Cette étude présente des contributions en traitement statistique du signal avec des applications biomédicales. La thèse est divisée en deux parties. La première partie traite de la détection des hotspots à l'interface des protéines. Les hotspots sont les résidus dont les contributions énergétiques sont les plus importantes dans l'interaction entre protéines. Les forêts aléatoires (Random Forests) sont utilisées pour la classification. Une nouvelle famille de descripteurs de hotspot est également introduite. Ces descripteurs sont basés seulement sur la séquence primaire unidimensionnelle d'acides aminés constituant la protéine. Aucune information sur la structure tridimensionnelle de la protéine ou le complexe n'est nécessaire. Ces descripteurs, capitalisant les caractéristiques fréquentielle des protéines, nous permettent de savoir la façon dont la séquence primaire d'une protéine peut déterminer sa structure tridimensionnelle et sa fonction. Dans la deuxième partie, le RDT (Random Distortion Testing), un test robuste d'hypothèse, est considéré. Son application en détection du signal a montré que le RDT peut résister aux imperfections du modèle d'observation. Nous avons également proposé une extension séquentielle du RDT. Cette extension s'appelle le RDT Séquentiel. Trois problèmes classiques de détection d¿écart/distorsion du signal sont reformulés et résolus dans le cadre du RDT. En utilisant le RDT et le RDT Séquentiel, nous étudions la détection d'AutoPEEP (auto-Positive End Expiratory Pressure), une anomalie fréquente en ventilation mécanique. C'est la première étude de ce type dans la littérature. L'extension à la détection d'autres types d'asynchronie est également étudiée et discutée. Ces détecteurs d'AutoPEEP et d'asynchronies sont les éléments principaux de la plateforme de suivi de manière automatique et continue l'interface patient-ventilateur en ventilation mécanique.

<p>The principle objective of this investigation was to develop an understanding of the physiological response and ecological aspects of winter torpor of small carnivores, specifically striped skunks (<i>Mephitis mephitis</i>) in the northern environment. An experiment was undertaken to investigate the physiological response of skunks to solitary and communal over-winter strategies. Solitary skunks were able to undergo daily torpor to conserve energy to survive the winter, whereas communal skunks were able to use social huddling to reduce energy expenditure and rarely entered torpor. Due to seasonal changes in life requirements, den selection criteria change throughout the year. I examined the landscape metrics and habitat characteristics surrounding dens to evaluate the hierarchical selection and use of dens during winter (i.e., for torpor) and summer (i.e., for parturition). Den structures commonly used for winter dens were buildings, whereas den structures used for maternity dens were rockpiles and underground burrows. Habitat surrounding den sites influenced den use; animals chose den sites closer to roads, water sources, habitat edges, and crop fields. Seasonal movements of skunks from winter dens to the following summer home ranges were examined with respect to winter grouping (i.e., solitary or communal) and winter den structure (i.e., underground burrow or building) to investigate factors that influence spatial distribution of skunks. Male and female skunks moved similar distances (~1.5 km) from winter dens to the center of home ranges established in summer, irrespective of winter grouping status and winter den structure use. Due to limited movement in spring, skunks from communal winter dens had higher spatial overlap of summer home ranges than did skunks from solitary dens, producing spatial aggregation of skunk activities surrounding winter communal den sites. Consequently, winter communal dens represent localized hotspots in the landscape. The effects of extrinsic variables (i.e., environment and diseases) and intrinsic characteristics (i.e., age, gender, and body condition) on cumulative winter survival rate were examined. Winter survival rates were driven mostly by winter condition (i.e., low ambient temperature and snow depth), rabies, and body condition. These results suggest that winter severity probably poses a limit on the northern distribution of the species.</p>

Sewage misconnections currently pose severe threats to water quality especially in urban areas in the UK. These misconnections lead to the discharge of untreated wastewater into receiving watercourses via surface water outfalls. Regular discharges from this source could lead to these watercourses failing to meet standards set by the Water Framework Directives. Despite the impacts resulting from this urban diffuse pollutant source, research into this area is limited. The study area is the River Lee, which is known to experience issues with water quality especially within the heavily urbanized lower Lee section. Misconnections are one of the major contributors to the poor water quality status of the River. In this study, the Lee was investigated using several parameters. The approach involved the monitoring of coliform bacteria to detect outfalls where misconnections were likely, then biofilm samples below selected outfalls were used for both clean and polluted sites to look for community types. Results showed severe pollution within some sections of the River particularly within the lower Lee. Pymmes Brook was used as a case study, both coliform bacteria and biofilm communities below outfalls were further investigated for clean and polluted sites. Results from the Pymmes Brook study also showed that this watercourse was experiencing severe issues with water quality, with elevated levels of coliform bacteria identified below polluted outfalls. Biofilm community data obtained during the pilot and experimental phases of study were analyzed using a range of multivariate techniques. Results of the analysis showed consistent x patterns in community structure within sites with similar water quality, with indicator species identified. Communities below polluted outfalls were composed mainly of species tolerant of organic pollution thus indicating a response of communities to misconnection discharges. Currently, the identification of misconnections are carried out through trackbacks, a process which is expensive and time consuming. During this study an inexpensive and rapid approach is proposed for assessing misconnections within a catchment. Using this method, misconnection hotspots are mapped out using coliform bacteria and biofilm communities. Using catchment data and predicted coliform bacteria from enumerated counts, misconnections within these hotspots are assessed. Having tested this approach on Pymmes Brook, a tributary of the River Lee, the results obtained were promising. Pending further verification, this system provides an economical and rapid tool for the assessment of misconnections within a catchment.

O recrutamento é extremamente importante no ambiente recifal, sendo o principal responsável pelo reabastecimento de populações adultas de peixes. Esse fenômeno é altamente complexo, não sendo claro se é influenciado apenas por processos estocásticos ou também por processos determinísticos. No presente estudo avaliamos a dinâmica temporal do recrutamento de diversas espécies de peixes recifais, identificando sítios de berçário (i.e. recrutamento estável e alto) e a influência de variáveis ambientais. Para tal, utilizamos dados de um monitoramento de médio prazo (i.e. 2001 a 2014) realizado no Banco dos Abrolhos (BA-Brasil). Foram amostrados mais de 45 sítios, sendo levantados dados sobre a comunidade de peixes, comunidade bentônica e outras variáveis ambientais. A partir desses dados, avaliamos a variação do recrutamento por sítio em dois períodos distintos (i.e. 2001-2008/2006-2014) e a influência de variáveis ambientais no recrutamento, através da técnica Boosted Regression Trees. Constatamos que diversas espécies de peixe apresentam-se com recrutamento estável em distintos sítios de amostragem. Também observamos um efeito positivo da densidade de peixes recifais coespecíficos adultos e da cobertura relativa de algas frondosas no recrutamento de diversas espécies analisadas. No geral, observamos que há certa espécie especificidade no processo de recrutamento, porém, em escalas espaciais maiores, os padrões podem estar ligados a características mais gerais, relacionadas a um grupo taxonômico mais elevado. Em relação aos sítios de berçário, um se destacou, sendo berçário de 5 diferentes espécies, incluindo Scarus trispinosus, uma das espécies prioritárias para conservação na região de Abrolhos. Assim, recomendamos a criação de uma área marinha de proteção integral que englobe o sítio em questão. Além disso, as descobertas deste trabalho nos permitem reforçar a teoria de que o recrutamento de peixes recifais pode ser influenciado por fenômenos determinísticos e não varia simplesmente de maneira estocástica. / Recruitment is extremely important in the reef environment, because it is the main source of population replenishment. Reef fish recruitment is a highly complex process and it is not clear whether it is influenced only by stochastic processes or also by deterministic processes. Herein, we aimed to investigate temporal dynamics of reef fish recruitment, identify nursery sites (i.e. predictably high recruitment sites) and evaluate the influence of environmental variables on recruitment. We used data from a medium-term time series (i.e. 2001-2014) of scientific surveys in Abrolhos Bank (BA-Brazil). We sampled more than 45 sites, for several consecutive years and recorded data about fish community, benthic community and other environmental variables. We assessed the variation of recruitment on each site, during two distinct periods (i.e. 2001-2008 / 2006-2014), and used the Boosted Regression Trees technique to evaluate the influence of environmental variables in recruitment. We found that several reef fish species present a low variable recruitment at different sampling sites. BRT showed a positive effect of the coverage of flesh algae and abundance of conspecific in the abundance of recruits (i.e. young-of-year) of many species. Overall, we notice that the recruitment traits seems to be species specific, but we also found indications that in larger spatial scales, recruitment spatial and temporal patterns may be related to general characteristics among species of the higher taxa. Nursery sites varied among species and one site was a nursery to 5 different reef fish species, including Scarus trispinosus, a species that require priority conservation in the Abrolhos Bank. Therefore, we recommend the creation of a new no-take marine protected area that encompasses this site. Our results also indicated that reef fish recruitment may be influenced by deterministic processes and do not vary only stochastically.

Nesta dissertação apresenta-se a evolução morfológica e sedimentológica no Arco Praial de Massaguaçú, Litoral Norte do Estado de São Paulo, em uma escala espaço-temporal histórica e de eventos. O Arco Praial de Massaguaçú localiza-se ao norte da Baia de Caraguatatuba e tem uma extensão de aproximadamente 7,5km. A metodologia consistiu na determinação da variação da linha de costa através da análise de fotografias aéreas de 1962, 1977, 1994 e 2001 e GPS para 2006. Foram obtidos 174 perfis bidimensionais e 16 perfis tridimensionais coletados em cinco levantamentos de campos entre os meses de novembro de 2006 e março de 2008 utilizando o método de DGPS. Foram coletadas ainda 176 amostras sedimentares na zona de espraiamento do Arco Praial, junto ao último ponto de cada perfil bidimensional, sendo uma coleta por perfil. Os resultados demonstraram que a maior parte da praia sofreu progradação entre os anos de 1962 e 1994, sendo observada mudança nesta tendência entre 1994 e 2006. Os dados de morfologia e sedimentologia mostraram grande variabilidade espaço temporal, sendo que estas parecem estar relacionadas a variações anuais de energia de onda. Foi identificada uma Zona de Erosão Acentuada (ZEA) na Parte Central do Arco Praial e dividiu-se a praia em cinco áreas de risco, onde este é menor nas extremidades do Arco Praial e aumenta em direção a região central. / This dissertation characterize the morphological and sedimentological evolution of Massaguaçú Bay Beach, São Paulo State, Northeast Brazil, in a Historical and events spatial-temporal scale. Massaguaçú Bay Beach is localized northward of Caraguatatuba Bay and has approximately 7.5Km length. The methodology consisted on the determination of the shoreline changes with Aerophotographic analyses of 1962, 1977, 1994 and 2001, 2006 shoreline was taken with GPS. The DGPS Method was used to obtain 174 two-dimensional profiles and 16 tri-dimensional profiles in 5 field campaigns conducted between November, 2006 and March, 2008. 176 sand samples were collect in the swash zone, next to the last position of each two-dimensional profile. Data showed that almost all beach demonstrated shoreline progradation between 1962 and 1994, this tendency change between 1994 and 2006 with the possibility of increase of the retraction processes. It was observed a great variability in morphological and sedimentological data, this appear to be related with variations on the wave height pattern during the year. It has identified an Erosional Hotspot in the central area of the beach and the beach has divided in five risck areas where the risck increase from the extremities to the center of the beach.

Submitted by (ana.araujo@ufrpe.br) on 2016-08-02T15:32:53Z No. of bitstreams: 1 Luciano Rodrigues da Silva.pdf: 1477739 bytes, checksum: e1ea61981eacbff2c9319865f5504f91 (MD5) / Made available in DSpace on 2016-08-02T15:32:53Z (GMT). No. of bitstreams: 1 Luciano Rodrigues da Silva.pdf: 1477739 bytes, checksum: e1ea61981eacbff2c9319865f5504f91 (MD5) Previous issue date: 2009-10-20 / Vegetation fires represent a natural hazard with severe ecological, social, health and economic consequences. Every year fires burn millions of hectares of forest worldwide and their number have been increasing, principally because of the increase in population and combustion material. The preservation of the environment depends on global and regional policies and methods of prevention and suppression of fires. To establish these methods it is necessarily to know the profile of fires: spatial location, time of occurrence, burned area, why they occur, and how they initiate and propagate. Recently, various methods of Statistical Physics (including data analysis and computational models) have been applied to provide additional information about spatial and temporal distribution of fire sequences, which is crucial for assessing various consequences of burning, such as emissions of gasses and particulates to the atmosphere, loss of biodiversity, loss of wildlife habitat, soil erosion etc. Several satellite systems (with different capabilities in terms of spatial resolution, sensitivity, spectral bands, and times and frequency of overpasses) are currently available for monitoring different fire characteristics: dry areas that are susceptible to wild fire outbreak, actively flaming fires, burned area and smoke, and trace gas emissions. Hotspots are satellite image pixels with infrared intensity corresponding to burning vegetation. A hotspot may represent one fire, or be one of several hotspots representing a larger fire. Together with other satellite data, thenumber of hot-spots can be used to estimate the burned area. In this work we study the dynamics of hotspots using the Detrended Fluctuation Analysis (DFA) method, which serves to quantify correlations in non stationary time series. We analyze daily hotspot temporal series detected in Brazil by various satellites during the period 1998-2008. The results show the existence of power-law long-range correlations that represent an important property of the underlying stochastic process. This property, also found in climatic phenomena, should be incorporated in theoretical models and computer simulations of the fire dynamics. / Incêndios em vegetação é um tipo de desastre natural com conseqüências ambientais, sociais econômicas, etc. Todos os anos incêndios destroem milhões de hectares das florestas e aumentam em número como conseqüência de vários fatores, principalmente de crescimento populacional e acúmulo de material combustível. A preservação de meio ambiente depende das políticas protecionistas globais e regionais adequadas às características de cada região. Para estabelecer essas políticas de controle e prevenção é necessário conhecer o perfil dos incêndios florestais: onde, quando e porque ocorrem. Além das estatísticas de ocorrências de incêndios os métodos emergentes da Física Estatística incluindo análise de dados e modelos computacionais, providenciam as informações adicionais sobre a distribuição e agrupamento espaço-temporal dos incêndios, que são cruciais para o estudo de várias conseqüências de fogo, como emissão de gases e partículas em atmosfera, perda de biodiversidade, erosão de solo, etc. Vários satélites (com características diferentes em termos de resolução espacial, bandas espectrais, tempo e freqüência de escaneamento) são disponíveis para monitoramento das varias características de fogos: áreas de risco, incêndios atualmente ativos, área queimada, fumaça, emissão de poluentes etc. Focos de calor são pixels na imagem de satélite com intensidade infravermelha correspondente a vegetação queimada. Um foco pode representar uma queimada, parte de um incêndio maior ou outras fontes de calor como, por exemplo, a reflexão de luz da superfície de um lago. O número de focos junto com outras informações providenciadas pelos satélites podem ser usados para estimar a área queimada, para detecção e monitoramento dos incêndios florestais, estimação de risco de fogo, e para avaliação da influencia de outros fatores ambientais. Neste trabalho estudamos a dinâmica de focos de calor no Brasil usando o método Detrended Fluctuation Analysis (DFA), desenvolvido para quantificar as correlações em séries temporais não estacionárias. Analisamos séries temporais diárias de focos de calor detectados no Brasil pelo vários satélites, durante o período 1998-2008. Os resultados mostram a existência de correlações de longo alcance persistentes, que representa uma propriedade importante dos processos estocásticos geradores desse fenômeno. Esta propriedade, também presente em fenômenos climáticos deveria ser incorporada em modelos teóricos e simulações computacionais de dinâmica de incêndios.

Abstract In visible light communication (VLC), light emitting diodes (LEDs) are used as transmitters; the air is the transmission medium and the photodiodes are used for receivers. This is often referred to as light fidelity (Li-Fi). In this thesis, we provide the methodology to evaluate the performance of VLC hotspot networks in the context of data downloading on the move scenarios by using throughput-distance relationship models. In this context, first we study the different properties of optical transceiver elements, noise sources, characterization and modelling of artificial light interference, different link topologies and then we introduce the throughput-distance relationship model. Secondly, the analytically based throughput-distance relationship has been developed for evaluating the performance of VLC hotspot networks in indoor environment in both day and night conditions. Simulation results reveal that background noise has a significant impact on the performance of VLC hotspots. As expected, in both indoor and outdoor environments the VLC hotspot performs better at night than during day. The performance of VLC hotspot networks is also quantified in terms of received file size at different bit error rate requirements and velocities of the mobile user. Thirdly, we study the performance of hybrid (Radio-Optical) WLAN-VLC hotspot and compare its performance with stand-alone VLC-only or WLAN-only hotspot cases. In this case, we also consider the data download on the move scenarios in an indoor environment for a single-user as well as for multi-user cases. In this hybrid WLAN-VLC hotspot, both the WLAN and the VLC are characterized by their throughput and communication range. Simulations have been performed to evaluate the performance of such network for data downloading on the move scenario by taking into account performance metrics such as filesize, average connectivity and system throughput. Simulation results reveal that the considered hybrid WLAN-VLC performs always better than stand-alone VLC-only or WLAN-only hotspot both for a single and multi-user cases. Finally, this thesis analyses the feasibility and potential benefits of using hybrid radio-optical wireless systems. In this respect, cooperative communication using optical relays are also introduced in order to increase the coverage and energy efficiency of the battery operated device. Potential benefits are identified as service connectivity and energy efficiency of battery operated device in an indoor environment. Simulation results reveal that user connectivity and energy efficiency depend on user density, coverage range ratio between single-hop and multi-hop, relay probabilities and mobility of the user. / Tiivistelmä Näkyvään valoon pohjautuvassa tiedonsiirrossa (VLC) valodiodeja (LED) käytetään lähettiminä, ilma on siirtokanava ja valoilmaisimia käytetään vastaanottimina. Tätä kutsutaan usein nimellä light fidelity (Li-Fi). Tässä työssä tarjoamme menetelmiä VLC ”hotspot” verkkojen suorituskyvyn arviointiin tiedonsiirtonopeus-etäisyysmalleilla skenaarioissa, jossa tietoa ladataan liikkeessä. Tässä kontekstissa tutkimme ensin optisen lähettimen komponenttien eri ominaisuuksia, kohinan lähteitä, keinovalon häiriömalleja ja tiedonsiirtolinkkien topologioita, jonka jälkeen esittelemme tiedonsiirtonopeuden ja etäisyyden välisen mallin. Toiseksi kehitetyn analyyttisen tiedonsiirto-etäisyys mallia käytetään arvioitaessa VLC hotspot verkkojen suorituskykyä sisäympäristössä sekä päivä että yö olosuhteissa. Simulointien tulokset osoittavat, että taustakohinalla on suuri vaikutus VLC verkkojen suorituskykyyn. Kuten odotettua, sisä- ja ulkotiloissa VLC hotspot toimii paremmin yöllä kuin päivällä. VLC hotspot verkkojen suorituskyky arvioidaan myös vastaanotetun tiedoston koon, eri bittivirhesuhteen vaatimuksilla ja liikkuvan käyttäjän nopeuden suhteen. Kolmanneksi tutkimme hybridi WLAN-VLC hotspot verkon suorituskykyä ja vertaamme sen suorituskykyä pelkän VLC- tai WLAN hotspot tapauksessa. Käsittelemme myös skenaarioita jossa tiedoston lataus tapahtuu liikkeessä sisätilassa yhden käyttäjän sekä monen käyttäjän tapauksissa. Tässä hybridi WLAN-VLC hotspot, sekä erilliset WLAN- ja VLC verkot ovat määritelty niiden tiedonsiirtonopeuden ja kantaman perusteella. Näiden verkkojen suorituskykyä arvioitaessa on tehty joukko tietokonesimulointeja verkossa tapahtuvasta tietojen lataamisesta liikkeessä ottamalla huomioon suorituskyvyn mittarit kuten tiedoston koko, keskimääräinen yhteyden kesto ja saavutettu läpäisy. Simuloinnin tulokset paljastavat, että hybridi WLAN-VLC toimii aina paremmin kuin pelkkä VLC tai WLAN hotspot sekä yhden että monen käyttäjän tapauksessa. Lopuksi työssä analysoidaan ehdotetun järjestelmän toteutettavuus ja mahdolliset edut käytettäessä hybridejä radio-optisia langattomia järjestelmiä. Tältä osin esitellään myös kooperatiiviseen viestintään perustuvat optiset releet parantamaan verkon kattavuutta ja energiatehokkuutta akkukäyttöisissä laitteissa. Mahdolliset hyödyt tunnistetaan palvelun konnektiivisuudessa ja energiatehokkuudessa akkukäyttöisissä laitteissa sisätiloissa. Simulointien tulokset osoittavat, että käyttäjien konnektiivisuus ja energiatehokkuus riippuvat käyttäjätiheydestä, kantaman ja etäisyyden välisestä suhteesta yhden hypyn ja monen hypyn välillä, releointi todennäköisyydestä ja käyttäjien mobiliteetista.

Dyer Island is thought to host one of the most abundant populations of white sharks on the planet; this is often credited to the large (55 – 60,000) Cape fur seal colony at Geyser Rock. Yet relatively little work has ever been produced from the area. This may be attributed to the harshness in its location as a study site, exposed to wind and swell from west to east which limits research periods. This study accounts for over 220 hrs of manual tracking at Dyer Island with a further 68 added from the inshore shallow areas of the bay. Sharks focused their movements and habitat use to reefs or channels that allowed access to Cape fur seals. Movement- Based Kernel Estimates (MKDE) were used to compute home range estimates for shark movements through and around the heterogeneous structures of Dyer Island and Geyser Rock. Inshore two core areas were revealed, one being the major reef system at Joubertsdam and the other at a kelp reef where the tracked shark had fed on a Cape fur seal. At Dyer Island one core area was identified in a narrow channel, ‘Shark Alley’, here a second tracked shark foraged for entire days within meters of rafting Cape fur seals. Rate of Movement (ROM) and Linearity (LI) of tracks were low during daytime and movements were focused around areas such as Shark Alley or other areas close to the seal colony before moving into deeper water or distant reefs with higher rates of ROM and LI at night. If moonlight was strong foraging would take place to the south of Geyser Rock but with higher ROM and LI than observed during the day. Foraging patterns in this study contrast studies from other sites in South Africa and home range and activity areas were comparatively much smaller than observed in Mossel Bay. It has been established that several known white sharks forage at Dyer Island and the other studied aggregation sites, such differences in foraging would suggest that they are able to adapt their foraging behaviour to suit the environment they are in; making them site specific in their foraging ecology. Both satellite and acoustic telemetry are revealing aggregation hotspots of white sharks in South Africa. It is important that such information is used to assist the recovery of the species which has been protected since 1991, yet is rarely considered in planning of coastal developments. / Dissertation (MSc)--University of Pretoria, 2012. / Zoology and Entomology / MSc / Unrestricted

Au cours de la méiose, les points chauds de recombinaison sont le siège de la formation de cassures double-brin de l’ADN. Ces dernières sont ensuite réparées par un processus qui, chez de nombreuses espèces, favorise la transmission des allèles G et C : la conversion génique biaisée vers GC (gBGC). L’intensité de cet important distorteur de la ségrégation méiotique varie fortement entre espèces mais les facteurs déterminant son évolution sont toujours inconnus. Nous avons donc voulu quantifier directement le biais de transmission chez la souris et comparer les paramètres dont il dépend avec d’autres mammifères. Dans cette étude, en couplant des développements bioinformatiques à une technique de capture ciblée d’ADN suivie de séquençage haut-débit (capture-seq), nous avons réussi à mettre au point une approche qui s’est révélée 100 fois plus performante pour détecter les événements de recombinaison que les méthodes existant actuellement. Ainsi, nous avons pu identifier 18 821 crossing-overs (COs) et non-crossovers (NCOs) à très grande résolution chez des individus uniques, ce qui nous a permis de caractériser minutieusement la recombinaison chez la souris. Chez cette espèce, les points chauds de recombinaison sont ciblés par la protéine PRDM9 et sont donc soumis à une deuxième forme de conversion génique biaisée (BGC) : le biais d’initiation (dBGC). La quantification du dBGC et du gBGC à partir de nos données nous a permis de mettre en lumière le fait que, au moment où des populations structurées s’hybrident, le gBGC des lignées parentales est propagé par un phénomène d’auto-stop génétique (genetic hitchhiking) provenant du dBGC. Nous avons ensuite pu observer que, chez les souris mâles, seuls les NCOs — et plus particulièrement les NCOs contenant un seul marqueur génétique— contribuent à l’intensité du gBGC. En comparaison, chez l’Homme, à la fois les NCOs et au moins une part des COs (ceux qui présentent des tracts de conversion complexes) distordent les fréquences alléliques. Ceci suggère que la machinerie de réparation des cassures double-brin qui induit le biais de conversion génique (BGC) présente des variations au sein des mammifères. Nos résultats sont aussi en accord avec l’hypothèse selon laquelle une pression de sélection limiterait l’intensité de ce processus délétère à l’échelle de la population. Cela se traduirait par une compensation de la taille efficace de population à de multiples niveaux : par le taux de recombinaison, par la longueur des tracts de conversion et par le biais de transmission. Somme toute, notre travail a permis de mieux comprendre la façon dont la recombinaison et la conversion génique biaisée opèrent chez les mammifères. / During meiosis, recombination hotspots host the formation of DNA double-strand breaks (DSBs). DSBs are subsequently repaired through a process which, in a wide range of species, is biased towards the favoured transmission of G and C alleles: GC-biased gene conversion (gBGC). The intensity of this fundamental distorter of meiotic segregation strongly varies between species but the factors dictating its evolution are not known. We thus aimed at directly quantifying the transmission bias in mice and comparing the parameters on which it depends with other mammals. Here, we coupled capture-seq and bioinformatic techniques to implement an approach that proved 100 times more powerful than current methods to detect recombination. With it, we identified 18,821 crossing-over (CO) and non-crossover (NCO) events at very high resolution in single individuals and could thus precisely characterise patterns of recombination in mice. In this species, recombination hotspots are targeted by PRDM9 and are therefore subject to a second type of biased gene conversion (BGC): DSB-induced BGC (dBGC). Quantifying both dBGC and gBGC with our data brought to light the fact that, in cases of structured populations, past gBGC from the parental lineages is hitchhiked by dBGC when the populations cross. We next observed that, in male mice, only NCOs — and more particularly single-marker NCOs — contribute to the intensity of gBGC. In contrast, in humans, both NCOs and at least a portion of COs (those with complex conversion tracts) distort allelic frequencies. This suggests that the DSB repair machinery leading to gBGC varies across mammals. Our findings are also consistent with the hypothesis of a selective pressure restraining the intensity of the deleterious gBGC process at the population-scale: this would materialise through a multi-level compensation of the effective population size by the recombination rate, the length of conversion tracts and the transmission bias. Altogether, our work has allowed to better comprehend how recombination and biased gene conversion proceed in the mammalian clade

The contamination of rivers with nitrate from agricultural diffuse sources is not just a risk for ecosystems and their services, but also a health risk for water users. The Great Lakes (USA and Canada) are suffering from eutrophication problems. The Midwest is one of the richest farming land and one of the most productive areas on the planet. Thus, agriculture is one of the biggest drivers of local economies, accounting for billions of dollars of exports and thousands of jobs. The Midwest encompasses the Corn Belt region, a specialised system in corn production. Many of its agricultural basins drain into the Great Lakes. Corn requires a heavy amount of fertilizer to keep the best-yielding varieties. Some of the soils also require artificial drainage due to their low permeability, and to enable agriculture. The Cedar Creek watershed (CCW) in northeastern Indiana in the Corn Belt region is used as a case study area in this dissertation. Intensive agriculture in the CCW is characterised mainly by corn and soybean production. Tile drains are used, ejecting nitrate directly into the water. To find hotspots of nitrate is, then, crucial to avoid water quality deterioration. Identification of critical source areas of nitrate (CSAs) impairing waters is challenging. There are, mainly, two methodologies to identify hotspots of nitrate for the implementation of Best Management Practices (BMP): the targeting technique and the optimization approach. The targeting technique tends to identify hotspots based on loads of nitrate, omitting geomorphological watershed characteristics, costs for BMP implementation, and their spatial interactions. On the other hand, the parsimonious strategy does contemplate the trade-off of the economic and environmental contribution but requires sophisticated computational resources and it is more data-intense. This research presents a new framework based on the synergistic combination of both methodologies for the identification of CSAs in agricultural watersheds. Changes in watershed response due to alternative BMP applications were assessed using the model Soil and Water Assessment Tool (SWAT). Outputs in SWAT (nitrate export rates and nitrate concentration at the subbasin level) were used to evaluate the changes in water quality for the CCW. The newly developed targeting technique (HosNIT) considers SWAT outputs and intrinsic watershed parameters such as stream order, crop distance to the draining stream, and downstream nitrate enrichment/dilution effects within the river network. HosNIT establishes a workflow, based on a threshold system for the parameters considered, in order to spatially identify priority areas from where nitrate is reaching water. The more precise hotspots of nitrate are identified, the more improved the allocation of limited resources for conservation practices will be. HosNIT allows for a more spatially accurate CSAs identification, which enables a parsimonious optimization for BMP implementation. This parsimonious strategy will test BMP’s performance based on the environmental contribution and cost at the hotspots determined by HosNIT. The optimised solution for the CCW comes from the environmental contribution (decrease percentage of nitrate concentration at outlets) per dollar spent. For this case study means a year average of 3.7% of nitrate reduction with the optimised selection of scenarios for the studied period.