L’aire de distribution des espèces est conditionnée à la fois par des facteurs biotiques et abiotiques et ses frontières dépendent généralement des limites physiologiques de l’espèce. Ainsi, en bordure d’aire de répartition, les populations se caractérisent par une diversité génétique moindre ainsi qu’une forte différentiation génétique et leur existence dépend d’un équilibre fragile entre événements de colonisation et d’extinction.Depuis les années 1970, l’augmentation et l’accélération des pressions anthropiques exercées sur les écosystèmes bouleversent ces équilibres et des modifications de l’aire de répartition sont observées chez certaines espèces dont le bivalve Macoma balthica, espèce clé des écosystèmes littoraux en Europe, dont la limite sud de répartition s’est décalée vers le nord-est au cours des quarante dernières années.Afin d’évaluer les capacités adaptatives de M. balthica et dans un but de conservation, deux approches complémentaires ont été menées dans des environnements contrastés qui ont permis de mettre en évidence des signes d’adaptation locale.D’une part, l’étude du génome neutre à l’aide des outils méthodologiques et concepts de la génétique des populations a permis d’inférer l’histoire démographique de l’espèce avec une attention particulière portée sur une baie en limite d’aire de répartition (Baie de Marennes Oléron, France) et sur une baie soumise à de fortes pressions physico-chimiques (Baie de Gdansk, Pologne). Nous avons mis en évidence notamment :(i) un polymorphisme significatif dans les populations en limite d’aire en opposition avec les attendus théoriques(ii) des ruptures au flux de gènes dans le golfe de Gascogne soumis au réchauffement des eaux de surface mais aussi le long d’un gradient environnemental dans la baie de Gdansk. D’autre part, l’étude moléculaire de la sélection a été menée par la méthode de pyroséquençage sur le transcriptome d’individus prélevés en milieux contrastés. Cette étude a permis de mettre en évidence des tendances d’expression différentielle de gènes de réponse générale au stress selon le milieu considéré. / Species distribution is conditioned by biotic and abiotic factors and its borders depend generally on physiological limits of species. At the edge of their distribution, populations are characterized by a less genetic diversity as well as a strong genetic differentiation and their existence depends on a fragile balance between colonization and extinction.Since the 1970s, the increase and the acceleration of the anthropological pressures exercised on ecosystems upset this balance. As a consequence, modifications of many species distributions are observed. As an example, the south end of the distribution of the bivalve Macoma balthica, a key species of the european littoral ecosystems has moved towards the northeast during the last forty years.In order to conserve this species, we need to estimate the adaptive capacities of M. balthica. Two complementary approaches were undertaken in contrasting environments. The neutral genome was studied using population genetics methods to the demographic history of the species with a particular attention at the edge of its distribution (Bay of Marennes Oléron, France) and in a bay subjected to strong physico-chemical pressures (Bay of Gdansk, Poland). We brought to light in particular:1) A significant polymorphism in the populations at the edge of the distribution in contrast to theoretical predictions.2) A geneflow rupture correlated with high sea surface temperature (in the Bay of Biscay) and also along an environmental gradient ( derived from multiple parameters) in the bay of Gdansk.The molecular study of natural selection was conducted by the method of pyroséquençage using transcriptome from individuals at specific locations. This study allowed us to bring to light tendencies of differential gene expression implicated in the general response to stress.

Abstract Tigers are endangered in the wild and face increasing threats from habitat loss and fragmentation. The majority of their range occurs in the Indian subcontinent, which is therefore a critical area for tiger conservation. Bengal tigers are distributed across many small protected areas in India. Two important Bengal tiger landscapes — Terai Arc Landscape (TAL) and Sundarbans in India were lacking in basic genetic information and needed to address the impact of anthropogenic pressure and climate change on their genetic makeup in order to identify conservation units. Therefore, I employed nuclear and mitochondrial genetic markers on TAL and Sundarbans tiger individuals to respond these demands for the first time. Thirty-nine heterologous microsatellite loci were screened on Bengal tigers and thirteen of these loci were selected to genotype Bengal tiger samples from western TAL (WTAL) and Sundarbans. After I had genotyped seventy-one Bengal tiger individuals from WTAL, I found cryptic population genetic structure, moderate gene flow and asymmetric migration among the subpopulation. Genetic diversity was moderate and there were no signs of population bottlenecks. In order to maintain the connectivity of subpopulations and avoid human—wildlife conflict, relocation of villages is necessary. Preventive measures against habitat encroachment and a ban on sand and boulder mining in the corridor area should also be implemented. Noninvasively-collected tiger samples from Sundarbans were analyzed for mitochondrial and microsatellite markers and compared with mainland (northern and peninsular) Bengal tiger populations in India. Sundarbans tigers were found to be genetically distinct and had lower genetic variation in comparison to other mainland tiger populations. Demographic analysis indicated recent historical isolation (600—2000 years ago) of the Sundarbans tiger from the mainland. Both historical and genetic evidence supported that the Sundarbans tiger was genetically connected to other mainland tigers until recently. Conclusively, genetic isolation from the mainland tiger population and adaptation to the mangrove ecosystem might have jointly shaped the genetic architecture of the Sundarbans tiger. Hence, the Sundarbans tiger needs special conservation attention for the preservation of its unique ability to adapt and for its genetic individuality. It should be managed as an evolutionary significant unit (ESU) under the adaptive evolutionary conservation (AEC) criteria. I also addressed a problem in the previously suggested sex-specific gene flow estimation method and recommended an alternative approach for a more precise estimation. / Tiivistelmä Tiikeri on nykyisin uhanalainen lajin elinympäristön supistumisen ja pilkkoutumisen vuoksi. Lajin tärkein esiintymisalue on Intian niemimaalla, joka on siten kriittisen tärkeä alue tiikerin suojelun kannalta. Intiantiikereitä esiintyy useilla pienillä suojelualueilla Intiassa. Kaksi tärkeää tiikerin esiintymisaluetta Intiassa ovat Terain kaaren (TAL) alue luoteis-Intiassa sekä Sundarbansin mangrovealue Bangladeshin rajalla. Näiden alueiden tiikereistä ei ole ollut olemassa geneettistä perustietoutta, jota tarvitaan, kun arvioidaan ihmisen toiminnan ja ilmastonmuutoksen aiheuttamia muutoksia tiikeripopulaatioiden geneettisessä koostumuksessa sekä kun määritellään lajin suojelun kannalta merkittäviä luonnonsuojeluyksikköjä. Tässä väitöskirjatutkimuksessa tutkittiin Terain kaaren ja Sundarbansin alueen tiikereiden geneettistä monimuotoisuutta ja rakennetta sekä tuman että mitokondrion geenimerkkien avulla. Tutkimuksessa selvitettiin kolmenkymmenyhdeksän tuman geenimerkin (mikrosatelliitin) soveltuvuutta intiantiikerin geneettisiin tutkimuksiin, ja näistä valittiin kolmetoista käytettäväksi läntisen Terain kaaren ja Sundarbansin alueiden tiikereiden geneettisiin tutkimuksiin. Terain kaaren alueelta tutkittiin seitsemänkymmenentäyksi intiantiikerinäytettä. Tulosten perusteella alueella on aikaisemmin havaitsematonta kryptistä populaatiorakennetta. Geenivirtaa eri alapopulaatioiden välillä oli kohtuullisen paljon, mutta se oli epäsymmetristä. Tiikereiden geneettinen monimuotoisuus oli melko suurta eikä geneettisillä menetelmillä havaittu eri alapopulaatioissa merkkejä populaation koon pullonkauloista. Jotta alapopulaatioiden välinen yhdistyneisyys säilyisi jatkossa, joidenkin kylien siirto toisaalle on välttämätöntä. Ihmisten luvaton levittäytyminen tiikerin elinalueita yhdistävillä käytävillä täytyisi saada hallintaan sekä kieltää hiekanotto ja kivenlouhinta. Sundarbansin alueelta ei-invasiivisesti kerätyt tiikerinäytteet tutkittiin sekä tuman että mitokondrion merkkigeenillä ja alueen tiikereiden geneettistä koostumusta verrattiin manner-Intian tiikeripopulaatioiden koostumukseen. Sundarbansin tiikereiden todettiin poikkeavan geneettisesti manneralueen tiikeripopulaatioista ja niiden geneettinen monimuotoisuus oli alhaisempaa kuin manneralueella. Koalesenssisimulaatiohin perustava demografinen analyysi viittasi Sundarbansin tiikereiden suhteellisen viimeaikaiseen (600—2000 vuotta sitten) erkanemiseen manneralueen tiikereistä. Sekä historialliset että geneettiset todisteet tukivat teoriaa, jonka mukaan Sundarbansin tiikereillä olisi ollut yhteyksiä mannermaan tiikereihin aivan viime aikoihin asti. Geneettinen isolaatio mannermaan tiikereistä ja adaptaatio mangrove-ekosysteemiin ovat yhdessä muovanneet Sundarbansin tiikereiden geneettistä arkkitehtuuria. Tämän vuoksi Sundarbansin tiikerit vaativat erityistä suojelua, jotta niiden geneettinen ainutlaatuisuus ja kyky sopeutua erityisolosuhteisiin säilyisivät myös tulevaisuudessa. Populaatiota täytyy hoitaa evolutiivisesti merkittävänä yksikkönä (evolutionary significant unit; ESU) adaptiivisen evolutiivisen suojelun (adaptive evolutionary conservation; AEC) kriteeristön mukaisesti. Tutkimuksessa kiinnitettiin huomiota myös ongelmiin, joita saattoi ilmetä aikaisemmin ehdotetuissa menetelmissä eri sukupuolten kautta kulkevan geenivirran määrän arvioimiseksi ja ehdotettiin vaihtoehtoista menetelmää tarkempien arvioiden saamiseksi.

Submitted by Fernando Henrique Machado (fernandomtb@hotmail.com) on 2018-04-23T13:30:20Z No. of bitstreams: 1 FHM - Tese 132 [PD].pdf: 9073445 bytes, checksum: 558a93dca350999137782573a2b01e5b (MD5) / Rejected by Bruna Bacalgini null (bruna@sorocaba.unesp.br), reason: Prezado, Solicitamos que realize correções na submissão seguindo as orientações abaixo: O pdf não pode estar protegido, por favor, faça a submissão novamente com arquivo pdf não protegido. Agradecemos a compreensão. on 2018-04-23T14:00:52Z (GMT) / Submitted by Fernando Henrique Machado (fernandomtb@hotmail.com) on 2018-04-23T14:39:49Z No. of bitstreams: 1 FHM - Tese 132 [PD].pdf: 9054390 bytes, checksum: 858ba049e3608953cf364a4045e9e325 (MD5) / Approved for entry into archive by Bruna Bacalgini null (bruna@sorocaba.unesp.br) on 2018-04-23T14:44:42Z (GMT) No. of bitstreams: 1 machado_fh_dr_soro.pdf: 9054390 bytes, checksum: 858ba049e3608953cf364a4045e9e325 (MD5) / Made available in DSpace on 2018-04-23T14:44:42Z (GMT). No. of bitstreams: 1 machado_fh_dr_soro.pdf: 9054390 bytes, checksum: 858ba049e3608953cf364a4045e9e325 (MD5) Previous issue date: 2018-03-01 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / As bacias hidrográficas localizadas em áreas densamente ocupadas e industrializadas sofrem diferentes pressões antrópicas, situação que compromete a qualidade e quantidade da água. Esse cenário, peculiar nas bacias hidrográficas dos rios Piracicaba, Capivari e Jundiaí (BH-PCJ), reflete também na sub-bacia hidrográfica do rio Jundiaí-Mirim (BH-JM), responsável pelo fornecimento de 95% da água consumida por Jundiaí-SP. Todavia, a vazão produzida nesta bacia é insuficiente para atender as demandas do município, necessitando da reversão sazonal das águas do rio Atibaia. Diante desse quadro de estresse hídrico, este estudo visou propor e analisar um conjunto de indicadores de segurança hídrica visando a melhoria da capacidade de planejamento e gestão dos recursos hídricos da BH-JM. Assim, utilizou-se de uma abordagem metodológica pautada na seleção, validação, aplicação e estruturação de indicadores de segurança hídrica em um modelo de causa-efeito. Os indicadores foram submetidos à avaliação por meio de um painel multidisciplinar de especialistas utilizando-se o método Delphi. Os indicadores validados pelo painel foram discutidos e, posteriormente, sistematizados a fim do estabelecimento das diretrizes. Os indicadores selecionados foram: (i) oferta de água; (ii) reservatórios de água; (iii) rede de distribuição; (iv) perdas na distribuição de água potável; (v) transposição de água; (vi) qualidade físico-química e biológica da água; e (vii) políticas públicas. Os principais resultados foram: (i) a série histórica analisada apontou um crescimento populacional de 1,8% a.a., conquanto a produção de água tratada cresceu a taxas inferiores (1,2% a.a.), onde verificou-se a redução constante do consumo per capta de 248 L hab.-1 dia-1 para 203 L hab.-1 dia-1 em um período de 17 anos; (ii) as áreas ocupadas por lagos e reservatórios foram ampliadas em 703% em um período de 4 décadas, sendo a maior área representada pelo reservatório de abastecimento público, do qual estimou-se receber uma carga de sedimentos de 1,5 mil t ano-1 ; (iii) o crescimento geométrico da rede de distribuição aumentou a taxas de 3,1% a.a., refletindo no aumento linear do número de ligações ativas de água; (iv) as perdas médias do sistema de distribuição de água potável encontra-se na ordem de 34% ao longo de quase duas décadas, representando perdas de aproximadamente 17,6 milhões de m3 ano-1 ou R$ 38,3 milhões ano-1 ; (v) uso cada vez mais frequente das águas revertidas do rio Atibaia, medida que pode emergir inúmeros desdobramentos e conflitos futuros pelo uso da água na região; (vi) alterações adversas na qualidade físico-química da água da BH-JM em decorrência da transposição, como o aumento na concentração de íons metálicos, turbidez, cloreto, dentre outros; (vii) identificou-se um amplo aparato jurídico-ambiental relacionadas à BH-JM, porém com baixa eficácia jurídica em suas aplicações. Em face dos resultados, 49 diretrizes de gestão foram propostas. Desse modo, a abordagem metodológica empregada revelou-se adequada e replicável para outras bacias, uma vez que: a partir do método Delphi foi possível estabelecer critérios de seleção de indicadores considerando a problemática em análise; a discussão individual dos indicadores permitiu uma melhor compreensão das dinâmicas envolvidas em cada indicador; a estruturação dos indicadores em um modelo-causal permitiu a sistematização das informações e, consequentemente, contribuiu para o estabelecimento das diretrizes. / The river basins located in densely occupied and industrialized areas are subject to different anthropogenic pressures, a condition that compromises directly the quality and quantity of water resources. This situation is common in the Piracicaba, Capivari, and Jundiaí river basins (BH-PCJ), southwestern Brazil, as well as in the Jundiaí-Mirim river basin (BH-JM) (sub-basin of the Jundiaí river). The BH-JM is a strategic area due to supply 95% of the raw water consumed by Jundiaí-SP. However, the available water flow in this basin is not enough to meet the local demands. This fact led to the need for seasonal interbasin water transfer from the Atibaia river. In view of this water stress scenario, this study aimed to propose and analyze a set of water security indicators for improving the planning and management capacity of the BHJM water resources. Therefore, a methodological approach based in selection, validation, application and structuring of water safety indicators was used in a cause-effect model. The indicators were submitted to the assessment through a multidisciplinary panel of experts using the Delphi method. The valid indicators from the panel were well discussed and, posteriorly, systematized for purpose of establishment of guidelines. The selected indicators were: (i) water supply; (ii) water reservoir; (iii) drinking water distribution system; (iv) drinking water losses in the distribution system; (v) interbasin water transfer; (vi) physical-chemical and biological water quality; (vii) public policies. The main results were: (i) the historical series analyzed showed a population growth rate of 1.8% p.a., while the potable water production was 1.2% p.a., where there was a constant reduction of consumption of 248 L inhabitant-1 day-1 to 203 L inhabitant-1 day-1 in 17 years; (ii) the areas occupied by lakes and reservoirs in BH-JM were increased by 703% in 4 decades, the largest area represented by the public supply reservoir, from which it was estimated that a sediment load of 1,5 thousand tons-1 ; (iii) the geometric growth of the distribution network was of 3.1% p.a., reflecting the linear increase in the number of hydrometric water connections; (iv) the average of drinking water losses in the distribution systems was around 34% over almost two decades, representing losses of about 17.6 million m3 year-1 or R$ 38.3 million year- 1 ; (v) increasingly frequent use of the interbasin water transfer from Atibaia river, a measure that may result in many unfolding and future conflicts over the use of water in the region; (vi) adverse changes in the physical-chemical quality of BH-JM water due to interbasin water transfer, such as the increase in the concentration of metallic ions, turbidity, chloride, among others; (vii) an ample environmental legislative framework related to BH-JM was identified, but with low legal effectiveness in their applications. In view of the results, 49 management guidelines were proposed. Therefore, the methodological approach used demonstrated to be adequate and replicable for other river basins, once that: the Delphi method developed allowed to set up criteria of indicators selection considering the research questions analyzed; the indicators discussion allowed a better understanding of the dynamics involved in each indicator; the indicators structuring in a causal model allowed the information systematization and, thus, it is contributed to the establishment the management guidelines. / Capes-DS

Dans le cadre des objectifs définis par la Directive Cadre sur l’Eau, ce travail de thèse porte sur la quantification du transfert de micropolluants organiques à la confluence entre la Fensch et la Moselle. Une nouvelle méthodologie a été développée pour déterminer les niveaux d’anthropisation dans les matrices environnementales. Basée sur la quantification exhaustive des marqueurs moléculaires, cette approche permet de comparer les apports naturels et anthropiques et de différencier les apports anthropiques selon leurs origines (combustion, pétrogénétique, eaux usées). Elle est parfaitement appropriée à l’étude de la matière organique des différentes matrices environnementales fournissant des informations beaucoup plus complètes que le dosage de quelques molécules cibles. Appliquée aux sédiments du système Fensch-Moselle, cette approche a permis d’analyser l’évolution des contributions organiques le long de la Fensch ainsi que leur transfert à la confluence avec la Moselle, tout en déterminant les sources principales de contamination. Ce travail souligne l’importance de l’hydrodynamisme sur la sédimentation et la biodégradation des micropolluants organiques. L’étude de ce système a également été l’occasion de développer deux outils utiles pour répondre à des questionnements environnementaux majeurs. Le premier, basé sur la déconvolution de l’unresolved complex mixture, permet de quantifier la masse de produits pétroliers accumulés dans des sédiments. Le second se base sur l’étude de la répartition des micropolluants organiques en phase aqueuse (dissous, colloïdale, particulaire) lors de la mobilisation de sédiments contaminés, permettant d’évaluer leur biodisponibilité / According to the objectives of the Water Framework Directive, this study deals with the quantification of the transfer of organic micropollutants at the confluence between Fensch and Moselle Rivers. A new methodology has been developed in order to quantify the anthropogenic pressure in environmental matrices. Based on the exhaustive quantification of molecular markers, this approach allows the comparison between natural and anthropogenic inputs and the differentiation between anthropogenic sources (pyrogenic, petrogenic, sewage waters). It is fully appropriate in order to study organic matter in different environmental matrices providing much more information than the quantification of few target compounds. In sediments of the system Fensch-Moselle, this approach has been applied in order to study the evolution of the anthropogenic pressure due to organic micropollutants along the Fensch River, their transfer at the confluence with the Moselle River and the major sources of contamination. This work highlights the relationship between hydrodynamism and settling and biodegradation of organic micropollutants. Together with the mutimolecular approach, two methodologies have been developed in order to answer to major environmental questionings. The first one, based on the deconvolution of unresolved complex mixture, allows quantifying the amount of petroleum by-products stored in sediments. The second one is based on the analysis of organic micropollutants in aqueous phases (dissolved, colloidal, particulate) during mobilization of contaminated sediments, which allows the evaluation of their bioavailability