Amplified fragment length polymorphism (AFLP) markers allow a rapid assessment of the level of genetic variation that would be difficult to evaluate using a limited number of morphological markers. AFLP was used to assess the level of genetic variation among 16 different Phalaenopsis species and hybrids. Ten AFLP primer combinations were used for genetic analysis of these Phalaenopsis and 95% of polymorphism in 16 Phalaenopsis species and hybrids was detected. The genetic similarity among Phalaenopsis species and hybrids ranged from 0.298 to 0.774 based on Dice coefficient. The dendrogram derived by UPGMA analysis clustered into two main groups. A significant linear relationship (r² = 0.524, P < 0.0001) was observed between known pedigrees and AFLP-derived genetic similarity for 136 pairwise comparisons of Phalaenopsis species and hybrids. The results indicate that there is an abundance of genetic diversity among within Phalaenopsis and that AFLP can be used to distinguish morphologically similar genotypes. In a second study, the effect of gametophytic selection on genetic diversity in Phalaenopsis was examined by AFLP analysis. Sixteen F1 seedlings resulting from cross-pollination that occurred within high (30 ºC) and low (14 ºC) temperature incubators between two hybrid Phalaenopsis [P. (Taisoco Windian à Sogo Yukidian) by P. hybrid unknown], were subjected to genetic analysis by AFLP. A total of 651 fragments ranging in size from 100 to 350 bp were detected using six primer combinations, of which 387 (59.4%) were polymorphic. Seedlings derived from different temperature treatments exhibited 25.5% to 35.9% polymorphism. The genetic similarity among 16 F1 seedlings ranged from 0.825 to 0.946 based on the Dice coefficient. A dendrogram based on 387 polymorphic markers was derived by UPGMA analysis resulting in three major groups and one subgroup. The dendrogram analysis showed clear clustering in Phalaenopsis hybrids pollinated under different temperature treatments, suggesting that several loci may have been selected during the divergent temperature stress treatments during pollination and early pollen tube growth. / Master of Science

Ancient DNA analysis of archaeological wheat remains may serve to clarify unknown or controversial points in the history of wheat. In the first part of this study, extraction and amplification of DNA from Anatolian charred ancient wheat seeds obtained from different locations and ages was attempted. None of the our extraction samples yielded any PCR amplification. The possible reasons for this result were investigated by constructing an artificial charring experiment. The results suggest that the chances of obtaining DNA from the charred archaeological samples used in this study by the methods used are very low. Moreover, strong PCR inhibition by these charred seed extracts was observed. The second part of the study aimed to develop new DNA based markers for ancient wheat DNA analysis. Markers linked to the brittle rachis character exhibiting domestication status were sought, but no result was obtained. Primers targeting plasmon sequences were developed and tested. A primer pair amplifying a 400 bp portion of the chloroplast TrnLTrnF intergenic region was focused upon. A short piece of this region was amplified using ancient wheat DNA extracted in another study. This short piece appeared non-polymorphicupon sequencing. The sequence spanning a wider portion of this region contained a number of length polymorphisms. Phylogenetic reconstruction using maximum parsimony showed that these polymorphisms were able to distinguish wheat taxa at the maternal ancestor level.

The specificity of fungal isolates from endemic Western Australian orchid species and hybrids in the tribe Diurideae was investigated using symbiotic seed germination and analysis of the fungal DNA by amplified fragment length polymorphism (AFLP). The distribution of the fungal isolates in the field was also assessed using two different seed baiting techniques. The information from these investigations is essential for developing protocols for reintroduction and translocation of orchid species. Two groups of orchids in the tribe Diurideae were studied. Firstly, a number of Caladenia species, their natural hybrids and close relatives from the southwest of Western Australia were selected because orchid species from the genus Caladenia are considered to have among the most specific mycorrhizal relationships known in the orchid family – an ideal situation for the investigation of mycorrhizal specificity. Secondly, species of Drakaea and close relatives, from the southwest of Western Australia and elsewhere in Australia, which are never common in nature and occur in highly specialised habitats, were selected to investigate the influence of habitat on specificity. Seed from the common species Caladenia arenicola germinated on fungal isolates from adult plants of both C. arenicola and its rare and endangered relative C. huegelii, while seed from C. huegelii only germinated on its own fungal isolates. The AFLP analysis grouped the fungal isolates into three categories: nonefficaceous fungi, C. huegelii type fungi, and C. arenicola type fungi. The group of C. huegelii type fungi included some fungal isolates from C. arenicola. An analysis of the AFLP fingerprints of C. arenicola fungal isolates from different collection locations showed that some, but not all, populations were genetically distinct, and that one population in particular was very variable. Despite being thought to have very specific mycorrhizal relationships, Caladenia species hybridise frequently and prolifically in nature, often forming self-perpetuating hybrid lineages. Five natural hybrids within Caladenia and its closest relatives were investigated. Symbiotic cross-germination studies of parental and hybrid seed on fungi from the species and the naturally occurring hybrids were compared with AFLP analyses of the fungal isolates to answer the question of which fungi the hybrids use. The germination study found that, while hybrid seeds can utilise the fungi from either parental species under laboratory conditions, it is likely that the natural hybrids in situ utilise the fungus of only one parental species. Supporting these observations, the AFLP analyses indicated that while the parental species always possessed genetically distinct fungal strains, the hybrids may share the mycorrhizal fungus of one parental species or possess a genetically distinct fungal strain which is more closely related to the fungus of one parental species than the other. The work on Caladenia hybrids revealed that C. falcata has a broadly compatible fungus that germinated seeds of C. falcata, the hybrid C. falcata x longicauda, and species with different degrees of taxonomic affinity to C. falcata. In general, germination was greater from species that were more closely related to C. falcata: seeds from Caladenia species generally germinated well on most C. falcata isolates; species from same subtribe (Caladeniinae) germinated well to the stage of trichome development on only some of the fungal isolates and rarely developed further; and seeds from species from different subtribes (Diuridinae, Prasophyllinae, Thelymitrinae) or tribes (Orchideae, Cranichideae) either germinated well to the stage of trichome development but did not develop further, or did not germinate at all. The AFLP analysis of the fungal isolates revealed that the fungi from each location were genetically distinct. In situ seed baiting was used to study the introduction, growth and persistence of orchid mycorrhizal fungi. A mycorrhizal fungus from Caladenia arenicola was introduced to sites within an area from which the orchid and fungus were absent, adjacent to a natural population of C. arenicola. In the first growing season, the fungus grew up to 50 cm from its introduction point, usually persisted over the summer drought into the second season and even into the third season, stimulating germination and growth to tuber formation of the seeds in the baits. Watering the inoculated areas significantly increased seed germination. Mycorrhizal relationships in Drakaeinae were less specific than in Caladeniinae. A study of the species Spiculaea ciliata revealed that this species, when germinated symbiotically, develops very rapidly and has photosynthetic protocorms, unlike all other members of the Drakaeinae. An AFLP analysis of the fungal isolates of this species grouped the isolates according to whether they had been isolated from adult plants or reisolated from protocorms produced in vitro. Isolates were genetically distinct when compared before germination and after reisolation. A cross-species symbiotic germination study of seeds of three Drakaea species and one Paracaleana species against fungal isolates from the same species and several other Drakaeinae species revealed lower specificity in this group than previously thought. A number of fungal isolates from Drakaea and Paracaleana species germinated two or more seed types, while all seed types germinated on fungal isolates from other species and the seed of Drakaea thynniphila germinated to some extent on every fungal isolate tested. An AFLP analysis of the Drakaeinae fungal isolates supported this information, revealing little genetic differentiation between the fungi of different orchid species. An ex situ seed baiting technique was used to examine the role of mycorrhizal fungi in microniche specialisation in the narrow endemic Drakaea. Soil samples from within and outside two Drakaea populations were tested for germination of the relevant seed types. In both cases, germination was significantly higher on soil samples from within than outside the populations, suggesting that the relevant mycorrhizal fungi may be restricted to the same microniches as the Drakaea species. The presence of similar fungi at distant, disjunct locations may be related to the extreme age and geological stabilityof the Western Australian landscape. The information from these investigations is essential for developing protocols for reintroduction and translocation of orchid species. It appears that the mycorrhizal relationships in these groups of orchids are not as specific as was previously thought. For reintroduction work, a broad sampling strategy is necessary, as it cannot be assumed that the same orchid species has the same fungus at different locations. A broadly compatible fungus may be of considerable utility in conservation work, such as in situations where a specific fungus appears to have poor saprophytic competence or where soil conditions have been altered. Seed baiting studies provide additional data on fungal distribution in situ. In general, molecular data do not provide information about efficacy or fungal distribution, so research programs that combine symbiotic germination studies with seed baiting investigations and genetic analyses of the fungi will provide the maximum benefit for designing more effective conservation programs.

Orientador: Suzete Aparecida Lanza Destéfano / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-20T14:37:32Z (GMT). No. of bitstreams: 1 Tonin_MarianaFerreira_D.pdf: 2371085 bytes, checksum: d7c915d664efeec24397b855164c65b9 (MD5) Previous issue date: 2012 / Resumo: Espécies pertencentes ao gênero Xanthomonas são responsáveis por doenças que podem causar grandes perdas econômicas em diversas culturas. Esses fitopatógenos têm sido objeto de diversos estudos taxonômicos resultando em significativas alterações na classificação em nível inter e infraespecífico. O presente estudo teve por objetivo caracterizar taxonomicamente bactérias do gênero envolvendo: (1) diferenciação e análises filogenéticas de espécies do gênero Xanthomonas; (2) esclarecimento da posição taxonômica de linhagens classificadas como Xanthomonas sp.; (3) diferenciação de patovares da espécie X. campestris; (4) desenvolvimento de primers específicos para X. campestris, X. translucens, X. cucurbitae e X. melonis. O par de primers rpoB2F/rpoB3R, desenhado a partir de sequências do gene rpoB, foi empregado em experimentos de amplificas;ao utilizando-se DNAs de 26 espécies do gênero Xanthomonas e os produtos de amplificas;ao (800 pb) foram digeridos com diversas endonucleases. Os perfis de restrição obtidos com a utilização da enzima Hae III permitiram a diferenciação da maioria das espécies, incluindo os patógenos de mesmo hospedeiro como X. albilineans e X. sacchari (patogênicas à cana-de-açúcar); X. cucurbitae . e X. melonis (patogênicas ao melão); X. vesicatoria, X. gardneri e X. euvesicatoria/X. perforans (patogênicas ao tomateiro). Ainda, os produtos de amplificação do gene rpoB foram seqüenciados e a árvore filogenética construída a partir destas sequências também possibilitou a diferenciação das espécies do gênero, indicando que o gene rpoB pode ser considerado um marcador molecular eficiente para o estudo das relações filogenéticas de espécies do gênero Xanthomonas. Os DNAs de linhagens classificadas como Xanthomonas sp. também foram analisados por meio de experimentos de amplificação com primers específicos para a espécie X. axonopodis, de hibridizas;ao DNA-DNA, e analise de multilocus utilizando-se sequências dos genes rpoB, rpoA, atpA, recA e região espaçadora 16S-23S DNAr. Os resultados mostraram que as linhagens de X. sp. pv. viticola, X. sp. pv. betae e X. sp. pv. paulliniae pertencem a espécie X. axonopodis, entretanto, não foi possível definir a posição taxonômica das linhagens de X. sp. pv. arracaciae, X. sp. pv. esculenti e X. sp. pv. eucalypti, embora várias ferramentas tenham sido utilizadas. Assim, somente estudos complementares deverão ser conduzidos visando esclarecer a classificação dessas linhagens. Nesse estudo também foram analisadas as espécies X. campestris, X. translucens, X. cucurbitae e X. melonis. Visando a diferenciação dos patovares da espécie X. campestris, os DNAs destas linhagens foram submetidos a experimentos de PCR-RFLP do gene rpoB e as digestões duplas utilizando-se Cfo I/Mbo I. Os resultados permitiram a diferenciação dos patovares X.c. pv. raphani, X.c. pv. barbariae, X.c. pv. incanae, X.c. pv. armoraciae e X.c. pv. campestris/ X.c. pv. aberrans. Ainda, os dados obtidos nas amilises do gene rpoB permitiram o desenvolvimento de primers específicos para as espécies X. campestris, patogênicas as crucíferas (rpoB2F/xcamR) e X. translucens, patogênicas a gramíneas e cereais (trans1F/trans2R). Alem disso, amilises de sequências da região espaçadora 16S-23S DNAr possibilitaram o desenho do par de primers mecF/mecR, especifico para X. cucurbitae e X. melonis, espécies patogênicas ao melão. A especificidade destes primers foi confirmada em experimentos de amplificação utilizando-se DNAs de algumas bactérias de diferentes gêneros isoladas de mesma espécie de plantas hospedeiras. O nível de sensibilidade da técnica de PCR utilizando-se os primers desenvolvidos foi de 0,1 pg para rpoB/xcam, de 0,01 ng para trans1F/trans2R e de 1 pg para mecF/mecR / Abstract: Xanthomonas species are responsible for diseases causing economic losses in many crops. These phytopathogens have been subject of several taxonomic studies resulting in significant changes at interespecific or infraspecific level. This study aimed the taxonomic characterization of Xanthomonas species including: (1) differentiation and phylogenetic analysis of Xanthomonas species; (2) clarification of taxonomic position of strains classified as Xanthomonas sp.; (3) differentiation of the pathovars of X. campestris; ( 4) development of specific primers for X. campestris, X. translucens, X. cucurbitae and X. melonis. The rpoB2F/rpoB3R primers, designed from rpoB gene sequences, were employed in amplification experiments using DNAs from 26 species of Xanthomonas genus and the products (800 bp) were digested with different restriction enzymes. Profiles using Hae III allowed to differentiate the most species of the genus, including pathogens the affect the same plant host as X. albilineans e X. sacchari (pathogenic to sugarcane); X. cucurbitae e X. melonis (pathogenic to melon); X. vesicatoria, X. gardneri and X. euvesicatoria/X. perforans (pathogenic to tomato). Amplification products of the rpoB gene were sequenced and the phylpgenetic tree constructed from these sequences also allowed the differentiation of the Xanthomonas species, indicating that the rpoB gene can be used as an efficient molecular marker for phylogenetic relationships studies within the Xanthomonas genus. DNA of the strains classified as Xanthomonas sp. were also analysed by the amplification experiments using specific primers for X. axonopodis species, DNA-DNA hybridization and multilocus sequence analysis of the genes rpoB, rpoA, atpA, recA and intergenic spacer region 16S-23S rDNA. Results showed that the strains of X. sp. pv. viticola, X. sp. pv. betae and X. sp. pv. paulliniae belong to X. axonopodis species, however, it was not possible to define the taxonomic position of X. sp. pv. arracaciae, X. sp. pv. esculenti and X. sp. pv. eucalypti, although different approaches have been used. Thus, further studies should be conducted in order to clarify their classification. In this study X. campestris, X. translucens, X. cucurbitae and X. melonis were also analyzed. In order to differentiate the pathovars of the X. campestris specie, the DNAs of these strains were submitted to PCR-RFLP analysis of the rpoB gene and the double digestions using Cfo I/Mbo I allowed the differentiation of the pathovars X. c. pv. raphani, X.c. pv. barbariae, X.c. pv. incanae, X.c. pv. armoraciae and X.c. pv. campestris/ X.c. pv. aberrans. Also, the data obtained in the rpoB gene analysis allowed the development of specific primers for the species X. campestris, pathogenic to crucifers (rpoB2F/xcamR) and X. translucens, pathogenic to grasses and cereals (trans1F/trans2R). Furthermore, intergenic spacer 16S-23S rDNA sequences analysis enabled the development of the mecF/mecR primers, specific for X cucurbitae and X melonis, both pathogenic to melon. The specificity of these primers was confirmed by amplification experiments using DNAs from bacteria belonging to different genera pathogenic to the same plant hosts. Sensitivity level of the PCR technique using the primers developed was 0,1 pg for rpoB/xcam, 0,01 ng for trans1F/trans2R and 1 pg for mecF/mecR / Doutorado / Genetica de Microorganismos / Doutor em Genetica e Biologia Molecular

In severe cases of ulcerative colitis (UC) unresponsive to current treatment options, patients require a complete proctocolectomy, or surgical removal of the colon. Ileal pouch anal anastomosis (IPAA) has become the preferred surgical technique for patients who require surgery, as this method restores rectal function. This procedure is also used to treat colorectal cancers such as adenocarcinoma and familial adenomatous polyposis (FAP). The surgery involves an abdominal colectomy with the construction of an ileal pouch created from folded tissue recovered from the ileal portion of the small intestine. Up to 50% of patients who require IPAA surgery experience an episode of pouchitis, a non-specific inflammation of the constructed ileal pouch with unknown etiology. Several hypotheses have been proposed regarding the pathogenesis of pouchitis. Current theories include bacterial overgrowth due to fecal stasis, microbial imbalance (dysbiosis), immune alteration, genetic susceptibility, metaplasia, ischemic complications of surgery, a recurrence of UC, or even a novel form of inflammatory bowel disease. The efficacy of antibiotics and probiotics in treating pouchitis and maintaining remission underscores the importance of gut microbiota in the development of this condition. In the study, we aimed to characterize the intestinal bacterial communities that inhabit IPAA pouches of both UC and FAP patients, in an effort to investigate the hypothesis that bacterial dysbiosis is involved in the pathogenesis of pouchitis. Mucosal biopsy and stool samples were analyzed from patients with UC and pouchitis (UCP), healthy UC controls (HUC) and healthy pouches with a background of FAP (FAP). Samples were examined through analysis of terminal restriction fragment length polymorphisms (TRF) and DNA sequencing. The data presented here demonstrate that a microbial imbalance exists in pouchitis, as bacterial communities in pouchitis differ significantly from healthy UC pouches and pouches constructed for FAP. Both methods identified potential groups of organisms that may play a role in the development of pouchitis, including decreases in protective Lactobacillus and Bacteroides and increases in mucin-degrading Clostridium and Akkermansia. A better understanding of the factors driving the pathogenesis of pouchitis will not only benefit patients with this disease, but also lead to a better understanding of the complex relationship that exists between the human host and the diverse community of organisms that inhabit the gastrointestinal tract.

No description available.

Fusarium head blight (FHB) is one of the most economically important diseases of small grains and continues to impact crops when environmental conditions are favorable to Gibberella zeae (Fusarium graminearum), the causal agent of the disease. Corn residues are considered to be primary sources of inoculum for epidemics of FHB. Therefore, knowledge of the movement of Gibberella zeae from a local source of infested corn residue is critical to the management of FHB in wheat and barley. Previous research made significant progress in defining the spatial dissemination of inoculum sources of G. zeae within agricultural fields, but was unable to clearly distinguish between within-field and background sources. Using amplified fragment length polymorphism, released clones of G. zeae were tracked within wheat and barley fields. This strategy allowed the distinction between the contributions of released clones to FHB, compared to that of background inocula. Corn residue infested with clones of G. zeae was placed into small replicated plots in winter wheat fields in New York and Virginia in 2007 and 2008 and wheat spikes were collected at 0, 3, 6, and ≥24 m from the inoculum sources. Recovery of released clones decreased an average of 90% between 3 and 6 m from inoculum sources. Various amounts of corn residue infested with a single clone of G. zeae were placed into small replicated plots in winter wheat and barley fields in Virginia from 2008 to 2010. The use of minimal or conventional tillage and a moderately resistant cultivar of wheat or barley may reduce the contribution of within-field inocula to FHB; however, environmental conditions play an important role in the effectiveness of these management strategies. With the increase of corn production due to incentives for ethanol-based fuel, overwintering sites for G. zeae on corn residue are likely to increase. Our work contributes to an increased understanding of the influence of overwintered corn residue to FHB which will also direct future research on how to reduce the inoculum potential from within-field sources. / Ph. D.

Master of Science / Department of Plant Pathology / Eduard D. Akhunov / Loretta C. Johnson / Big bluestem (Andropogon gerardii Vitman) is an ecologically dominant grass of the North American grasslands with precipitation-dependent productivity. However, climatic predictions for big bluestem’s dominant range in the Great Plains include increased periods of drought. The main objectives of this research were to determine the extent of neutral and non-neutral genetic differentiation and diversity among putative big bluestem ecotypes using amplified fragment length polymorphism (AFLP) markers. This is the first study of both neutral and non-neutral genetic diversity of big bluestem which also includes source populations of well-described ecotypes studied in reciprocal common gardens. A total of 378 plants were genotyped from 11 source prairies, originating from one of three ecoregions (Central Kansas, Eastern Kansas, and Illinois). Using two AFLP primer sets, 387 polymorphic markers (error rate 9.18%) were found. Un-rooted neighbor joining tree and principle-component analyses showed continuous genetic differentiation between Kansas and Illinois putative ecotypes, with genetic overlap occurring between Kansas ecotypes. Analysis of molecular variance showed high diversity within-prairie sites (80%) relative to across-prairies (11%), and across- ecoregions (9%) (p<0.001). Within-prairie genetic diversity levels were similar among ecoregions (84-92%), with the highest genetic variation maintained in Illinois prairies (92%). Population structure analyses supported K=6 genetic clusters across the environmental gradient, with Kansas prairies belonging to three main genetic groups, and Illinois prairies having largely divergent allele frequencies from Kansas prairies. Interestingly, BAYESCAN analysis of the three putative ecotypes identified eight F[subscript]ST-outlier AFLP loci under potential diversifying selection. Frequency patterns of loci under diversifying selection were further linked to geo-environmental descriptors including precipitation, temperature severity, diurnal temperature variation, prairie location, and elevation. The observed allele frequency divergence between Kansas and Illinois ecotypes suggests tallgrass restorations should consider possible maladaptation of non-local ecotypes and genetic swamping. However, high within-prairie genetic variation may help individual big bluestem populations withstand climatic variability.

Submitted by Ana Damasceno (ana.damasceno@unipampa.edu.br) on 2016-10-10T19:11:40Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Padrões de distribuição e estrutura genética de schinus molle l. na região do pampa brasileiro.pdf: 1391928 bytes, checksum: 2218d5b0fe88623d4d79a44918949a55 (MD5) / Made available in DSpace on 2016-10-10T19:11:41Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Padrões de distribuição e estrutura genética de schinus molle l. na região do pampa brasileiro.pdf: 1391928 bytes, checksum: 2218d5b0fe88623d4d79a44918949a55 (MD5) Previous issue date: 2014-08-08 / Um dos principais aspectos para a ecologia de populações e evolução é o entendimento da conectividade entre os indivíduos e seus grupos. O bioma Pampa apresenta diversos componentes florísticos de grande importância ecológica, e sua estrutura de campo, estépico-savana, vem sendo fragmentada e impactada pelo sistema de produção e pela falta de manejo desse bioma naturalmente frágil. A partir da informação da diversidade genética de populações nativas é possível entender o atual estado de fragmentação ambiental, esclarecer se há fluxo-gênico entre populações, e sugerir formas de manejo que possam garantir a sobrevivência da biodiversidade local. Nesse estudo, Schinus molle L. (Anacardiaceae) foi empregada para avaliar a dinâmica ecológica, a diversidade e a estrutura genética em espécies arbóreas no bioma Pampa. A dinâmica de expansão prevista para a espécie foi determinada através de modelagem de nichos ecológicos e estrutura e diversidade genética foram avaliadas em nove populações amostradas dentro do bioma Pampa stricto sensu, utilizando marcadores microssatélite e AFLP. O mapa da modelagem de nichos ecológicos de S. molle sugere a expansão da espécie sobre o campo, como um fenômeno natural da dinâmica ecológica do bioma. A estrutura genética intra- e inter-populacional sugere limitações ao fluxo gênico e, a diversidade genética intra-populacional é baixa se comparada a espécies com as mesmas características biológicas. O isolamento entre populações e o pequeno tamanho destas parece ser o principal fator interferindo negativamente no ambiente. A manutenção de conexões entre as populações é a ação imediata sugerida para preservar a espécie e o bioma. / One of the main aspects for the population ecology and evolution is the understanding of the connectivity among individuals and their groups. The Pampa biome presents several floristic elements of high ecological importance and its grassy structure, steppic-savanna, has been fragmented and impacted by the production system and by the absence of management of this naturally fragile biome. From the information about genetic diversity of native populations, it is possible to understand the current status of the environment degradation, highlighting the presence of gene flow among populations and to suggest management strategies that could guarantee the survival of the local biodiversity. In this study, Schinus molle L. (Anacardiaceae) was employed to evaluate the ecological dynamic, the genetic diversity and structure in tree species of the Pampa biome. The expected expansion dynamic for this species was determined through ecological niche modeling and the genetic diversity and structure were evaluated in nine populations sampled within the Pampa stricto sensu, using microsatellite and AFLP markers. The ecological niche modeling map of S. molle suggests the species expansion over the grassland as a natural phenomenon of the biomes ecological dynamic. The intra- and inter-population genetic structure suggests limitations to the gene flow and the intra-population genetic structure is low in comparison to species with the same biological traits. The isolation among populations and their small size seems to be the main factor negatively interfering in the environment. The maintenance of connections among the populations is the immediate action suggested to safeguard the species and the biome.

Terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrosequencing were used to characterize the microbiota of the tonsil of the soft palate of 126 unfit and 18 healthy pigs. The T-RFLP analysis method was first optimized for the study of the pig tonsil microbiota and the data compared with culture-based identification of common pig pathogens. Putative identifications of the members of the microbiota revealed that the phyla Firmicutes, Proteobacteria and Bacteroidetes were the most prevalent. A comparison of the T-RFLP analysis results grouped into clusters to clinical conditions revealed paleness, abscess, PRRS virus, and Mycoplasma hyopneumoniae to be significantly associated with cluster membership. T-RFLP analysis was also used to select representative tonsil samples for pyrosequencing. These studies confirmed Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria to be the core phyla of the microbiota of the tonsil of the soft palate of pigs. / OMAFRA Animal Health Strategic Investment