Advancements in molecular sequencing have revealed unexpected cryptic genetic diversity and contrasting evolutionary histories within genes and between genomes of many organisms; often in disagreement with recognized taxonomy. Incongruent patterns between the mitochondrial and nuclear evolutionary history can have several plausible explanations, but widespread systematic conflict inevitably challenges our conceptions of species boundaries when there is discordance between coevolving and coinherited genomes. It is unknown to what degree mitonuclear conflict drives the process of divergence, or how ubiquitous these patterns are across the tree of life. To understand the evolutionary relevance of intergenomic discordance we must identify the conflicting patterns that exist in natural systems by generating robust estimates of the underlying species history, quantify support for alternative hypotheses of lineage formation, and describe patterns of genetic variation present in robust nuclear genomic datasets. Empirically testing correlations between mitonuclear genomic conflict and reduced gene flow at the organism level will contribute toward a better understanding of lineage boundaries and how intergenomic interactions shape the process of divergence. Mitochondrial introgression has been inferred in many salamander systems with limited perspective from nuclear sequence data. Within dusky salamanders (Desmognathus), these patterns have been observed between morphologically and geographically disparate populations. I sequenced regions throughout the nuclear genome to reconstruct species trees, performed population-level analyses testing concordance between the mitochondrial, nuclear datasets, and nuclear genes with mitochondrial functions with the expectation that coevolutionary interactions among genomes are more likely to manifest in these regions. I also estimated migration rates between populations that may have experienced historical mitochondrial introgression to evaluate phylogeographic patterns. Using these data we definitively reject species models in which genetic boundaries are based solely on mitochondrial data, favoring geographic models instead. Furthermore, analyses soundly reject current taxonomic models based on morphological characteristics, suggesting there is greater lineage diversity than is currently recognized. I also used empirical assays of pre-zygotic reproductive mating behavior within and among populations containing diverse mitochondrial lineages to test metrics of reproductive isolation, and to determine if introgression shapes the evolution of complex traits directly influencing rates of divergence. These results may explain incongruent patterns observed between the mitochondrial and nuclear data as a function of inheritance and population dynamics rather than directly functioning to suppress nuclear gene flow. This research builds upon recent studies suggesting that speciation is a highly complex and often non-bifurcating process in which introgression can have a profound and lasting signature on the nuclear evolutionary history. Mechanisms responsible for divergence with gene flow challenge evolutionary biologists to reevaluate our notions and definitions of species boundaries to accommodate seemingly conflicted genomic patterns within and between genomes.

Les circulations de fluides aux interfaces entres les socles cristallins et leur couvertures sédimentaires sont des événements majeurs de transferts élémentaires dans la croûte. Dans de nombreux contextes, des fluides de bassins peuvent pénétrer dans les socles de faible perméabilité, interagir avec eux, y lessiver des métaux, et donner lieu à des concentrations métalliques, notamment en Pb, Zn, Cu, Ag et U. Les gisements d’uranium de type discordance du bassin d’âge protérozoïque de l’Athabasca (Canada), sont des témoins essentiels de ce type de circulations de fluides, et sont des objets modèles pour comprendre les mécanismes et les conséquences de tels événements. Les inclusions fluides permettent d’échantillonner et d’analyser directement les paléofluides. Malgré les difficultés d’analyse, ces objets de taille micrométriques apportent des informations importantes sur les propriétés des fluides. Les techniques d’analyse disponibles (microthermométrie, LA-ICP-MS, écrasement-lessivage, écrasement sous vide) permettent de reconstituer la température, la pression, la composition chimique détaillée des fluides, dont les teneurs en métaux, ainsi que la composition isotopique de l’hydrogène de l’eau, du chlore et du carbone du CO2 dissous. De plus, l’analyse de la composition isotopique de l’oxygène et du carbone des minéraux dans lesquels sont piégées les inclusions fluides apporte des informations complémentaires sur la température des fluides et les interactions fluides-roches. Cette approche a été utilisée sur six gisements d’uranium du Bassin de l’Athabasca, et a permis d’apporter les résultats suivants, potentiellement généralisables à l’ensemble du bassin. (1) Deux saumures, une calcique et une sodique ont circulé et se sont mélangées à la base du bassin et dans le socle au cours de la formation des gisements à environ 150 ± 30°C. (2) Ces deux saumures ont transporté de l’uranium, dont les concentrations exceptionnelles et très hétérogènes (entre 0.2 et 600 ppm) indiquent qu’il a été lessivé dans le socle. (3) Ces saumures ont une origine commune et se sont formées essentiellement par évaporation en surface de l’eau de mer, et mélange avec des fluides issus de la dissolution de minéraux évaporitiques. (4) La saumure calcique s’est formée par interaction entre la saumure sodique et les roches du socle. (5) Les interactions des saumures avec les minéraux et le graphite du socle, la radiolyse de l’eau, et la synthèse de bitumes ont contrôlé la composition isotopique en oxygène, hydrogène et carbone de ces saumures. / Fluid circulations between crystalline basements and their sedimentary covers are major events for element transfer in the crust. In numerous settings, basinal fluids penetrate the low-permeability basement, interact with basement lithologies, leach metals, leading to metal concentrations, notably Pb, Zn, Cu, Ag and U. Unconformity-related uranium deposits from the Proterozoic Athabasca Basin (Canada) are crucial witnesses and useful tools for the understanding of mechanisms and consequences of such fluid events. Fluid inclusions allow us to directly sample and analyze paleofluids. Despite analytical difficulties, these micrometer size objects provide key information on fluid properties. Available analytical techniques (microthermometry, LA-ICP-MS, crush-leach, in-vacuo crushing) provide reconstruction of temperature, pressure, detailed fluid chemistry, including metal concentrations, as well as isotopic composition of water hydrogen, chlorine and of dissolved CO2 carbon. In addition, analysis of isotopic composition of oxygen and carbon from minerals in which fluid inclusions are trapped provide supplementary information on fluid temperatures and fluid-rock interactions. This approach was used on six uranium deposits from the Athabasca Basin and provided the following results, which can be potentially generalized to the entire basin. (1) Two brines, a calcium-rich brine and a sodium-rich brine have circulated and mixed at the base of the basin and in the basement at the time of formation of uranium deposits, at temperature close to 150 ± 30°C. (2) Both brines have transported uranium, whose exceptional and highly heterogeneous concentrations (0.2 to 600 ppm) indicate that it was leached in the basement. (3) Both brines share a common origin and were formed mainly by surface evaporation of seawater and mixing with fluids originating from dissolution of evaporitic minerals. (4) The calcium-rich brine was formed by interaction between the sodium-rich brine and basement lithologies. (5) Interaction with basement minerals and graphite, water radiolysis, and bitumen synthesis were the main controls on the oxygen, hydrogen and carbon isotopic composition of brines.

Phylogenetics is crucial in the study of evolutionary processes and the determination of appropriate conservation units, and often these efforts are complicated by hybridization and introgression. Aliciella subsection Subnuda consists of seven species of herbaceous plants occurring in Utah and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of ITS and cpDNA regions and RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from the cpDNA and ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny robustly resolves relationships between six clades, supportive of merging of two species. We employ STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results provide evidence of hybridization among and between all species in the subsection. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression.

Both borderline personality disorder (BPD) and posttraumatic stress disorder (PTSD) are associated with emotion dysfunction and often co-occur. Emotional reactivity is also evident in some studies in BPD and PTSD. Despite the frequent co-occurrence of these diagnoses, only a few studies have examined the independent and joint effects of BPD and PTSD on emotional functioning. Some data suggest that co-occurring PTSD may drive discordance between domains of emotional reactivity in BPD, dampening physiological reactivity but increasing subjective reactivity. Low reliance on acceptance-based emotion regulation may also account for this divergence. The current study examined the independent and interactive effects of BPD and PTSD on emotional reactivity, regulation, and concordance across physiological and subjective measures. We also examined the role of acceptance in driving concordance across physiological and subjective measures. Participants (N = 195) underwent a diagnostic interview and completed a computerized task including neutral and negative emotion inductions. We examined subjective and physiological outcomes after both inductions. Linear regressions were used to examine relationships between diagnostic group and self-reported reactivity and regulation outcomes, as well the mediating role of acceptance on discordance. Multilevel models were used to examine the associations between diagnostic criteria and time on reactivity and regulation outcomes. We found that BPD and BPDxPTSD, but not PTSD, were significantly associated with greater difficulty regulating and accepting emotions. No significant differences in physiological reactivity and regulation were present across diagnostic groups, and acceptance was not found as a mediator between diagnostic groups and discordance indices. We discuss possible interpretations of our reactivity and regulation findings. Investigating BPD and PTSD’s association with reactivity and regulation, along with the role of emotional acceptance on these outcomes, will extend our understanding of diagnostic profiles and potentially pinpoint how acceptance can be utilized to influence emotional concordance.

The phenomenon of HIV discordance has been in existence for a long time along with HIV. However, very limited attention has been given to HIV discordance. This phenomenological study aimed at gaining a deeper understanding on the lived experiences of sero-discordant couples in Botswana. Reports show that discordance in Botswana is around 17%. The main objectives of this study were to identify HIV discordant couples living in Botswana and explore their knowledge and understanding of the situation, explore the psychological, social and sexual experiences of the HIV discordant couples and determine its impact in their lives, and examine the meaning they attach to such experiences and challenges they face as well as their coping strategies. A qualitative phenomenological approach using face to face in-depth interviews was used to explore and describe meanings and experience as lived by the HIV discordant couples. The study sample consisted of forty-six (N=46) (twenty-nine (n=29) females and seventeen (n=17) males) participants selected using purposive sampling from three cities in Botswana. The Inclusion criteria were that participants should be aged 21 years and above; with no known diagnosis of mental illness; having been in a discordant relationship for at least six months at the time of data collection; living in Botswana and willing to participate in the study. The findings were that there are three forms of discordance, which are: discordant unaware which are couples who went into the relation unaware of their HIV status. Discordant aware; those who got into the relationship already knowing each other’s HIV status and discordantly discordant which are those with differing HIV status and differing motives of going into the relationship. These are the couples that conceal their status from one another. The results revealed intense emotional/psychological, sexual and social stresses as experienced by couples. HIV discordant goes through three phases of initial shock, conflict and resolution. The researcher recommends the OPEN DESK MODEL to be integrated in the health facilities to encompass the concept of a family or couple and as a unit. / Health Studies / D. Litt. et Phil. (Health Studies)

The phenomenon of HIV discordance has been in existence for a long time along with HIV. However, very limited attention has been given to HIV discordance. This phenomenological study aimed at gaining a deeper understanding on the lived experiences of sero-discordant couples in Botswana. Reports show that discordance in Botswana is around 17%. The main objectives of this study were to identify HIV discordant couples living in Botswana and explore their knowledge and understanding of the situation, explore the psychological, social and sexual experiences of the HIV discordant couples and determine its impact in their lives, and examine the meaning they attach to such experiences and challenges they face as well as their coping strategies. A qualitative phenomenological approach using face to face in-depth interviews was used to explore and describe meanings and experience as lived by the HIV discordant couples. The study sample consisted of forty-six (N=46) (twenty-nine (n=29) females and seventeen (n=17) males) participants selected using purposive sampling from three cities in Botswana. The Inclusion criteria were that participants should be aged 21 years and above; with no known diagnosis of mental illness; having been in a discordant relationship for at least six months at the time of data collection; living in Botswana and willing to participate in the study. The findings were that there are three forms of discordance, which are: discordant unaware which are couples who went into the relation unaware of their HIV status. Discordant aware; those who got into the relationship already knowing each other’s HIV status and discordantly discordant which are those with differing HIV status and differing motives of going into the relationship. These are the couples that conceal their status from one another. The results revealed intense emotional/psychological, sexual and social stresses as experienced by couples. HIV discordant goes through three phases of initial shock, conflict and resolution. The researcher recommends the OPEN DESK MODEL to be integrated in the health facilities to encompass the concept of a family or couple and as a unit. / Health Studies / D. Litt. et Phil. (Health Studies)

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: This PhD study investigated the organisational structure of medical communicative facilities and the related communicative experiences of health care providers and patients in HIV and AIDS care centres where there is language discordance between physicians and patients. Such discordance refers specifically to communication in contexts where patients and health care providers speak a number of different, mostly mutually unintelligible first languages (L1s) and where speakers have varying levels of proficiency in a lingua franca such as English. This study considers key moments within the organisational communication structure to assess how well the structure meets its communicative aims. The sites of care that provided empirical data in this study, were a public health clinic which is a division of a state hospital, and a privately run day care clinic both located near Maseru, the capital city of Lesotho. The participants were drawn from four categories, namely physicians, nurses, lay interpreters and patients. Data collection was done through semi-structured interviews, focus group discussions and direct observations of the study sites. The data was later transcribed interpreted and analysed according to insights gained from Organisation Theory on the one hand and Thematic Analysis and Qualitative Data Analysis on the other hand. The most important result of the study is the recognition of organisational fragmentation of care into different units which helps to facilitate communication where patients and physicians show marked language discordance. Further results illuminate several challenges that are encountered by participants in mediating and making meaning where language diversity is such that physicians’ linguistic repertoire does not match the repertoires of patients and local HCPs. The study highlights several institutional and interpersonal strategies that are used to overcome these challenges and to assure effective communication in the particular institutions. It also shows how some of these strategies fail to fully address the communicative challenges identified. The findings of this study suggest that in multilingual clinical contexts there is a need for more dedicated attention to interpreting practices, to the kinds of material distributed among patients and, more generally, to make consultative decisions on improved systems to put in place in order to facilitate communication related to quality health care. / AFRIKAANSE OPSOMMING: Hierdie PhD-studie het die organisatoriese struktuur van mediese kommunikatiewe geleenthede en die verwante ervarings van beroepsmense in gesondheidsorg van pasiënte in HIV-versorgingsentra ondersoek, waar die taalvaardighede van dokters en pasiënte nie gesinchroniseer is nie. Die taaldissonansie verwys spesifiek na kommunikasie in kontekste waar pasiënte en beroepsmense in gesondheidsorg 'n verskeidenheid tale praat wat meestal onderling onverstaan-bare eerste tale (T1e) is van sprekers met ongelyke vlakke van vaardigheid in 'n lingua franca soos Engels. Die studie vestig aandag op sleutelmomente binne die struktuur van die kommunikasie van die organisasie om vas te stel hoe goed die bepaalde struktuur sy kommunikatiewe doelstellinge verwesenlik. Die terreine van gesondheidsorg wat empiriese data vir hierdie navorsing voorsien het, was 'n openbare kliniek wat verbonde is aan 'n staatshospitaal, en 'n privaat dagsorgkliniek wat albei naby Maseru, die hoofstad van Lesotho, geleë is. Die deelnemers behoort aan vier kategorieë, naamlik dokters, verpleegpersoneel, leke-vertalers/-tolke en pasiënte. Data insameling is gedoen deur middel van semigestruktureerde onderhoude, fokus groepbesprekings and direkte waarrneming by die betrokke instansies. Die data is later getranskribeer, geinterpreteer en geanaliseer volgens insigte uit Organisasie Teorie aan die een kant en Tematiese Analise en Kwalitatiewe Data Analise aan die ander kant. Die belangrikste bevinding van die studie is herkenning van die organisatoriese fragmentering van die sorg in verskillende eenhede wat help om kommunikasie te fasiliteer binne ‘n konteks waar pasiënte en dokters merkbare taaldissonansie vertoon. Verdere bevindinge werp lig op verskeie uitdagings wat deelnemers ervaar in die bemiddeling en skep van betekenis waar taaldiversiteit sodanig is dat die talige repertoires van die mediese praktisyns nie aangepas is by die talige repertoires van die pasiënte of plaaslike mediese beamptes nie. Die studie vestig aandag op verskeie institusionele en interpersoonlike strategieë wat gebruik word om uitdagings te oorkom en om effektiewe kommunikasie binne die betrokke instansies te verseker. Dit wys ook hoe sommige van hierdie strategieë misluk in die aanspreek van bepaalde kommunikatiewe uitdagings. Die bevindinge bevestig dat in die omgewing van ‘n veeltalige kliniek daar ‘n behoefte is aan meer toegewyde aandag aan tolkingspraktyke, aan die soort materiaal wat onder pasiënte versprei word, en in meer algemene terme, aan die neem van besluite gegrond op konsultasie sodat verbeterde stelsels geimplimenteer kan word om kommunikasie wat verband hou met goeie kwaliteit gesondheidsorg, te help bedien. / The African Doctoral Academy for financial support

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

De nouveaux gisements d’uranium, entièrement inclus dans le socle du bassin d’Athabasca (Province de la Saskatchewan, Canada), ont été récemment découverts, faisant d’eux une cible d’exploration privilégiée. Leur mode de formation est encore discuté, ne facilitant pas leur découverte. Afin de mieux les comprendre, une étude multidisciplinaire a été entreprise sur trois de ces gisements : Eagle Point, Millennium et P-Patch. Les oxydes d’uranium ont des caractéristiques chimiques variables fonction des conditions de cristallisation et d’altération postérieures à leur dépôt. Les âges U-Pb obtenus sont conformes à ceux des minéralisations à la discordance, tout comme le sont les abondances en terres rares, indiquant des circulations fluides à grande échelle et des processus physico-chimiques de formation identiques pour les deux types de gisements. Les saumures liées à la formation des gisements circulent massivement dans le socle, en partie grâce à la réouverture de structures et microstructures métamorphiques antérieures. La microfracturation globale des roches, fonction du contexte tectonique local, va directement déterminer le degré d’altération du socle et l’évolution du chimisme des saumures. L’altération du socle par les saumures est progressive et favorise une déstabilisation fractionnée des minéraux, permettant le transfert de nombreux éléments du socle vers le bassin. Les minéraux accessoires du socle porteurs d’uranium et de terres rares sont altérés à totalement dissous et sont donc une source majeure de ces éléments pour la formation des minéralisations. Des fluides météoriques tardifs (<300 Ma) déstabilisent les oxydes d’uranium antérieurs et favorisent la cristallisation de fronts d’oxydo-réduction / New basement-hosted uranium deposits in Athabasca Basin (Saskatchewan, Canada) were recently discovered. This ore type is now a new exploration target. The formation processes of basement-hosted ores are discussed and their discovery is not obvious. To better understand this deposit type, a multidisciplinary study has been focussed on three deposits: Eagle Point, Millennium and P-Patch. The basement-hosted uranium oxides have variable chemical characteristics function of their crystallisation and posterior alteration conditions. U-Pb isotopic ages are in accordance with uranium oxides localized at the unconformity. The same tendency is observed too for Rare Earth Elements (REE) concentrations. Physico-chemical conditions and fluid circulations are thus close to for the two types of deposit. The brines associated to deposit formation circulate in the basement, for a part, thanks to metamorphic structures and microstructures reopenings under the same stress field than those occurring during the late metamorphic episodes. Microfracturing determines directly the alteration degree of the rock and thus the chemistry evolution of the brines. Basement alteration by brines is progressive and favours the successive destabilisation of mineral, permitting the transfer of several elements from the basement to the basin. Basement accessory minerals are altered to totally dissolved, indicating that the basement is a main source of uranium and REE for the mineralization formation. Late meteoric fluids (<300 Ma) destabilized previous uranium oxides and favour the crystallization of uranium redox-front in hydrothermal alteration halo

Comprendre les mécanismes neurophysiologiques et les bases neurales de la conscience est un défi médico-scientifique majeur. A cette fin, il faut opérer une distinction entre les mécanismes neuraux des états de conscience, et ceux qui sous-tendent l'accès conscient à un contenu mental particulier (ou la prise de conscience). Les données expérimentales ayant contrasté état conscient/ état non conscient (coma, sommeil, sédation) d'une part, et perception consciente/inconsciente d'un même stimulus d'autre part, sont en faveur de l'implication d'un réseau d'aires cérébrales fronto-pariétales à la fois dans l'état et dans l'accès conscient à une information donnée. La comparaison état conscient/ état non conscient est malheureusement limitée par les différences de vigilance existant entre ces états. Nous avons cherché à contourner ce problème en nous focalisant sur deux populations de malades présentant un niveau de vigilance proche mais différant sous l'angle de l'état de conscience : patients éveillés, non conscients (état végétatif) versus patients éveillés et minimalement conscients (état de conscience minimale). Nos résultats, obtenus en utilisant les potentiels évoqués auditifs cognitifs à haute densité spatiale, sont en faveur de l'implication du même réseau d'aires cérébrales fronto-pariétales que celui mentionné ci-dessus, à la fois dans l'état et l'accès conscient. L'activation de ce réseau est contemporaine de l'apparition d'une P300b en potentiels évoqués qui semble constituer un marqueur très spécifique de conscience. Notre travail nous a permis également d'identifier un possible nouveau marqueur de la conscience qu'est la variation contingente négative (CNV). / Understanding the neurophysiological mechanisms and neural bases of consciousness is a major scientific and medical challenge. To do this, one has to distinguish neural mechanisms of conscious state from those subserving conscious access to a given mental state (that is awareness). Experimental data having contrasted conscious / non conscious state (coma, sleep, sedation) on the one hand, and conscious/ unconscious processing of a very same stimulus on the other hand are in favour of the implication of a network of lateral and medial frontal and parietal areas in both conscious state and conscious access. The comparison of conscious/ non conscious state is unfortunately limited by arousal difference between these two states. So, we endeavoured to overcome this problem by exploring two categories of patients with a same level of arousal but a different state of awareness: unaware awaked patients (vegetative state) versus awaked and minimally conscious patients (minimally conscious state). Our results obtained by using high-density auditory event related potentials argue in favour of the implication of the very same network of frontal and parietal areas than the one described above in both conscious state and conscious access to a given information. This network activation is associated with the emergence of a P300b wave, on event related potentials, which seems to be a very specific marker of consciousness. Our work also give us the opportunity to discover a potential new marker of consciousness, namely the contingent negative variation (CNV).