We report on a small collection of parachuting frogs from Sumatra and Java. Three new species are described. Rhacophorus achantharrhena is similar to R. dulitensis and R. prominanus and differs from these species by a suite of characters including morphology of the supratympanic fold, digital webbing, coloration, and morphometrics. These three species are unusual in having white visceral and parietal peritonea. Rhacophorus catamitus is a small species similar to R. angulirostris and differing from this species by having a calcar at the heel and reduced digital webbing. Rhacophorus barisani resembles R. baluensis but differs from this species in color pattern, habitus, webbing of the fingers, and morphology of the dermal appendages. A new specimen of Sumatran R. pardalis is described and compared to the holotype of R. pulchellus. Rhacophorus prominanus is reported from Gunung Rajabasa, Lampung. Two specimens are described and compared to Bornean R. dulitensis and R. prominanus from the Malay Peninsula. Rhacophorus tunkui Kiew is a junior subjective synonym of Rhacophorus prominanus Smith. Finally, we describe new specimens of Rhacophorus margaritifer from Cibodas, Java, Skeletons of the new species and of R. margaritifer are described in detail. Superficial jaw and throat musculature appears to be relatively conservative within the genus.

Place-based biological conservation planning and recovery delineates “places” – spatial extents with favourable conditions for the recovery and management of multiple species simultaneously. Places represent geographic areas where constituent species are more likely to benefit from a specific set of recovery and management actions. Currently, place-based conservation planning is focused on prioritizing already-identified places. Findlay and McKee (2016) propose an approach to identify and delineate places by grouping geographical units based on species-at-risk (SAR) co-localization in (a) geographical, and (b) threat space. The following research is a practical application of the Findlay-McKee Methodology (FMM), using southern Ontario as a case study. I develop a parameterized algorithm to operationalize the design principles laid out in the FMM. I first define metrics to characterize the variation in SAR overlap and the degree to which sets of SAR share common threats. Next, I explore how the spatial extent of places (place size) changes as a function of tolerance for dissimilarity in both measures. The case study allowed me to evaluate the benefits and limitations of the FMM. I conclude that the FMM has the potential to be a defensible method for characterizing places based on SAR community overlap and inter-species threat similarity. However, the FMM’s applicability is limited by the availability of datasets at an appropriate resolution for analysis; uncertainty in selecting appropriate thresholds of tolerance for dissimilarity; and the criteria used to designate seed planning units. Given the increasing popularity of multi-species and ecosystem level recovery and conservation management, developing an efficient and effective process to guide place selection is crucially important. I recommend further research focus on empirically determining the number of places in a planning region and identifying at what tolerance thresholds places lose their ability to delineate areas where a comparatively small number of recovery actions will confer widespread benefits.

An intensive sampling of all ant species encountered on 6 Hawaiian Islands: Big Island, Maui, Oahu, Kauai, Molokai, and Lanai took place between 1988 and 1996. Species presence and absence was recorded at each site. Using remote sensing, variables were added insitu and used throughout my analysis. Species accumulation curves suggest that sampling was comprehensive. There is a significant trend between island area and species richness which validates the Theory of Island Biogeography for invasive species. Islands were found to be significantly nested by area, order, and tourism. Cluster analysis shows a link between elevation, land-use and island, and species presence. Predictive models can be built to predict spread of particular ant species as they continue toward equilibrium.

Buffelgrass (Pennisetum ciliare (L.) Link), a non-native perennial bunchgrass, invades ecologically intact areas of the Sonoran Desert. It competitively excludes native plants and increases fire frequency and intensity. Since the 1990s, whole buffelgrass plants have been manually uprooted and removed to control the invasion in southern Arizona. Uprooting plants results in bare, disturbed soil which promotes buffelgrass seed germination. This study examined whether leaving entire uprooted buffelgrass plants (thatch) on a field site reduces future buffelgrass establishment compared to removing uprooted plants from the site. A secondary goal was to determine whether light reduction and autoallelopathy were major factors in the negative effect of thatch on buffelgrass seedling density. Field plots with an average of 8,095 kg/ha thatch had 1.9 buffelgrass seedlings/m(2) which was significantly fewer than the 2.9 seedlings/m(2) in plots without thatch. Thatched portions of thatch plots (50% of their total area) had only 0.7 seedlings/m(2). In the greenhouse, which reduced outdoor light intensity by 35.2%, buffelgrass seeds sown in bare soil resulted in significantly higher seedling density than beneath buffelgrass thatch. Potential autoallelopathic chemicals leached from partially decomposed buffelgrass thatch and leached thatch had an intermediate but not significant (p = 0.09) effect on seedling numbers. Results suggest that leaving uprooted buffelgrass plants has the benefit of reducing seedling establishment in the area disturbed by uprooting.

From all the species that arrive to a novel environment, very few manage to form a viable population. The guppy, a very successful invader, is a highly social species that performs some of its vital tasks (e.g., foraging, avoiding predators) in groups. This thesis aimed to quantify heterospecific association benefits that enhance invasion success. Interactions between invaders and natives could be one of the environmental characteristics of a place that increase its risk of invasion. I evaluated the tendency of an invasive species to associate with native individuals with similar ecological requirements. I tested the hypothesis that invaders gain exploring, acquisition of information and foraging benefits when socializing with natives. In these experiments I used the guppy as the invasive model species and endangered native Mexican topminnows (Poeciliopsis infans, Skiffia bilineata, Ameca splendens, Zoogoneticus tequila, Xenotoca eiseni and Girardinichthys viviparous). I found that guppies shoal with other species in Trinidad (Poecilia picta and Poecilia sphenops), where they are native (Chapter 2) and that this trait remains when they are invasive (Chapter 3). Guppies are equally willing to explore novel environments when accompanied by heterospecifics or conspecifics. Guppies are more willing to explore complex environments than simple ones. Moreover, when exploring simple environments they have a higher association tendency, regardless of the partner' species (Chapter 4), which could lead them to acquire the benefits of grouping behaviour and avoid Allee effects - the disadvantages of being part of a small group. In the contexts in which they were tested guppies gained as much information by associating with heterospecifics as with conspecifics (Chapter 5). Finally, I found that when shoaling in bigger shoals guppies are able to locate food faster and spent more time foraging. The benefits of increased shoal size were maintained when the additional guppies were replaced with heterospecifics. However, they derive more benefits from the species they are more willing to associate with (Chapter 6). These results uncover a mechanism enabling founding individuals to survive during the most vulnerable phase of an invasion and help explain why guppies have established viable populations in many parts of Mexico as well as in every continent except Antarctica.

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Sepsis-related multiple organ dysfunction syndrome is a leading cause of death in intensive care units. There is overwhelming evidence that oxidative stress plays a significant role in the pathogenesis of sepsis-associated multiple organ failure; however, reactive oxygen species (ROS)-associated biomarkers and/or diagnostics that define mortality or predict survival in sepsis are lacking. Lung or peripheral blood gene expression analysis has gained increasing recognition as a potential prognostic and/or diagnostic tool. The objective of this study was to identify ROS-associated biomarkers predictive of survival in patients with sepsis. In-silico analyses of expression profiles allowed the identification of a 21-gene ROS-associated molecular signature that predicts survival in sepsis patients. Importantly, this signature performed well in a validation cohort consisting of sepsis patients aggregated from distinct patient populations recruited from different sites. Our signature outperforms randomly generated signatures of the same signature gene size. Our findings further validate the critical role of ROSs in the pathogenesis of sepsis and provide a novel gene signature that predicts survival in sepsis patients. These results also highlight the utility of peripheral blood molecular signatures as biomarkers for predicting mortality risk in patients with sepsis, which could facilitate the development of personalized therapies.

Nos recherches abordent, par une approche multidisciplinaire, l’écologie spatiale et la dynamique d’invasion du ravageur de l’épicéa Ips typographus (Coleoptera : Scolytinae) en Belgique. Bien que cette espèce ne puisse pas être considérée au sens strict comme invasive en Belgique où elle est implantée depuis le milieu du 19ème siècle, de très vraisemblables introductions de souches exotiques en provenance de Russie et des Pays baltes, en font un modèle exceptionnel pour l’étude de ces processus. Une analyse en milieu urbain, suivant des transects centre-périphérie, a d’une part suggéré l’introduction probable de ces souches exotiques et d’autre part permis d’étudier ce ravageur forestier dans un milieu qui lui est a priori défavorable. Il en résulte que, malgré un effet de la structure urbaine sur l’abondance du scolyte, sa présence a été observée partout, y compris dans les zones densément bâties du centre de Bruxelles. Cela suggère, en terme de dispersion, que cette espèce est capable d’atteindre des arbres isolés, et en terme d’infestation, que tout épicéa constitue un hôte potentiel tant en milieu forestier qu’en milieu ouvert ou urbain. Une étape préliminaire dans l’estimation des risques liés aux invasions biologiques est d’effectuer une analyse de filière, afin d’analyser les différentes voies d’introduction et les risques liés aux pays d’origine des marchandises importées. Sur base de l’analyse de l’ensemble des sources de données statistiques disponibles, nous avons déterminé l’ampleur du commerce de grumes d’épicéa entre l’est de l’Europe et la Belgique, les modes de transport utilisés, les origines et destinations des grumes, ainsi que la variabilité de la localisation et du nombre des différents points d’entrée de ces marchandises sur le territoire belge d’une année à l’autre, depuis le début des importations en 1996. Notre analyse illustre les difficultés inhérentes à ce genre d’étude, particulièrement au niveau de la disponibilité des données à une échelle appropriée. Par une approche de modélisation, nous avons envisagé différents scénarios de dispersion de souches introduites d’Ips typographus afin d’estimer l’expansion de celles-ci en Belgique. Notre modèle a permis de mettre en évidence l’importance de la bonne connaissance de certains paramètres biologiques caractétistiques de l’espèce étudiée (phénologie, capacité de dispersion, taux de croissance). Par ailleurs, les volumes d’importation et la localisation des points d’entrée des marchandises semblent jouer un rôle secondaire. Enfin, nous avons utilisé des marqueurs génétiques afin d’essayer de prouver l’introduction de souches russes et baltes du scolyte de l’épicéa en Belgique. Des échantillons ont été collectés dans neuf pays européens ainsi que sur l’ensemble du territoire wallon. La structure génétique observée n’a pas permis de mettre en évidence une différenciation entre les populations de l’est et de l’ouest de l’Europe. La présence d’haplotypes communs à l’est et à l’ouest rejoint l’hypothèse d’une homogénéisation des populations en relation avec le large pouvoir de dispersion du typographe. Cependant, un grand nombre de mutations a été observé entre 2 haplotypes. Des introductions d’origines lointaines telles que la Sibérie ne sont donc pas improbables. Les résultats détaillés de chacune de ces études sont développés dans les différents articles constituant cette thèse. La discussion générale met ceux-ci en relation et aborde les perspectives découlant de nos recherches.

Probabilistic models have been successfully applied for a wide variety of problems, such as but not limited to information retrieval, computer vision, bio-informatics and speech processing. Probabilistic models allow us to encode our assumptions about the data in an elegant fashion and enable us to perform machine learning tasks such as classification and clustering in a principled manner. Probabilistic models for bio-acoustic data help in identifying interesting patterns in the data (for instance, the species-specific vocabulary), as well as species identification (classification) in recordings where the label is not available. The focus of this thesis is to develop efficient inference techniques for existing models, as well as develop probabilistic models tailored to bioacoustic data. First, we develop inference algorithms for the supervised latent Dirichlet allocation (LDA) model. We present collapsed variational Bayes, collapsed Gibbs sampling and maximum-a-posteriori (MAP) inference for parameter estimation and classification in supervised LDA. We provide an empirical evaluation of the trade-off between computational complexity and classification performance of the inference methods for supervised LDA, on audio classification (species identification in this context)as well as image classification and document classification tasks. Next, we present novel probabilistic models for bird sound recordings, that can capture temporal structure at different hierarchical levels, and model additional information such as the duration and frequency of vocalizations. We present a non-parametric density estimation technique for parameter estimation and show that the MAP classifier for our models can be interpreted as a weighted nearest neighbor classifier. We provide an experimental comparison between the proposed models and a support vector machine based approach, using bird sound recordings from the Cornell Macaulay library. / Graduation date: 2011 / Access restricted to the OSU Community at author's request from Dec. 30, 2010 - Dec. 30, 2011

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