THE USE OF SIMULATIONS IN EVOLUTIONARY POPULATION GENETICS: APPLICATIONS ON HUMANS, OWLS AND VIRTUAL ORGANISMS

Summary (in English) Computer simulations provide a practical way to address scientific questions that would be otherwise intractable. In evolutionary biology, and in population genetics in particular, the investigation of evolutionary processes frequently involves the implementation of complex models, making simulations a particularly valuable tool in the area. In this thesis work, I explored three questions involving the geographical range expansion of populations, taking advantage of spatially explicit simulations coupled with approximate Bayesian computation. First, the neutral evolutionary history of the human spread around the world was investigated, leading to a surprisingly simple model: A straightforward diffusion process of migrations from east Africa throughout a world map with homogeneous landmasses replicated to very large extent the complex patterns observed in real human populations, suggesting a more continuous (as opposed to structured) view of the distribution of modern human genetic diversity, which may play a better role as a base model for further studies. Second, the postglacial evolution of the European barn owl, with the formation of a remarkable coat-color cline, was inspected with two rounds of simulations: (i) determine the demographic background history and (ii) test the probability of a phenotypic cline, like the one observed in the natural populations, to appear without natural selection. We verified that the modern barn owl population originated from a single Iberian refugium and that they formed their color cline, not due to neutral evolution, but with the necessary participation of selection. The third and last part of this thesis refers to a simulation-only study inspired by the barn owl case above. In this chapter, we showed that selection is, indeed, effective during range expansions and that it leaves a distinguished signature, which can then be used to detect and measure natural selection in range-expanding populations. Résumé (en français) Les simulations fournissent un moyen pratique pour répondre à des questions scientifiques qui seraient inabordable autrement. En génétique des populations, l'étude des processus évolutifs implique souvent la mise en oeuvre de modèles complexes, et les simulations sont un outil particulièrement précieux dans ce domaine. Dans cette thèse, j'ai exploré trois questions en utilisant des simulations spatialement explicites dans un cadre de calculs Bayésiens approximés (approximate Bayesian computation : ABC). Tout d'abord, l'histoire de la colonisation humaine mondiale et de l'évolution de parties neutres du génome a été étudiée grâce à un modèle étonnement simple. Un processus de diffusion des migrants de l'Afrique orientale à travers un monde avec des masses terrestres homogènes a reproduit, dans une très large mesure, les signatures génétiques complexes observées dans les populations humaines réelles. Un tel modèle continu (opposé à un modèle structuré en populations) pourrait être très utile comme modèle de base dans l'étude de génétique humaine à l'avenir. Deuxièmement, l'évolution postglaciaire d'un gradient de couleur chez l'Effraie des clocher (Tyto alba) Européenne, a été examiné avec deux séries de simulations pour : (i) déterminer l'histoire démographique de base et (ii) tester la probabilité qu'un gradient phénotypique, tel qu'observé dans les populations naturelles puisse apparaître sans sélection naturelle. Nous avons montré que la population actuelle des chouettes est sortie d'un unique refuge ibérique et que le gradient de couleur ne peux pas s'être formé de manière neutre (sans l'action de la sélection naturelle). La troisième partie de cette thèse se réfère à une étude par simulations inspirée par l'étude de l'Effraie. Dans ce dernier chapitre, nous avons montré que la sélection est, en effet, aussi efficace dans les cas d'expansion d'aire de distribution et qu'elle laisse une signature unique, qui peut être utilisée pour la détecter et estimer sa force.

Evolution of decision-making and learning under fluctuating social environments

The capacity to learn to associate sensory perceptions with appropriate motor actions underlies the success of many animal species, from insects to humans. The evolutionary significance of learning has long been a subject of interest for evolutionary biologists who emphasize the bene¬fit yielded by learning under changing environmental conditions, where it is required to flexibly switch from one behavior to another. However, two unsolved questions are particularly impor¬tant for improving our knowledge of the evolutionary advantages provided by learning, and are addressed in the present work. First, because it is possible to learn the wrong behavior when a task is too complex, the learning rules and their underlying psychological characteristics that generate truly adaptive behavior must be identified with greater precision, and must be linked to the specific ecological problems faced by each species. A framework for predicting behavior from the definition of a learning rule is developed here. Learning rules capture cognitive features such as the tendency to explore, or the ability to infer rewards associated to unchosen actions. It is shown that these features interact in a non-intuitive way to generate adaptive behavior in social interactions where individuals affect each other's fitness. Such behavioral predictions are used in an evolutionary model to demonstrate that, surprisingly, simple trial-and-error learn¬ing is not always outcompeted by more computationally demanding inference-based learning, when population members interact in pairwise social interactions. A second question in the evolution of learning is its link with and relative advantage compared to other simpler forms of phenotypic plasticity. After providing a conceptual clarification on the distinction between genetically determined vs. learned responses to environmental stimuli, a new factor in the evo¬lution of learning is proposed: environmental complexity. A simple mathematical model shows that a measure of environmental complexity, the number of possible stimuli in one's environ¬ment, is critical for the evolution of learning. In conclusion, this work opens roads for modeling interactions between evolving species and their environment in order to predict how natural se¬lection shapes animals' cognitive abilities. - La capacité d'apprendre à associer des sensations perceptives à des actions motrices appropriées est sous-jacente au succès évolutif de nombreuses espèces, depuis les insectes jusqu'aux êtres hu¬mains. L'importance évolutive de l'apprentissage est depuis longtemps un sujet d'intérêt pour les biologistes de l'évolution, et ces derniers mettent l'accent sur le bénéfice de l'apprentissage lorsque les conditions environnementales sont changeantes, car dans ce cas il est nécessaire de passer de manière flexible d'un comportement à l'autre. Cependant, deux questions non résolues sont importantes afin d'améliorer notre savoir quant aux avantages évolutifs procurés par l'apprentissage. Premièrement, puisqu'il est possible d'apprendre un comportement incorrect quand une tâche est trop complexe, les règles d'apprentissage qui permettent d'atteindre un com¬portement réellement adaptatif doivent être identifiées avec une plus grande précision, et doivent être mises en relation avec les problèmes écologiques spécifiques rencontrés par chaque espèce. Un cadre théorique ayant pour but de prédire le comportement à partir de la définition d'une règle d'apprentissage est développé ici. Il est démontré que les caractéristiques cognitives, telles que la tendance à explorer ou la capacité d'inférer les récompenses liées à des actions non ex¬périmentées, interagissent de manière non-intuitive dans les interactions sociales pour produire des comportements adaptatifs. Ces prédictions comportementales sont utilisées dans un modèle évolutif afin de démontrer que, de manière surprenante, l'apprentissage simple par essai-et-erreur n'est pas toujours battu par l'apprentissage basé sur l'inférence qui est pourtant plus exigeant en puissance de calcul, lorsque les membres d'une population interagissent socialement par pair. Une deuxième question quant à l'évolution de l'apprentissage concerne son lien et son avantage relatif vis-à-vis d'autres formes plus simples de plasticité phénotypique. Après avoir clarifié la distinction entre réponses aux stimuli génétiquement déterminées ou apprises, un nouveau fac¬teur favorisant l'évolution de l'apprentissage est proposé : la complexité environnementale. Un modèle mathématique permet de montrer qu'une mesure de la complexité environnementale - le nombre de stimuli rencontrés dans l'environnement - a un rôle fondamental pour l'évolution de l'apprentissage. En conclusion, ce travail ouvre de nombreuses perspectives quant à la mo¬délisation des interactions entre les espèces en évolution et leur environnement, dans le but de comprendre comment la sélection naturelle façonne les capacités cognitives des animaux.

Immunofluorescence test on Schistosoma mansoni worm paraffin sections (IgM-IFT) for the study of schistosomiasis transmission in Campinas, São Paulo, Brazil

The detection of IgM antibodies for Schistosoma mansoni using gut-associated antigens (IgM-IFT) was compared to the parasitological Kato-Katz method for study of the transmission of schistosomiasis in an urban area in Campinas. About 400 schoolchildren whose ages ranged from 6 to 18 years, were observed for a period of two years. Blood samples on filter paper and fecal samples were collected, at intervals of six months. Serological (IgM-IFT) prevalence rates of 1.2%, 4.3%, 3.6%, 2.9% and 3.4% were obtained in five surveys carried out. S. mansoni eggs were detected in only one child out of the 225 children (0.4%) who were submitted to the Kato-Katz method (three slides for each fecal sample) in the 1st survey. Sixty eight children who submitted five blood samples, one for each survey, were found IFT negative throughout the study. No child was found to be IFT positive in all five surveys, and only four children showed IFT positive results in at least four surveys. Seroconversion from IFT negative to positive was observed from the 1st to the 2nd survey in six chidren, from the 2nd to the 3rd survey in three children, from the 3rd to the 4th survey in four children, and from the 4th to the 5th survey in two cases. However, confirmation of S. mansoni infection using the fecal examination was not possible in any of the cases. Also, in most of them the IFT result oscillated from negative to positive and vice versa. Our data implied that recent transmission of schistosomiasis in the study area was not possible.

Immunotherapy for Visceral Leishmaniasis: Ability of Factors Produced during Anti-leishmania Responses of Skin Test Positive Adults to Inhibit Peripheral Blood Mononuclear Cell Activities Associated with Visceral Leishmaniasis

The course of human Leishmania chagasi infections appears to be determined by the balance between type 1 (T1) CD4+ and CD8+ T suppressor (Ts) cell activities. Skin test positive adults living in hyperendemic areas who have no history of visceral leishmaniasis (VL) have T1 CD4+ T cell immunodominant responses against L. chagasi. The cytokines they secrete during anti-leishmania responses are a probable source of cytokines which inhibit the CD8+ Ts cells associated with VL. The ability of supernatants generated from peripheral blood mononuclear cells derived from skin test positive adults to reverse immune responses which appear to be mediated by CD8+ Ts cells was assessed in three sets of screening assays. The supernatants displayed three candidate factors. One, which could be explained by Leishmania antigens in the supernatant, decreased high endogenous IL-10 secretion characteristic of one class of VL patients. A second activity decreased high endogenous proliferation characteristic of the same class of patients without decreasing antigen specific proliferation. The third activity inhibited or killed CD8+ T cells but not CD4+ T cells. These activities might be useful in treating VL.

Humoral Immune Response Kinetics in Philander opossum and Didelphis marsupialis Infected and Immunized by Trypanosoma cruzi Employing an Immunofluorescence Antibody Test

Philander opossum and Didelphis marsupialis considered the most ancient mammals and an evolutionary success, maintain parasitism by Trypanosoma cruzi without developing any apparent disease or important tissue lesion. In order to elucidate this well-balanced interaction, we decided to compare the humoral immune response kinetics of the two didelphids naturally and experimentally infected with T. cruzi and immunized by different schedules of parasite antigens, employing an indirect fluorescence antibody test (IFAT). Both didelphids responded with high serological titers to different immunization routes, while the earliest response occurred with the intradermic route. Serological titers of naturally infected P. opossum showed a significant individual variation, while those of D. marsupialis remained stable during the entire follow-up period. The serological titers of the experimentally infected animals varied according to the inoculated strain. Our data suggest that (1) IFAT was sensitive for follow-up of P. opossum in natural and experimental T. cruzi infections; (2) both P. opossum and D. marsupialis are able to mount an efficient humoral immune response as compared to placental mammals; (3) experimentally infected P. opossum and D. marsupialis present distinct patterns of infection, depending on the subpopulation of T. cruzi, (4) the differences observed in the humoral immune responses between P. opossum and D. marsupialis, probably, reflect distinct strategies selected by these animals during their coevolution with T. cruzi.

Role of disease activity for decision making ability in early multiple sclerosis

Background and purpose: Decision making (DM) has been defined as the process through which a person forms preferences, selects and executes actions, and evaluates the outcome related to a selected choice. This ability represents an important factor for adequate behaviour in everyday life. DM impairment in multiple sclerosis (MS) has been previously reported. The purpose of the present study was to assess DM in patients with MS at the earliest clinically detectable time point of the disease. Methods: Patients with definite (n=109) or possible (clinically isolated syndrome, CIS; n=56) MS, a short disease duration (mean 2.3 years) and a minor neurological disability (mean EDSS 1.8) were compared to 50 healthy controls aged 18 to 60 years (mean age 32.2) using the Iowa Gambling Task (IGT). Subjects had to select a card from any of 4 decks (A/B [disadvantageous]; C/D [advantageous]). The game consisted of 100 trials then grouped in blocks of 20 cards for data analysis. Skill in DM was assessed by means of a learning index (LI) defined as the difference between the averaged last three block indexes and first two block indexes (LI=[(BI-3+BI-4+BI-5)/3-(BI-1+B2)/2]). Non parametric tests were used for statistical analysis. Results: LI was higher in the control group (0.24, SD 0.44) than in the MS group (0.21, SD 0.38), however without reaching statistical significance (p=0.7). Interesting differences were detected when MS patients were grouped according to phenotype. A trend to a difference between MS subgroups and controls was observed for LI (p=0.06), which became significant between MS subgroups (p=0.03). CIS patients who confirmed MS diagnosis by presenting a second relapse after study entry showed a dysfunction in the IGT in comparison to the other CIS (p=0.01) and definite MS (p=0.04) patients. In the opposite, CIS patients characterised by not entirely fulfilled McDonald criteria at inclusion and absence of relapse during the study showed an normal learning pattern on the IGT. Finally, comparing MS patients who developed relapses after study entry, those who remained clinically stable and controls, we observed impaired performances only in relapsing patients in comparison to stable patients (p=0.008) and controls (p=0.03). Discussion: These results raise the assumption of a sustained role for both MS relapsing activity and disease heterogeneity (i.e. infra-clinical severity or activity of MS) in the impaired process of decision making.

New bench test for venous cannula performance assessment.

Cannula design is of prime importance for venous drainage during cardiopulmonary bypass (CPB). To evaluate cannulas intended for CPB, an in vitro circuit was set up with silicone tubing between the test cannula encased in a movable preload reservoir and another static reservoir. The pressure-drop (DeltaP) value (P-drainage - P-preload) was measured using Millar pressure transducers. Flow rate (Q) was measured using an ultrasound flowmeter. Data display and data recording were controlled using a LabView application, custom made particularly for our experiments. Our results demonstrated that DeltaP, Q, and cannula resistance (DeltaP/Q) values were significantly decreased when the cannula diameter was increased for Smart and Medtronic cannulas. Smartcanula showed 36% and 43% less resistance compared to Medtronic venous and Medtronic femoral cannulas, respectively. The cannula shape (straight- or curved-tips) did not affect the DLP cannula resistance. Out of five cannulas tested, the Smartcanula outperforms the other commercially available cannulas. The mean (DeltaP/Q) values were 3.3 +/- 0.08, 4.07 +/- 0.08, 5.58 +/- 0.10, 5.74 +/- 0.15, and 6.45 +/- 0.15 for Smart, Medtronic, Edwards, Sarns, and Gambro cannulas, respectively (two-way ANOVA, p < 0.0001). In conclusion, the present assay allows discrimination between different forms of cannula with high or low lumen resistance.

Comparison of quantiferon-TB gold with tuberculin skin test for detecting latent tuberculosis infection prior to liver transplantation.

Screening for latent tuberculosis infection (LTBI) is recommended prior to organ transplantation. The Quantiferon-TB Gold assay (QFT-G) may be more accurate than the tuberculin skin test (TST) in the detection of LTBI. We prospectively compared the results of QFT-G to TST in patients with chronic liver disease awaiting transplantation. Patients were screened for LTBI with both the QFT-G test and a TST. Concordance between test results and predictors of a discordant result were determined. Of the 153 evaluable patients, 37 (24.2%) had a positive TST and 34 (22.2%) had a positive QFT-G. Overall agreement between tests was 85.1% (kappa= 0.60, p < 0.0001). Discordant test results were seen in 12 TST positive/QFT-G negative patients and in 9 TST negative/QFT-G positive patients. Prior BCG vaccination was not associated with discordant test results. Twelve patients (7.8%), all with a negative TST, had an indeterminate result of the QFT-G and this was more likely in patients with a low lymphocyte count (p = 0.01) and a high MELD score (p = 0.001). In patients awaiting liver transplantation, both the TST and QFT-G were comparable for the diagnosis of LTBI with reasonable concordance between tests. Indeterminate QFT-G result was more likely in those with more advanced liver disease.

Making Chronic Conditions Count: 5. Chronic Airflow Obstruction

Chronic conditions are responsible for a significant proportion of early deaths. They reduce qualityof life in many of the adults living with them, represent substantial financial costs to patients andthe health and social care system, and cause a significant loss of productivity to the economy.This report contains estimates and forecasts of the population prevalence of chronic airflowobstruction, and it shows how it varies across the island and what change is expected between2007, 2015 and 2020.

Making Chronic Conditions Count: 1. Diabetes

Chronic conditions are responsible for a significant proportion of early deaths. They reduce quality of life in many of the adults living with them, represent substantial financial costs to patients and the health and social care system, and cause a significant loss of productivity to the economy. This report contains estimates and forecasts of the population prevalence of diabetes, and it shows how it varies across the island and what change is expected between 2007, 2015 and 2020.

Making Chronic Conditions Count: 2. Coronary Heart Disease (Angina and Heart Attack)

Chronic conditions are responsible for a significant proportion of early deaths. They reduce quality of life in many of the adults living with them, represent substantial financial costs to patients and the health and social care system, and cause a significant loss of productivity to the economy. This report contains estimates and forecasts of the population prevalence of coronary heart disease (angina and heart attack), and it shows how it varies across the island and what change is expected between 2007, 2015 and 2020.

Making Chronic Conditions Count: 3. Hypertension

Chronic conditions are responsible for a significant proportion of early deaths. They reduce quality of life in many of the adults living with them, represent substantial financial costs to patients and the health and social care system, and cause a significant loss of productivity to the economy. This report contains estimates and forecasts of the population prevalence of hypertension and shows how it varies across the island and what change is expected between 2007, 2015 and 2020.

Making Chronic Conditions Count: 4. Stroke

Chronic conditions are responsible for a significant proportion of early deaths. They reduce quality of life in many of the adults living with them, represent substantial financial costs to patients and the health and social care system, and cause a significant loss of productivity to the economy. This report contains estimates and forecasts of the population prevalence of stroke, and it shows how it varies across the island and what change is expected between 2007, 2015 and 2020.