Forecasting changes in population genetic structure of alpine plants in response to global warming.

Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways because of adaptation to their environment. Here, we introduced ancestry distribution models, that is, statistical models of the spatial distribution of ancestry proportions, for forecasting intra-specific changes based on genetic admixture instead of species occurrence data. Using multi-locus genotypes and extensive geographic coverage of distribution data across the European Alps, we applied this approach to 20 alpine plant species considering a global increase in temperature from 0.25 to 4 °C. We forecasted the magnitudes of displacement of contact zones between plant populations potentially adapted to warmer environments and other populations. While a global trend of movement in a north-east direction was predicted, the magnitude of displacement was species-specific. For a temperature increase of 2 °C, contact zones were predicted to move by 92 km on average (minimum of 5 km, maximum of 212 km) and by 188 km for an increase of 4 °C (minimum of 11 km, maximum of 393 km). Intra-specific turnover-measuring the extent of change in global population genetic structure-was generally found to be moderate for 2 °C of temperature warming. For 4 °C of warming, however, the models indicated substantial intra-specific turnover for ten species. These results illustrate that, in spite of unavoidable simplifications, ancestry distribution models open new perspectives to forecast population genetic changes within species and complement more traditional distribution-based approaches.

Mate choice evolution, dominance effects, and the maintenance of genetic variation.

Female mate choice influences the maintenance of genetic variation by altering the mating success of males with different genotypes. The evolution of preferences themselves, on the other hand, depends on genetic variation present in the population. Few models have tracked this feedback between a choice gene and its effects on genetic variation, in particular when genes that determine offspring viability and attractiveness have dominance effects. Here we build a population genetic model that allows comparing the evolution of various choice rules in a single framework. We first consider preferences for good genes and show that focused preferences for homozygotes evolve more easily than broad preferences, which allow heterozygous males high mating success too. This occurs despite better maintenance of genetic diversity in the latter scenario, and we discuss why empirical findings of superior mating success of heterozygous males consequently do not immediately lead to a better understanding of the lek paradox. Our results thus suggest that the mechanisms that help maintain genetic diversity also have a flipside of making female choice an inaccurate means of producing the desired kind of offspring. We then consider preferences for heterozygosity per se, and show that these evolve only under very special conditions. Choice for compatible genotypes can evolve but its selective advantage diminishes quickly due to frequency-dependent selection. Finally, we show that our model reproduces earlier results on selfing, when the female choice strategy produces assortative mating. Overall, our model indicates that various forms of heterozygote-favouring (or variable) female choice pose a problem for the theory of sexual ornamentation based on indirect benefits, rather than a solution.

Antimicrobial susceptibility patterns, emm type distribution and genetic diversity of Streptococcus pyogenes recovered in Brazil

Streptococcus pyogenes is responsible for a variety of infectious diseases and immunological complications. In this study, 91 isolates of S. pyogenes recovered from oropharynx secretions were submitted to antimicrobial susceptibility testing, emm typing and pulsed-field gel electrophoresis (PFGE) analysis. All isolates were susceptible to ceftriaxone, levofloxacin, penicillin G and vancomycin. Resistance to erythromycin and clindamycin was 15.4%, which is higher than previous reports from this area, while 20.9% of the isolates were not susceptible to tetracycline. The macrolide resistance phenotypes were cMLSB (10) and iMLSB (4). The ermB gene was predominant, followed by the ermA gene. Thirty-two emm types and subtypes were found, but five (emm1, emm4, emm12, emm22, emm81) were detected in 48% of the isolates. Three new emm subtypes were identified (emm1.74, emm58.14, emm76.7). There was a strong association between emm type and PFGE clustering. A variety of PFGE profiles as well as emm types were found among tetracycline and erythromycin-resistant isolates, demonstrating that antimicrobial resistant strains do not result from the expansion of one or a few clones. This study provides epidemiological data that contribute to the development of suitable strategies for the prevention and treatment of such infections in a poorly studied area.

Genetic variability in Arbuscular Mycorrhizal Fungi : effect on gene transcription of "Oryza Sativa"

AbstractArbuscular Mycorrhizal Fungi (AMF) form obligate symbioses with the majority of land plants. These fungi influence the diversity and productivity of plants. AMF are unusual organisms, harbouring genetically different nuclei in a common cytoplasm (known as heterokaryosis). Genetic variability has been shown between AMF individuals coming from the same population. Recent findings showed that genetic exchange between genetically different AMF individuals was possible. Additionnaly, segregation was shown to occur at spore formation in AMF. These two processes were shown to increase genetic variability between AMF individuals.Because of the difficulty to study these organisms, almost nothing is known about the effect of intra-specific genetic variability in AMF on the plant transcriptome. The aim of this thesis was to bring insights into the effect of intra-specific genetic variability in AMF on plant gene transcription. We demonstrated that genetic exchange could influence expression of some symbiosis specific plant genes and the timing of the colonization of the fungi in plant roots. We also showed that segregation could have a large impact on plant gene transcription. Taken together, these results demonstrated that AMF intra-specific variability could profoundly affect the life of plants by altering various molecular pathways. Moreover, results obtained on rice open a field of research on AMF genetics in impromvment of growth in agricultural plants and should be taken into account for future experiments.RésuméLes champignons endomycorhiziens arbusculaires (CEA) forment une symbiose obligatoire avec la majorité des plantes sur terre. Ces champignons peuvent influencer la diversité et la productivité des plantes avec lesquelles ils forment la symbiose. Les CEA sont des organismes particuliers de part le fait qu'ils possèdent des noyaux génétiquement différents (appelés hétérocaryosis) dans un cytoplasme commun. Il a été montré qu'il existait de la variabilité génétique intra-specific chez les CEA. De plus, des études recentes ont montré que l'échange génétique chez les CEA était possible entre des individus génétiquement différents tout comme la ségrégation qui a aussi été démontrée au moment de la formation des nouvelles spores chez les CEA. Ces deux processus ont été montrés comme pouvant créer aussi de la variabilité génétique intra-specific.Du fait de la difficulté de travailler avec les CEA et à cause de la nouveauté de ces recherches, très peu de choses sont connues sur l'effet de l'échange génétique et de la ségrégation chez les CEA sur les plantes, et particulièrement au niveau moléculaire. Le but de cette thèse a été d'apporter la lumière sur les effets de la viariabilité génétique intra-specific chez les CEA, sur la transcription des gènes chez la plante. Nous avons pu montrer que l'échange génétique pouvait avoir des effets sur l'expression de gènes spécifiques à cette symbiose mais aussi pouvait influencer le timing de colonisation des racines de plantes par les CEA. Nous avons aussi montré que la ségrégation pouvait grandement influencer le transcriptome complet de la plante, et pas seulement les voies métaboliques spécifiques à la symbiose comme cela avait été montré auparavant.L'ensemble de ces résultats démontre l'importance de la variation intra-specific chez les CEA sur les plantes et leur implication sur leur cycle de vie en changeant l'expression de voies métaboliques. De plus, ces résultats obtenus sur le riz ouvrent un champ de recherches sur les plantes destinées à l'agriculture et devraient être pris en compte pour des expériences futures.

Genetic diversity of chloroquine-resistant Plasmodium vivax parasites from the western Brazilian Amazon

The molecular basis of Plasmodium vivax chloroquine (CQ) resistance is still unknown. Elucidating the molecular background of parasites that are sensitive or resistant to CQ will help to identify and monitor the spread of resistance. By genotyping a panel of molecular markers, we demonstrate a similar genetic variability between in vitro CQ-resistant and sensitive phenotypes of P. vivax parasites. However, our studies identified two loci (MS8 and MSP1-B10) that could be used to discriminate between both CQ-susceptible phenotypes among P. vivax isolates in vitro. These preliminary data suggest that microsatellites may be used to identify and to monitor the spread of P. vivax-resistance around the world.

Genetic Polymorphisms and Susceptibility to Fungal Infections

Invasive fungal infections (IFI) are life-threatening diseases that are of particular concern in specific debilitated or immunosuppressed populations. Invasive candidiasis (IC) is the most frequent of the IFI, being one of the major causes of nosocomial bloodstream infection and a feared complication in patients with recurrent gastrointestinal surgery or prolonged stay in the intensive-care unit [1,2]. Patients with hematological malignancies or prolonged chemotherapy-induced neutropenia, and those with allogeneic hematopoietic stem cell transplantation (allo-HSCT), represent the groups at highest risk for developing invasive aspergillosis (IA), which is associated with a high mortality rate despite the increasing availability of antifungal therapies [3,4]. An increasing incidence of IA has also been reported in non-neutropenic immunosuppressed populations such as solid-organ transplant recipients or steroid-treated patients with chronic pulmonary diseases [5]. Early diagnosis of IFI is crucial for improving chances of survival [6], but is particularly challenging owing to the lack of reliable diagnostic methods [7,8]. Significant efforts during the last few decades have focused on the prevention of these severe complications. Antifungal prophylaxis in high-risk patients has been shown to reduce the incidence of IA in patients with onco-hematological malignancies [9] and that of IC in surgical intensive-care unit patients [10]. However, its widespread use raises concerns about costs, toxicity, and the risk of emergence of resistant fungal species such as non-Aspergillus moulds or non-albicansCandida spp. [4,11,12]. Prophylactic strategies usually rely on the identification of host risk factors resulting from clinical conditions (type and duration of immunosuppression, underlying diseases, and extrinsic interventions) [8,13]. Recent advances in the field of immunogenetics may change our perspective of, and approach to, preventive strategies with the identification of subgroups of patients exhibiting a genetic predisposition to IFI.

Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1.

Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation.

Evaluation of the IL2/IL21, IL2RA and IL2RB genetic variants influence on the endogenous non-anterior uveitis genetic predisposition.

BACKGROUND Recently, different genetic variants located within the IL2/IL21 genetic region as well as within both IL2RA and IL2RB loci have been associated to multiple autoimmune disorders. We aimed to investigate for the first time the potential influence of the IL2/IL21, IL2RA and IL2RB most associated polymorphisms with autoimmunity on the endogenous non-anterior uveitis genetic predisposition. METHODS A total of 196 patients with endogenous non-anterior uveitis and 760 healthy controls, all of them from Caucasian population, were included in the current study. The IL2/IL21 (rs2069762, rs6822844 and rs907715), IL2RA (2104286, rs11594656 and rs12722495) and IL2RB (rs743777) genetic variants were genotyped using TaqMan® allelic discrimination assays. RESULTS A statistically significant difference was found for the rs6822844 (IL2/IL21 region) minor allele frequency in the group of uveitis patients compared with controls (P(-value)=0.02, OR=0.64 CI 95%=0.43-0.94) although the significance was lost after multiple testing correction. Furthermore, no evidence of association with uveitis was detected for the analyzed genetic variants of the IL2RA or IL2RB loci. CONCLUSION Our results indicate that analyzed IL2/IL21, IL2RA and IL2RB polymorphisms do not seem to play a significant role on the non-anterior uveitis genetic predisposition although further studies are needed in order to clear up the influence of these loci on the non-anterior uveitis susceptibility.

Genetic variability in G2 and F2 region between biological clones of human respiratory syncytial virus with or without host immune selection pressure

Human respiratory syncytial virus (HRSV) is an important respiratory pathogens among children between zero-five years old. Host immunity and viral genetic variability are important factors that can make vaccine production difficult. In this work, differences between biological clones of HRSV were detected in clinical samples in the absence and presence of serum collected from children in the convalescent phase of the illness and from their biological mothers. Viral clones were selected by plaque assay in the absence and presence of serum and nucleotide sequences of the G2 and F2 genes of HRSV biological clones were compared. One non-synonymous mutation was found in the F gene (Ile5Asn) in one clone of an HRSV-B sample and one non-synonymous mutation was found in the G gene (Ser291Pro) in four clones of the same HRSV-B sample. Only one of these clones was obtained after treatment with the child's serum. In addition, some synonymous mutations were determined in two clones of the HRSV-A samples. In conclusion, it is possible that minor sequences could be selected by host antibodies contributing to the HRSV evolutionary process, hampering the development of an effective vaccine, since we verify the same codon alteration in absence and presence of human sera in individual clones of BR-85 sample.

The effect of host plant and isolation on the genetic structure of phytophagous insects: A preliminary study on a bruchid beetle

Genetic differentiation is a consequence of the combination of drift and restriction in gene flow between populations due to barriers to dispersal, or selection against individuals resulting from inter-population matings In phytophagous insects, local adaptation to different kinds of host plants can sometimes lead to reproductive isolation and thus to genetic structuring, or even to speciation Acanthoscelides. obtectus Say is a bean bruchid specialized on beans of the Phaseolus vulgaris group, attacking both wild and domesticated forms of P vulgaris., and P coccineus This study reveals that the genetic structure of populations of this bruchid is explained mainly by their geographical location and is not related to a particular kind (wild or domesticated) of bean In contrast, the species of bean might have led, to some extent, to genetic structuring in these bruchids, although our sampling is too limited to address such process unambiguously. If confirmed, it would corroborate preliminary results found for the parasitoid species that attack Acanthoscelides species, which might show a genetic structure depending on the species of host plant

Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices.

Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants that improve plant nutrient acquisition and promote plant diversity. Although within-species genetic differences among AMF have been shown to differentially affect plant growth, very little is actually known about the degree of genetic diversity in AMF populations. This is largely because of difficulties in isolation and cultivation of the fungi in a clean system allowing reliable genotyping to be performed. A population of the arbuscular mycorrhizal fungus Glomus intraradices growing in an in vitro cultivation system was studied using newly developed simple sequence repeat (SSR), nuclear gene intron and mitochondrial ribosomal gene intron markers. The markers revealed a strong differentiation at the nuclear and mitochondrial level among isolates. Genotypes were nonrandomly distributed among four plots showing genetic subdivisions in the field. Meanwhile, identical genotypes were found in geographically distant locations. AMF genotypes showed significant preferences to different host plant species (Glycine max, Helianthus annuus and Allium porrum) used before the fungal in vitro culture establishment. Host plants in a field could provide a heterogeneous environment favouring certain genotypes. Such preferences may partly explain within-population patterns of genetic diversity.

Clinical and genetic findings in a large cohort of patients with ryanodine receptor 1 gene-associated myopathies.

Ryanodine receptor 1 (RYR1) mutations are a common cause of congenital myopathies associated with both dominant and recessive inheritance. Histopathological findings frequently feature central cores or multi-minicores, more rarely, type 1 predominance/uniformity, fiber-type disproportion, increased internal nucleation, and fatty and connective tissue. We describe 71 families, 35 associated with dominant RYR1 mutations and 36 with recessive inheritance. Five of the dominant mutations and 35 of the 55 recessive mutations have not been previously reported. Dominant mutations, typically missense, were frequently located in recognized mutational hotspot regions, while recessive mutations were distributed throughout the entire coding sequence. Recessive mutations included nonsense and splice mutations expected to result in reduced RyR1 protein. There was wide clinical variability. As a group, dominant mutations were associated with milder phenotypes; patients with recessive inheritance had earlier onset, more weakness, and functional limitations. Extraocular and bulbar muscle involvement was almost exclusively observed in the recessive group. In conclusion, our study reports a large number of novel RYR1 mutations and indicates that recessive variants are at least as frequent as the dominant ones. Assigning pathogenicity to novel mutations is often difficult, and interpretation of genetic results in the context of clinical, histological, and muscle magnetic resonance imaging findings is essential.

Genetic and environmental effects on early life-history traits in salmonids

Les changements environnementaux, tels la température ou les maladies infectieuses, peuvent influencer l'évolution en induisant de la sélection, mais ceci à la seule condition qu'il y ait assez de diversité génétique pour les traits en question ou pour l'expression plastique de ces traits. Au cours cette thèse, nous avons étudié l'effet de potentielles pressions environnementales sur différents phénotypes de trois représentants des sous familles des salmonidés: l'ombre commun (Thymallus thymallus; Thymallinae), la truite de rivière {Salmo trutta; Salmoninae) et le corégone Coregonus palaea (Coregoninae). Les salmonidés se prêtent particulièrement bien à ce type d'expériences car étant hautement sensibles aux conditions environnementales, ils montrent une large variabilité dans leurs traits morphologiques, comportementaux ainsi que d'histoire de vie, tout en bénéficiant d'un large intérêt général. Nous avons testé si le sexe de l'ombre commun pouvait être modifié par la température, ce qui pourrait ainsi expliquer un changement abrupte de sex ratio observé dans l'une des plus grandes populations de Suisse. Nous n'avons trouvé aucun indice permettant de conclure que la température puisse induire ce changement chez l'ombre commun ou chez la truite de rivière. De plus nous avons étudié la plasticité de développement ainsi que d'éclosion, et avons observé des différences entre familles ainsi qu'entre populations. Alors que ces différences comportementales entre populations suggéraient une adaptation aux conditions environnementales locales, cette prédiction n'a pas été confirmée par une expérience de transplantation réciproque d'embryons entre cinq rivières de la même région. Cette étude a montré que les embryons ne survivaient pas mieux dans leur rivière d'origine, indiquant donc une absence d'adaptation locale. Nous avons aussi montré que la mortalité embryonnaire était influencée autant par des "bons gènes" que par des "gènes compatibles", que la qualité des mâles pouvait être signalée par leur coloration, et que le fait d'élever des poissons dans une pisciculture pouvait aboutir a des relations contre-intuitives entre la coloration des mâles et la qualité de leur jeunes. Nos résultats contribuent ainsi à une meilleure compréhension de l'effet de diverses pressions environnementales sur la morphologie, le comportement ou les traits d'histoire de vie chez les salmonidés. - Environmental changes, such as changes in temperatures or infection levels, can induce selection and drive evolution if there is sufficient genetic variation for the traits or the plasticity in trait expression. In this thesis, we investigated the influence of potential environmental stressors on various phenotypes in representatives of the three salmonid subfamilies: the European grayling (Thymallus thymallus; Thymallinae), the brown trout (,Salmo trutta; Salmoninae), and the whitefish Coregonus palaea (Coregoninae). Salmonids are ideal study species, as they seem sensitive to changing environmental conditions, show considerable variability in morphological, behavioral, and life history traits, and are of broad public interest. We investigated whether temperature-induced sex reversal could explain the sex-ratio distortion found in one of Switzerland's largest grayling populations. We found no evidence of temperature-induced sex reversal in either graylings or brown trout. We also examined plasticity in embryo development and the timing of hatching. We found variation at the level of family and population. Although behavioral differences between populations suggested adaptation to local environmental conditions, no indications of local adaptation could be found in reciprocal transplant experiments carried out over five rivers in the same region. We also demonstrate that embryo development and viability is influenced by 'good genes' and 'compatible genes', that the genetic quality of sires can be signaled by their grey coloration, and that raising larvae in a hatchery environment can produce counter-intuitive relationships between male phenotypes and offspring viability. Our results contribute to the understanding of how changing environmental conditions affect the phenotypes and the heritability of early life-history traits in salmonids.