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Ma thèse s’intéresse à l’influence des comportements culturels sur la diversité génétique neutre des populations humaines, en particulier les populations d’Asie intérieure. Notamment, ces travaux explorent comment certains comportements affectent l’histoire démographique des populations, en agissant sur l’intensité des migrations et de la dérive génétique. Pour ce faire, j’ai étudié des données génétiques, au regard de données ethnologiques, collectées dans des populations habitant actuellement en Asie intérieure, qui diffèrent, entre autres, par leur organisation sociale. La première partie de cette thèse cherche à retracer l’histoire du peuplement de l’Asie intérieure, de l’âge du Bronze jusqu’à nos jours à partir données génomiques d’ADN moderne et ancien. Les résultats montrent que les populations actuelles forment deux groupes génétiques distincts correspondant à deux groupes linguistiques (Turco-Mongol et Indo-Iranien) et reflétant des composantes ancestrales contrastées. En étudiant la diversité génétique de marqueurs uniparentaux, j’ai montré des différences génétiques sexe-spécifiques telles qu’une différenciation des populations réduite pour l’ADN mitochondrial par rapport à celle du chromosome Y. Cette homogénéité génétique des populations pourrait être causée par de la patrilocalité, une règle de résidence commune à toutes les populations étudiées et entrainant principalement des migrations féminines entre populations. D’autre part, j’ai observé des différences de diversité génétique entre les groupes d’Asie intérieure pour le chromosome Y, que j’ai interprété à la lumière des différences de règles de filiation suivies par ces deux groupes : l’un des groupes est patrilinéaire, c’est-à-dire que la filiation sociale est héritée du père ; l’autre groupe est cognatique, et la transmission est indifférenciée entre les parents. La patrilinéarité conduirait à la formation de noyaux d’hommes apparentés par la lignée masculine dans la population et donc partageant le même chromosome Y, ce qui réduirait la diversité génétique du chromosome Y des populations patrilinéaires, comparées aux cognatiques. La diversité mitochondriale est, par contre, similaire entre patrilinéaires et cognatiques, illustrant le fait que seule la diversité génétique masculine est affectée par la patrilinéarité. Enfin, pour étudier le processus d’ethnogénèse, j’ai calculé l’âge génétique des groupes ethniques patrilinéaires et j’ai montré que cet âge biologique est plus ancien que les âges historiques, suggérant que l’ethnie, du moins chez les Turco-Mongols d’Asie intérieure, est une construction en partie sociale, plutôt qu’une entité entièrement biologique. Dans la troisième partie, je me suis intéressée aux mécanismes d’évitement de la consanguinité, que j’ai estimée au moyen de données génomiques. J’ai notamment testé l’hypothèse selon laquelle des unions exogames, entre conjoints nés dans des villages différents, permettraient de réduire la consanguinité. Malgré une importante variabilité du taux d’exogamie entre populations et entre groupes linguistiques dans notre jeu de données, je n’ai trouvé aucune différence significative de consanguinité. A l’échelle des individus, j’ai pu mettre en évidence le fait que certains descendants de couples exogames sont néanmoins consanguins. Cette situation est particulièrement répandue pour des conjoints nés à moins de 40 km l’un de l’autre, à tel point que leurs descendants sont statistiquement plus consanguins que les descendants de couples endogames. Ces résultats illustrent que, chez l’Homme, des comportements culturels d’alliance peuvent s’opposer aux attendus de la biologie évolutive. Ainsi, mes travaux illustrent plusieurs cas de figure, à des échelles géographiques et temporelles différentes, où des comportements culturels ont modifié et laissé une signature génétique particulière sur la diversité des populations humaines d’Asie intérieure. / My PhD thesis is about the influence of cultural behaviours on the neutral genetic diversity of human populations from Inner Asia. Notably, I investigated how specific behaviours may affect the demographic history of populations, by acting on the intensity of migration and genetic drift. To do so, I combined genetic and ethnological data, collected in present-day Inner Asian populations that belong to two major cultural and linguistic groups and have different social organisations.The first part of this work aims at understanding how Inner Asia was peopled, from the Bronze Age to nowadays. This was done in the framework of an international collaboration, through the study of both ancient and modern genomic data. The results obtained showed that modern populations are divided in two distinct genetic groups, mirroring the two cultural groups, and exhibiting contrasted ancestral components. I was then interested in exploring the influence of cultural behaviours on the sex-specific genetic structure of present-day populations from Inner Asia. By studying the genetic diversity of uniparental markers, namely mitochondrial DNA and the Y chromosome, I was able to characterize sex-specific genetic differences, such as a reduced population differentiation for mitochondrial DNA as compared to the Y chromosome. This maternal genetic homogeneity between populations may be explained by patrilocality, a residence rule shared by all the studied populations and generating mostly female migrations between populations. On the other hand, I showed there were some significant differences in genetic diversity between the two cultural groups for the Y chromosome. This observation may be related to the different filiation rules of these two groups. Indeed, one is patrilineal: the social filiation is inherited from the father, while the other is cognatic: the transmission is undifferentiated between the parents. It could then be that patrilineality leads to the formation of cores of related men within the population, who share the same Y chromosome. This population structuration would result in a reduced genetic diversity for the Y chromosome in patrilineal populations, compared to cognatics. As expected, the mitochondrial diversity is comparable between patrilineal and cognatic group, comforting the idea that patrilineality affects only the male genetic diversity. Finally, to investigate the ethnogenesis process, I calculated the genetic age of patrilineal ethnic groups from STR markers of the Y chromosome. I showed that this biological age is older than the one from historical sources, which suggests that, at least for Turko-Mongolic from Inner Asia, the ethnic group is partly a social construct, rather than an actual biological entity. In the third part, I focused on whether dispersal can be an inbreeding avoidance mechanisms by dispersal. Notably, I tested the hypothesis that exogamous unions, between spouses born in different villages, would lead to less inbreeding than endogamous unions. Despite a strong variation of the exogamous rate between the populations of the studied dataset, no significant difference was found for inbreeding, which was estimated from a genome-wide dataset. At the individual scale, I showed that some of the descendants of exogamous unions are inbred. This is especially true for spouses born less than 40 km away, in which case their descendants are statistically more inbred than those from endogamous unions. This shows that, in human populations, specific matrimonial behaviours, driven by culture, may contradict the results expected by evolutionary biology.In conclusion, my work shows several cases, at different time and geographic scales, where cultural behaviours left a footprint into the genetic diversity of Inner Asian populations.

Golden mice (Ochrotomys nuttalli) are generally an elusive and rare species throughout their geographic range in the southeastern United States. They are considered to be habitat specialists that prefer dense understory consisting of shrubs and vines. Golden mice are less vagile, and likely disperse shorter distances than other sympatric species such as the white-footed mouse (Peromyscus leucopus). Conversely, white-footed mice are considered habitat generalists that inhabit a variety of habitat types, are more vagile, and disperse farther than golden mice. Because of this it is likely that golden mice have a lower genetic diversity and are more genetically subdivided than white-footed mice. In southern Illinois, golden mice are on the periphery of their range, which is one of the reasons they are on the state-threatened list in Illinois. It has been hypothesized that populations on the periphery of a species range will have more population structure and lower genetic diversity than populations in the core of the range. Tissue samples for golden mice and white-footed mice were collected from 24 sites throughout southern Illinois and 24 sites throughout the golden mouse core range. I analyzed 13 and 10 microsatellite markers as well as 594 and 624 base pairs of the mitochondrial control region for golden mice and white-footed mice, respectively, to characterize and compare the genetic diversity and population structure of both species. Overall haplotype diversity (0.76) and nucleotide diversity (0.20%) was lower in golden mice compared to white footed mice (0.99 and 1.97%). Results of an AMOVA using the mitochondrial control region revealed more subdivision among the 3 populations of golden mice (Φst = 0.099, P < 0.001) than among the 3 populations of white-footed mice (Φst = 0.058, P < 0.001). Microsatellite loci showed a similar trend with overall FST values of 0.027 (P < 0.001) for golden mice and 0.004 (P = 0.137) for white-footed mice. I intended to compare golden mouse individuals from southern Illinois and the core of the range, but too few individuals were collected from the core. More samples need to be collected throughout the core of the range to better understand the population genetics of golden mice in the core of the range compared to the periphery.

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The thesis focused to population ecology and genetics of subalpine species Gentiana pannonica. Pollination ecology of species and generative reproduction in different habitat (primary vs. secondary) were investigated in the field. Genetic variation and structure of G. pannonica populations were studied in three disjunct parts of its distribution range: the Eastern Alps, the Bohemian Forest, and the Giant Mts. Present distribution of G. pannonica in the central past of the Bohemian Forest were processed.

Made available in DSpace on 2016-04-01T17:55:01Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-10-15. Added 1 bitstream(s) on 2016-04-01T18:00:50Z : No. of bitstreams: 1 000860445.pdf: 1297564 bytes, checksum: 7fa2ff28bbc7d5672a1c49b6aaceef4a (MD5) / Anaplasma marginale é o mais prevalente patógeno transmitido por carrapatos em bovinos nas regiões tropicais e subtropicais do mundo. A Proteína Principal de Superfície 1 alpha (MSP1a) do A. marginale contém um número variável de sequências repetidas na região animo-terminal e tem sido utilizada para a caracterização da diversidade genética desse patógeno. Nós realizamos um estudo longitudinal para averiguar a diversidade genética do A. marginale em um rebanho bovino leiteiro de Seropédica no estado do Rio de Janeiro e Taiaçu no estado de São Paulo, Brasil. Vinte bezerras foram avaliadas a cada três meses durante o primeiro ano de vida por esfregaço sanguíneo, Ensaio de Imunoadsorção Enzimático Indireto (ELISA), Reação de Imunofluorescência Indireta (RIFI) e Reação em Cadeia da Polimerase (nPCR/qPCR). Adicionalmente, as amostras positivas para o gene msp1a usando nPCR foram sequenciadas. A frequência do A. marginale variou de 10 - 90% no esfregaço sanguíneo, 20 - 80% no ELISA/RIFI e 15 - 100% na qPCR. O número de copias da msp1a por mL de sangue variou de 1,04 x 101 a 6.76 x 1012 (Seropédica RJ) e 1.20 x 101 a 5.17 x 106 (Taiaçu SP). Os resultados mostraram que a diversidade genética do A. marginale, em um grupo de bezerras até 1 ano de idade em Taiaçu (SP) foi baixa, com apenas três diferentes estirpes identificadas, mostrando o genótipo E. No entanto, os resultados mostraram que o diversidade genética do A. marginale, em um grupo de bezerras até 1 ano de idade em Seropédica (RJ) foi elevada, com dezenove diferentes estirpes identificadas, mostrando o genótipo E e G. As estirpes 4-63-27 (27.4%) e α-β3-Γ (77.8%) foram as mais comumente observadas em bezerras do estado do Rio de Janeiro e São Paulo, respectivamente. O novo conjunto de repetição da MSP1a 190 foi descrito em bezerras de Taiaçu e vinte e uma repetições em tandem da MSP1a resultou em novas sequências com alterações de... / Anaplasma marginale is the most prevalent tick-borne pathogen in cattle in tropical and subtropical regions of the world. The A. marginale major surface protein 1 alpha (MSP1a) contains a variable number of tandem repeats in the amino terminal region and has been used for the characterization of pathogen genetic diversity. We conducted a longitudinal study to ascertain the genetic diversity of A. marginale in in a dairy cattle herd in Seropédica state of Rio de Janeiro and Taiaçu state of São Paulo, Brazil. Twenty calves were evaluated every three months during the first year of life by blood smear, Enzyme-linked Immunosorbent Assay (ELISA), Indirect Fluorescent Antibody Test (IFAT) and Polymerase Chain Reaction (nPCR/qPCR). Additionally, samples positive for the msp1a gene using nPCR were sequenced. The prevalence of A. marginale ranged from 10 to 90% according to blood smears, 20-80% using ELISA/IFAT and 15-100% using qPCR. The number of msp1a copies per mL of blood ranged from 1,04x101 to 6.76x1012 (Seropédica RJ) and 1.20 x 101 to 5.17 x 106 (Taiaçu SP). The results showed that the genetic diversity of A. marginale in a group of calves up to 1 year of age from Taiaçu (SP) was low, with only three different strains identified, showing the microsatellite genotype E. However, the results showed that the genetic diversity of A. marginale in a group of calves up to 1 year of age from Seropédica (RJ) was high, with nineteen different strains identified, showing the microsatellite genotype E and G. The strains 4-63-27 (27.4%) and α-β3-Γ (77.8%) were the most commonly observed in calves of Seropédica RJ and Taiaçu SP, respectively. The new MSP1a tandem repeat 190 was described in calves from Taiaçu and twenty-two MSP1a tandem repeats resulted in new sequences with amino acid changes, which were labeled as 165-186 in calves from Seropédica. In Seropedica, three animals were born infected, with strains 4-63-27, 78-242-25-31 and ...

Made available in DSpace on 2014-06-11T19:26:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-07-04Bitstream added on 2014-06-13T18:54:06Z : No. of bitstreams: 1 faria_act_me_jabo.pdf: 1121101 bytes, checksum: 31146cb54a347b3fc8cc68d8a356b030 (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Xanthomonas aliblineans é um importante patógeno da cana-de-açúcar, causando grandes perdas na produção. Este trabalho teve como objetivos o desenvolvimento de um antissoro específico para X. albilineans bem como a caracterização molecular e fenotípica de um banco de isolados de diferentes regiões do Brasil. O antissoro foi produzido a partir da imunização de coelhos da raça Nova Zelândia, utilizando com antígeno, o isolado 2256 utilizado neste trabalho. Os isolados foram obtidos de canas sintomáticas, coletadas a campo, utilizando-se meio de cultura seletivo XAS. “Simple Sequence Repeats” - SSRs obtidas a partir da análise do genoma de X. albilineans foram utilizadas para o desenho de 15 “primers”, e o polimorfismo avaliado em gel de poliacrilamida corados com nitrato de prata. O antissoro desenvolvido foi altamente específico para X. albilineans. Os 15 “primers” amplificaram um total de 54 alelos polimórficos. A análise de agrupamento mostrou a existência de variabilidade genética entre os isolados coletados em diferentes estados brasileiros, os quais foram divididos em três grupos principais, embora não foi possível agrupar esses indivíduos por local de coleta. A avaliação da patogenicidade mostrou a existência de diversidade patogênica entre os isolados, embora vários deles não tenham sido distinguidos molecularmente pelo marcadores utilizados. Dois alelos foram identificados como associados a patogenicidade, sendo que um deles, , está localizado no loco que codifica a síntese de peptídeos não ribossomais (non ribosomal peptide synthetase – NRPS), os quais estão associados à virulência de muitas bactérias fitopatogênicas / Xanthomonas albilineans is an important pathogen of sugarcane, causing important losses in production. This study aimed to develop an antiserum specific for X. albilineans and the phenotypic and molecular characterization of a set of isolates from different regions of Brazil. The antiserum was produced from immunizing New Zealand rabbits, using as antigen, the isolated 2256 used in this work. The isolates were obtained from symptomatic canes, collected in the field, using selective culture media XAS. Simple Sequence Repeats - SSRs obtained from the analysis of the genome of X. albilineans were used to design 15 primers and the polymorphism analyzed on polyacrylamide gels stained with silver nitrate. The antiserum developed was highly specific for X. albilineans. The 15 primers amplified a total of 54 polymorphic alleles. Cluster analysis showed the existence of genetic variability among isolates collected in different Brazilian states, which were divided into three main groups, although it was not possible to group these individuals based on collect site. The evaluation showed the presence of pathogenic diversity among isolates, although many of them have not been distinguished with the molecular markers used. Two alleles were identified as being associated with pathogenicity, one of which is located in the site encoding the non-ribosomal peptide synthetase - NRPS, which are associated with virulence of many pathogenic bacteria

Made available in DSpace on 2014-06-11T19:26:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-06-29Bitstream added on 2014-06-13T19:33:26Z : No. of bitstreams: 1 oliveira_lz_me_jabo.pdf: 921703 bytes, checksum: a718a5abe40d58b514f5d9794b51f351 (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O objetivo do presente trabalho foi estudar a divergência genética entre árvores matrizes de Tabebuia caraiba (Mart.) Bur. no município de Macapá, no Estado do Amapá, por meio de caracteres biométricos de flores, frutos, sementes e processo germinativo. A divergência genética foi avaliada pela análise de agrupamento, através do método de Ward, K-means e pelo algoritmo de Tocher, obtidos a partir da matriz de dissimilaridade pela Distância Euclidiana. Para verificação da importância relativa de cada variável para a divergência genética utilizou-se a análise de Componentes Principais. As 119 árvores matrizes foram distribuídas em 21 grupos no método de Ward e 23 grupos para o algoritmo de Tocher. O método K-means auxiliou na exclusão de 11 caracteres pouco discriminatórios. Dos caracteres mais importantes para a divergência genética, destacam-se o comprimento do fruto, largura do fruto, comprimento da ala maior da semente, massa de matéria seca da semente, largura do cotilédone, largura da folha e massa de matéria seca da plântula. Há variabilidade entre as árvores matrizes de T. caraiba quanto aos caracteres avaliados e o estudo da divergência possibilita a identificação de árvores matrizes para a colheita de sementes, que subsidiem programas de conservação genética / The objective of this work was to study the genetic diversity among trees of Tabebuia caraiba (Mart.) Bur. at city of Macapá, Amapá State, by means of biometric characters of flowers, fruits, seeds and germination process. Genetic divergence was assessed by cluster analysis by Ward method, K-means algorithm and the Tocher, obtained from the matrix of the Euclidean Distance. To verify the relative importance of each variable to the genetic divergence we used the Principal Component analysis. The 119 selected trees were divided into 21 groups in the method of Ward and 23 groups for the algorithm Tocher. The K-means method aided in the exclusion of 11 characters less discriminatory. Among the most important traits for genetic divergence, we highlight the fruit length, fruit width, length of greater wing of the seed dry weight of seed, cotyledon width, leaf width and dry weight of seedlings. There is variability among the trees of T. caraiba about the traits and the study of divergence allows the identification of mother trees for seed collection, programs that support conservation genetics

Made available in DSpace on 2014-06-11T19:33:40Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-02-27Bitstream added on 2014-06-13T19:23:54Z : No. of bitstreams: 1 luz_fjf_dr_jabo.pdf: 696825 bytes, checksum: e6fae364aaea139b88622f336be9f094 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) / Com o objetivo de ampliar o conhecimento sobre uma coleção de pimentas da Embrapa Roraima, foram realizadas caracterizações morfológica com descritores do IPGRI e molecular com marcadores fAFLP, de 58 acessos de Capsicum chinense. Os resultados da avaliação morfológica detectaram que, 39% dos acessos não se agruparam e entre os mesmos observou-se uma dissimilaridade de até 70%, com 50% de média. A caracterização molecular revelou uma dissimilaridade média de 22,3% entre os acessos levando à conclusão de que há uma pequena variabilidade genética entre os acessos, considerando o genoma como um todo. Os resultados demonstraram que as diferenças morfológicas estariam baseadas apenas em uma parte do genoma das pimentas, focada em características visíveis e mensuráveis pelo ser humano. Por outro lado, a variação observada a partir do DNA genômico por meio do marcador molecular utilizado não foi suficiente para ratificar as diferenças morfológicas observadas. Ambas as formas de caracterizar os acessos foram úteis e necessárias para o conhecimento dos mesmos, revelando informações valiosas para estratégias de conservação e uso das pimentas da Amazônia. / In order to raise the knowledge about a pepper collection from Embrapa Roraima, IPGRI morphological descriptors and fAFLP molecular marker were used to characterize 58 acessions of Capsicum chinense, contributing with information about the diversity of those plants. The results of morphological evaluation showed that 39% of the accessions did not group together and it also detected a great dissimilarity among the accessions, reaching values above 70%, with a 50% medium. The molecular characterization showed an average dissimilarity of 22,3%, indicating little genetic variability on the collection evaluated, considering the total genome of the plants. These results demonstrate that variation detected by morphological descriptors would be related to only a small part of pepper genome, focusing on human visible and measurable traits. The variation observed directly on the genome by the molecular marker used was not sufficient to confirm the morphological differences observed among the accessions. Both ways of characterizing the accessions were useful and necessary to their knowledge, revealing valuable information for conservation strategies and the use of amazon peppers.

Made available in DSpace on 2014-06-11T19:34:59Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-04-26Bitstream added on 2014-06-13T19:44:45Z : No. of bitstreams: 1 rosa_dd_dr_botfca.pdf: 3769642 bytes, checksum: 6f5fb83fe76a081fea96b890323e30f2 (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Dentro do setor de horticultura, as plantas da família Brassicaceae são de grande expressão, tanto em volume, como em valor agregado na comercialização, por isso, destaca-se o cultivo intensivo de brassicas, como as variedades de Brassica oleraceae L. (Couve, repolho, Couve-flor, Brócolos, Couve de Bruxelas), Brassica napus L. e Brassica oleraceae L. var. pekinensis L. (Couve chinesa), sendo a base de sustentação econômica dos pequenos e médios produtores de hortaliças. Como outras culturas de plantio intensivo, as brassicas também enfrentam inúmeros problemas com doenças, dentre estes está a “hérnia das crucíferas”, doença de enorme risco potencial ao produtor, visto seu difícil ou inexistente controle e por condenar a área, impedindo futuros cultivos de brassicas. O agente causal da “hérnia das crucíferas” (Plasmodiophora brassicae Woronin) é um endoparasita obrigatório, pertencente ao reino Protozoa, habitante do solo, sendo um dos fitopatógenos de solo menos estudados no mundo, mas sabe-se que este apresenta raças patogênicas, ou patotipos, sendo que algumas dessas já são conhecidas, principalmente os que ocorrem na Europa e no Japão sabem-se, também, que estas raças “quebram”, com certa freqüência, a pouca resistência que os melhoristas conseguem incorporar nas variedades comerciais, fazendo com que quase não haja variedade resistente disponível no mercado, principalmente ao mercado brasileiro onde, possivelmente, haja raças ainda não relatadas. O objetivo deste estudo visou conhecer a variabilidade genética e patogênica de isolados de P. brassicae oriundos das principais regiões produtoras de Brassicas do estado de São Paulo, utilizando para isso: a) testes em variedade diferenciais, nacionais e importadas, com isolados monospóricos e não monospóricos para determinação das raças; b) estudo da agressividade dos isolados frente... / Within the horticulture sector, the plants of the Brassicaceae family are widespread in both volume and value-added marketing, so we highlight the intensive cultivation of brassicas, such as varieties of Brassica oleracea L. (Kale, cabbage, cauliflower, broccoli, Brussels sprouts), Brassica napus L. and Brassica oleracea L. var. pekinensis L. (Chinese cabbage), and the basis of economic support for small and medium producers of vegetables. Like other intensive planting crops, the brassicas are also facing many problems with diseases, among these is the club root, disease of great potential risk to the producer, because its difficult or no control and order the area, preventing future crops brassicas. The agent causal of the club root (Plasmodiophora brassicae Woronin) is an obligatory endoparasites belonging to the kingdom Protozoa, inhabitant of soil, being one of the pathogens in soil less studied in the world, but it is known that this presents pathogenic races, or pathotypes, and some of these are already known, especially those taking place in Europe and Japan knows it, too, that these races break with some frequency, the little resistance that breeders can incorporate into commercial varieties, making that almost no resistant variety available in the market, especially the Brazilian market where perhaps there is not race related. This study aimed to investigate the genetic variability and pathogenic isolates of P. brassicae come from the main producing regions Brassicas state of Sao Paulo, using for this: a) testing range differential, domestic and imported, with no single spores and spore for the determination of races, b) study of the aggressiveness of the isolates in the face of cultivars available in the market, c) study of genetic variability within and between populations, using markers RAPD and Microsatellite d) genetic characterization through sequencing of genetic regions... (Complete abstract click electronic access below)