an important factor controlling this fish’s distribution. The results indicate that H. guttatus has a wide temperature tolerance range (a characteristic of a ‘good’ invader), that preference is a more informative metric for predicting invasion than absolute tolerances, and that resource-poor environments may promote searching behaviors that cause an invasive fish to increase its range. In Chapter 3, the results of a field survey are analyzed and temperature, pH, depth and the presence of vegetation are all found to be related to H. guttatus presence. Invasion risk of several as-of-yet uninvaded sites in Cuatro Ciénegas is assessed. In Chapter 4, competitive and predatory interactions of H. guttatus on an endemic, threatened cichlid (Herichthys minckleyi) and a macroinvertebrate community respectively are investigated. The results suggest that while H. guttatus does not directly impact H. minckleyi through competition in these conditions, it may inhibit reproduction and alter H. minckleyi’s behavior through aggressive interactions. In Chapter 5, all results are synthesized and a determination of the invasive status of H. guttatus in Cuatro Ciénegas is made. The results presented here will be useful in identifying areas with a high risk of invasion by this popular ornamental fish, thus allowing the implementation of policy and management actions to prevent or at least ameliorate the impacts of an invasion and will add to the growing knowledge of how invasive species affect native systems. / text

Introduced species present one of the greatest threats to biodiversity of native species, and knowledge of introduced species ecology is imperative for the development of management plans to ensure conservation of native species populations. We sought to determine the distribution and nesting behavior of an introduced population of red-bellied squirrels (Sciurus aureogaster) on islands of the Florida Keys currently managed as part of Biscayne National Park, and document potential for the species to impact native flora and fauna. Squirrels were difficult to observe in the dense vegetation of the subtropical forest, so we relied on their leaf nests, which were highly visible in the canopy of trees, to determine current presence and distribution on the Park's islands. We found nests throughout the mixed-hardwood forests of Elliott Key and Sands Key, and also documented a single, old nest on Old Rhodes Key, the first ever documentation of the species that far south in the Upper Keys. Nests were located in tall trees with more canopy linkages than random focal trees, and nests were placed in the upper canopy on the north side of the nest tree more often than expected by chance. Squirrels selected West Indies mahogany (Swietenia mahagoni) to place nests more often than available in the forest. Squirrels used areas with greater tree density and canopy cover, but lower recent hurricane damage and fewer woody shrub stems, than areas available at random in the forest. Squirrels built nests only in mixed-hardwood forest. Overall, this introduced species exhibited nest site selection behavior similar to other tree squirrels, and appears capable of continued spread despite the initial site of introduction on an oceanic island. Knowledge obtained from this research is being used by managers and applied to an eradication program to remove this invasive species from Biscayne National Park.

The present thesis deals with the related themes of mortality and growth in coral reef fishes. In the first chapter, a nine-year dataset from Bermuda is used to quantify how reef fish populations respond to the introduction of a trap-fishing ban, finding that herbivores exhibit extremely strong recovery, but that stock-recruitment relationships may be decoupled by a numerical response in a meso-predator. In the second chapter, a dataset from Bonaire is used to test the efficacy of the widely-used coefficient of natural mortality, M, in modelling a population of stoplight parrotfish (Sparisoma viride). As determined from simulation models, this statistical coefficient performs considerably less well than a novel mechanistic function that partitions mortality into size- and age-based processes and achieves extremely good fits to the field data. The third chapter presents a new approach to estimating growth parameters of reef fish from tagging data that exploits the disproportionate response of certain parameters to misestimates in the true age of the tagged individuals. The method works considerably better than the most widely used method when sample sizes are small, as is commonly the case in reef fish tagging studies where recapture rates tend to be low. The fourth and final chapter uses non-lethal stable isotope techniques to tease apart the invasion dynamics of Indo Pacific lionfish (Pterois spp.) that are currently colonising the wider Caribbean. The results show that lionfish exhibit habitat-specific ontogenetic shifts in prey selection, inflicting elevated mortality on small, bommie-dwelling fishes on forereefs but switching to seagrass-foraging invertivores as they grow. Lionfish also display ontogenetically shifting competition with native Nassau grouper (Epinephelus striatus), which may provide a greater barrier to invasion success on patch reefs than on fore reefs, where competitive overlap is diminished. The thesis concludes with a discussion of some lines of enquiry that could not be undertaken owing to time or data limitations, but which may hold as much interest for the reader as they do for the author.