Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2016-12-20T16:03:47Z No. of bitstreams: 2 Tese - Luciana Cristina Vitorino - 2015.pdf: 8226538 bytes, checksum: 818b91ae152e61751eb80f72e40d2ef6 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-12-26T13:21:49Z (GMT) No. of bitstreams: 2 Tese - Luciana Cristina Vitorino - 2015.pdf: 8226538 bytes, checksum: 818b91ae152e61751eb80f72e40d2ef6 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2016-12-26T13:21:49Z (GMT). No. of bitstreams: 2 Tese - Luciana Cristina Vitorino - 2015.pdf: 8226538 bytes, checksum: 818b91ae152e61751eb80f72e40d2ef6 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2015-12-09 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / There is strong evidence that the Neotropical vegetation has been influenced by climate changes at the end of the Tertiary and Quaternary. The response of vegetation to the cold weather and dry these periods, consistent with the occurrence of the last glacial maximum, still remains in debate. It is suggested that the areas currently occupied by the Cerrado and seasonal forests (SDTFs) are remnants of a continuous vegetation that existed in the past. From the perspective of that species widely distributed in savannas and Brazilian SDTFs could help unravel the role of climate change Pleistocene on the current distribution pattern of genetic diversity in these vegetation types, we sampled 17 populations of Tabebuia serratifolia in SDTFs and 24 populations Tabebuia ochracea in savannas and sequenced intergenic non-coding regions of chloroplast (psbA-trnH, trnG-trnS e trnC-ycf6) as well as the nuclear region ITS (nrDNA). Later, we used coalescent analysis, Ecological Niche Modeling techniques (ENM) and simulations of demographic hypothesis for these species in an attempt to broaden the understanding of the changes undergone by neotropical landscape during the last ice age cycles. The sampled populations for both species showed high genetic diversity for both markers (hcpDNA = 0.8731 and hnrDNA = 0.7723 - T. serratifolia and hcpDNA = 0.927 and hnrDNA = 0.637 - T. ochracea), and large structure (Fst(cpDNA) = 0.528, P < 0.001 and Fst(ITS) = 0.742, P < 0.001 - T. serratifolia and Fst(cpDNA) = 0.742, P < 0.001 and Fst(ITS) = 0.544, P < 0.001 - T. ochracea). The coalescing analysis showed the time to the most recent common ancestor between haplotypes of the sampled populations, oldest to T. serratifolia (~ 3.4 Ma - 95% CI 1.9 - 6.8), which for T. ochracea (~ 1.9 Ma - 95% CI 0.1 - 2.3). The two species show standard recent population expansion and the niche modeling revealed for the T. serratifolia a higher potential distribution area during Holoceno medium while for T. ochracea the highest suitability area was predicted for maximum glacial last (LGM - 21ka), going in favor the hypothesis that the savannas and STDFs have submitted in the past, a wider distribution than currently known. / Há fortes evidências de que a vegetação Neotropical tenha sido influenciada por alterações climáticas ocorridas no final do período Terciário e no Quaternário. A resposta da vegetação ao clima mais frio e seco desses períodos, condizente com a ocorrência do último máximo glacial, ainda permanece em debate. Sugere-se que as áreas atualmente ocupadas pelo Cerrado e florestas estacionais (SDTFs) sejam remanescentes de uma vegetação contínua que existia no passado. Sob a perspectiva de que espécies amplamente distribuídas em savanas e SDTFs brasileiras pudessem ajudar a desvendar o papel das mudanças climáticas do Pleistoceno sobre o padrão atual de distribuição da diversidade genética nessas formações vegetais, nós amostramos 17 populações de Tabebuia serratifolia em SDTFs e 24 populações de Tabebuia ochracea em savanas e sequenciamos regiões intergênicas não codificantes de cloroplasto (psbA-trnH, trnG-trnS e trnC-ycf6), bem como a região nuclear ITS (rDNA). Posteriormente, utilizamos análises coalescentes, técnicas de Modelagem de Nicho Ecológico (ENM) e simulações de hipóteses demográficas para essas espécies, na tentativa de ampliar o entendimento das mudanças sofridas pela paisagem neotropical durante os últimos ciclos de glaciação. As populações amostradas para as duas espécies apresentaram alta diversidade genética para ambos os marcadores (hcpDNA = 0.8731 e hnrDNA = 0.7723 – T. serratifolia e hcpDNA = 0.927 e hnrDNA = 0.637 – T. ochracea), e grande estruturação (Fst(cpDNA) = 0.528, P < 0.001 e Fst(ITS) = 0.742, P < 0.001 – T. serratifolia e Fst(cpDNA) = 0.742, P < 0.001 e Fst(ITS) = 0.544, P < 0.001 – T. ochracea). As análises coalescentes mostraram um tempo para o ancestral comum mais recente, entre os haplótipos das populações amostradas, mais antigo para T. serratifolia (~3.4 Ma - 95% CI 1.9 - 6.8), que para T. ochracea (~1.9 Ma - 95% CI 0.1 - 2.3). As duas espécies apresentaram padrão de expansão populacional recente sendo que a modelagem de nicho revelou, para T. serratifolia, maior área de distribuição potencial durante o Holoceno médio enquanto que para T. ochracea a maior área de adequabilidade foi predita para o último glacial máximo (LGM – 21ka), indo de encontro à hipótese de que as savanas e as STDFs possam ter apresentado, no passado, uma distribuição mais ampla que a conhecida atualmente.

For neutral genes, uniparental inheritance is expected to reduce effective population size relative to biparentally inherited genes. In finite populations, the ensuing genetic drift can cause stronger spatial and temporal differentiation. An intrapopulation polymorphism in chloroplast DNA was used to examine relative spatial and temporal population structure of chloroplast and allozyme markers in the annual plant Phacelia dubia. There was significant differentiation among populations at chloroplast markers but not for allozyme loci. A fine-scale analysis showed significant structure among sites within populations for chloroplast markers and local heterozygote deficiencies at allozyme loci. These spatial analyses suggest that gene flow via pollen exceeds that via seed. Temporal variation in chloroplast markers, assessed over a 10-year period, was evident in two of four populations, and allozyme loci were characterized by temporal variation in rare-allele frequencies. Population structure appeared to be related to the intensity and type of human disturbance influencing each population. Habitat destruction promoted isolation and enhanced differentiation, whereas mowing increased seed dispersal and reduced differentiation for chloroplast markers. At this time, genetic drift appears to be the primary force shaping chloroplast gene frequencies.

Há controvérsia sobre os processos responsáveis pela atual distribuição de Florestas Tropicais Sazonalmente Secas (FTSS) na América do Sul. Este tipo de vegetação compreende uma grande proporção de todas as espécies neotropicais. Entender o que modela a sua distribuição pode fornecer novas perspectivas para a evolução deste bioma e contribuirpara os aspectos de sua conservação. O trabalho avaliou a evolução deste bioma no sul do Brasil, onde as FTSS e as Florestas Tropicais (FT) são amplamente intercaladas. Para isso, foi reconstruídaa história filogeográfica do cacto, Cereus hildmannianus, uma espécie característica e abundante das FTSS. Métodos de datação molecular, estrutura populacional e filogeografia foram realizadas para avaliar os eventos histórico-demográficospor meio de uma amostragem densa que compreendeu 24 populações e cerca de 150 amostrasde, pelo menos, uma dentre as seis regiões genômicas nuclear e cloroplastidiais selecionadas. A partir disso, foi investigado um possível cenário da dinâmica populacional de C. hildmannianus. Os resultados indicam uma separação da espécie em dois grupos principais (ST: 0,788) com eventos de expansão populacional: umem regiões costeiras e o outro no interior do sul do Brasil, concondante com a distribuição dos núcleos das FTSS. O tempo do ancestral comum mais recente de C. hildmannianus, há 2,56 milhões de anos, remete a especiação deste ao período pré-Glacial. Os resultados do padrão de distribuição de C. hildmannianus foram concordantes com as áreas de endemismo para outros táxons das FTSS. Os eventos de dispersão e de vicariância entre as FTSS e as FT podem estar associados às mudanças paleoclimáticas durante os períodos glaciais do Quaternário, promovendo eventos de retração/expansão nestas florestas. A compreensão desses padrões na história biogeográfica de populações naturais podem auxiliar futuros planos de conservação deste bioma, na América do Sul. / There is controversy about the processes responsible for the current distribution of Seasonally Dry Tropical Forests (SDTF) in South America. This vegetation type comprises a large proportion of all Neotropical species. Understanding what shapes your distribution may provide new insights into the evolution of this ecosystem and contribute to aspects of conservation. The study evaluated the evolution of this biome in southern Brazil, where SDTF and Rainforests are widely interspersed. For this, we reconstructed the phylogeographic history of the cactus, Cereus hildmannianus, a kind of characteristic and abundant SDTF. Molecular dating methods, population structure and phylogeography were performed to evaluate the historical and demographic events through a dense sampling which comprised 24 populations and about 150 samples of at least one among the six nuclear and chloroplast genomic regions selected. From this, we investigated a possible scenario of population dynamics of C. hildmannianus. The results indicate a separation of the species into two main groups (ST: 0.788) with events of population expansion: one in coastal regions and the other inside the south of Brazil, concondante with the distribution of the nuclei of SDTF. The time of the most recent common ancestor of C. hildmannianuswere 2.56 million years ago, this speciation refers to the pre-Glacial. The results of the distribution pattern C. hildmannianus were consistent with areas of endemism for other taxa of SDTF. The events of dispersal and vicariance between SDTF and Rainforests may be related to paleoclimatic changes during glacial periods of the Quaternary, promoting events shrinkage /expansion in these forests. Understanding these patterns in the biogeographic history of natural populations may aid future conservation plans this biome in South America.

Nothofagus moorei is a long-lived, Gondwana relict cool temperate rainforest tree. Nothofagus-dominated rainforests were widespread across much of eastern Australia during the mid-Tertiary but today, N. moorei occurs only as a series of disjunct, isolated populations in south-east Queensland and northern New South Wales. Clonal regeneration via coppicing is reported to be a common feature of most N. moorei populations, while successful sexual regeneration is believed to be rare, occurring largely only in niches with high light levels and limited competition. While clonal propagation enables population persistence and individual longevity, it cannot generate novel genotypes. Isolated populations, potentially high levels of clonality, low-potential for successful sexual regeneration, long-lived individuals and predicted global warming effects make N. moorei vulnerable to local, if not total, population extinction. The current study aimed to assess the relative conservation status of extant N. moorei populations in order to develop appropriate conservation management strategies for long-term population persistence. Levels of genetic diversity and population structure were examined across the remaining natural distribution of N. moorei using nuclear amplified fragment length polymorphism (AFLP), microsatellite and chloroplast DNA markers. In total 607 individuals were sampled from 20 populations and 5 geographical regions: Lamington/Border Ranges, Ballow, Dorrigo/New England, Werrikimbe and Barrington. Genetic results were then analysed to assess conservation status of each population and geographical region. Microsatellite and AFLP data identified comparatively high levels of genetic diversity in all remnant populations sampled. The prevalence of coppicing in the northern Lamington/Border Ranges populations appears to have had little impact on relative levels of genetic diversity, heterozygosity or population structure. Population differentiation was limited, with the majority of genetic variation retained within populations, no regional structuring and high levels of admixture. Analysis of cpDNA variation showed that the three Dorrigo/New England populations were divergent from all other populations, suggesting an ancient divergence in N. moorei prior to Pleistocene glaciations. While levels of genetic diversity were essentially the same across all populations, Bayesian analysis of genetic structure did identify four populations with differing gene pool proportions which would be important to include in conservation efforts in addition to individuals from other populations. Similarly, individuals from four significantly differentiated groups identified using traditional F-statistics suggests individuals from each of these four groups should be included in future conservation plans. In order to maintain ancient chloroplast lineages, populations from the Dorrigo/New England region should also be assigned special conservation value. Populations of N. moorei appear to have retained significant levels of genetic diversity and show little population divergence in spite of marked reductions in the natural distribution since the Early Miocene. Sampling of these ancient trees however, suggests current levels of diversity in N. moorei actually reflect past diversity and differentiation, and that there have been insufficient generations since the historical contraction in distribution for genetic diversity to be adversely affected and regional differentiation to evolve. Long-term persistence of N. moorei is still threatened by future accelerated climate change and the limited preferred habitat that remains where N. moorei can expand its range. While the ability to regenerate clonally may enable long-term persistence of N. moorei, populations are still likely to continue to decline as climatic conditions will increasingly favour sub-tropical and warm temperate species across much of N. moorei's northern distribution. Southern populations of N. moorei, in contrast, could expand their ranges into eucalypt woodlands as predicted climate becomes warmer and wetter. However, this will ultimately be determined by the frequency of fires, with increased fire frequencies favouring the expansion of eucalypts and contraction and possible local population extinction of N. moorei dominated cool temperate rainforests.

Há controvérsia sobre os processos responsáveis pela atual distribuição de Florestas Tropicais Sazonalmente Secas (FTSS) na América do Sul. Este tipo de vegetação compreende uma grande proporção de todas as espécies neotropicais. Entender o que modela a sua distribuição pode fornecer novas perspectivas para a evolução deste bioma e contribuirpara os aspectos de sua conservação. O trabalho avaliou a evolução deste bioma no sul do Brasil, onde as FTSS e as Florestas Tropicais (FT) são amplamente intercaladas. Para isso, foi reconstruídaa história filogeográfica do cacto, Cereus hildmannianus, uma espécie característica e abundante das FTSS. Métodos de datação molecular, estrutura populacional e filogeografia foram realizadas para avaliar os eventos histórico-demográficospor meio de uma amostragem densa que compreendeu 24 populações e cerca de 150 amostrasde, pelo menos, uma dentre as seis regiões genômicas nuclear e cloroplastidiais selecionadas. A partir disso, foi investigado um possível cenário da dinâmica populacional de C. hildmannianus. Os resultados indicam uma separação da espécie em dois grupos principais (ST: 0,788) com eventos de expansão populacional: umem regiões costeiras e o outro no interior do sul do Brasil, concondante com a distribuição dos núcleos das FTSS. O tempo do ancestral comum mais recente de C. hildmannianus, há 2,56 milhões de anos, remete a especiação deste ao período pré-Glacial. Os resultados do padrão de distribuição de C. hildmannianus foram concordantes com as áreas de endemismo para outros táxons das FTSS. Os eventos de dispersão e de vicariância entre as FTSS e as FT podem estar associados às mudanças paleoclimáticas durante os períodos glaciais do Quaternário, promovendo eventos de retração/expansão nestas florestas. A compreensão desses padrões na história biogeográfica de populações naturais podem auxiliar futuros planos de conservação deste bioma, na América do Sul. / There is controversy about the processes responsible for the current distribution of Seasonally Dry Tropical Forests (SDTF) in South America. This vegetation type comprises a large proportion of all Neotropical species. Understanding what shapes your distribution may provide new insights into the evolution of this ecosystem and contribute to aspects of conservation. The study evaluated the evolution of this biome in southern Brazil, where SDTF and Rainforests are widely interspersed. For this, we reconstructed the phylogeographic history of the cactus, Cereus hildmannianus, a kind of characteristic and abundant SDTF. Molecular dating methods, population structure and phylogeography were performed to evaluate the historical and demographic events through a dense sampling which comprised 24 populations and about 150 samples of at least one among the six nuclear and chloroplast genomic regions selected. From this, we investigated a possible scenario of population dynamics of C. hildmannianus. The results indicate a separation of the species into two main groups (ST: 0.788) with events of population expansion: one in coastal regions and the other inside the south of Brazil, concondante with the distribution of the nuclei of SDTF. The time of the most recent common ancestor of C. hildmannianuswere 2.56 million years ago, this speciation refers to the pre-Glacial. The results of the distribution pattern C. hildmannianus were consistent with areas of endemism for other taxa of SDTF. The events of dispersal and vicariance between SDTF and Rainforests may be related to paleoclimatic changes during glacial periods of the Quaternary, promoting events shrinkage /expansion in these forests. Understanding these patterns in the biogeographic history of natural populations may aid future conservation plans this biome in South America.

Orientadores: Flavio Antonio Maës dos Santos, Maria Imaculada Zucchi / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-25T23:19:56Z (GMT). No. of bitstreams: 1 Silvestrini_Milene_D.pdf: 3891912 bytes, checksum: 6bb6bd65f788f261b8387e6c9daf17f8 (MD5) Previous issue date: 2014 / Resumo: A estrutura genética espacial de populações de plantas pode variar ao longo dos estádios ontogenéticos, através das gerações e entre diferentes condições ambientais. Estas mudanças são direcionadas por fatores ecológicos e evolutivos. As espécies pioneiras apresentam histórias de vida e estruturas populacionais características que são afetadas principalmente pelas mudanças ambientais geradas por distúrbios naturais ou antrópicos. O objetivo deste trabalho foi investigar como as características do ciclo de vida, os processos ecológicos e fatores genéticos associados aos distúrbios afetam a diversidade e estrutura genética de populações de uma espécie arbórea pioneira. Nós estudamos Croton floribundus Spreng. (Euphorbiaceae), uma espécie arbórea pioneira abundante em clareiras e em áreas secundárias da Floresta Estacional Semidecidual, em duas áreas com níveis contrastantes de distúrbios antrópicos: uma floresta primária e uma floresta secundária em estádio inicial de sucessão. A fim de abordar a principal questão deste estudo, nós avaliamos o padrão de distribuição da espécie sob as diferentes condições ambientais geradas por distúrbios naturais e antrópicos (Capítulo I); testamos e caracterizamos iniciadores universais cloroplastidiais (cpSSR) para C. floribundus (Capítulo II); desenvolvemos e caracterizamos marcadores microssatélites nucleares (SSR) para C. floribundus bem como examinamos algumas características citogenéticas da espécie com o objetivo de testar a ocorrência de poliploidia e avaliar sua implicação para o uso dos marcadores SSR (Capítulo III); avaliamos a diversidade e estrutura genética de C. floribundus entre duas classes de tamanho e entre populações em uma floresta primária e uma floresta secundária em estádio inicial de sucessão (Capítulo IV). C. floribundus foi frequente e igualmente distribuído em clareiras de todos os tamanhos na floresta primária, mas sua estrutura populacional variou entre áreas com níveis contrastantes de distúrbio antrópico. Seis locos cpSSR foram otimizados e caracterizados em C. floribundus. O estudo citogenético permitiu a caracterização mais precisa dos locos SSR, bem como forneceu novos dados sobre a origem e a evolução da espécie. O número de bivalentes observados na meiose, n = 56 (2n = 8x = 112), mostrou a ocorrência de poliploidia em todas as populações estudadas. Altos níveis de diversidade genética foram encontrados para C. floribundus. A dispersão de sementes e as colonizações (e extinções) foram determinantes para a estrutura genética em fina escala encontrada nas populações de C. floribundus em ambos os tipos de florestas. Além disso, os efeitos destes processos associados aos distúrbios antrópicos parecem aumentar fortemente a diferenciação genética entre as populações na floresta em estádio inicial de sucessão. As análises de marcadores moleculares nucleares e cloroplastidias sugeriram que o fluxo gênico por pólen é responsável por manter a diversidade genética dentro das populações de C. floribundus tanto na floresta primária quanto na floresta secundária em estádio inicial de sucessão. Nesta última, o fluxo gênico por sementes parece ser igualmente importante. Os resultados obtidos mostraram que a dinâmica de clareiras, o processo de colonização e a dispersão de pólen e sementes afetam a diversidade e estrutura genética da espécie arbórea pioneira, aumentando-os ou diminuindo-os conforme o número de colonizadores, número de populações-fonte, as taxas de fluxo gênico e o nível de perturbação antrópica da área / Abstract: The spatial genetic structure of plant populations may vary across life stages, across generations and among different environmental conditions. These changes are driven by evolutionary and ecological forces. Pioneer tree species exhibit particular life histories and population structures that are mainly affected by environmental changes generated by natural or human disturbances. Our aim was to investigate how the life-history traits, ecological processes, and the genetic factors associated to natural and human disturbances can affect the genetic diversity and structure of populations of a pioneer tree species. We studied Croton floribundus Spreng. (Euphorbiaceae), a pioneer tree species abundant in gaps and secondary areas of the semi-deciduous tropical forest, in two areas with contrasting levels of human disturbance: a primary forest and an early successional forest. In order to address the main question of this study, we examined the pattern of distribution of the species under the different environmental conditions generated by natural and human disturbances (Chapter I); tested and characterized universal chloroplast microsatellite (cpSSR) primers for C. floribundus (Chapter II); developed and characterized nuclear microsatellite (SSR) markers for C. floribundus as well as examined some cytogenetic traits of the species in order to test for polyploidy and to evaluate its implications for the appropriate use of the SSR markers (Chapter III); and evaluated the genetic diversity and structure of C. floribundus between two size classes and among populations in the primary forest and in the early successional forest (Chapter IV). C. floribundus was widespread and equally distributed along the gap size range in the primary forest, but its population structure varied between areas with contrasting levels of human disturbance. Six universal cpSSR loci were optimized and characterized for C. floribundus. The cytogenetic study allowed the accurate characterization of SSR loci as well as provided new data on the origin and evolution of the species. The number of bivalents observed in meiosis n=56 (2n=8x=112) showed the occurrence of polyploidy in all populations studied. High genetic diversity levels were found for C. floribundus. Seed dispersal and colonizations (and extinctions) were determinants of the fine-scale genetic structure of C. floribundus in both forest types. Also, their effects associated to the human disturbances seem to strongly increase the genetic differentiation among populations in the early successional forest. Analysis of nuclear and chloroplast markers suggested that gene flow by pollen is responsible for maintaining the genetic diversity within populations of C. floribundus in both primary and early successional forests. In the latter, gene flow by seeds seem to be equally important. The results showed that gap dynamics, colonization process, and pollen and seed dispersal affect the genetic diversity and structure of the pioneer tree species by increasing or decreasing them depending mainly on the number of colonizers, the number of source populations, the gene flow rates, and the level of human disturbance of the area / Doutorado / Ecologia / Doutora em Ecologia

No description available.

Thesis (MSc)--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: Erica is a genus of about 860 species world wide, with 700 of these found in South Africa’s southwestern and southern Cape, making it by far the most speciose genus in the Cape Floristic Region. This poses a particular challenge in the construction of a molecular phylogeny of the genus. The choice of suitably variable gene regions is a crucial decision on which the successful phylogenetic reconstruction of this important genus is critically dependent. The aim of this project was therefore to determine which DNA regions, both chloroplast and nuclear, would be sufficiently variable to give adequate informative characters that may be useful at the species level phylogenetic reconstruction. A subset of 30 species, representing the range of morphological diversity and pollinator preference within Erica, was selected for study. For each of these species the variability in eight chloroplast regions (trnL-F, matK, trnS-G, rps12- rpl20, psbAtrnH, trnC-D, rps4-trnT and trnT-L) and the nuclear ITS region was investigated. The psbA-trnH, trnC-D, rps4-trnT and trnT-L chloroplast regions were found to be problematic to amplify and to possess too few Parsimony Informative Characters to be of use in phylogenetic reconstruction. Four of the chloroplast regions, trnS-G, trnL-F, matK and rpS12-rpL20 and the nuclear ITS region could be amplified and sequenced with success. The ITS region was found to be reasonably variable, with the chloroplast genes showing less variability. The DNA extraction method employed showed itself to be of critical importance in the success of the study. Two DNA extraction protocols, both modified from the original Doyle and Doyle (1987) method, were tested. The one included double the amount of β-mercaptoethanol and Polyvinylpyrrolidone (PVP) and the other included an extended phenol: chloroform: isoamylalcohol step. These variables, together with the effectiveness of these methods on fresh vs. silica dried plant samples, were investigated to determine which of the two would yield high quantities and qualities of DNA and result in the best method for the extraction of DNA from Erica species. / AFRIKAANSE OPSOMMING: Erica is ‘n genus van omtrent 860 spesies wêreldwyd, met 700 van hierdie spesies aanwesig in die suidwes en suid Kaap van Suid Afrika, wat dit by verre die mees spesieryke genus in die Kaapse Floristiese Streek maak. Dit stel ’n besondere uitdaging in die konstruksie van ’n molekulêre filogenie van die genus. Die keuse van geskikte variërende geen-areas is ‘n belangrike besluit waarvan die suksesvolle filogenetiese rekonstruksie van hierdie belangrike genus krities afhanklik sal wees. Die doel van hierdie projek was dus om te bepaal watter DNS areas, buide chloroplas en kern, genoegsaam varieer om voldoende informatiewe kenmerke te lewer om bruikbaar te wees in ’n spesie-vlak molekulêre rekonstruksie. ’n Subgroep van 30 spesies, wat die reeks van morfologiese diversiteit en bestuiwer voorkeure in Erica verteenwoordig, is dus vir die studie geselekteer. Vir elk van hierdie spesies is die variasie in agt chloroplast areas (trnL-F, matK, trnS-G, rps12- rpl20, psbA-trnH, trnC-D, rps4-trnT en trnT-L) en die kern ITS area ondersoek. Dit was problematies om die psbA-trnH, trnC-D, rps4-trnT en trnT-L chloroplast areas te amplifiseer, en daar is gevind dat hulle te min Parsimonie Informatiewe Kenmerke besig om bruikbaar te wees in filogenetiese rekonstruksie. Vier van die chloroplas areas, trnS-G, trnL-F, matK en rpS12-rpL20 en die kern ITS kon suksesvol geamplifiseer word en die basisvolgordes kon suksesvol bepaal word. Daar is gevind dat die ITS area redelik variërend is, terwyl chloroplas areas minder variasie getoon het. Die DNS ekstraksie metode wat gebruik is het die kritiese belang van die ekstraksie metode in die sukses van die studie bewys. Twee DNS protokolle, beide gemodifiseer van die oorspronklike Doyle en Doyle (1987) metode, is getoets. Die een het dubbel die hoeveelheid β-mercaptoetanol en Polyvinylpyrrolidone (PVP) bevat, en die het ’n uitgebruide fenol: chloroform: isoamylalkohol stap ingesluit. Hierdie veranderlikes, saam met die effektiwiteit van hierdie metodes op vars teenoor silika-gedroogde plant monsters, is ondersoek om vas te stel watter een van die twee die hoogste kwaliteit en kwantiteit DNS sou lewer en dus sal lei tot die beste DNS ekstraksie metode vir Erica spesies.

Les oliviers cultivés et leurs parents sauvages (oléastres), représentent deux variétés botaniques de l'espèce Olea europaea, subsp. var. europaea et var. sylvestris, respectivement. Selon des études génétiques et archéobotaniques antérieures, l'existence de populations d'oléastres dans l'est et l'ouest du bassin méditerranéen remonte à avant le néolithique. La domestication de l'olivier aurait eu lieu au moins dans ces deux zones. Néanmoins, la lignée maternelle qui caractérise les oléastres de l'est de la Méditerranée est majoritaire au sein des variétés méditerranéennes. Une telle signature génétique est probablement le résultat de migrations humaines essentiellement d'est en ouest. En dépit de ces travaux, les origines et les processus de diversification à l'ouest de la méditerranée demeurent méconnus. L'objectif de cette thèse est d'étudier les origines et les processus de diversification chez l'olivier à l'ouest de la Méditerranée. Deux hypothèses sont formulées: (i) une co-existence entre variétés sélectionnées localement et variétés introduites à partir de l'est de la Méditerranée et maintenues par clonage, (ii) une sélection à partir des formes de l'est introgressées par les populations locales à l'ouest de la Méditerranée. Dans une première partie, nous avons examiné les processus de diversification par une analyse des pratiques paysannes à une échelle localisée et dans une zone d'extrême diffusion : le Maroc. Il s'agissait de comprendre comment les paysans traitent la diversité variétale dans un contexte fortement impacté par une seule et même variété, la ‘Picholine marocaine'. Sur la base d'enquêtes semi-dirigées menées auprès des paysans dans les agro-écosystèmes traditionnels et selon une approche d'ethnobiologie, nous avons mis en évidence l'importance des logiques de classifications locales (usage, origine, âge, conservation de l'huile, méthode de propagation…) dans le traitement, le maintien et la gestion de la diversité variétale. Nos résultats montrent la présence d'un système de dénomination basée sur des catégories englobantes où les types d'oliviers sont regroupés sous des noms génériques en fonction des critères socioculturels et techniques plutôt que sur des critères morphologiques. Nous avons montré que ces catégories sont définies par des contours permissifs permettant aux types d'oliviers d'être classées dans plusieurs catégories. Nous soutenons l'hypothèse que ce système de classification permet de maintenir la diversité et est une force motrice pour la diversification variétale dans ces agro-écosystèmes caractérisés par une faible diversité d'oliviers. Dans une seconde partie, nous avons examiné les processus de diversification variétale par une approche basée sur la phylogéographie à l'échelle de la Méditerranée. Les analyses génétiques des variétés méditerranéennes d'olivier basées sur l'utilisation des marqueurs microsatellites nucléaires et chloroplastiques selon une approche bayésienne montrent une structure génétique est-ouest. La plupart des variétés de l'ouest de la méditerranée ont une lignée maternelle de l'est mais un génome nucléaire proche du "pool" génétique de l'ouest de la Méditerranée, ce qui indique une sélection à partir des formes de l'est introgressées par le "pool" génétique ouest et suggère que la sélection des oliviers à partir du semis n'a pas cessé aux premières étapes de domestication. Nos analyses sur les pratiques paysannes montrant que l'oléastre issu de semis fait partie intégrante de l'agro-écosystème et fait l'objet de sélection et d'usage (greffage sur oléastre, utilisation de l'huile de l'oléastre), ce qui plaide en faveur de l'hypothèse de l'introgression. En adoptant l'approche ABC (Approximative Bayesianne Computation), nous montrons que le scénario basé sur l'introgression des oliviers de l'est par les oléastres de l'ouest est le plus probable avec une introgression. / Olive cultivars and their wild relatives (also named oleasters) represent two botanical varieties of Olea europaea subsp. europaea, respectively var. europaea and var. sylvestris. Archaeobotanical and genetic studies showed the occurrence of Oleasters populations in east and west Mediterranean areas before the Neolithic. The domestication of the olive tree has taken place at least in these two areas. However, the maternal lineage that characterizes the eastern Mediterranean oleasters predominates among Mediterranean olive varieties. Such genetic signature is probably the result of human migrations mainly from east to west. Nevertheless, the origins and processes of olive diversification in the western Mediterranean remain unknown. The objective of this thesis is to study the origins and processes of olive diversification in the western Mediterranean areas. Two assumptions are formulated: (i) a co-existence between locally selected and introduced olive varieties from the eastern Mediterranean and maintained by cloning, (ii) a selection from the eastern olive varieties and their introgression by local populations of the western Mediterranean pool. Firstly, we examined the process of olive diversification through analysis of farming practices on a localized scale and in an area of extreme diffusion, in Morocco. Our aim is to understand how farmers treat the olive varietal diversity in a highly impacted context by a single variety, the ‘Picholine marocaine'. Based on semi-structured surveys conducted with farmers in traditional agro-ecosystems and using an approach of ethnobiology, we highlighted the importance of local classification logic (use, origin, age, conservation oil, propagation methods ...) in the treatment, maintenance and management of the varietal diversity. Our results show the presence of a naming system based on inclusive categories which olives types are grouped under generic names based on cultural and technical criteria rather than morphological criteria. We have shown that these categories are defined by permissive contours allowing the olive types to be classified in several categories. We support the hypothesis that this classification system helps to maintain diversity and is a driving force for varietal diversification in these agro-ecosystems characterized by a low diversity of olive trees. Secondly, we examined the varietal olive diversification process by an approach based on a phylogeographic study at a Mediterranean scale. Genetic analyses of Mediterranean olive varieties based on the nuclear and chloroplast microsatellites markers and a Bayesian approach show an east-west genetic structure. Most of western olive varieties have a maternal lineage of the oleasters Mediterranean east, but a nuclear genome close to the gene pool of western Mediterranean, indicating a selection from the eastern forms that were introgressed by the western Mediterranean gene pool and suggests that selection from seedling has not ceased in the early stages of domestication. Our analyzes on the farmers' practices show that oleasters from seedling is an integral part of the agroecosystem and are subject to selection and use (grafting, use of oil oleasters), which argues in favor of the introgression hypothesis. By adopting the ABC approach (Approximate Computation Bayesianne), we show that the scenario based on the introgression of olive varieties of the east by the western oleasters is the most likely scenario. We enrich the knowledge about the domestication process in the western Mediterranean by crossing analysis of farmers' practices and phylogeographic study of olive trees in the Mediterranean basin. Results were discussed with respect to ex-situ versus in-situ conservation and with the questions raised by the evolution of plant diversity involving clonal and sexual propagation.

L'introgression est un processus fréquent et qui a d'importantes conséquences évolutives. L'objectif de ce travail était de tester un modèle neutre d'introgression chez des épicéas du Plateau tibétain et des régions voisines. Le travail a permis de mettre en évidence que la direction de l'introgression pouvait être prédite par la dynamique passée des populations d'arbres, et que l'importance de cette introgression était inversement proportionnelle à l'intensité des échanges génétiques au sein de l'espèce invasive, grâce à la comparaison de la structure génétique basée sur des marqueurs chloroplastiques (à hérédité paternelle) et mitochondriaux (à hérédité maternelle). / Introgression is a widespread phenomenon with potentially profound evolutionaryconsequences. Recently, significant progress in our understanding of introgression hasbeen made with the development of a neutral model. This model predicts that, whenone species invades an area already occupied by a related species, introgression ofneutral genes takes place mainly from the local species towards the invading ones. Inaddition, following a contact between two hybridizing species, the model predicts thatintrogression should be particularly frequent for genome components experiencinglittle gene flow. However, to date, there was no empirical example available, in whichone species expanded into the range of a closely related one and two markers withcontrasted rates of gene flow had been studied for both species. Only in such a casecould the two predictions outlined above be tested simultaneously. In addition, basedon these two predictions, species delimitation should be more efficient when usingmolecular markers experiencing high rates of gene flow. The present thesis was designed to test the hypotheses of this model. The biologicalmodel used was conifers, a group in which introgression and hybridization arecommon because of incomplete reproductive isolation. The species investigatedbelong to the genus Picea (spruce). We focused on two species complexes,represented by monographic clades in a phylogenetic study using the chloroplast genematK. All species studied occur in the Qinghai-Tibetan Plateau (QTP) and adjacenthighlands. The phylogeography of these species complexes was reconstructed usingorganelle markers (mitochondrial DNA, mtDNA and chloroplast DNA, cpDNA). Inconifers, mtDNA and cpDNA have contrasted modes of inheritance. The former ismaternally inherited, transmitted by seeds experiencing little gene flow while thelatter is paternally inherited, transmitted by both pollen and seeds experiencing highlevels of gene flow. Therefore, uniparentally inherited mtDNA and cpDNA markersexperience different rates of gene flow in such a group, providing an ideal model to test the relationship between rates of gene flow, introgression and species delimitation.Two mtDNA fragments (nad1intron b/c; nad5 intron1) and three cpDNA fragments(ndhK-C；trnL-trnF；trnS-trnG) were sequenced for nine species belonging to thePicea asperata and P. likiangensis species complex.(1) Nine mtDNA and nine cpDNA haplotypes were detected in 459 individualsfrom 46 natural populations in five species of P. asperata complex. As found in mostconifer species studied so far, low variation is present in the two mtDNA intronsalong with a high level of differentiation among populations (GST = 0.90). In contrast,higher variation and lower differentiation among populations was found at cpDNAmarkers (GST = 0.56). The cpDNA, although far from being fully diagnostic, is morespecies-specific than mtDNA: four groups of populations were identified usingcpDNA markers, all of them related to species or groups of species, whereas formtDNA, geographical variation prevails over species differentiation. A literaturereview shows that mtDNA variants are often shared among related conifer species,whereas cpDNA variants are more species-specific. Hence, increased intraspecificgene flow appears to decrease differentiation within species but not among species.[...]