Si les patrons d'expression de la diversité génétique des essences forestières à distribution grégaire des forêts tropicales humides ont fait l'objet de nombreuses études, les connaissances sur les essences forestières disséminées et représentées à très faible densité à l'hectare (dites rares) restent encore embryonnaires. Ces dernières suivent elles les mêmes patrons de distribution de la diversité génétique? Quels facteurs biotiques et abiotiques régissent l'organisation spatiale et l'évolution de la diversité génétique chez ce type d'espèce ? Afin d'améliorer les connaissances sur la biologie des espèces rares, nous nous proposons au travers de marqueurs microsatellites nucléaires(nuc) et chloroplastiques(cp) (i) d'analyser le régime de reproduction chez une espèce rare (ii) d'évaluer sa capacité de dispersion des gènes via les graines et le pollen , et enfin de(iii) décrire l'organisation spatiale de la diversité génétique à fine et à large échelle. Nous avons abordé ces questions avec Baillonella toxisperma (le Moabi), une essence commerciale dite rare (1 adulte/15ha à 20 ha), à multi- usages, représentée à travers les différentes écozones du bassin du Congo. Trois résultats majeurs découlent de nos travaux : (i) En dépit d'un isolement prononcé des adultes, B. toxisperma présente un régime de reproduction allogame prépondérant (tm ≈ 98%) avec des taux réduits d'autofécondation (1 - tm < 3%) probablement favorisé par la protandrie. (ii) Comme attendu dans le cas d'arbres disséminés, l'intensité de sa structure génétique spatiale à fine échelle est faible (Spnuc = 0.003 ; Spcp = 0.015) et reflète bien les flux de gènes à longues distances mesurés via le pollen [σp = 9.8 km à 10.8 km] et les graines [σs = 4.0 km à 6.3 km], probablement dû aux disperseurs efficaces que sont la chauve-souris, l'éléphant et l'homme. A large échelle spatiale, un signal phylogéographique a été détecté entre les individus situés de part et d'autre de l'équateur thermique, notamment entre ceux du massif forestier Camerounais et du Gabon (Rst = 0.313 > Rstp = 0.115, P < 0.001). Deux sous-groupes du massif forestier gabonais qui séparent les individus des forêts côtières de l'Ouest, de ceux des forêts planitaires de l'intérieur des terre, à l'Est, ont également été détectés, et présentent une différenciation génétique modérée (FST = 0.068, P < 0.001). La divergence génétique entre ces trois groupes pourrait s'expliquer par un isolement géographique qui remonterait aux perturbations climatiques du pléistocène et de l'Holocène sur la forêt tropicale humide africaine, et qui serait encore aujourd'hui maintenu par un isolement dans la reproduction du fait d'un asynchronisme dans la période de floraison entre leurs individus. La mise en évidence de ces trois groupes génétiques suggère une répartition biogéographique de B. toxisperma dans le bassin du Congo en partie façonnée par le climat actuel et passé. Nos conclusions peuvent servir d'outils d'aide à la décision pour les programmes de conservation et d'aménagement durable de la biodiversité en Afrique centrale. / If genetic diversity patterns of gregarious rainforest forest trees are well known, few knowledges are available about low density tree species. Does those last one follow the same genetic distribution pattern? Which biotic and abiotic factors underline the spatial structure and evolution of the genetic diversity of such species? In order to improve the knowledge of the biology of such species, we have propose through nuclear microsatellite(nuc) and chlorosplastic (cp) markers to (i) analyse the reproductive system of a low density tree species, (ii) assess its dispersal capacity through seeds and pollen, and finally to (iii) describe the spatial genetic structure at a fine and large scale. We have addressed those questions with Baillonella toxisperma Pierre (commonly named Moabi), a commercial tree of many uses, known to be rare (1 ind/15ha à 20 ha) and distributed through different ecologicals areas of Congo basin. Three main results rise from our study: (i) Despite a strong isolation of the adults, B. toxisperma has a dominant allogamous reproductive system (tm ≈ 98%) with a reduce rate of self-pollination (1- tm< 3%) which is probably due to occurrence of protandry. (ii) As expected in the case of low density trees, the spatial statistic (Sp) of the fine spatial genetic structure is very low [Spnuc = 0.003 ; Spcp = 0.015]. Those reflected a very high gene flow mediated through pollen [σp = 9.8 km à 10.8 km] and seeds [σs = 4.0 km à 6.3 km], that probably mediated by efficient dispersal vectors like bats, human and elephant. At a large scale, a phylogenetic signal has been detected between individuals located in both side of the thermic equator, mainly between those from the block forest of Cameroon and Gabon [RST = 0.313 > RSTp = 0.115, P < 0.001]. Two discretes genetics units from the Gabon block forest which separate individuals of the West coastal forests from the lowland forest ones (in the inland) have also been detected and showed a moderate genetic differentiation [FST = 0.068, P < 0.001]. The genetic differentiation between these three units could be explained by a geographical isolation during past climatic disturbances in the African rainforest, occurred in the Pleistocene and Holocene, and which will be still maintained up to date by a reproductive isolation caused by flowering asynchrony periods among individuals. The occurrence of these three genetic units suggests a biogeographical repartition of B. toxisperma in the Congo basin that is mainly due to the past and current climate. Our conclusions may lead to implement conservation strategies and sustainable management programm for biodiversity in Central Africa.

Les Sicydiinae amphidromes constituent une part importante des peuplements piscicoles insulaires de la région Indo-Pacifique et sont vulnérables à de nombreuses pressions anthropiques (i.e. pêcherie, dégradation et fragmentation des habitats). La reproduction a lieu en eau douce, puis les jeunes dévalent en mer où ils débutent leur croissance pendant quelques mois avant de coloniser les rivières. L’objectif est d’acquérir des connaissances sur les traits de vie de S. lagocephalus (cosmopolite) et de C. acutipinnis (endémique). Les travaux de terrain démontrent que le choix de l’habitat quotidien est fortement lié aux interactions sociales, alors que l’habitat de fraie montre une forte sélection pour des conditions morphodynamiques favorisant l’oxygénation des oeufs. Les mâles sélectionnent des sites de ponte et gardent les oeufs. L’étude expérimentale de la survie en eau douce confirme que tous les embryons libres possèdent la capacité à rejoindre la mer. L’analyse des traits de vie marins à partir des otolithes des post-larves révèle des variations saisonnières d’âge et de taille au recrutement, en lien avec la croissance et la température marine. L’examen histologique des ovaires permet de décrire les variations spatiales et temporelles de l’activité de reproduction chez les femelles en rivière et de déterminer la fécondité et la taille de première reproduction. Les variations inter et intra-spécifiques des traits de vie sontcomparées en lien avec la répartition géographique des deux espèces. Ces travaux permettent d’identifier des perspectives concrètes dans le domaine de la gestion et de la conservation sur la base des caractéristiques de la stratégie amphidrome. / Amphidromous Sicydiinae are particularly widespread among fish freshwater assemblages of the Indo-Pacific region and are vulnerable to anthropogenic pressures (i.e. fishery, degradation and fragmentation of habitats). Spawning and hatching happen in freshwater, then offspring drift downstream to the sea where they begin their growth for a few months before recruiting in the rivers. This study aims at acquire knowledge about life traits of S. lagocephalus (cosmopolite) and C. acutipinnis (endemic). Field sampling shows that the usual habitat choice is related to social interactions, whereasspawning habitat shows a strong selection for morphodynamic conditions which favor eggs oxygenation. Males select spawning sites and care for the eggs. The experimental study of freshwater survival confirms that free embryos survival and swimming capacities are enough to drift to the ocean. Marine life history analysis, based on postlarvae otoliths examination, reveals a seasonal variation of both age and size-atrecruitment related to the larval growth rate and the sea temperature. Histological examination of ovaries is used to describe the spatial and temporal variation of reproductive activity of mature females in the rivers, and to determine fecundity and size at first reproduction. Inter and intra-specific variations of life history traits are compared in relation to the respective geographical distribution of both species. This study identifies concrete prospects for management and conservation based on the features of amphidromous life history strategy.

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Postcopulatory sexual selection—sperm competition and cryptic female choice—has become a major area of research over the past 40 years. Within this field there are many outstanding questions at every level of analysis, from proximate to ultimate. The fitness consequences for both sexes in the period after copulation and before fertilization are considerable, but are obscured within the female reproductive tract. Our understanding of postcopulatory mechanisms is especially sparse in taxa other than birds and insects. Nearly nothing is known in reptiles except that multiple paternity is common and widespread, and often results from long-term sperm storage across breeding seasons. We present some of the very first data on the determinants of fertilization success in the context of sperm competition in reptiles, a group that accounts for 30% of terrestrial vertebrates. In the first chapter, "Asymmetric gametic isolation between two populations of red-sided garter snakes", we discuss the use of between-population crosses to reveal gametic isolation. The effect of population density and operational sex ratios on mating systems and the speciation process has fueled theoretical debate. We attempted to address these issues using two populations of red-sided garter snakes (Thamnophis sirtalis parietalis) from Manitoba, Canada. Our study populations differ markedly in their density mating aggregations, with a 10-fold difference between them. Using microsatellite markers for paternity analysis of litters produced from within and between population crosses. We found that the population with highest aggregation density, and presumably with the highest level of sexual conflict (i.e., when the evolutionary interests of the sexes differ) over mating, was also the population that exhibited homotypic sperm precedence. The less dense population showed a distinct postcopulatory male-size advantage. We also demonstrated that sperm stored within the female over hibernation can father 20-30% of offspring in a litter. In the second chapter, "Sperm competition and mate-order effects in red-sided garter snakes", we test whether females use mate-order effects to ensure that a larger (fitter) male will sire her offspring. Does that second male should have precedence in sperm competition? We tested for second-male precedence using singly-mated females that mated with a second male. Average proportion of paternity was shared equally among the first (P₁, i.e., proportion of offspring from a litter fathered by the first male to mate) and second males (P₂) to mate, and stored sperm (P[subscript ss]). This may be a case where last male precedence breaks down with more than two males. All females were spring virgins (they had not mated that spring, but may have stored sperm from fall matings); thus sperm stored presumably from fall matings is important in this system. As the interval between matings increased P₁ increased at the expense of P[subscript ss]. As the second male to mate's copulation duration increased, P₁ also increased at the expense of P₂. This last result may indicate female influence over sperm transfer during coerced matings. Copulatory plugs (CPs) are found in many taxa, but the functional significance is debated. Male garter snakes produce a gelatinous copulatory plug during mating that occludes the opening of the female reproductive tract for approximately two days. In chapter three, "Not just a chastity belt: the role of mating plugs in red-sided garter snakes revisited", we experimentally tested the role of the CPs. In snakes, sperm are produced in the testes and delivered through the ductus deferens, and the copulatory plug is thought to be produced by the sexual segment of the kidney and conveyed through the ureter. We manipulated the delivery of the two fluids separately by ligating the ducts. We confirmed that the CP is not formed in ureter-ligated males and that sperm leaks out immediately after copulation. The CP is analogous to a spermatophore. The protein matrix contains most of the sperm which are liberated as the plug dissolves within the female's vaginal pouch. One of the fundamental principles in sperm competition is that increased sperm numbers increase the odds of winning in competitions for fertilization success and males will adjust their ejaculate relative to competition and the quality of his mate. In chapter four, "Sperm depleted males and the unfortunate females who mate with them", we detect significant among-male variation in the number of sperm ejaculated, and that male mate-order reduces sperm numbers. Male sperm numbers drop significantly from one mating to the next, and this has implications for sperm competiveness, as Thamnophis sirtalis exhibits a disassociated reproductive tactic, in that sperm stores are produced outside the breeding season, and thus cannot be replenished after mating. Interestingly, however, the on average the mobility of the sperm increased for a male's second mating. Therefore, increased sperm quality may compensate for reduced numbers in a competitive context. Further, females increase their remating rate when mating with males that are unable to deliver sperm. In chapter five, "Sexual conflict during mating in red-sided garter snakes as evidenced by genital manipulation", we revisited the CP in the context of sexual conflict. Sex-differences in optimal copulation duration can be a source of conflict, as increased copulation duration may be advantageous for males as it delays female remating. Males of many species actively guard females to prevent them from remating, and in some cases males produce copulatory plugs to prevent remating. If precopulatory choice is limited at the time of her first mating, conflict may be especially onerous to a female. The size of the plug is influenced by the copulation duration. We experimentally tested the contribution of male and female control over copulation duration. We ablated the largest basal spine on the male's hemipene and found a reduction in copulation duration and an increase in the variation of plug mass. Further, we anesthetized the female's cloaca and found copulation duration increased, which suggests that males benefit from increased copulation duration while females actively try to reduce copulation duration. Therefore, sexual conflict is manifest in divergent copulation duration optima for males and females. / Graduation date: 2013

Made available in DSpace on 2016-06-02T20:20:30Z (GMT). No. of bitstreams: 1 3280.pdf: 5102569 bytes, checksum: f511b08e43998ea79e0f9b0ac5ed969b (MD5) Previous issue date: 2010-08-06 / Universidade Federal de Sao Carlos / Population genetic parameters and genetic relatedness estimates were carried out for Roseate Spoonbill (Platalea ajaja), Wood Stork (Mycteria americana) and Great Egret (Ardea alba egretta) reproductive colonies in Amapa, Pantanal and Rio Grande do Sul (RS), Brazil. Microsatellite genotypes were used to investigate kinship patterns between nestlings sampled inside the same nests, using a variety of analytical approaches. Unrelated nestling-pairs were observed in Roseate Spoonbill nests (6.12% of analyzed nests) and in Wood Stork nests (11.34%); half-siblings were present in Roseate Spoonbill nests as well (1.36%). Only full-siblings were detected inside Great Egret nests. Conspecific brood parasitism (CBP) and extra-pair paternity were proposed to account for the presence of unrelated nestmates and half-siblings, respectively, in Roseate Spoonbill and Wood Stork nests. Those results suggest the occurrence of a mating system different than genetic monogamy in natural populations of those waterbirds. Genetic relatedness was also investigated for adults and offspring, as well as for supposed siblings in Roseate Spoonbill families kept in three zoological facilities in the U.S. Paternity and maternity allocation analyses through maximum-likelihood revealed that errors were present in zoo&#8223;s studbooks in relation to the familial records. We also identified mating between related individuals that were not detected previously by zookeepers. Population genetic parameters were also estimated and demographic processes were assessed for Great Egret reproductive colonies in the Pantanal and Rio Grande do Su, Brazil. Bayesian clustering analyses, assignment tests, analysis of molecular variance, F-statistics estimates, allelic frequency distribution and the G-W index revealed that: i) Pantanal reproductive colonies are genetically differentiated from Rio Grande do Sul colonies; ii) an IBD-like pattern alone cannot explain that differentiation; and iii) genetic signal of a reduction of population size was present for two colonies in the Pantanal and one in Rio Grande do Sul. Results were discussed considering a metapopulation dynamic and also considering that populations from both Brazilian regions represent distinct units and deserve to be treated separately when planning and carrying out conservation and management programs that aim to preserve the species&#8223; genetic diversity. / Estudos de genética de populações e de parentesco genético foram desenvolvidos em colhereiro (Platalea ajaja), cabeça-seca (Mycteria americana) e garça-branca-grande (Ardea alba egretta), de colônias reprodutivas do Amapá, Pantanal e Rio Grande do Sul (RS), Brasil. Genótipos em locos de microssatélites foram utilizados para se investigar os padrões de relacionamento entre ninhegos amostrados dentro dos mesmos ninhos com diferentes metodologias de análise. Pares de ninhegos não-relacionados foram encontrados nos ninhos de colhereiro (6,12% dos pares analisados) e de cabeça-seca (11,34%); meio-irmãos foram observados nos ninhos de colhereiro (1,36%). Em garça branca grande foi detectada apenas a presença de irmãos-completos dentro dos ninhos. Parasitismo de ninho intraespecífico e paternidade extra-par podem explicar a presença de ninhegos não-relacionados e meio-irmãos nos ninhos de colhereiro e cabeça-seca, o que indica a presença de um sistema de acasalamento diferente da monogamia genética nas populações naturais dessas espécies. Relações de parentesco entre adultos e filhotes e entre supostos irmãos foram determinadas em famílias de colhereiro de três zoológicos dos EUA. Análises de atribuição de maternidade e paternidade por máxima verossimilhança revelaram erros nos registros dos zoológicos quanto às relações progenitor-progênie e identificaram acasalamentos entre indivíduos aparentados que não tinham sido registrados. Parâmetros genético-populacionais e processos demográficos foram investigados em populações de garça-branca-grande do Pantanal e do Rio Grande do Sul. Análises Bayesianas, testes de alocação de indivíduos, análises de variância molecular, estimativa de estatísticas F, exame da distribuição das freqüências alélicas e cálculo do índice de G-W permitiram identificar que: i) há diferenciação genética significativa entre colônias reprodutivas do Pantanal e do Rio Grande do Sul; ii) o padrão de isolamento pela distância não explica essa diferenciação; e iii) duas populações no Pantanal e uma população no RS apresentaram sinais genéticos de redução demográfica. Os resultados foram discutidos considerando que as populações de garça-branca-grande localizadas no Pantanal e no Rio Grande do Sul são unidades populacionais independentes e devem se tratar separadamente no planejamento e desenvolvimento de programas de manejo para a conservação da diversidade genética total da espécie.

Studies of mating systems and social organisation have been central to understanding of the evolution of social behaviour. The European badger Meles meles is a good species in which to study these processes, as its complex social system provides an opportunity to investigate how both natural and kin selection shape the evolution of mating systems and social structure. In this thesis, I use behavioural and genetic data to describe the mating system and social organisation of a high-density badger population and examine the occurrence of cooperative breeding. I genotyped 915 (85%) badgers trapped in Wytham Woods (1987–2005), 630 of which were cubs, and assigned both parents to 331 cubs with 95% confidence. This revealed a polygynandrous mating system, with up to five mothers and five fathers per social group. Mounting behaviour was also polygynandrous and I show the strongest evidence to date for multiple-paternity litters. I demonstrate, for the first time, that groups consisted of close and distant kin: approximately one third of group members were first-order kin, and overall group members had slightly lower relatedness levels than half-siblings. Within groups, adult and yearling females had higher pairwise relatedness than males, and neighbouring groups contained relatives. These findings result from the high level (42%) of extra-group paternities, 86% of which were assigned to neighbouring males. For the first time I show that females avoided inbreeding by mating with extra-group males; however, incestuous matings did occur. Promiscuous and repeated mountings were observed, which may reduce male–male aggression and infanticide, but may also promote sperm competition, genetic diversity, and / or genetic compatibility. Just under a third of adult males and females were assigned parentage each year and I quantify, for the first time, reproductive skew within badger groups. Correlations between relatedness, group productivity, and reproductive skew were not consistent with the predictions of incomplete-control models; rather, resource availability may play a role. Older and younger badgers displayed reduced annual breeding success, with male success increasing initially with experience. The Restraint, Constraint, and Selection Hypotheses did not explain the age-related breeding pattern in females. Variance in lifetime breeding success (LBS) was greater for males. Males that only bred within or only outside of their groups had half the LBS of males that did both. Females that were assigned maternity probably bred cooperatively and allonursed non-offspring, which has not been demonstrated previously. No benefit was established, however, in terms of litter size, probability of offspring breeding, or offspring lifetime breeding success, with more mothers in a group. In conclusion, badger social groups are fostered through kinship ties. Polygynandry and repeated mounting may have evolved originally to reduce male–male aggression and infanticide by males, through paternity masking. Although plural breeding occurs, group living appears to be costly. Motivation to disperse may be reduced through high-levels of extra-group paternities, which may also reduce inbreeding. Cooperative breeding among mothers may represent a low-cost behaviour with indirect benefits due to high levels of relatedness between female group-members. Badger sociality therefore represents an early stage in the evolution of social behaviour.