The Rhodophyta (red algae) are an ancient crown group of the Eukarya (ca. 1400-1500 million years), comprised of 5000 - 6000 species. Gametophytes of taxa excluding the speciose Class Florideophyceae are typically of very simple unicellular, filamentous or foliose morphologies. These simple morphologies are often homoplasious (resulting from convergent or parallel evolution) and can be indistinguishable among distinct taxa, leading to cryptic species. As a result, historical morphology-based taxonomy is often not congruent with evolutionary history. Intraspecific genetic variation is not yet characterized for non-Florideophyceae taxa. Here the intraspecific genetic variation was characterized for a locally endemic, morphologically distinct bangiophyte red alga, Bangia maxima Gardner using inter simple sequence repeat (ISSR) patterns from 91 individual filaments across seven local populations. A high degree of genetic variation was observed over very small distances (< 25 cm) and very little genetic exchange was observed between populations. It is possible that B. maxima is a true endemic species and its population dynamics may differ from other Bangia species. Metrics of sequence-based identification rely on genetic divergence among isolates to distinguish taxonomic units independent of morphology. Such metrics are especially useful for morphologically simple or cryptic species. The mitochondrial cytochrome oxidase c subunit 1 gene has been proposed for the Florideophyceae. An evaluation of this gene as a metric for non-Florideophyceae taxa was undertaken and limited utility was demonstrated in most lineages of Rhodophyta due to poor or inconsistent amplification and conflicts with nuclear and plastid phylogenies. Patterns of genetic divergence among taxa are used to infer evolutionary relationships. The nuclear ribosomal small subunit (nSSU rRNA) is the taxonomically broadest pool of gene sequence data for the Rhodophyta. The use of stochastic models of nucleotide evolution is the most common approach to inferring phylogenies using this gene, ignoring much of its evolutionary information as different characters that contribute to secondary structure (e.g. paired nucleotides) are treated independently. The incorporation of structural information leads to more biologically realistic evolutionary models increasing phylogenetic resolution. Parametric models incorporating structural information were used here to more fully resolve phylogenies for all known Rhodophyta lineages. Novel phylogenetic topologies were observed and well supported for each Class within the Rhodophyta resulting in a number of formally proposed or suggested taxonomic revisions. These include phylogenetic resolution of Rhodophyta Classes, support for the introduction of 11 genera within the Bangiales and support for various taxonomic revisions within the Florideophyceae previously proposed but not yet fully adopted. As structure evolves more slowly than its constituent sequence, secondary structure elements can further resolve evolutionary relationships, especially in lineages as old as the Rhodophyta. A novel encoding of secondary structure elements and subsequent multivariate analysis was performed for all known Rhodophyta nSSU rRNA gene sequences, reinforcing phylogenetic results. Computer programs developed for these analyses are publicly available. The analyses presented here significantly advanced understanding of the evolutionary distribution of cryptic species within the Rhodophyta. Furthermore, useful methods for the characterization of such species are presented, as is a demonstration of the utility of biologically realistic sequence models parameterizing nSSU rRNA structure in resolving ambiguous phylogenetic relationships. Most importantly, this work also represents a significant improvement toward taxonomy congruent with evolutionary history for the Rhodophyta.

The horticultural industry is responsible for approximately half of the invasive plant introductions in North America. To reduce these introductions, voluntary initiatives are preferred over government regulations. This thesis aims to evaluate the effectiveness of two types of voluntary initiatives. At the gardener level, I investigated the effectiveness of alternative species promotion campaigns, called “Grow Me Instead” programs. Adult gardeners visiting the Royal Botanical Gardens in Hamilton, Ontario, as well as customers at two garden centres, participated in a conjoint analysis which measured their preferences for various traits of potential ground cover species. Results showed that gardeners generally prefer plant species having invasive characteristics, suggesting these programs may not be as effective as initially believed. At the retailer level, this study aimed to build upon the work done by Burt and colleagues (2007) to obtain further understanding of the relative strength of internal (ethical motivations) and external (legislation, stakeholder pressures and economic opportunities) factors for motivating participation in voluntary initiatives. Telephone interviews were conducted with 30 industry professionals from southern Ontario to assess their adoption of the St. Louis Voluntary Codes of Conduct. Results found that participation rates of industry professionals in southern Ontario were lower for every specific initiative than those interviewed by Burt et al. (2007). Industry professionals presently experience the most pressure to participate from a sense of personal responsibility and the desire to create a green business image. Pressure was significantly higher from these sources than from pressure from employees. Together these two studies identified several barriers to the efficacy of voluntary initiatives as well as some reasons for optimism. To ensure the success of future voluntary initiatives, efforts must be made to encourage these two groups to work together. Understanding how both retailers and gardeners respond to voluntary initiatives will assist in the development of more effective programs and lead to fewer horticultural invasive species introductions in the future.

Genetic diversity has rarely been the focus of study in species at risk in Canada. <i>Tradescantia occidentalis</i> is one of 157 species listed by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC 2005a). This species is nationally threatened due to the limited number of populations, their geographic isolation from each other and from the main distribution in the United States of America, and habitat loss. The National Recovery Team for Plants at Risk in the Prairie Provinces and the Alberta Western Spiderwort Recovery Team have called for research into the habitat requirements, demography, and genetic diversity of <i>T. occidentalis</i> in Canada. As a result, this study was designed to address the following objectives: 1) to conduct an inventory of the Canadian populations, 2) to investigate intra- and interpopulation genetic diversity in <i>Tradescantia occidentalis</i>, and 3) to provide recommendations for the conservation management of this species. <p>Information on demography and plant communities in <i>Tradescantia occidentalis</i> habitats indicated that the numbers of individuals in the Saskatchewan and Manitoba populations were similar to previous surveys; however, the Alberta population was significantly larger in number than prior estimates, indicating population growth. Taxonomic lists were prepared for each province in habitats with and without <i>T. occidentalis</i>. Community types, as separated by RA analysis, differed by province and not by association with <i>T. occidentalis</i>. Euphorbia esula, an invasive species in Canada, was observed in the Saskatchewan and Manitoba populations but was absent in Alberta. <p> Using amplified fragment length polymorphisms (AFLPs), genetic diversity was assessed at the intra- and interpopulation levels. Relatively low levels of intrapopulation variation were observed in Saskatchewan and Alberta, while higher levels were found in Manitoba. Gene flow via pollen or propagule transfer may account for higher genetic diversity among the closely situated Manitoba populations. The lack of correlation between dendrogram topology and geographic distribution suggests panmixia in all populations. Levels of intrapopulation diversity were low to moderate depending on primer combination used, indicating that populations are isolated within each province. <p>Information on population demography and genetic diversity are important within a conservation context. The large number of individuals within each population and the perceived increase in some populations suggest that the existing populations of <i>Tradescantia occidentalis</i> are relatively stable. Although levels of genetic diversity are low in Saskatchewan and Alberta compared to Manitoba, it appears that all populations are adapted to their local environments based on their apparent size and stability. The most viable conservation strategy for this species is in situ protection. This should include controlling invasive plant species, monitoring grazing, and preventing further habitat fragmentation. Ex situ methods must also be explored. Transplantation of individuals from one population to the next may not be a successful conservation strategy due to the moderate level of population differentiation. Alternatively, it is recommended that a seed bank from each population be implemented in case of a drastic population decline.

Flavonoids are of great interest for their antioxidant and health-promoting activities. Ascorbate (vitamin C) has antioxidant activities but also sometimes displays pro-oxidant activities <i>in vitro</i> and reportedly <i>in vivo</i>. This research investigated to what extent flavonoids moderate oxidative stress from vitamin C <i>in vivo</i>.<p>Dietary experiments were conducted in two phases using adult male Wistar rats. First, all animals were maintained for two weeks on a control flavonoid-free diet with the dietary requirement (27 IU) of vitamin E/kg diet. In the subsequent four weeks, the animals were treated in four groups (8 rats/group), being fed the following diets: flavonoid-free control (C), ascorbate-supplemented (7.55 mmol/kg diet) (A), flavonoid-supplemented (2.67 mmol/kg diet) (F) and flavonoids (2.67 mmol/kg diet) plus ascorbate (7.55 mmol/kg diet)-supplemented (T). Measurements were done on in vivo biomarkers of oxidative stress, tissue antioxidants and on tissue in vitro susceptibility to oxidative stress.<p>In the combined feeding of ascorbate plus flavonoids, endogenous thiobarbituric acid reactive substances (TBARS) increased in liver by 114%. No effects of dietary ascorbate or flavonoids were seen on endogenous TBARS in brain or heart, or on plasma thiols or erythrocyte fragility.<p><i>In vitro</i>, the susceptibility to TBARS formation of liver homogenate (incubated for 60 min at 37ºC in air) showed a significant 60% increase in ascorbate-fed animals compared to control, but no increase in animals fed ascorbate plus flavonoids, suggesting that the additional feeding of flavonoids helped to prevent the increase produced by ascorbate-feeding. Incubation of liver mitochondria with 300 µM ascorbate in vitro produced a large (2-7 fold) increase in TBARS, but there was no difference among mitochondria from the different feeding groups.<p>The ability of flavonoid-feeding in protecting against oxidative stress from ascorbate in vivo could not be demonstrated in this study, even showing pro-oxidant effects of flavonoids in combination with ascorbate in liver. However, in vitro tests in liver suggest a protective effect of flavonoid-feeding against susceptibility to oxidative stress from ascorbate. Further investigations are needed in order to resolve the differences observed in vitro and in vivo and to determine the endogenous effects of specific flavonoids under ascorbate-induced oxidative stress.

The fungus <i>Colletotrichum truncatum</i> (Schw.) Andrus and Moore causes lentil anthracnose, which is a major challenge to lentil production in Western Canada. The pathogen infects leaves and stems, resulting in defoliation, stem girdling, plant wilting, and possibly plant death. Two races, Ct0 and Ct1, have been identified in the pathogen population in Canada. However, the differences in the infection process between the two races have not been described in detail. Currently, several lentil cultivars, such as CDC Redberry, CDC Robin, CDC Rosetown, CDC Rouleau, and CDC Viceroy, have resistance against race Ct1, whereas there are no cultivars showing resistance to race Ct0. The objective of this study was to investigate differences in the infection process between race Ct0 and race Ct1 using the fully susceptible cultivar Eston and the race Ct1-resistant cultivar CDC Robin. Experiments on glass well slides showed that race Ct0 had no inherently different conidium germination rate compared to race Ct1, and that differences in conidium germination between the two races on lentil plants were the result of specific interactions between the two races and lentil resistance. Investigations of the infection process of the two races on detached and attached leaves of both lentil cultivars were conducted starting 12 h postinoculation (hpi) until 72 hpi, including conidium germination, appressorium formation, and leaf penetration. Results indicated that differences in virulence of the two races may be related to the ability of conidia to germinate and form appressoria, as well as the ability of primary infection hyphae to grow in response to cues from the lentil cultivars. Furthermore, resistance of lentil to isolates of race Ct1 appeared to involve an inhibition in and/or delay of the spread of primary infection hyphae inside the plant tissue. Results of infection studies of one isolate from each race on attached leaves did not completely agree with results of the same isolates on detached leaves. Based on this study, race Ct0 and race Ct1 do not appear to be classical physiological races, but may represent aggressive races or some intermediate forms.

<p>This dissertation focuses on solving some common problems associated with ecological field studies. In the core of the statistical methodology, lies spatial modeling that provides greater flexibility and improved predictive performance over existing algorithms. The applications involve prevalence datasets for hundreds of plants over a large area in the Cape Floristic Region (CFR) of South Africa.</p><p>In Chapter 2, we begin with modeling the categorical abundance data with a multi level spatial model using background information such as environmental and soil-type factors. The empirical pattern is formulated as a degraded version of the potential pattern, with the degradation effect accomplished in two stages. First, we adjust for land use transformation and then we adjust for measurement error, hence misclassification error, to yield the observed abundance classifications. With data on a regular grid over CFR, the analysis is done with a conditionally autoregressive prior on spatial random effects. With around ~ 37000 cells to work with, a novel paralleilization algorithm is developed for updating the spatial parameters to efficiently estimate potential and transformed abundance surfaces over the entire region.</p><p>In Chapter 3, we focus on a different but increasingly common type of prevalence data in the so called <italic>presence-only</italic> setting. We detail the limitations associated with a usual presence-absence analysis for this data and advocate modeling the data as a point pattern realization. The underlying intensity surface is modeled with a point-level spatial Gaussian process prior, after taking into account sampling bias and change in land-use pattern. The large size of the region enforces using an computational approximation with a bias-corrected predictive process. We compare our methodology against the the most commonly used maximum entropy method, to highlight the improvement in predictive performance.</p><p>In Chapter 4, we develop a novel hierarchical model for analyzing noisy point pattern datasets, that arise commonly in ecological surveys due to multiple sources of bias, as discussed in previous chapters. The effect of the noise leads to displacements of locations as well as potential loss of points inside a bounded domain. Depending on the assumption on existence of locations outside the boundary, a couple of different models -- <italic>island</italic> and <italic>subregion</italic>, are specified. The methodology assumes informative knowledge of the scale of measurement error, either pre-specified or learned from a training sample. Its performance is tested against different scales of measurement error related to the data collection techniques in CFR.</p><p>In Chapter 5, we suggest an alternative model for prevalence data, different from the one in Chapter 3, to avoid numerical approximation and subsequent computational complexities for a large region. A mixture model, similar to the one in Chapter 4 is used, with potential dependence among the weights and locations of components. The covariates as well as a spatial process are used to model the dependence. A novel birth-death algorithm for the number of components in the mixture is under construction.</p><p>Lastly, in Chapter 6, we proceed to joint modeling of multiple-species datasets. The challenge is to infer about inter-species competition with a large number of populations, possibly running into several hundreds. Our contribution involves applying hierarchical Dirichlet process to cluster the presence localities and subsequently developing measures of range overlap from posterior draws. This kind of simultaneous inference can potentially have implications for questions related to biodiversity and conservation studies. .</p> / Dissertation

<p>The effects of climate change on forest dynamics will be determined by tree responses at different life-stages and different scales -- from establishment to maturity and from individuals to populations. Studies incorporating local factors, such as natural enemies, competition, or tree physiology, with sufficient variation in climate are lacking. The importance of global and regional climate variation vs. local conditions and responses is poorly understood and may only be addressed with large datasets capturing sufficient environmental variation. This dissertation uses several large datasets to examine tree demographic and ecophysiological responses to light, moisture, predation, and climate in eastern temperate forests of North Carolina. </p><p> First, I use a 19-yr seed rain record from 13 forest plots in the piedmont, transition zone, and mountains to examine how climate-mediated seed maturation and density-dependent seed predation processes increase population reproductive variation in nine temperate tree species (Chapter 1). I address several hypotheses explaining interannual reproductive variation, such as resource matching, predator satiation, and pulse resource dynamics. My results indicate that (1) interannual reproductive variation increased as a result of seed maturation and seed predation processes, (2) seed maturation rates increased under warm, wet conditions, and (3) seed predation rates exhibited negative and positive density-dependence, depending of tree species and type of seed predator (specialist insects vs. generalist vertebrates). Because positive density-dependent seed predation dampened and negative density-dependent seed predation amplified the effects of climate-mediated maturation on reproductive variation, this study showed evaluations of tree reproduction need to incorporate both climate and seed predation.</p><p> Next, I use an 11-yr record of annual tree seedling growth and survival in 20 tree species planted in the piedmont and mountains to quantify individual tree seedling growth and survival responses to spatial variation in resources and temporal variation in climate (Chapter 2). First, I tested whether height-mediated growth provides an advantage to large individuals in all environments by amplifying responses to light and moisture or only when those resources were plentiful. Second, I tested whether allometric and survival responses differed among species based on life-history strategies. Individual height amplified tree seedling growth. However, some species exhibited amplification at moderate to high resource levels as well as depression of growth in large individuals growing in low light and moisture environments. Shade intolerant species exhibited an increasing ratio of height to diameter growth and increasing survival probability with both increasing light and moisture resources. Conversely, shade tolerant species exhibited decreasing height to diameter ratio with increasing light, possibly because of biomass allocation toward acquisition of limiting light resources. Despite relative small effects of drought and winter temperature of tree seedling demography, the results of this study indicate that individual tree seedlings sensitive to light and moisture environments, such as large seedlings and seedlings of shade intolerant species, growing in shaded or xeric sites may be particularly vulnerable to climate induced mortality. </p><p> Finally, I examine interannual and interspecific variation in canopy conductance using four years of environmental (vapor pressure deficit, above canopy light, and soil moisture) and stem sap flux data from heat dissipation probes for six co-occurring tree species. I developed a state-space modeling framework for predicting canopy conductance and transpiration which incorporates uncertainty in canopy and observation uncertainty. This approach is used to evaluate the degree to which co-occur deciduous tree species exhibited drought tolerating and drought avoiding canopy responses and whether these patterns were maintained in the face of interannual variation in environmental drivers. Comparisons of canopy conductance responses to environmental forcing across species and years highlighted the importance of tree sensitivity to moisture limitation, both in terms of high vapor pressure deficit and low soil moisture, and tree hydraulic characteristics within diverse forest communities. The state-space model produced similar parameter estimates to the more traditional boundary line analysis, performed well in terms of in-sample and out-of-sample prediction of sap flux observations, and provided for coherent incorporation of parameter, process, and observation errors in predicting missing data (i.e., gap-filling), canopy conductance, and transpiration.</p><p> Much needs to be learned about forest community responses to climate change, however these responses depend on local growing conditions (light and moisture), the life-stage being examined (seedlings, juveniles, or mature trees), and the scale of inference (individuals, canopies, or populations). Because climate change will not occur in isolation from other factors, such as stand age or disturbance, studies must characterize tree responses across multidimensional gradients in growing conditions. This dissertation addresses these challenges using large demographic and ecophysiological datasets well-suited for global change research.</p> / Dissertation

There is a great challenge to deal with psychid taxonomy due to the sexual dimorphism and conservative morphology of male. The genus Eumeta is widely distributed among Asia, Australia and Africa, with taxa resembling each other in morphological aspects. This historical confusion was originated from misidentification of type specimen and difficulty of specimen vouchering. Previous studies also recorded Eumeta of Taiwan, but taxa still uncertain actually. In present study, reared specimens were used to acquire morphology of different development and larval case style, and corroborated each other with barcode of life. As the results, Eumeta minuscula and E. variegata were confirmed in Taiwan. A highly variation of male morphology with genitalia asymmetry were described. Additionally, the male 8th tergite and sternite were suggested valuable for species identification. Having examined the type series specimen and original description, 13 species distributed in orient were grouping. Except E. minuscula and E. crameri were smaller and identifiable, a mass of ambiguous species included E. variegata, E. maxima, E. layardi, E. japonica, E. pryeri, E. sikkima, E. wallacei, E. javanica, E. wallacei var. bougainvillea, E. formosicola and E. kiushiuana were defined as E. variegata species-complex, and then revised this complex mainly with Taiwanese specimens. Due to the morphological variety of whole examination involving with those of Taiwan, 8 species were treated as junior synonym of E. variegata, excluding E. japonica, E. javanica and E. kiushiuana that remain undetermined because the types have not examined. Preliminary result of molecular work also supported this treatment as well, except an individual of China (Yunnan) that more information is needed.

The avian influenza virus can be transmitted from sick birds to other birds by fecal and oral secretion. Therefore, when birds with avian influenza virus enter domestic bird farms and make contacts, it is possible to carry the virus in and transmit it to domestic birds. Since the outbreak of the avian influenza in Taiwan, most bird farms had set up the screen. Yet, the actual effectiveness of screen coverage rate has not been researched. This study will discuss further regarding the results of different screen coverage rate in preventing wild birds¡¦ entering to poultry farms in Kaohsiung area. Field observations were carried out at the wetlands in Kaohsiung county, including Old Railroad Bridge artificial wetland, Fongshan reservoir and 20 poultry farms which were less than five kilometers away from wetlands from September 2008 to October 2009. Chicken and duck farms were analyzed respectively, and the screen coverage rate was categorized into full, partial and no coverage, respectively. The aims of the study were to investigate the effect of screen coverage on the entrance of wild birds to the farms, and found out the potential bridge species near poultry farms. By observing different levels of screen coverage in poultry farms, migratory birds¡¦ activity, and the contact situation between wild and domestic birds, we can analyze the contact level of high risk species and speculate possible transmission path of the avian influenza, and understand the effectiveness of the screens. Also, showing the correlation between the density of domestic poultry and the number of wild bird enterance. The result showed, in terms of screen with different coverage rates, the number of bird species within the duck farms had significant different in full and no coverage. The number of total birds within the duck and chicken farms with full coverage was significant less than partial coverage. Both in chicken and farms, screen had a great effectively in preventing small sized birds entering, yet not on big sized birds. The density of domestic poultry and the number of wild bird enterance showed negative correlation only in chicken farms with partial coverage. In terms of the wild land birds entering poultry farms, Passeer montanus is the largest species, followed by Hirundo rustica and Streptopelia tranquebarica. As for aquatic birds, it is mainly of Ardeidae, Scolopacidae, Charadriidae and Rallidae. Among all, Passeer montanus, Hirundo rustica, Streptopelia tranquebarica, and Bubulcus ibis are not migratory birds and highly pathogenic avian influenza virus species which move between poultry farms and wetlands. Therefore, they were considered bridge species. Due to the bridge species makes direct contacts with poultry, it might be the spreader of the virus. Decreasing the possibility of wild birds¡¦ contact with poultry is an important mechanism for avian influenza control. Also, based on the model of European Food Safety Authority (ESFA), risk assessments will be conducted on Kaohsiung County wetland¡¦s migratory birds¡¦ highly pathogenic avian influenza virus H5N1 transmission to poultry farms.

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