O objetivo desta tese foi o estudo da influência do aditivo redutor de retração (SRA) e o aditivo compensador de retração (SCA) em argamassas e pastas de cimento de escória ativada com silicato de sódio. A metodologia foi centrada na análise da retração por secagem e autógena, com o estudo de outras características que influenciam no fenômeno da retração, como as propriedades mecânicas. Para o avanço no conhecimento do efeito dos aditivos no comportamento do cimento de escória, foi caracterizada a microestrutura com a determinação da análise por termogravimetria, porosimetria e difração de raios X. Neste estudo foram empregados os seguintes teores de aditivo, porcentagem relativa à massa de aglomerante: 0,5%, 1%, 1,5% e 2% do aditivo SRA e 5%, 10% e 15% do aditivo SCA. Para a análise da influência da relação a/agl foram empregadas três teores: 0,40, 0,48 e 0,56. No estudo das amostras de referência, sem a utilização de aditivo, observou-se que o aumento da relação a/agl causa o aumento da retração por secagem e da retração autógena do cimento de escória ativada. A diminuição da resistência mecânica com o aumento da relação a/agl, o que torna o esqueleto sólido mais susceptível à deformações, e o aumento das tensões capilares, em razão do aumento da quantidade de água livre para ser evaporada, são os principais fatores para o aumento da retração por secagem. No caso da retração autógena, seu aumento é atribuído ao aumento da auto-secagem com o aumento do volume de poros com diâmetro na faixa de mesoporos, além da diminuição da resistência mecânica. O aditivo redutor de retração (SRA) conseguiu reduzir a retração por secagem em percentuais de 40% até 74% aos 28 dias, no entanto, este tipo de aditivo não obteve êxito no combate a retração autógena. Com relação à resistência mecânica, o aditivo SRA causou a redução de até 40%, efeito atribuído à diminuição do grau de hidratação e retardo do refinamento da porosidade. O aditivo compensador de retração (SCA) amenizou a retração por secagem e a retração autógena, reduzindo em até 64% e 70%, respectivamente, porém reduziu em até 60% a resistência mecânica do cimento de escória ativada. Com relação à microestrutura, o aditivo SCA diminuiu o grau de hidratação e aumentou a porosidade total, com o aumento da proporção do volume de macroporos. / The aim of this research was the study of the influence of shrinkage reducing admixture (SRA) and shrinkage compensating admixture (SCA) in mortars and pastes of blast furnace slag activated with sodium silicate. The method was centered in the analysis of free drying and autogenous shrinkage, with other characteristics that affect the shrinkage, as the mechanical properties. The microstructure behavior was accomplished with thermogravimetry (TG), mercury intrusion porosimetry (MIP) and X-ray diffraction (XRD). The samples were prepared with 0,5%, 1%, 1,5% and 2% of SRA admixture and 5%, 10% and 15% of SCA admixture, by binder mass. The effect of water/binder ratio was accomplished in three contents: 0,40, 0,48 and 0,56. In the reference mixtures, without admixtures, it was observed that an increase of water/binder ratio incurs in an increase of drying and autogenous shrinkage of alkali activated slag. The explanations for drying shrinkage behavior are the decrease of mechanical strength as consequence of water/binder increase, that turns the porous structure more susceptible to deformations, and the increase of the capillary tensions, attributed to the increase of free water to be evaporated. The increase of autogenous shrinkage with water/binder ratio is attributed to the increase of pore volume with diameter in the mesopores range, besides the decrease of the mechanical strength. The shrinkage reducing admixture (SRA) diminish drying shrinkage of 40% up to 74% at 28 days, however, this type of admixture was not capable to combat the autogenous shrinkage. About mechanical strength, the SRA admixture incurs in a decrease up to 40% of compression strength that it was attributed to the decrease of the hydration degree and retard of pore size refinement. The shrinkage compensating admixture (SCA) softened drying and autogenous shrinkage, reducing in up to 64% and 70%, respectively. However, the SCA admixture decreases in up to 60% mechanical strength of alkali activated slag. About microstructure, SCA admixture reduced the hydration degree and it increased the total porosity, with the increase of macropores volume.

De nombreuses méthodes ont été développées dans le but d’estimer les apports génétiques (taux de mélange) de populations parentales au pool génétique d’une population mélangée. Certaines de ces méthodes ont été implémentées dans des logiciels, permettant une estimation plus ou moins rapide et précise des taux de mélange. Une comparaison complète des logiciels ADMIX (méthode des moindres carrés pondérés), ADMIX95 (méthode basée sur les identités géniques), Admix 2.0 (méthode basée sur la coalescence), Mistura (méthode de maximum de vraisemblance), LEA (méthode bayésienne de vraisemblance), et LEADMIX (méthode de maximum de vraisemblance basée sur la coalescence) a été menée. L’analyse a été faite à deux niveaux : intra-logiciel (test de chaque logiciel sous un jeu de paramètres définis), inter-logiciel (comparaison des logiciels entre eux). Les taux de mélange ont été estimés à partir de quatre types de marqueurs : autosomaux (groupes sanguins et gènes KIR), et uniparentaux (ADNmt et chromosome Y). Notre étude révèle que la précision et la fiabilité des estimations dépendent de l’adéquation du mélange étudié avec le modèle de la méthode employée, mais également d’un choix judicieux des loci et des populations parentales utilisés. La variabilité des estimations lors de modifications, même minimes, des paramètres de l’étude, nous amène à considérer que les contributions ne doivent pas être présentées sous forme de taux de mélange, mais d’« intervalles indicatifs de mélange » soulignant les tendances migratoires générales. / Different methods have been developed to estimate the genetic admixture contributions of parental populations to a hybrid one. Most of these methods are implemented in different software programs that provide estimates having variable accuracy. A full comparison between ADMIX (weighted least square), ADMIX95 (gene identity), Admix 2.0 (coalescent-based), Mistura (maximum-likelihood), LEA (likelihood-based) and LEADMIX (maximum-likelihood) software programs has been carried out, both at the “intra” (test of each software programs) and “inter” level (comparisons between them). We tested all of these programs on a real human population data set, using four kinds of markers, autosomal (Blood groups and KIR genes) and uniparental (mtDNA and Y-Chromosome). We demonstrated that the accuracy of the results depends not only on the method itself but also on the choice of loci and of parental populations. We consider that the results of admixture contribution rates obtained from human population data set should not be considered as an accurate value but rather as an indicative result and we suggest using an “Admixture Indicative Interval” as a measurement of admixture.

BACKGROUND: Uruguay exhibits one of the highest rates of breast cancer in Latin America, similar to those of developed nations, the reasons for which are not completely understood. In this study we investigated the effect that ancestral background has on breast cancer susceptibility among Uruguayan women. METHODS: We carried out a case-control study of 328 (164 cases, 164 controls) women enrolled in public hospitals and private clinics across the country. We estimated ancestral proportions using a panel of nuclear and mitochondrial ancestry informative markers (AIMs) and tested their association with breast cancer risk. RESULTS: Nuclear individual ancestry in cases was (mean ± SD) 9.8 ± 7.6% African, 13.2 ± 10.2% Native American and 77.1 ± 13.1% European, and in controls 9.1 ± 7.5% African, 14.7 ± 11.2% Native American and 76.2 ± 14.2% European. There was no evidence of a difference in nuclear or mitochondrial ancestry between cases and controls. However, European mitochondrial haplogroup H was associated with breast cancer (OR = 2.0; 95% CI 1.1, 3.5). CONCLUSIONS: We have not found evidence that overall genetic ancestry differs between breast cancer patients and controls in Uruguay but we detected an association of the disease with a European mitochondrial lineage, which warrants further investigation.

Following their dispersal out of Africa, humans colonised all continents of the world save one, Antarctica. Whilst Europe was initially peopled soon after this exodus, paleoclimatic, archaeological, and historical evidence suggest that successive waves and migrations of people have contributed to the population resident in Europe today. I therefore examined the impact of past events on the European population through the analysis of DNA sampled both from contemporary Europeans, and from worldwide populations pertinent to its history. I genotyped and analysed data from the Y chromosomes of over 2,000 haplogroup R-M269 European men from over 30 different populations and, in combination with comparable datasets gathered from the literature, show that there it is not possible to assign a date to the origin of this lineage in Europe, and thus that any conclusion as to the ancient or recent spread of this lineage in Europe is unfounded. I also show that commonly used Y chromosome lineage dating techniques based on STR variation are biased by the markers used and conclusions based on such dates should be viewed with a large amount of caution. I next use genome-wide SNP data from 1,550 individuals from 95 worldwide populations to explore the population structure of Europe and present an analysis of the detailed structure of Europe in a novel analytical framework using ChromoPainter and fineSTRUCTURE. Admixture analysis based this data reveals distinct genomic inputs to peripheral European populations, from North Africa, Sub-Saharan Africa, the Middle East, and East Asia, and provides dates for this admixture within the last 1,000 years that correspond to the emergence and decline of empires and kingdoms in these regions of Europe. This novel analysis highlights the importance of recent historical events on European population structure, but also suggests a degree of ancient structure across European populations. Taken together, these analyses demonstrate the substantial effects of both ancient and recent migrations and mixture on the contemporary genetic structure of Europe.

Apesar da intensa mistura étnica na formação da população Brasileira, pequenos grupos isolados ainda podem ser encontrados, principalmente representados pelas tribos indígenas e comunidades remanescentes de quilombo. As comunidades de Barra (BA), São Gonçalo (BA) e Valongo (SC) apresentam diferentes histórias demográficas de formação. Os AIMs (Marcadores Informativos de Ancestralidade) são capazes de revelar essas diferenças pois apresentam grandes diferenciais de freqüência () entre os principais grupos populacionais parentais (africanos, ameríndios, europeus) e, por esta razão, constituem polimorfismos com maior poder discriminante em estimativas de mistura étnica. No presente trabalho, foram testados oito AIMs na análise de três remanescentes de quilombo, comparados a duas amostras de população urbana brasileira. Um destes marcadores, o alelo CYP1A1*2C, foi testado em sete aldeias de quatro tribos da Amazônia Central Brasileira, completando a análise dos outros sete marcadores previamente realizados nestas populações ameríndias. Os objetivos, além da descrição formal de tais populações, incluíam comparar eventuais diferenças entre as comunidades quilombolas e verificar a eficiência relativa destes marcadores em estudos deste tipo. A comparação das freqüências do alelo CYP1A1*2C entre os ameríndios e populações mundiais confirma este alelo como um excelente AIM para diferenciar ameríndios de europeus e africanos, informação importante em estimativas de mistura em populações trihíbridas Brasileiras. As freqüências de oito AIMs (FY-Null, RB, LPL, AT3, Sb19.3, APO, PV92 e CYP1A1*2C) foram então estimadas nas comunidades remanescentes de quilombo de Barra (n=47), São Gonçalo (n=51) e Valongo (n=25) e nas populações urbanas de Jequié (n=47) e Hemosc (Hemocentro de Santa Catarina, n=25) a partir dos fenótipos determinados por PCR e PCRRFLP. As análises estatísticas empregaram programas já descritos (GENEPOP, DISPAN, GDA, STRUCTURE, MVSP e ADMIX 2 e 3). As freqüências alélicas e genotípicas diferenciam todas as comunidades remanescentes e urbanas, fato corroborado pelos valores de FST (p<0,01) par a par entre elas. Outros valores de FST mostram similaridades da comunidade de Barra com africanos e da amostra Hemosc com Europeus, o que é confirmado pelas estimativas do componente africano em Barra (95%) e europeu no Hemosc (83%), como também pelas análises de componente principal. Nestas últimas, o locus FY foi a variável de maior peso (loading) sobre o primeiro componente principal e o PV92 o locus de maior peso sobre o segundo componente principal. Este método demonstrou-se particularmente adequado, pois, em ambas as análises, os dois componentes principais explicaram mais do que 95% da variância total. As estimativas dos componentes africano, europeu e ameríndio em São Gonçalo (68%, 22% e 10%) e JQ (52%, 31% e 17%) mostram que os AIMs geram estimativas de contribuição africana maiores do que as obtidas por STRs autossômicos, YSTRs e marcadores clássicos nas mesmas populações. A estimativa do componente africano em Valongo (68%) foi menor que a obtida a partir dos marcadores clássicos. Isto poderia ser considerado como evidência da maior eficiência destes marcadores na quantificação do componente africano, uma vez que o aumento das estimativas não foi generalizado e, portanto, provavelmente não viciado. Conclui-se que os AIMs seriam mais eficientes para o cálculo da proporção relativa dos diferentes componentes formadores destas populações, pois conduziriam a estimativas mais realistas. / In spite of the high degree of inter-ethnic admixture that characterizes the formation of the Brazilian population, small isolated groups, mainly represented by indigenous Amerindian tribes and communities known as quilombo remnants, can still be found. Barra (BA), São Gonçalo (BA) and Valongo (SC) are communities that presented different demographic histories during their formations. The AIMs (Ancestry Informative Markers) are capable of disclosing such differences due to the fact that they present large frequency differentials () between the major ethnic groups that gave origin to the Brazilian population. This provides more reliable information for interethnic admixture estimates. Given that, the present study aimed at establishing the differences regarding inter-ethnic admixture between these three quilombo remnants, which present different demographic histories. The CYP1A1*2C allele frequencies were established in four indigenous tribes from the Brazilian Amazon, which are characterized by low admixture degrees with non-Amerindian people (2-3%), and were compared with frequencies obtained in worldwide populations. This comparison evidenced that such allele is extremely useful for setting Amerindians apart from Europeans and Africans, which is an outstanding feature for estimation of admixture proportions in Brazilian tri-hybrid populations. Allele frequencies of eight AIMs (FY-Null, RB, LPL, AT3, Sb19.3, APO, PV92 and CYP1A1*2C) were obtained in three quilombo remnant communities, Barra (n=47), São Gonçalo (n=51) and Valongo (n=25), and in urban population samples from Jequié (n=47) and Hemosc (n=25), by means of PCR and PCR-RFLP. Statistical analysis were carried out employing the GENEPOP, DISPAN, GDA, STRUCTURE, MVSP and ADMIX 2 and 3 softwares. Allele and genotype frequencies are able to differentiate all quilombo remnant and urban samples, an aspect corroborated by the pair-wise FST (p<0.01) values. Other FST estimates reveal similarities between Barra and Africans and between Hemosc and Europeans, which are supported by the respective African and European admixture estimates in Barra (95%) and Hemosc (83%) and by the Principal Component Analysis. In the latter analysis, the FY locus consisted in the variable with greatest influence (loading) over the first component. On the other hand, the variable PV92 exhibited the highest influence over the second component analysis. This method has proven to be very reliable, given that, in both analyses, the first two principal components explained more than 95% of the total variance. African, European and Amerindian inter-ethnic admixture estimates in São Gonçalo (68%, 22% and 10%) and JQ (52%, 31% and 17%) emphasize the fact that the AIMs provides higher African contribution estimates than the ones obtained by means of autosomal and Y-linked STRs and classical markers in the same populations. African contribution estimated in Valongo (68%) was lower than the one obtained by means of classical markers. Taken together, these estimates may be an evidence of higher effectiveness of this set of markers in quantifying the African component, as long as the increase in African contribution was not generalized and, hence, probably unbiased. In conclusion, the AIMs are more effective in estimating the admixture proportions of the different ethnic components that gave origin to these populations, given that they resulted in more reliable estimates.

L'emploi de certaines additions minérales et organiques dans la confection du mortier et du béton contribue à une modification du processus d'hydratation du ciment. L'incorporation de ces additions minérales entraîne également une modification de la distribution granulaire, l'apparition de nouveaux sites de nucléation et une nouvelle activité des surfaces des grains. Ceci nécessite le malaxage avec des superplastifiants qui viennent défloculer les grains, libérer l'eau piégée dans les interstices et améliorer l'ouvrabilité du béton. Ces modifications des propriétés physicochimiques des composants du béton affectent directement les propriétés rhéologiques du mortier et du béton à l'état frais ainsi que ses composantes finales.L'objectif principal de ce travail est focalisé sur la prédiction des modifications rhéologiques apportées par les additions minérales aux mortiers afin de trouver les meilleures compositions d'une mise en œuvre convenable. Une étude expérimentale est entamée sur des mortiers normalisés où le ciment ordinaire est substitué partiellement par différentes additions minérales telles que la fumée de silice, le laitier des hauts fourneaux, la pouzzolane naturelle et le calcaire. Avec l'eau de gâchage, on a ajouté plusieurs types de superplastifiants avec différents dosages où les paramètres rhéologiques du mortier ont été mesurés respectivement par un mini cône et un rhéomètre.Les paramètre rhéologiques obtenus varient sensiblement avec chaque type d'addition minérale et dépendent de ses propriétés et son interaction avec le superplastifiant et les grains de ciment. Le superplastifiant à base de polycarboxylates est plus efficace en présence du ciment contenant du calcaire ou du laitier conduisant à une amélioration des propriétés rhéologiques. Par contre, le mortier devient plus visqueux s'il contient un fort pourcentage de pouzzolane naturelle. Une relation mathématique est proposée qui exprime la variation de chaque paramètre rhéologique selon le taux de substitution du ciment et le dosage en superplastifiant. Cette relation est exprimée par le produit de trois paramètres; l'effet de l'addition minérale, l'effet du superplastifiant et l'effet de leur interaction. Les coefficients de corrélation trouvés sont proches de l'unité et justifient bien la convenance de ce choix. L'application de cette nouvelle relation à d'autres résultats trouvés par d'autres chercheurs présente une grande satisfaction avec des résultats satisfaisant et des coefficients de corrélation allant 0,9 à 0,98. / The use of some organic and inorganic admixtures in the production of mortar and concrete contributes to a change in the cement hydration process. The incorporation of these mineral additions also causes a change in the grain distribution, the appearance of new nucleation sites and a new activity of the grain surfaces. This requires mixing with superplasticizers which deflocculates grains, releases the trapped water in the interstices and improves the workability of concrete. These changes in the physicochemical properties of the cement paste directly affect the rheological properties of mortar and concrete in the fresh state and its final components.The main objective of this work is focused on the prediction of rheological changes of mineral additions mortars and finds the best composition for a suitable casting. An experimental study is underway on standardized mortars where ordinary cement is partially substituted by different mineral additions such as silica fume, blast furnace slag, natural pouzzolan and limestone powder. With the mixing water, was added several types with different dosages of superplasticizers where the rheological parameters of the mortar were measured respectively by a rheometer apparatus and a mini cone test.The Theological parameters obtained vary with each type of mineral addition and depend on its properties and its interaction with the superplasticizer and cement grains. The polycarboxylate superplasticizer is more effective in the presence of limestone powder or cement containing slag resulting in improved rheological properties. However, the mortar becomes more viscous if it contains a high percentage of natural pozzolan. A mathematical relationship is provided which expresses the variation of each rheological parameter according the substitution rate of the cement and superplasticizer dosage. This relationship is expressed by the product of three parameters; the effect of the mineral addition, the effect of the superplasticizer and the effect of their interaction. The correlation coefficients found are close to unity and well justify the appropriateness of this choice. The application of this new relationship to other results found by other researchers has high satisfaction with satisfactory results and correlation coefficients ranging from 0.9 to 0.98

The upland (Pseudacris feriarum) and midland (P. triseriata) chorus frogs are closely related cryptic species that are best distinguished genetically. The distribution of these species within the Commonwealth of Kentucky has previously been defined by only a handful of genetic samples, making delineation of range limits for each species difficult. Accurate understanding of species distributions, and the genetic structure within them, are vitally important for conservation management of amphibian species. In this study, I have collected genetic samples from across the putative ranges of P. triseriata and P. feriarum in Kentucky and used next-generation sequencing technology to generate more fine-scale estimates of species ranges. The genetic data generated in this study support the delineation of two species in Kentucky, and the species assignments of all individuals and populations are in general concordance with the previously hypothesized species distributions. However, I have identified two previously unrecognized contact zones for these species and revealed areas of hybridization. By delineating species distributions and identifying potentially important regions of genetic admixture, this study will be informative to future conservation management and conservation genetic research of chorus frogs in Kentucky.

When hollow concrete masonry is used for construction in high seismic regions, structural designs typically require fully grouted walls. The grouting process is labor-intensive, time-consuming and has a high energy demand due to requirements of consolidation in each and subsequent grout lifts. Self-consolidating grout with admixtures has been successfully used without segregation in walls of up to 12.67 ft. in height. Investigation of self-consolidating grout mixes without admixtures has potential for sustainability improvement. This thesis reports on the compression strength and consolidation observations of self-consolidating characteristics of no vibration/no admixture grout made by substituting various proportions of Portland cement with Type F fly ash and/or ground granulated blast furnace slag (GGBFS). The percentages of Portland cement replacement evaluated were 0%, 50%, 60%, and 70% for Type F fly ash. The percentages of Portland cement replacement evaluated were 0%, 60%, 70% and 80% for Type F fly ash and GGBFS. Grout compressive strengths were evaluated from individually filled grout specimens constructed in concrete masonry hollow core units, dry cured, and tested after 7, 14, 28, 42, 56, and 130 days. Also, hollow concrete masonry walls were built 12.67 ft. tall and grouted. The relative performance was assessed by comparing to conventional grouted masonry and evaluating consolidation characteristics around mortar fins and reinforcement; compressive strength tests after 130 days of curing, and rebar pull-out tests were taken from various wall heights. All experimental grouts had acceptable consolidation characteristics but fly ash replacement grouts did not meet the compressive strength requirements.

Les études préexistantes identifient quatre taxons de base (C. reticulata les mandariniers, C. maxima les pamplemoussiers, C. medica les cédratiers et C. micrantha) à l'origine de l'ensemble des formes cultivées suite à des événements de réticulations. Il en résulte des structures génotypiques complexes, généralement fixées par l'apomixie, fortement hétérozygotes et formées d'une mosaïque de grands fragments chromosomiques d'origines phylogénétiques différentes. La structuration de la variabilité phénotypique suggère que la différenciation initiale des taxons ancestraux est à l'origine d'une part importante de la variabilité utile des agrumes. La connaissance de l'origine des formes cultivées et de leurs structures phylogénomiques est donc indispensable à la bonne gestion des collections et à l'optimisation des programmes d'amélioration génétique. A cette fin, cette thèse explore différentes approches d'analyse de la diversité des génomes. Elle a bénéficié de l'évolution rapide des NGS et propose une utilisation raisonnée des outils disponibles en fonction des questions de recherches. Une analyse plus poussée a été conduite sur les limettiers et citronniers. Le pyroséquençage 454 (Roche) d'amplicons a été utilisé pour décrypter la structure en mosaïque interspécifique du chromosome 2 de 50 variétés à partir d'une information haplotypique multiloci et pour identifier des marqueurs diagnostiques des taxons ancestraux. Ces marqueurs ont permis, en association avec des SSR et indels, d'apporter un nouvel éclairage sur l'origine des limettiers et citronniers, par un génotypage exhaustif des collections Inra/Cirad et Ivia. Enfin, les données de re-séquençage complet Illumina de sept variétés de limettiers et de citronniers comparées à celles de représentants des taxons ancestraux nous ont permis de reconstituer la structure interspécifique de leurs génomes et de schématiser leurs caryotypes phylogénomiques. Les différentes approches ont conduit à des conclusions convergentes. Nos résultats confirment les hypothèses concernant la séquence évolutive à l'origine des bigaradiers (C. aurantium), des orangers (C. sinensis) et des pomelos (C. paradisi) à partir des pools géniques de C. maxima et C. reticulata. Ils mettent en évidence de fréquentes introgressions de C. maxima dans le génome de mandariniers considérées comme représentatifs de C. reticulata. Les contributions relatives de ces deux taxons ancestraux aux génomes de nombreuses variétés de petits agrumes (mandariniers, tangors et tangelos) ont pu être estimées. Les limettiers et citronniers résultent de multiples évènements de réticulation et C. medica est identifié comme parent mâle de la majorité des variétés diploïdes. Deux grands groupes de citronniers, sont différenciés, ceux issus d'hybridations directes C. reticulata × C. medica et ceux impliquant trois taxons ancestraux (C. maxima, C. reticulata et C. medica). Le bigaradier serait le parent femelle à l'origine des citronniers type Lisbonne (C. limon). Les limettiers de type Mexicain (C. aurantifolia) seraient issus d'une hybridation directe C. micrantha × C. medica. Enfin, les limes à gros fruits, triploïdes, ont deux origines. Les types Tahiti résulteraient probablement de la fécondation d'un ovule de citronnier type Lisbonne par un gamète diploïde de limettier type Mexicain. L'autre grand type serait issu d'un backcross entre C. aurantifolia (gamète diploïde) et C. medica. Ces connaissances sur la structure génomique des espèces secondaires permettent d'envisager une reconstruction d'idéotypes à partir du germplasm des taxons ancestraux. Elles ouvrent également la voie à des études de génétique d'association s'appuyant sur la phylogénomique des gènes impliqués dans l'élaboration des caractères de qualité, de résistance et d'adaptation. Enfin, les marqueurs diagnostiques d'espèces développés trouveront de nombreuses applications pour la caractérisation des collections et diverses études de génétiques. / Citrus fruit, the most important fruit crop in the world, show a wide phenotypic diversity. Previous studies (molecular markers) identified four ancestral taxa (Citrus reticulata Blanco, mandarins; C. maxima (Burm.) Merr., pummelos; C. medica L., citrons; C. micrantha Wester, papedas) as the ancestors of all cultivated Citrus after reticulate evolutions. As a result, modern citrus varieties have complex and highly heterozygous genotypic structures, generally fixed by apomixis, and formed by a mosaic of large chromosomal fragments of different phylogenetic origins. Furthermore, the structuration of the phenotypic variability suggests that the initial differentiation of the basic taxa is the main source of most of the variability of the useful citrus phenotypic diversity. A thorough knowledge of the origin of cultivated citrus and their phylogenomic structure are essential for the management of biological resources and breeding program optimization. This thesis explores different approaches for analyzing genome diversity in order to identify the phylogenetic origins of the various horticultural citrus groups and to decipher their phylogenomic genome's structures. We focused on limes and lemons. This thesis takes advantage of the rapid evolution of NGS and proposes a rational use of available tools, based on research questions. Roche 454 parallel sequencing of amplicons provides multi-loci haplotype information on 500 base fragments. It was used to decipher the interspecific mosaic structure of chromosome 2 for fifty varieties and to identify ancestral taxa diagnostic SNP markers. The genotyping of all limes and lemons of the Inra/Cirad and Ivia germplasms with these markers, in association with SSR and indel markers, allowed to propose new hypothesis on the origins of limes and lemons. Data from Illumina whole genome re-sequencing of 7 varieties of limes and lemons, compared to those of representatives of the ancestral taxa, allowed to infer the interspecific structure of their genomes and to map out, for the first time, their phylogenomic karyotypes. The different approaches led to similar conclusions. Our results confirm previous hypothesis about the evolutionary steps at the origin of sour orange (C. aurantium), sweet orange (C. sinensis) and grapefruit (C. paradisi) involving C. maxima and C. reticulata gene pools. They highlight frequent introgressions of C. maxima in the genome of mandarin varieties despite the fact they were considered as representative of C. reticulata. We were also able to quantify the relative proportions of these two ancestral taxa in the genome of many varieties of small citrus fruit (mandarin hybrids, tangors and tangelos). Our work on limes and lemons demonstrate that C. medica is the male parent of this varietal group at the diploid level. Two groups of lemons are clearly differentiated: one from direct hybridizations between C. reticulata and C. medica, and one from crosses between hybrids (C. maxima × C. reticulata) and C. medica. Sour orange seems to be the female parent of ‘Eureka' type lemons (C. limon). The ‘Mexican' limes (C. aurantifolia) seems to come from a direct hybridization C. micrantha × C. medica. Finally, triploid big fruit limes have two major origins. The ‘Tahiti' type probably results from an ‘Eureka' type lemon (C. limon) ovule fecundated by a diploid gamete of a ‘Mexican' type lime (C. aurantifolia), while the other type would come from a back-cross between C. aurantifolia (diploid gamete) and C. medica. This new insights in genomic structure of secondary species makes to consider possible a reconstruction of these ideotypes from ancestral taxa germplasm. They also open new ways for association genetic studies based on phylogenomics of genes involved in the development of quality, resistance and adaptation traits. Finally, developed specific taxa diagnostic markers will find many applications for the characterization of collections and further genetic studies.

Today, groups considered Hispanic in the United States consist of populations whose complex genetic structures reflect intermixed diverse groups of people who came in contact during Spanish colonization in Latin America. After coming in contact and wiping out most of the Native Americans who occupied North and Latin America, the Spanish also introduced West African individuals for labor to begin developing crops to be shipped back to Europe, resulting in the Trans-Atlantic African slave trade. These migration events and differential gene flow among males and females that occurred throughout Latin America have led to populations that have been genetically transformed from what they were prior to Spanish arrival (Madrigal, 2006). Genetic research commonly refers to individuals considered Hispanic as "tri-hybrids" of Native American, European, and African ancestry (Bertoni et al., 2003; Gonz[aacute]lez-Andrade et al., 2007). This research focuses on populations from present-day Mexico, Puerto Rico, and Cuba, all of whom experienced various population histories as these three ancestral groups came in contact. Published genetic research demonstrates that individuals from Mexico tend to have the highest mean proportion of Native American ancestry, while Puerto Rican individuals have the highest mean proportion of European ancestry, and Cuban individuals have the highest mean proportion of African ancestry (Bonilla et al., 2005; Lisker et al., 1990; Mendizabal et al., 2008; Tang et al., 2007; Via et al., 2011). The present research utilizes craniometric data from these three groups to determine whether the cranial morphology reflects similar population relationships and mean ancestry proportions as found in genetic research through Mahalanobis distance (D2), canonical discriminant function, and normal mixture cluster analyses. Sex-biased ancestry asymmetry was also tested by separating each group by sex and running the same analyses. The results show that all three groups considered Hispanic (Mexico, Puerto Rico, and Cuba) are significantly different from each other; however, when proxy ancestral groups are included (Guatemalan Mayan, Indigenous Caribbean, Spanish, and West African), the Mexican and Guatemalan Mayan samples are the most similar, followed by the Mexican and Indigenous Caribbean samples and the Puerto Rican and Cuban samples. The results of the normal mixture analyses indicate that Mexico has the highest mean ancestry proportion of Native American (Guatemalan Mayan) (72.9%), while the Puerto Rican and Cuban samples both have a higher mean European ancestry proportion, with 81.34% and 73.6% respectively. While the Cuban sample is not reflective of the genetic research in regards to ancestry proportion results, with the highest proportion of African ancestry over European and Native American ancestry, it does have the highest proportion of African ancestry among the three groups (18.4%). When separated by sex, the results indicate that the Mexican and Puerto Rican samples may show some evidence in sex-biased ancestry proportions, with the male individuals having a larger proportion of European ancestry and the female individuals having a larger proportion of Native American or African ancestry. Cuba, on the other hand, does not follow this trend and instead displays a higher proportion of European ancestry in females and a higher proportion of Native American and African ancestry in the males. Techniques in the field of forensic anthropology in the United States are constantly being reanalyzed and restructured based on the changing demographics of the population, especially with the arrival of individuals from Latin America (Ennis et al., 2011). Recent samples of American Black and White individuals were included in the Mahalanobis distance (D2) and canonical discriminant function analyses in place of the ancestral proxy groups to determine the craniometric relationship of the groups within the United States. The results show that the Mexico and Guatemala samples are the most similar (D2=2.624), followed by the Cuba and American Black samples (D2=3.296) and the Puerto Rico and American White samples (D2=4.317), which each cluster together in pairs. These results reflect the population histories that took place during colonialism, with the largest amount of slave trade occurring in Cuba over the other two countries. From an applied perspective, clarification is needed in the biological definition of Hispanic and the degree of heterogeneity in each social group, as well as the relationship among groups, in order to accurately develop techniques in forensic anthropology for human identification.