Many sharks have life history characteristics (e.g., slow growth, late age at maturity, low fecundity, and long gestation periods) that make their populations vulnerable to collapse due to overfishing. The porbeagle (Lamna nasus), bull shark (Carcharhinus leucas), great hammerhead (Sphyrna mokarran), and smooth hammerhead (S. zygaena), are all commercially exploited. The population genetic structure of these species was assessed based on globally distributed sample sets using mitochondrial control region (mtCR) sequences and/or nuclear markers. Complex patterns of evolutionary and demographic history were inferred using coalescent and statistical moment-based methods. All four species showed statistically significant genetic partitioning on large scales, i.e., between hemispheres (L. nasus mtCR φST = 0.8273) or oceanic basins (C. leucas nuclear FST = 0.1564; S. mokarran mtCR φST = 0.8745, nuclear FST = 0.1113; S. zygaena mtCR φST = 0.8159, nuclear FST = 0.0495). Furthermore, S. zygaena mtCR sequences indicated statistically significant matrilineal genetic structuring within oceanic basins, but no intrabasin structure was detected with nuclear microsatellites. S. mokarran showed statistically significant genetic structure between oceanic basins with both nuclear and mitochondrial data, albeit with some differences between the two marker types in fine scale patterns involving northern Indian Ocean samples. A microsatellite assessment of C. leucas demonstrated no population structuring within the Atlantic or Indo-Pacific, with the exception that samples from Fiji were differentiated from the remaining Indo- Pacific Ocean locations. In contrast, the L. nasus mitochondrial and nuclear ITS2 sequences revealed strong northern vs. southern hemispheric population differentiation, but no differentiation within these hemispheres. These geographic patterns of genetic structure were used to determine the source of fins obtained from the international fin trade and to develop forensic tools for conservation.

Thesis (PhD)--Stellenbosch University, 2008. / ENGLISH ABSTRACT: Introduced species displace native species and alter ecological communities, affect agriculture as well as human health and are economically costly to eradicate. Long term monitoring of introduced species including the documentation of levels of genetic variation is therefore of the utmost importance. This study investigated the distribution of genetic variation in two introduced species distributed across South Africa the bud gall-forming wasp Trichilogaster acaciaelongifoliae and the Argentine ant Linepithema humile. The bud gall-forming wasp was introduced into South Africa as a biological control agent to curb the spread of the invasive long-leaved wattle Acacia longifolia. In addition to the intended (target) host, the bud gall-forming wasp has also colonised A. floribunda, a noninvasive ornamental plant. Limited genetic variation was found across South Africa based on the mitochondrial DNA cytochrome oxidase subunit I (COI) gene. Only 3 haplotypes characterized 53 individuals collected from 23 localities (nucleotide diversity £k = 0.002 ¡Ó 0.001, haplotype diversity h = 0.482 ¡Ó 0.045). No significant partitioning of genetic variation was found across South Africa including between host plants (target host = A. longifolia, non target host = A. floribunda) or between the core (sites of introduction) and edge (naturally dispersed) sites (ƒ¶ST = 0.094, P = 0.288). The limited genetic variation and the absence of significant genetic structure are congruent with patterns described for many other introduced species and may suggest that propagule pressure plays only a minor role in species establishment and spread of the gall-forming wasp across South Africa. Mitochondrial and nuclear markers were used to describe the distribution of genetic variation within Argentine ants across their introduced range in South Africa. For the mitochondrial DNA, low genetic diversity was found for the COI gene with only five haplotypes, separated by single mutational changes, characterizing 101 specimens from 35 localities (nucleotide diversity π = 0.001 ± 0.001, haplotype diversity h = 0.151 ± 0.048). Notwithstanding the low levels of genetic diversity, mitochondrial variation was significantly structured (ST = 0.54, P < 0.001) across the landscape. In contrast, microsatellite analyses of 230 ants from 23 localities, employing six polymorphic microsatellite markers, revealed a relatively high amount of genetic diversity (HE = 0.51 ± 0.22). Significant population structure was similarly evident (RST = 0.14, P < 0.001) with the localities of Elim2, Porterville2 and Bloemfontein2 clustering as a distinct population from the remainder of the localities. Importantly, individuals from these localities also had a unique mitochondrial haplotype and, when taken with the nuclear results, may indicate the occurrence of more than one introduction event (and possibly more than one colony) in South Africa. This is further underscored by the presence of unique microsatellite alleles in these three populations. In an attempt to establish the source populations for the introduction of Argentine ants into South Africa, mitochondrial cytochrome b sequences were generated for a subset of ants representing the two major genetic clades across South Africa. A comparison with the published data from across the world including the native range of the Argentine ant in South America grouped Argentine ants from South Africa with three potential source populations namely Ocampo and Rosario in Argentina and Passo do Lontra in Brazil. The results of this study underscore the role of human-mediated dispersal in shaping the levels of genetic variation in both species. Human-mediated dispersal can lead to genetic homogenization across populations. / AFRIKAANSE OPSOMMING: Indringer spesies verplaas of verander ekologiese gemeenskappe, beinvloed landbou asook menslike gesondheid en is ekonomies duur om te verwyder. Langtermyn monitering van indringer spesies asook die dokumentasie van genetiese variasie is dus baie belangrik. Hierdie studie bestudeer die verspreiding van genetiese variasie in twee indringer spesies wat regoor Suid-Afrika voorkom, naamlik die kroongal-vormende wespe Trichilogaster acaciaelongifoliae en die Argentynse mier Linepithema humile. Die kroongal-vormende wesp is na Suid Afrika gebring as biologiese beheeragent om die verspreiding van indringer lang-blarige wattle Acacia longifolia te beveg. Die kroongalvormende wespe het sowel die teiken spesies, asook A. floribunda, ‘n nie-indringer ornamentele plant gekoloniseer. Beperkte genetiese variasie is gevind regoor Suid Afrika gebasseer op die mitochondriale DNA sitokroom-oksidasie subeenheid I (COI) geen. Slegs 3 haplotipes karakteriseer 53 indiviue van 23 bevolkings (nukleotied diversiteit π = 0.002 ± 0.001, haplotiep diversiteit h = 0.482 ± 0.045). Geen beduinde groepering van genetiese variase is gevind regoor Suid Afrika nie (ST = 0.094, P = 0.288). Hierdie bevinding geld onafhanklik van die gasheer plant (teiken gasheer = A. longifolia, nie-teiken gasheer = A. floribunda). Ook is geen beduidende genetiese groepering gevind tussen die sentrale (plek van inisiele blootstelling) en perifêre (natuurlik verspreide) lokaliteite nie. Die kleinskaalse genetiese variase en die afwesigheid van beduidende genetiese struktuur wat hier gevind is, verskil van die patrone wat voorheen vir baie ander indringer-spesies beskryf is. Dit mag daarop dui dat ‘propagule’ druk slegs ’n klein rol speel in spesies-vestiging en verspreiding van die galvormende wespe regoor Suid-Afrika. Mitochondriale asook kern merkers is gebruik om die verspreiding van genetiese variasie in Argentynse miere in Suid Afrika te beskryf. Vir die mitochondriale DNA is lae genetiese variase gevind vir die COI geen, met slegs 5 haplotipes, gedifferensieer deur enkele mutasie veranderinge wat 101 monsters van 35 lokaliteite karakteriseer (nukleotied diversiteit π = 0.001 ± 0.001, haplotiep diversiteit h = 0.151 ± 0.048). Desondanks die lae genetiese variasie, is gevind dat mitochondriale variasie beduidend gestruktureerd is (ST = 0.54, P < 0.001) oor die landskap. Hierteenoor het mikrosatelliet analises van 230 miere van 23 lokaliteite, deur gebruik te maak van ses polimorfiese mikrosatelliet merkers, ’n relatiewe hoë hoeveelheid genetiese diversiteit aangedui. Beduidende bevolkingstruktuur was ook gevind (RST = 0.14, P < 0.001) in die areas Elim2, Porterville2 en Bloemfontein2 wat saam groepeer as eiesoortige bevolkings vergeleke met die res van die areas. Ook van belang is dat individue van die areas ’n unieke mitochondriale haplotipe besit, en in kombinasie met die kern resultate, mag dit die voorkoms van meer as een blootstellingsgeleentheid (en moontlik meer as een kolonie) in Suid Afrika aandui. Hierdie bevinding word verder beklemtoon deur die teenwoordigheid van unieke mikrosatelliet allele in die drie bevolkings. In ‘n poging om die oorsprong van die oorsprong-bevolking vir die blootstelling van Argentynse miere in Suid Afrika vas te stel, is mitochondriale sitokroom b volgordes gegenereer vir ’n substel miere wat die twee hoof genetiese klades in Suid Afrika voorstel. Vergelyking met gepubliseerde data van regoor die wêreld, insluitende die endemiese gebied van die Argentynse mier in Suid Amerika, het die Argentynse mier van Suid Afrika met drie potensiele oorsprong-bevolking verbind, naamlik Ocampo en Rosario in Argentina en Passo do Lontra in Brazil.

This thesis assessed effects of Amazonian deforestation on artificial association networks of bacteria to bacteria and to abiotic soil factors and networks based on categories of bacterial functions and abiotic soil factors, and sought a better insight into community of Acidobacteria in Amazon soils under agricultural management of soybean based on culture-dependent and molecular approaches. Bacterial community was studied based on next-generation sequencing technologies (Roche GS FLX Titanium and Illumina HiSeq 2000 platforms), quantitative real-time PCR, fingerprinting technique and basic procedures for bacteria culture. The general objective of this thesis was achieved by development of three different studies. The Study 1 analyzed the total bacterial community based on 16S ribosomal DNA pyrotag (425 thousand sequences), shotgun metagenomics (266 million sequences) and environmental parameters from soil samples collected in three real replicate of intact Amazon rainforest and adjacent deforested site after 2-4 months of forest clearing and burning in the Brazilian Amazon. This study showed that deforestation of Amazon forest soils led to a consistent decline in the abundance of Verrucomicrobia and alterations in verrucomicrobial community structure, and simplified association networks among different bacterial taxonomic groups and abiotic soil factors. In order to adapt to this condition function-based associations network were enhanced, indicating a higher degree of risk spreading for the maintenance of soil functioning. The Study 2, in turn, correlated relative abundance of Acidobacteria subgroups - based on approximately 33 thousand sequences of acidobacterial 16S rRNA genes - and abiotic soil factors, and showed differential response of Acidobacteria subgroups to abiotic soil factors in Amazon forest soils into soybean croplands. This study opened the possibilites to explore acidobacterial subgroups as early-warning bio-indicators of agricultural soil management effects in the Amazon area. Lastly, the Study 3 reported the culturability and molecular detection of Acidobacteria subgroups 1 and 3 concomitantly to other bacterial groups from Amazon soils on enriched culture medium with carbon source and incubated for relatively long period in hypoxic atmosphere (2% O2 [vol/vol], 2% CO2 [vol/vol] and 96% N2 [vol/vol]), and validated the combination of traditional procedures for bacteria culture and molecular techniques for recover and detection of Acidobacteria from Amazon soils / Este trabalho de tese avaliou o efeito do desmatamento sobre redes artificiais de associação entre grupos taxonômicos de Bacteria e fatores abióticos do solo e redes baseadas em funções bacterianas e fatores abióticos do solo, e utilizou técnicas moleculares e abordagem dependente de cultivo para compreender a dinâmica da comunidade de Acidobacteria em solos da floresta Amazônica convertidos em áreas agrícolas para produção de soja. Para estudo das comunidades bacterianas foram utilizadas tecnologias de sequenciamento de nova geração (plataformas 454 GS FLX Titanium da Roche e Illumina HiSeq 2000), PCR quantitativo em tempo-real, método de fingerprinting e procedimentos tradicionais para cultivo de bactérias. O objetivo geral desta tese foi alcançado com o desenvolvimento de três diferentes estudos. O Estudo 1 considerou aproximadamente 425 mil sequências do gene 16S rRNA de Bacteria e 266 milhões de sequências de DNA bacteriano obtidas por análise metagenômica a partir de solos coletados em três réplicas verdadeiras de floresta intacta na Amazônia e área desmatada adjacente após corte e queima da cobertura vegetal. Com isso, este estudo mostrou que o desmatamento declina a abundância e altera a estrutura de comunidade de Verrucomicrobia no solo e simplifica as redes artificiais de associação entre diferentes grupos bacterianos. A rede artificial de associação entre categorias funcionais e fatores de solo revelou-se mais complexa em solos desmatados, indicando um alto grau de dispersão de risco para a manutenção do funcionamento do solo. Por sua vez, o Estudo 2 correlacionou a abundância de subgrupos de Acidobacteria - com base em aproximadamente 33 mil sequências do gene 16S rRNA de Acidobacteria - com fatores abióticos do solo, e mostrou que subgrupos de Acidobacteria respondem diferentemente aos efeitos do manejo agrícola de solos da floresta Amazônica dentro de áreas de produção de soja. Este estudo abriu possibilidades de explorar subgrupos de Acidobacteria como bio-indicadores dos efeitos do manejo agrícola do solo na região da Amazônia. Por fim, o Estudo 3 reportou a culturabilidade e detecção molecular de Acidobacteria subgrupos 1 e 3 e outros grupos bacterianos presentes em solos Amazônicos em meio de cultura enriquecido com carbono e incubado sob atmosfera hipóxica (2% O2 [vol/vol], 2% CO2 [vol/vol] e 96% N2 [vol/vol]), atestando, assim, a combinação de procedimentos tradicionais de cultivo e técnicas moleculares para a recuperação e detecção de Acidobacteria de solos da Amazônia

O presente trabalho esteve inserido em um projeto mais amplo de cooperação internacional intitulado Conservation and Sustainable Management of Below-Ground Biodiversity CSMBGBD/ BiosBrasil, implementado pela United Nations Environment Programmer (UNEP) na bacia do Alto Solimões, Amazônia Ocidental, estado do Amazonas. Esta região é território remanescente de povos indígenas e permanece conservada, sendo um importante hotspot de biodiversidade. Ainda assim, as áreas de estudo foram caracterizadas por paisagens antropizadas com diferentes sistemas de usos da terra. Amostras de solos foram coletadas em um período de elevado índice pluviométrico, nos anos de 2008 e 2009, em áreas caracterizadas por floresta primária tropical, cultivos semiperenes de mandioca manejados por prática agrícola de corte-equeima, pastagens implantadas nos anos de 1970 e áreas florestais em estádios avançados de regeneração (>10 anos de abandono). As amostras foram analisadas pelas técnicas de DGGE, ARISA, clonagem e sequenciamento a fim de obter uma caracterização das estruturas de comunidades de Archaea, Bacteria e microfungos e da composição e diversidade de um grupo funcional de Archaea envolvido no processo de oxidação de amônia nos ambientes do solo. Os resultados permitiram concluir que o uso da terra tem um grande efeito sobre as estruturas de comunidades de Archaea, Bacteria e microfungos presentes no solo e sugerem que longo período de abandono das áreas é necessário para cumprir com a resiliência dos ecossistemas amazônicos no contexto de recomposição da paisagem. Adicionalmente, os dados revelaram que a riqueza e a diversidade de comunidades de Archaea oxidadoras de amônia foram capazes de refletir sensivelmente as alterações percebidas nos ambientes do solo em decorrência do desmatamento de áreas de floresta primária e uso subsequente com cultivo agrícola tradicional e pastagem na região do Alto Solimões, Amazônia Ocidental. / The present study was part of a wider project of international cooperation entitled Conservation and Sustainable Management of Below-Ground Biodiversity CSMBGBD/ BiosBrasil, established by the United Nations Environment Programmer (UNEP) at the basin of Alto Solimões, Western Amazon, Amazonas State. This region is a remanescent territory of indigenous people and remains conserved, being considered an important hotspot of biodiversity. Even though, the studied areas were characterized by mosaic landscapes under different land use systems. Soil samples were collected in a period of high pluviometric index in the years 2008 and 2009 in areas characterized by tropical rainforest, semi permanent manioc cultivation under agricultural management of slash-and-burn, pasture established in the 1970s and forested areas at a higher stage of regeneration (>10 years abandoned). The samples were analyzed by DGGE, ARISA techniques, cloning and sequencing in order to obtain a characterization of the community structure of Archaea, Bacteria and microfungi and the composition and diversity of an archaeal functional group involved in the process of ammonia oxidation in the soil environments. The results allowed to conclude that land use has a great effect on the community structure of Archaea, Bacteria and microfungi present in the soil and suggest that long period of abandon of the areas is necessary to accomplish with the resilience of Amazonian ecosystems in the context of landscape recomposition. Additionally, the data revealed that richness and community diversity of ammonia oxidizing Archaea were able to sensitively reflect the changes observed in the soil environment due to deforestation of rainforest areas and subsequent use with traditional agriculture cultivation and pasture in the region of Alto Solimões, Western Amazon.

Novos marcadores genéticos foram caracterizados para jacaré-de-papo-amarelo (Caiman latirostris) pela construção de bibliotecas enriquecidas de DNA microssatélite. Um microssatélite foi desenvolvido a partir de uma biblioteca enriquecida de DNA microssatélite (ACC/TGG)n e 12 a partir de uma biblioteca enriquecida de DNA microssatélite (AC/TG)n. Esses marcadores foram testados em indivíduos da espécie Caiman latirostris e resultaram em sete novos microssatélites polimórficos. Adicionalmente quatro marcadores microssatélites de Alligator mississipiensis previamente transferidos para Caiman latirostris foram utilizados. Amostras de sangue jacarés-de-papo-amarelo originárias de várzeas associadas ao Rio Piracicaba e alguns de seus tributários no estado de São Paulo, Brasil, foram avaliadas quanto à variação genética entre populações e o parentesco entre indivíduos. Foi detectada variabilidade entre indivíduos originários de sitos diferentes, mesmo entre aqueles com pequena distância geográfica. Os resultados sugerem que os grupos amostrados em cada sítio são compostos predominantemente por indivíduos aparentados. Uma possível combinação de alta taxa de mortalidade e baixa taxa de natalidade pode ser a explicação do baixo número de indivíduos dispersos com sucesso por geração entre os sítios estudados. Esses marcadores podem auxiliar na compreensão dos processos metapopulacionais que aparentemente ocorrem na espécie. / New genetic markers were characterized for the broad-snouted caiman (Caiman latirostris) by constructing libraries enriched for microsatellite DNA. One microsatellite was developed from a (ACC/TGG)n enriched microsatellite DNA library and 12 from a (AC/TG)n enriched microsatellite DNA library. These markers were tested in Caiman latirostris individuals and resulted in seven new polymorphic microsatellites for the specie. Additionally four Alligator mississipiensis microsatellite markers previously transferred for Caiman latirostris were used. Samples from broad-snouted caimans from small wetlands associated with the Piracicaba River and some of its tributaries in the state of São Paulo, Brazil were used to study the genetic variation between populations and parentage between individuals. Genetic variability was detected among individuals from different sites, even those within a small geographic distance. The results suggest that the groups sampled at each site are composed predominantly of related individuals. A possible combination of high mortality and low natality rates in the fragmented Caiman latirostris populations may explain the low number of successfully dispersed individuals per generation observed between the sites studied. These markers might help to understand the metapopulation processes that are occurring within this species.

Phlebotomine sand flies (Diptera, Psychodidae) are small blood sucking insects which are only proven vectors of neglected tropical disease called leishmaniasis. Sand flies of the genus Phlebotomus act as vectors in the Old World and those of genus Lutzomyia are vectors in the New World. However, not all of them are capable of transmitting the disease. It is therefore crutial to conclusively determinate the species and have up-to-date knowledge of their natural occurence. Routine identification based on morphological characters is challenging due to intraspecific variability of these or their possible damage during the capture and preparation. In adition, correct assessment of distinctive cahracters, especially for females, is difficult and requires certain expertise. Thus, approaches of molecular taxonomy have been recently increasingly used for sand flies species determination. This thesis presents usage of DNA sequencing and MALDI-TOF protein profiling for routine determination of sand flies caught in southeastern Europe and adjacent regions, where we have lack of information of present sand flies species. Another part of this thesis focus on closer examination of relations between selected closely related species within species complexes. Key words: Phlebotomus, molacular identification, DNA...

Submitted by Francine Silva (francine.silva@unipampa.edu.br) on 2019-03-28T18:51:45Z No. of bitstreams: 1 Diversidade e estrutura genética populacional em luehea divaricata mart. & zucc. na região da fronteira oeste do Rio Grande do Sul, baseada em marcadores microssatélites.pdf: 1894891 bytes, checksum: 4bdf370c0584966a24bc7d1c50440ac3 (MD5) / Made available in DSpace on 2019-03-28T18:51:45Z (GMT). No. of bitstreams: 1 Diversidade e estrutura genética populacional em luehea divaricata mart. & zucc. na região da fronteira oeste do Rio Grande do Sul, baseada em marcadores microssatélites.pdf: 1894891 bytes, checksum: 4bdf370c0584966a24bc7d1c50440ac3 (MD5) Previous issue date: 2013-02-26 / Pertencente à família Malvaceae, o Açoita-cavalo (Luehea divaricata) é uma espécie florestal que ocorre naturalmente desde o Rio Grande do Sul até o sul da Bahia, sendo muito utilizada na confecção de móveis e, também, como fitoterápico. Por ser uma espécie pioneira de rápido crescimento, característica das florestas aluviais, apresenta, em condições de regeneração natural, uma grande quantidade de indivíduos, mostrando ser uma espécie recomendável para a regeneração natural de áreas degradadas. O Açoita-cavalo é uma das espécies nativas mais importantes do ponto de vista fitossociológico, ocorrendo em praticamente todas as bacias hidrográficas do Rio Grande do Sul, na floresta ombrófila mista, na floresta estacional decidual, na floresta estacional semidecidual, na savana, na savana estépica e nas áreas de tensão ecológicas. O objetivo deste trabalho foi caracterizar a diversidade e estrutura genética de cinco populações naturais de L. divaricata na região da Fronteira Oeste do Rio Grande do Sul, no bioma Pampa. Amostras foliares foram coletadas de indivíduos adultos encontrados nas áreas (n=128). O DNA foi extraído com o kit Invisorb Spin Plant Mini Kit (Invitek) e cinco loci microssatélites foram amplificados via PCR. Os alelos foram resolvidos em gel de poliacrilamida (a 10%) e os dados, analisados com auxílio do programa GenAlEx 6.4, FSTAT 2.9.3 e ARLEQUIN 3.1. Os resultados indicaram altos níveis de diversidade genética dentro das populações. A heterozigosidade esperada (He) e o índice de Shannon (I) foram de 0.627 e 1.223, respectivamente. A análise AMOVA mostrou que a maior parte da diversidade genética ocorre dentro das populações (76.12%). O índice de fixação nas populações estudadas demonstrou haver excesso de homozigotos em relação ao equilíbrio de Hardy-Weinberg. Os valores da distância genética de Nei indicaram alta divergência genética entre as populações, em função da baixa eficiência do fluxo gênico entre as populações. Os valores obtidos indicaram que o fluxo gênico está próximo do suficiente para prevenir a diferenciação populacional devido à deriva genética nas populações estudadas, e esse fluxo, deve ocorrer, principalmente, via pólen (por entomofilia), dado que a dispersão das sementes (por anemocoria) teoricamente alcançaria maiores distâncias. Essa baixa dispersão de sementes se deve, provavelmente, à fragmentação e consequente isolamento entre as populações estudadas. Estes resultados sugerem quea dispersão de propágulos reprodutivosem duas, das cinco populações, de certa forma é eficiente, poisapresentaram baixo grau de endogamia. Assim, programas de conservação dos recursos genéticos desta espécie tendem a ser efetivos se o fluxo de polinizadores for mantido,e,pela criação de corredores ecológicos para a conservação da conectividade entre os fragmentos. Além disso, os dados obtidos mostram que as populações estudadasdevem ser priorizadas em programas de conservação genéticada espécie,devido à alta diversidade genética observada,e,ao nível de fragmentação das áreas de remanescentes florestais na região do Pampa. / Belonging to the family Malvaceae, the Açoita-cavalo (Luehea divaricata) is a forest species that occurs naturally from the Rio Grande do Sul State to Bahia State, largely employed in the furniture manufacturing and as medicinal plant. It is a fast-growing pioneer species, characteristic of riparian forests, it presents in natural regeneration conditions, a large quantity of individuals, being indicated for the natural recovery of degraded areas. The açoita-cavalo is one of the most important native species for the phytosociology, occurring virtually in all hydrographical components of the Rio Grande do Sul, in the mixed ombrophylous forest, seasonal deciduous forest, seasonal semidecidual forest, savanna, stepic-savanna and in areas of ecological tension. This study aimed to characterize the genetic diversity and structure of five natural populations of L. divaricata in the region of “Fronteira Oeste” in the Rio Grande do Sul State, within the Pampa biome. Leave samples were collected from adult individuals found in the areas (n=128). DNA was isolated using the Invisorb Plant Mini Kit (Invitek) and five microsatellite loci were amplified through PCR. The alleles were resolved in polyacrylamide gels (10%) and the data analyzed with the software GenAlEx 6.4, FSTAT 2.9.3 e ARLEQUIN 3.1. The results revealed high levels of genetic diversity within the populations. The expected heterozigosity (He) and the Shannon index (I) equaled 0.627 and 1.223, respectively. The AMOVA analysis revealed that the larger amount of the genetic diversity occurs within the populations (76.12%). The fixation index in the studied populations presented an excess of homozygotes in respect of the Hardy-Weinberg equilibrium The values of the Nei’s genetic distance point to high genetic divergence among the populations, consequence of the low efficiency of the gene flow among populations. The results indicate that gene flow is close enough to prevent population differentiation due to genetic drift in the populations studied, and this flow should occur mainly through pollen (by entomophily), since the seed dispersion (by anemocory), theoretically reaches longer distances. This low level of seed dispersion likely is due to the fragmentation and consequent isolation of the studied populations. These results suggest that the dispersal of reproductive propagules in two of the five populations in some ways is efficient because it presented low inbreeding. Thus, programs of genetic resources conservation of this species may be more efficient by maintaining the flow of pollinators, and the creation of ecological corridors for the conservation of connectivity between fragments. In addition, the obtained data reveals that the studied populations should be prioritized in programs of species genetic conservation, due to the relatively high level genetic diversity observed and the level of fragmentation of the areas of forest remnants in the Pampa region.

Le présent travail s’intéresse à l’étude de la diversité des communautés procaryotiques, basée sur le gène codant pour l’ARNr 16S et sur les gènes codants pour la sous-unité β du sulfite réductase dissimilatrice (dsrB) et la sous-unité alpha de la méthyl-coenzyme M réductase (mcrA), pour étudier la diversité de la communauté des bactéries sulfato-réductrices et des méthanogènes, respectivement à partir des échantillons collectés en saison sèche ou pluvieuse du Chott El Jerid. Les analyses des séquences du gène codant pour l’ARNr 16S ont montré que les bactéries regroupées aux Proteobacteria et Firmicutes sont détectés dans les deux saisons alors que les séquences appartenant au groupe taxonomique Bacteroidetes, Actinobacteria et Betaproteobacteria sont apparues uniquement dans la saison pluvieuse. Le groupe Deinococcus-Thermus sont observés que dans la saison sèche. Dans le domaine des archées, la plupart des séquences appartiennent au phylum Euryachaeota, détecté dans les deux saisons, alors que, le phylum Crenarchaeota apparait uniquement dans la saison pluvieuse. En plus, les bactéries sulfato-réductrices, appartenant à la classe Deltaproteobacteria, sont fréquents notamment à la saison pluvieuse prouvée déjà par les deux techniques DGGE et qPCR. A partir des cultures d’enrichissement, de nombreuses bactéries anaérobies fermentaires appartiennent aux familles Halanaerobiaceae et Halobacteroidaceae. Les analyses phylogénétiques ainsi que les caractéristiques phénotypiques et physiologiques montrent une nouvelle souche Sporohalobacter salinus proche de l’espèce Sporohalobacter lortetii, seule espèce décrite à ce jour du genre Sporohalobacter. / The present work concerns microbial biodiversity of prokaryotic communities, sulfate-reducing bacteria, and methanogens targeting the 16S rRNA gene and functional gene markers encoding the dissimilatory sulfite reductase β-subunit gene (dsrB) and alpha subunit of the methyl-coenzyme M reductase (mcrA), respectively from samples collected in the dry and wet seasons from Chott El Jerid. Phylogenetic analysis targeting the 16S rRNA gene showed that bacteria were grouped to Proteobacteria and Firmicutes detected at both seasons, whereas, Bacteroidetes, Actinobacteria and Betaproteobacteria were present only in the wet season. Deinococcus-Thermus group were observed in the dry season. Archaeal sequences were belonged to the phyla of Euryarchaeota in both seasons and Crenarchaeota was appeared in wet season. Sulfate-reducing bacteria, related to Deltaproteobacteria class were dominant mainly in wet season proved by two techniques DGGE and QPCR. From enrichment cultures, anaerobic fermentative bacteria were isolated in pure cultures, related to Halanaerobiaceae and Halobacteroidaceae families. Phylogenetic analysis, phenotypic and physiological characteristics showed a novel strain Sporohalobacter salinus related to Sporohalobacter lortetii, an unique species of genus Sporohalobacter described until now.

Padrões de assimetria sexual na dispersão e relações de parentesco são fatores intimamente relacionados e considerados fundamentais para a compreensão da estrutura social dos primatas. Apesar da relevância desses dois assuntos, pouco se sabe sobre como eles afetam o comportamento individual e a estrutura social nos primatas neotropicais. Assim, essa pesquisa teve como objetivos: determinar o padrão de dispersão de uma população selvagem de macacosprego (Sapajus nigritus) por meio de análises genéticas e examinar o efeito do parentesco sobre a estrutura social dos grupos de S. nigritus. Esta pesquisa foi realizada no Parque Estadual Carlos Botelho, localizado no município de São Miguel Arcanjo/SP. Todo material genético foi obtido através de amostras fecais dos indivíduos adultos e subadultos de três grupos sociais. Após a extração do DNA, parte dele foi amplificada através da técnica da Reação em Cadeia da Polimerase. Para as análises genéticas utilizamos marcadores moleculares do tipo microssatélites. Os métodos de amostragem por varredura instantânea e ad libitum foram utilizados para o registro do comportamento dos indivíduos adultos de dois grupos. Os dados genéticos obtidos nesta tese indicaram que ambos os sexos dispersam, pois: 1) o grau de parentesco intragupo entre machos não diferiu do grau de parentesco entre fêmeas, 2) não houve diferenciação genética ao analisar a distribuição das frêquencias alélicas de machos e de fêmeas, e 3) não houve diferença entre machos e fêmeas quanto à probabilidade de terem nascido dentro dos grupos sociais nos quais foram amostrados. Os resultados de associações espaciais e interações sociais indicaram que as fêmeas adultas não formam fortes relações sociais entre si, sendo pouco afiliativas. Os machos adultos estabelecem fracas relações sociais, que podem ser classificadas como tolerantes e caracterizadas pela ausência de catação e pela baixa frequência de interações agonísticas. As relações sociais mais fortes observadas dentro de cada grupo social foram entre machos e fêmeas. Além de machos e fêmeas associarem-se espacialmente e catarem-se mais do que as díades compostas somente por fêmeas ou por machos, eles também interagiram de maneira agonística numa menor frequência. As díades consideradas como aparentadas não demonstraram ser mais afiliativas ou manter maior proximidadade espacial quando comparadas com as díades não aparenteadas. O baixo grau de parentesco/familiaridade parece ser um fator importante como uma explicação geral para as fracas relações sociais de fêmeas no PECB. No entanto, em termos individuais, aparentemente, esse fator exerceu pouca influência sobre as relações sociais entre as fêmeas e entre os machos. Os resultados apresentados nesta tese ampliam o conhecimento sobre relações sociais em primatas neotropicais e os possíveis fatores que as afetam. O padrão de dispersão e a estrutura social são elementos do sistema social de primatas neotropicais altamente flexíveis, variando entre populações da mesma espécie ou mesmo entre grupos de uma mesma população. Além disso, a alegada assimetria sexual na dispersão talvez não seja passível de generalização entre as populações de Sapajus, e talvez dispersão de ambos os sexos nesse gênero possa ser mais comum do que previamente se considerava / Sex-biased dispersal patterns and kinship are related factors extremely important to understand the social structure of primates. In spite of their importance, little is known about how these factors affect individual behavior and the social structure of neotropical primates. Therefore, the aims of this research were: to determine the dispersal pattern of a wild population of black capuchin monkeys (Sapajus nigritus) through genetic analyses, and to verify the effect of kinship on the social structure of groups of S. nigritus. This research was conducted at Carlos Botelho State Park, in the municipality of São Miguel Arcanjo/SP. We used DNA from fecal samples of adult and subadult members from three wild social groups. DNA was amplified by Polymerase Chain Reaction and microsatellite molecular markers were used. Behavioral data were collected systematically for two groups, and we used scan sampling and ad libitum methods to record the behavior of adults. Genetic data indicated that both sexes disperse from their natal groups, since: 1) relatedness between males was not statistically different from relatedness between females, 2) there was no difference between males and females in population genetic differentiation, and 3) there was no difference between males and females in the probability of being born in the group from which they were sampled. The results of the spatial association and social interactions analysis indicate that females are little affiliative and do not form strong relationships among themselves. Adult males established weak relationships, being classified as tolerant, and characterized by no grooming interactions and by low frequency of agonism. The strongest social relationships observed within each group were between males and females. They associated and groomed more than female dyads and male dyads. Moreover, there were fewer agonistic interactions between males and females as compared to same sex dyads. Related and unrelated dyads showed similar rates of association and affiliative behavior. The low level of relatedness/familiarity might be an important factor contributing to the weak social relationship among females in the PECB. However, at the individual level, kinship had low influence on male and female social relationships. The results presented here extended our knowledge about social relationships of neotropical primates and about the factors that influence the relationships. The dispersal pattern and the social structure are flexible elements of social systems, and can vary among populations of the same species or among groups of the same population. In addition, male-biased dispersal is not a general characteristic for all populations of Sapajus, and dispersal by both sexes might be more commom than previously thought

This thesis assessed effects of Amazonian deforestation on artificial association networks of bacteria to bacteria and to abiotic soil factors and networks based on categories of bacterial functions and abiotic soil factors, and sought a better insight into community of Acidobacteria in Amazon soils under agricultural management of soybean based on culture-dependent and molecular approaches. Bacterial community was studied based on next-generation sequencing technologies (Roche GS FLX Titanium and Illumina HiSeq 2000 platforms), quantitative real-time PCR, fingerprinting technique and basic procedures for bacteria culture. The general objective of this thesis was achieved by development of three different studies. The Study 1 analyzed the total bacterial community based on 16S ribosomal DNA pyrotag (425 thousand sequences), shotgun metagenomics (266 million sequences) and environmental parameters from soil samples collected in three real replicate of intact Amazon rainforest and adjacent deforested site after 2-4 months of forest clearing and burning in the Brazilian Amazon. This study showed that deforestation of Amazon forest soils led to a consistent decline in the abundance of Verrucomicrobia and alterations in verrucomicrobial community structure, and simplified association networks among different bacterial taxonomic groups and abiotic soil factors. In order to adapt to this condition function-based associations network were enhanced, indicating a higher degree of risk spreading for the maintenance of soil functioning. The Study 2, in turn, correlated relative abundance of Acidobacteria subgroups - based on approximately 33 thousand sequences of acidobacterial 16S rRNA genes - and abiotic soil factors, and showed differential response of Acidobacteria subgroups to abiotic soil factors in Amazon forest soils into soybean croplands. This study opened the possibilites to explore acidobacterial subgroups as early-warning bio-indicators of agricultural soil management effects in the Amazon area. Lastly, the Study 3 reported the culturability and molecular detection of Acidobacteria subgroups 1 and 3 concomitantly to other bacterial groups from Amazon soils on enriched culture medium with carbon source and incubated for relatively long period in hypoxic atmosphere (2% O2 [vol/vol], 2% CO2 [vol/vol] and 96% N2 [vol/vol]), and validated the combination of traditional procedures for bacteria culture and molecular techniques for recover and detection of Acidobacteria from Amazon soils / Este trabalho de tese avaliou o efeito do desmatamento sobre redes artificiais de associação entre grupos taxonômicos de Bacteria e fatores abióticos do solo e redes baseadas em funções bacterianas e fatores abióticos do solo, e utilizou técnicas moleculares e abordagem dependente de cultivo para compreender a dinâmica da comunidade de Acidobacteria em solos da floresta Amazônica convertidos em áreas agrícolas para produção de soja. Para estudo das comunidades bacterianas foram utilizadas tecnologias de sequenciamento de nova geração (plataformas 454 GS FLX Titanium da Roche e Illumina HiSeq 2000), PCR quantitativo em tempo-real, método de fingerprinting e procedimentos tradicionais para cultivo de bactérias. O objetivo geral desta tese foi alcançado com o desenvolvimento de três diferentes estudos. O Estudo 1 considerou aproximadamente 425 mil sequências do gene 16S rRNA de Bacteria e 266 milhões de sequências de DNA bacteriano obtidas por análise metagenômica a partir de solos coletados em três réplicas verdadeiras de floresta intacta na Amazônia e área desmatada adjacente após corte e queima da cobertura vegetal. Com isso, este estudo mostrou que o desmatamento declina a abundância e altera a estrutura de comunidade de Verrucomicrobia no solo e simplifica as redes artificiais de associação entre diferentes grupos bacterianos. A rede artificial de associação entre categorias funcionais e fatores de solo revelou-se mais complexa em solos desmatados, indicando um alto grau de dispersão de risco para a manutenção do funcionamento do solo. Por sua vez, o Estudo 2 correlacionou a abundância de subgrupos de Acidobacteria - com base em aproximadamente 33 mil sequências do gene 16S rRNA de Acidobacteria - com fatores abióticos do solo, e mostrou que subgrupos de Acidobacteria respondem diferentemente aos efeitos do manejo agrícola de solos da floresta Amazônica dentro de áreas de produção de soja. Este estudo abriu possibilidades de explorar subgrupos de Acidobacteria como bio-indicadores dos efeitos do manejo agrícola do solo na região da Amazônia. Por fim, o Estudo 3 reportou a culturabilidade e detecção molecular de Acidobacteria subgrupos 1 e 3 e outros grupos bacterianos presentes em solos Amazônicos em meio de cultura enriquecido com carbono e incubado sob atmosfera hipóxica (2% O2 [vol/vol], 2% CO2 [vol/vol] e 96% N2 [vol/vol]), atestando, assim, a combinação de procedimentos tradicionais de cultivo e técnicas moleculares para a recuperação e detecção de Acidobacteria de solos da Amazônia