Biodiversity across the globe is threatened. Rapid surveying and monitoring techniques are required to understand the origin of the threats to biodiversity and to enable conservation actions to be undertaken. Kuwait is an arid desert country with a small flora of only 402 species. This flora is endangered by environmental factors, overgrazing, and human activities. DNA barcoding the flora and using Next Generation Sequencing (NGS) technologies allowed us to identify plants to species level, conduct a molecular taxonomic revision, and distinguish plant diversity found in soil environmental DNA samples. After investigating the discriminatory power of five commonly used DNA markers from plastid (matK, rbcL, trnH-psbA, trnL) and a nuclear genome (ITS2) on four largest genera of the flora using phylogenetics reconstruction tree based methods, two barcoding markers (rbcL and ITS2) were assigned to build a DNA reference library of the flora. Furthermore, the DNA reference library was tested to identify the plant diversity found below-ground level and comparing it with that above-ground, using environmental soil samples collected from both species rich and poor habitats in Kuwait by applying high-throughput sequencing methods. The DNA database provided in this study could be used as a reference library for the identification process and contribute towards the future of molecular taxonomy, biodiversity and ecological research in Kuwait.

abstract: Novel resource inputs represent an increasingly common phenomenon in ecological systems as global change alters environmental factors and species distributions. In semiarid riparian areas, hydric pioneer tree species are being replaced by drought-tolerant species as water availability decreases. Additionally, introduced omnivorous crayfish, which feed upon primary producers, allochthonous detritus, and benthic invertebrates, can impact communities at multiple levels through both direct and indirect effects. In arid and semiarid systems of the American Southwest, crayfish may be especially important as detrital processors due to the lack of specialized detritivores. I tested the impact of virile crayfish (Orconectes virilis) on benthic invertebrates and detrital resources across a gradient of riparian vegetation drought-tolerance using field cages with leaf litter bags in the San Pedro River in Southeastern Arizona. Virile crayfish increased breakdown rate of drought-tolerant saltcedar (Tamarix ramosissima), but did not impact breakdown of Fremont cottonwood (Populus fremontii), Gooding's willow (Salix goodingii), or seepwillow (Baccharis salicifolia). The density and composition of the invertebrate community colonizing leaf litter bags were both heavily influenced by litter species but not directly by crayfish presence. As drought-tolerant species become more abundant in riparian zones, their litter will become a larger component of the organic matter budget of desert streams. By increasing breakdown rates of saltcedar, crayfish shift the composition of leaf litter in streams, which in turn may affect the composition and biomass of colonizing invertebrate communities. More research is needed to determine the full extent to which these alterations change community composition over time. / Dissertation/Thesis / M.S. Biology 2012

Environmental degradation is accelerating worldwide, yet environmental conservation remains limited by funding. Tackling this limitation requires not only absolute increases in funding, but improved prioritisation of actions. On a global scale island ecosystems are of high priority, with invasive species one of their most significant threats. In this thesis I investigate prioritisation of invasive grazing species control, incorporating ecological, economic, and social concerns, on the island of Bonaire, Caribbean Netherlands. To enable the trade-off of potential grazer control options for their ecological impacts I modelled the relationship between of grazer density and vegetation, and watershed vegetation and the coral reef. I found negative relationships for goat and pig grazing with grass presence, and for donkey grazing with ground cover. Coral cover below 10m showed a positive relationship to ground cover, and, surprisingly, a negative relationship to tree biomass. Because conservation action is most likely to be sustainable when connected to funding, I conducted choice experiments with SCUBA divers, which estimated a positive willingness to pay for reef health improvements achieved using terrestrial grazer control. Through communication with local policy makers and practitioners I identified three options for grazer control, eradication, population reduction, or fencing, and estimated costs and social acceptability for each option. Though the ecological models predicted eradication to have the highest impacts on the terrestrial and marine ecosystem, lower costs and higher social acceptability identified fencing as the most suitable option for grazer control on Bonaire in the short term, with the potential to be funded through a fee on SCUBA divers. Through linking ecological, economic, and social considerations within a real world conservation context I illustrate the importance of looking beyond only ecological improvements when prioritising conservation action. This research is directly applicable to policy and practise on Bonaire.

Philosophiae Doctor - PhD (Biotechnology) / High temperature stress is synonymous with the attenuation of plant growth, metabolism and eventually death resulting in major loss of crop productivity worldwide. Part of the metabolic perturbations associated with heat stress leads to the excessive formation of reactive oxygen species (ROS), which have highly deleterious effects on cellular homeostasis. Naturally, through millions of years of evolution and adjustment, plants have developed antioxidant enzymes that neutralize harmful ROS species offering a protective role in the annulment of oxidative damage in response to high temperature. The aim of this study was to measure the activity of several antioxidant enzymes in response to heat stress in Zea mays.

Submitted by CAMILA CHIODA DE ALMEIDA (milachioda@gmail.com) on 2018-08-03T16:19:20Z No. of bitstreams: 1 Camila_doutorado tese definitiva.pdf: 1977508 bytes, checksum: 8f88b2d3a8deefe001caf55b7c3ef036 (MD5) / Approved for entry into archive by Neli Silvia Pereira null (nelisps@fcav.unesp.br) on 2018-08-03T18:26:54Z (GMT) No. of bitstreams: 1 almeida_cc_dr_jabo.pdf: 1977508 bytes, checksum: 8f88b2d3a8deefe001caf55b7c3ef036 (MD5) / Made available in DSpace on 2018-08-03T18:26:54Z (GMT). No. of bitstreams: 1 almeida_cc_dr_jabo.pdf: 1977508 bytes, checksum: 8f88b2d3a8deefe001caf55b7c3ef036 (MD5) Previous issue date: 2018-07-04 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Assim como nos bovinos, a búfala pode ter mastite, sendo o Staphylococcus aureus o principal causador desta enfermidade. No entanto, é possível que sua prevalência possa estar superestimada. Este estudo objetivou comparar métodos fenotípico e genotípico na identificação de S. aureus em amostras de leite bubalino e ambiente de ordenha bem como propor uma nova PCR quantitativa em tempo real para identificação do mesmo. Para isso, de um total de 408 amostras obtidas de leite de búfalo, ambiente de ordenha e mãos de ordenhadores, 32 cepas presuntivas de S. aureus foram identificadas com base em seu crescimento fenotípico característico em ágar Baird Parker, reações positivas de Gram e catalase, capacidade de coagular plasma de coelho, e resultado positivo no ensaio de PCR Sa442 específico para a espécies. No entanto, testes adicionais revelaram que destas 32 estirpes, apenas 10 isolados apresentaram resultado positivo na aglutinação em látex, incluindo um S. chromogenes e um S. agentis. A análise de MALDI-TOF MS revelou que oito das 32 cepas eram S. aureus, 19 S. chromogenes, três S. agnetis e uma S. xylosus. Todas as oito cepas identificadas como S. aureus pela análise de MALDI-TOF e confirmadas pelo sequenciamento do 16S rRNA foram positivas na PCR do gene cydB específico para S. aureus. Além disso, foi encontrada uma cepa positiva para o gene sea, nove para o gene cna, uma para o gene sei, duas para o gene sem, uma para o gene seg, seis para o gene seh, 15 para o gene eno 11 para o gene ebps duas para o gene fib e 14 para o gene fnbA. Das cepas Isoladas, apenas uma apresentou resistência a clindamicina, uma a vancomicina, uma para a rifampicina, nove para a penicilina, 15 para a eritromicina, duas para a ciprofloxacina e três para o cotrimoxazole. Resistência a dois antimicrobianos foi observado em oito cepas, a três antimicrobianos em uma cepa e a quatro antimicrobianos em uma cepa. Finalmente, sete das oito cepas de S. aureus foram positivas para a nova PCR em tempo real do gene coa, duas das 19 cepas S. cromogenes e a única cepa de S. xylosus também foram positivas. Em conjunto, nossos achados sugerem que S. agentis e S. chromogenes podem ser identificados erroneamente como S. aureus pelos testes de aglutinação em látex, PCR para Sa442 PCR e Staphyclin latex enquanto MALDI-TOF MS e um teste de PCR cydB específico para S. aureus podem identificar com precisão S. aureus de leite de búfala e amostras ambientais e que estas cepas podem apresentar genes que codificam enterotoxinas e resistência aos antimicrobianos. / Like cattle, buffalo may have mastitis, with Staphylococcus aureus being its main cause. However, it is possible that its prevalence may be overestimated. This study aimed to compare phenotypic and genotypic methods for S. aureus identification in samples of buffalo milk and milking environment as well as to propose a new quantitative real time PCR for its identification. For this, a total of 408 samples obtained from buffalo milk, milking environment and milkers hand, 32 presumed S. aureus strains were identified based on their characteristic phenotypic growth in Baird Parker agar, positive reactions of Gram and catalase, ability to coagulate rabbit plasma, and positive result in the species-specific Sa442 PCR assay. However, additional tests revealed that of these 32 strains, only 10 isolates tested positive for latex agglutination, including a S. chromogenes and a S. agentis. Analysis of MALDI-TOF MS revealed that eight of the 32 strains were S. aureus, 19 were S. chromogenes, three were S. agnetis and one was S. xylosus. All eight strains identified as S. aureus by MALDI-TOF analysis and confirmed by 16S rRNA sequencing were positive in S. aureus specific cydB gene PCR. In addition, a positive strain was found for the sea gene, nine for the cna gene, one for the sei gene, two for the sem, one for the seg gene, six for the seh gene, 15 for the eno 11 gene for the gene ebps two for the fib gene and 14 for the fnbA gene. Of the isolates, only one showed resistance to clindamycin, one to vancomycin, one to rifampicin, nine to penicillin, 15 to erythromycin, two to ciprofloxacin and three to cotrimoxazole. Resistance to two antimicrobials was observed in eight strains, three antimicrobials in one strain and four antimicrobials in one strain. Finally, seven of the eight strains of S. aureus were positive for the new real-time PCR of the coa gene, two of the 19 S. chromogenes strains and the only strain of S. xylosus were also positive. Taken together, our findings suggest that S. agentis and S. chromogenes can be misidentified as S. aureus by the agglutination assays of Sa442 PCR and Staphyclin latex while MALDI-TOF MS and a cydB PCR test specific for S. aureus can identify with accurate S. aureus of buffalo milk and environmental samples and that these strains may have enterotoxin genes and antimicrobial resistance genes in buffaloes.

Submitted by Johnsson Rodrigo (r.johnsson@gmail.com) on 2013-09-02T11:56:44Z No. of bitstreams: 1 RAFAEL.pdf: 2923056 bytes, checksum: ed2c8fd6018c384a933ac0da4bea2317 (MD5) / Approved for entry into archive by Alda Lima da Silva(sivalda@ufba.br) on 2013-09-26T18:15:11Z (GMT) No. of bitstreams: 1 RAFAEL.pdf: 2923056 bytes, checksum: ed2c8fd6018c384a933ac0da4bea2317 (MD5) / Made available in DSpace on 2013-09-26T18:15:11Z (GMT). No. of bitstreams: 1 RAFAEL.pdf: 2923056 bytes, checksum: ed2c8fd6018c384a933ac0da4bea2317 (MD5) / CAPES, FAPESB, CNPq / A revisão da família Hylidae realizada recentemente (2005) teve como base principalmente caracteres moleculares e examinou 228 das 860 espécies conhecidas para a referida família. Os autores apontaram lacunas deixadas em seu trabalho, entre elas uma carência de teste de monofilia para o possível clado de Dendropsophus decipiens. Com o objetivo de testar a monofilia do grupo de D. decipiens e explorar seu relacionamento interno realizei uma análise filogenética usando uma abordagem morfológica com 82 caracteres de morfologia externa e esqueleto cranial das formas adultas e larvares de 31 táxons. Foi obtida uma árvore mais parcimoniosa apenas de 470 passos, valores de suporte alto para o grupo de D. decipiens (também para os outros grupos incluídos na análise) e baixos para as relações entre os grupos. A monofilia do grupo de Dendropsophus decipiens é suportada com base em oito sinapomorfias (2 da larva e 6 do adulto) e a hipótese de relacionamento entre as espécies obtida é (D. berthalutzae (D. haddadi (D. decipiens, D. oliveirai))). Dos caracteres apontados para definir formalmente o grupo apenas a posição de início da nadadeira dorsal na junção do corpo com a cauda e coloração da cauda congruem com as sinapomorfias aqui encontradas. Da discussão que historicamente envolve a diferenciação do grupo de D. decipiens em relação ao grupo de D. microcephalus, aqui é observado que as diferenças refletem o caráter único do girino deste último grupo de espécies. Com base nos resultados obtido aqui recomendo o reconhecimento do grupo de D. decipiens como unidade independente do grupo de D. microcephalus. Uma descrição do girino de D. haddadi é provida. / Salvador

Medical cartography can provide valuable insights into the epidemiology and ecology of infectious diseases, providing a quantitative representation of the distribution of these pathogens. Such methods therefore provide a key step in informing public health policy decisions ranging from prioritising sites for further investigation to identifying targets for interventions. By increasing the resolution at which risk is defined, policymakers are provided with an increasingly informed approach for considering next steps as well as evaluating past progress. In spite of their benefits however, global maps of infectious disease are lacking in both quality and comprehensiveness. This thesis sets out to investigate the next steps for medical cartography and details the use of species distribution models in evaluating global distributions of a variety of zoonotic diseases of public health importance. Chapter 2 defines a methodology by which global targets for infectious disease mapping can be quantitatively assessed by comparing the global burden of each disease with the demand from national policymakers, non-governmental organisations and academic communities for global assessments of disease distribution. Chapter 3 introduces the use of boosted regression trees for mapping the distribution of a group of vector-borne diseases identified as being a high priority target, the leishmaniases. Chapter 4 adapts these approaches to consider Ebola virus disease. This technique shows that the West African outbreak was ecologically consistent with past infections and suggests a much wider area of risk than previously considered. Chapter 5 investigates Marburg virus disease and considers the variety of different factors relating to all aspects of the transmission cycle that must be considered in these analyses. Chapters 6 and 7 complete the mapping of the suite of viral haemorrhagic fevers by assessing the distribution of Crimean-Congo haemorrhagic fever and Lassa fever. Finally, Chapter 8 considers the risk that these viral haemorrhagic fevers present to the wider African continent, quantifying potential risk of spillover infections, local outbreaks and more widespread infection. This thesis addresses important information gaps in global knowledge of a number of pathogens of public health importance. In doing so, this work provides a template for considering the global distribution of a number of other zoonotic diseases.

Meadows are critical in arid and semi-arid Argentinean Patagonia because of their importance for regional biodiversity. Despite this, little information on the spatial distribution of meadows is available and no analysis of the potential effect of climate change on meadows has been performed, which hampers conservation planning. In this study, I modeled the spatial distribution of meadows and investigated how climate change may affect the current distribution of meadows in arid and semiarid Patagonia by 2050. In addition, I investigated conservation status and areas of desertification vulnerability of those areas predicted to contain meadows. I used high-resolution imagery available in Google Earth software to visually estimate presence and absence of meadows. To model current and future distribution of meadows I used these observations and different socio-environmental predictor variables. I implemented generalized linear, additive, boosting, and random forest models, as the basis for a mean ensemble technique. I predicted future distribution of meadows using four different general circulation models and the A2 SERES scenario. The final ensemble model was an accurate representation of the current distribution of meadows in Patagonia and indicates they are severely under-represented within protected areas. I determined that overall meadow abundance is going to decrease by 2050 given the changes in climate. However, there were two contrasting trends: severe reduction of meadows in northwest Patagonia and Tierra del Fuego Island, and an expansion of suitable areas for meadows in the south and a small section in the northwest. This first regional map of meadow distribution across Argentinean Patagonia and information on meadows vulnerability to climate change represent key information for planning actions to conserve this critical habitat.

There are numerous examples of how exotic insect pests and pathogens have altered the dominance of native tree species and the ecological processes and function related to those species. While targeted species may persist in a functionally altered state via vegetative sprouting, the widespread decimation of a species can have dramatic direct and indirect consequences for organisms in multiple trophic levels. Devastation due to alien insect herbivores poses the greatest threat to native insect larvae that specialize on the impacted host species. The loss of pollinators whose larvae feed on impacted species and provide services for native plants may also be a serious but yet undocumented indirect threat of these exotic invasions. The disruption of mutualistic relationships between native species will have negative consequences for those species and could potentially benefit exotic species. In the southeastern US, laurel wilt disease (LWD) is impacting numerous species in the Lauraceae family, with the majority of cases observed on Persea borbonia, a common sub-canopy tree found in many Coastal Plain habitats. This species is also known to be the primary larval host of the palamedes swallowtail (Papilio palamedes). While infection rates and crown dieback are catastrophically high (>90%), basal resprouting is a common response in P. borbonia. The exotic Cinnamomum camphora is the only Lauraceae species that has shown resistance to LWD and could benefit from opportunities to replace P. borbonia and other Lauraceae species threatened by LWD. The primary objectives of this study were four fold: 1) to quantify P. borbonia sprouting responses in the field and greenhouse and determine the effect of P. borbonia removal on the composition and abundance of woody and herbaceous plant species in the understory layer, 2) to test the relative suitability of C. camphora as an alternative larval host for P. palamedes, 3) to determine the reliance of the Platanthera ciliaris on P. palamedes for successful pollination and the relative availability of alternative long-tongued pollinators, and 4) to forecast how disease-induced shifts in the relative abundance of native (P. borbonia) and exotic (C. camphora) fruit may alter patterns of consumption and subsequent dispersal of C. camphora by birds. The field component (Grand Bay National Estuarine Research Reserve (GBNERR), Jackson County, MS) of chapter two involved the removal of P. borbonia main stems to mimic the impacts of LWD which resulted in a significant increase (~50%) in light transmission. All treated individuals produced sprouts and the size and number of sprouts was positively related to initial tree size. Following the removal of P. borbonia from treatment plots, Ilex vomitoria showed the greatest increase in basal area after two years. Both woody seedlings and herbaceous plants showed no significant trends in composition and/or abundance over time. In the greenhouse (Southern Illinois University, Carbondale, IL), the stem and leaf biomass of vegetative sprouts was significantly greater in a high-nutrient treatment. Light treatments had no effect on sprout production. Results from chapter two suggest that the loss of P. borbonia from the canopy layer may have little direct effect on plant community dynamics. In addition, I found that sprout production is vigorous in P. borbonia and the capacity to persist and tolerate future disturbances may be enhanced on more nutrient-rich sites. In chapter three, I used laboratory experiments and field observations to compare larval performance and adult female preference of P. palamedes between C. camphora and P. borbonia foliage. My results indicate moderate survivorship on C. camphora (46%) compared to P. borbonia (87%) and there were no differences in first and fourth instar growth rates between treatments. Fourth instars consumed less C. camphora foliage than P. borbonia, but metabolic efficiency did not differ between treatments. In the field and laboratory, I found no oviposition preference for C. camphora relative to P. borbonia. While females laid eggs on C. camphora during laboratory trials, the same number of eggs was also laid on inanimate objects. I conclude that C. camphora is suitable for larval development but host-switching to this species by P. palamedes will be primarily constrained by oviposition behaviors. In chapter four, I monitored pollinator visitation and measured nectar spur lengths of P. ciliaris flowers and proboscis lengths of its floral visitors (at GBNERR). Papilio palamedes was the primary visitor (44 visits) but Phoebis sennae was also observed (4 visits). There were no significant differences among P. ciliaris nectar spurlength and the proboscis lengths of P. palamedes and P. sennae. Fruit set was 55 ± 10.8% with access to pollinators and 0% on bagged inflorescences (pollinators excluded). Although I found a positive relationship between visitation and inflorescence size, there was no such pattern in fruit set, indicating that fruit set was not limited by pollinator visitation within the range of visitation rates I observed. Phoebis sennae may provide supplemental pollination service but is likely constrained by habitat preferences that do not always overlap with those of P. cilaris. Although additional observations are needed, my results suggest that expected LWD-induced declines of P. palamedes will threaten the reproductive success and persistence of P. ciliaris populations. In chapter five, I investigated redundancy between C. camphora and P. borbonia with respect to fruit characteristics (physical and chemical) and selectivity by frugivorous birds (at GBNERR). Across two winter survey periods I observed fruit removal from artificial infructescences. I manipulated background species upon which displays were hung (Myrica cerifera and Triadica sebifera) and the accessibility of the displays. Using motion-activated cameras I confirmed foraging bouts on both P. borbonia and C. camphora fruits by three bird species (Dumetella carolinensis, Turdus migratorius, and Catharus guttatus). There was no significant difference in selectivity between fruit types during year one of my surveys but there was a significant preference for C. camphora in year two, which coincided with significantly lower mean daily temperatures. Background tree species and accessibility had no apparent effect on fruit preference. Total polyphenols and pulp:seed ratio were significantly higher in C. camphora fruit. I conclude that the fruits of C. camphora and P. borbonia represent nearly substitutable resources for native birds. However, native species may prefer C. camphora fruit in times of energetic stress. The decline of P. borbonia will likely increase the consumption and dispersal of C. camphora fruits. Additional studies are required to determine if such changes could ultimately increase the distribution and abundance of this exotic species. Combined, the chapters of this dissertation present substantial empirical evidence for the potential multi-trophic level impacts of an exotic plant disease. While it remains unclear how dramatic these impacts will be, the approach used here is vital for understanding and mitigating the long-term ecological effects of species/disease invasions.

This thesis consists of three sections, all of which are linked to the ecology of infectious disease and the decline of amphibians caused by chytridiomycosis. This thesis represents a detailed analysis of factors that allow the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), to persist in the Peruvian Andes. Collectively, these three sections elaborate on the current knowledge of the disease, how it persists in an area, as well as recommendations for future disease mitigation. Chapter one is a review of environmental and biological factors that contribute to the persistence of Bd. Here we address the use of biotic and abiotic reservoirs by the pathogen that allow Bd to persist. Biological reservoirs include both amphibian and non-amphibian hosts, thus allowing Bd to persist and proliferate when susceptible host densities recover. More than 40% of all amphibian populations are in decline and more than a third are at risk of extinction making it important to develop conservation measures for endangered and diminishing biodiversity. By understanding disease dynamics between reservoirs and other susceptible hosts, mitigation strategies can be developed to save amphibian populations from loss of genetic diversity or extinction. Chapter two addresses the current distribution and disease status of Bd in the Kosñipata Valley in southeastern Peru. We investigated the post-epizootic distribution and prevalence of Bd by examining trends in Bd prevalence across multiple sample periods. We modeled infection prevalence using logistic regression as a function of species, sample period, reproductive mode, life stage, and elevation and their two-way interactions. The most parsimonious model of prevalence contained two-way interactions between sample period and elevation, and reproductive mode and life stage. Overall we observed that prevalence varied over time; prevalence was higher in 2012-2015 than it was in 2008-2009. The interaction between elevation and sample period revealed that while prevalence decreased with elevation during the wet season, it generally increased with elevation during the dry season. We concluded that the prevalence of Bd in the Kosñipata Valley appears to have stabilized over time, indicating enzootic Bd. Long-term monitoring of infection in hosts is important because temporal patterns in prevalence and infection intensity are associated with changes in population abundance which could lead to future changes in the disease state. Chapter three examines Hypsiboas gladiator as a proposed reservoir species for Bd. We conducted field surveys to determined prevalence and calculated Bd loads across life stages, and calculated zoospore shedding rates of H. gladiator and sympatric species. Results showed that H. gladiator had the highest prevalence and Bd load, followed by Pristimantis toftae and then P. platydactylus. We tried to determine if prevalence and Bd load varied with distance from streams but found no direct evidence to support our claims. We also conducted susceptibility trials of H. gladiator to Bd. Results from our susceptibility trials are inconclusive. Shedding rates were higher in 2014 than 2013 for all species and varied by year. At this time we cannot determine if H. gladiator is a reservoir species for Bd.