Female mating rates vary widely, even among closely related species, but the reasons for this variation are not fully understood. Across Drosophila species, female mating frequencies are positively associated with sperm length. This association may be due in part to sperm limitation, with longer-spermed species transferring fewer sperm, or to cryptic female choice. However, a previously overlooked factor is sperm metabolic rate, which may correlate with sperm length. If faster-metabolizing sperm accumulate agerelated cellular damage more quickly, then females should remate sooner to obtain fresh sperm. Alternatively, frequent female mating may select for increased sperm competitiveness via increased metabolism. Here, we measure sperm metabolism across 13 Drosophila species and compare these measures to published data on female mating rate and on sperm length. Using fluorescent lifetime imaging microscopy, we quantify NAD(P)H metabolism ex vivo, in intact organs. Phylogenetically controlled regression reveals that sperm metabolic rate is positively associated with sperm length and with female mating frequency. Path analysis shows sperm length driving sperm metabolism and sperm metabolism either driving or being driven by female mating rate. While the causal directionality of these relationships remains to be fully resolved, and the effect of sperm metabolism on sperm aging and/or sperm competitiveness remains to be established, our results demonstrate the importance of sperm metabolism in sexual selection.

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

Cis-regulatory changes in e.g. promoters or enhancers that affect the expression of a linked focal gene have long been thought to be important for adaptation. In this thesis, I investigate the selective importance and genomic correlates of cis-regulatory variation and divergence in the genus Capsella, using massively parallel sequencing data. This genus provides an opportunity to investigate cis-regulatory changes in response to polyploidization and mating system shifts, as it harbors three diploid species, the outcrosser Capsella grandiflora and the selfers Capsella orientalis and Capsella rubella, as well as the tetraploid Capsella bursa-pastoris. We first identify cis-regulatory changes associated with adaptive floral evolution in connection with the recent switch to self-fertilization in C. rubella and show that cis-regulatory changes between C. rubella and its outcrossing close relative C. grandiflora are associated with differences in transposable element content. Second, we show that variation in positive and purifying selection is important for the distribution of cis-regulatory variation across the genome of C. grandiflora. Interestingly, the presence of polymorphic transposable elements is strongly associated with cis-regulatory variation in C. grandiflora. Third, we show that the tetraploid C. bursa-pastoris is of hybrid origin and investigate the contribution of both parental species to gene expression. We show that gene expression in the tetraploid is partly explained by cis-regulatory divergence between the parental species. Nonetheless, within C. bursa-pastoris there is a great deal of variation in homeolog expression. In summary, this thesis explores the role of cis-regulatory changes for adaptive morphological changes in connection to a shift in mating system, the role of cis-regulatory divergence between progenitor species for an allopolyploid as well as the impact of positive and purifying selection on cis-regulatory variation within a species.

Thesis (MScAgric)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Botrytis cinerea Pers. Fr. [teleomorph Botryotinia fuckeliana (de Bary) Whetzel] causes serious losses of over 200 crops worldwide, including rooibos seedlings and pears. This pathogen is characterized by morphological, physiological and genetic diversity. The genetic diversity and population structure have not been investigated for B. cinerea populations in South Africa. Botrytis cinerea collected from rooibos seedlings and in pear orchards in the Western Cape of South Africa were investigated in the present study. The study was done with the aid of microsatellite markers, the amplification of mating type alleles MAT1-1 and MAT1-2 and determination of resistance towards various fungicides. Population dynamics was inferred and a similar picture emerged in both production systems. Botrytis cinerea annually causes severe losses of rooibos seedlings (Aspalathus linearis) in nurseries situated in the Clanwilliam region. Sampling was done in five nurseries and the cryptic species status of the isolates obtained was determined through restriction enzyme digestion of the Bc-hch gene. All but one (206 out of 207) of the isolates belonged to Group II or B. cinerea ‘sensu stricto’. Analysis of the B. cinerea Group II population, using seven microsatellite loci, was performed to assess the genetic population structure. Total gene diversity (H) was high, with a mean of 0.67. Two of the nurseries populations’ sample sizes were severely limited after clone correction, yet 100 genotypes were discerned among the 206 isolates genotyped. The percentage of maximal genotypic diversity (G) ranged between 16 and 68 for the five populations, with a total value of 17 for the 100 genotypes. One genotype, represented by 27 clones, was isolated from four nurseries. Relatively low but significant population differentiation was observed in total between nurseries (mean FST = 0.030, P = 0.001). The distribution of mating types MAT1-1 and MAT1-2 differed significantly from the ratio of 1:1 for the total population plus two of the nurseries’ populations. Three nursery populations had an equal mating type distribution. The index of association (IA) analyses suggests that the populations are asexually reproducing. Analysis of molecular variance (AMOVA) indicated that 97% of the total genetic variation is distributed within subpopulations. Fungicide resistance frequency against iprodione for 198 of the genotyped isolates displayed highly varying levels of resistance amongst the five nurseries. The mean total incidence of resistance towards iprodione was 43%, ranging from 0% to 81% for the five nurseries. Baseline sensitivity towards pyrimethanil yielded an average EC50 value of 0.096 mg/L. Botrytis cinerea isolates were collected from pear blossoms (Pyrus communis) in four orchards. Two orchards in the Ceres area and two in the Grabouw area were sampled from. A total of 181 isolates were collected from the four orchards. Incidence of blossom infection in the orchards ranged from 3% to 17%. Overall, there was a high incidence of isolates that had only the Boty transposable element (74%) compared to those harbouring both (Boty and Flipper), simultaneously (transposa, 24%). One isolate examined had the Flipper element only. Cryptic species status according to restriction enzyme digestion of the Bc-hch gene indicated that all the isolates belonged to Group II or B. cinerea ‘sensu stricto’. Analysis of the Group II population, through the use of seven microsatellite loci, was performed to assess the genetic population structure. Total gene diversity (H) was high, with a mean of 0.69 across all populations. Although two of the subpopulations displayed a high clonal proportion, overall 91 genotypes were discerned among the 181 isolates. The percentage of maximal genotypic diversity (G) ranged between 18 and 33 for the four populations, with a total value of 14 for the 91 genotypes. One genotype, represented by 27 clones, was isolated from all orchards. Moderate, but significant population differentiation was present in total among orchards (mean FST = 0.118, P = 0.001). The distribution of the mating types, MAT1-1 and MAT1-2, did not differ significantly from a 1:1 ratio for the total population as well as the subpopulations. Index of association (IA) analyses, on the other hand, suggests that the populations reproduce asexually. Analysis of molecular variance (AMOVA) indicated that 88% of the total genetic variation is distributed within subpopulations, 9% between subpopulations and only 3% between production areas. Fungicide resistance frequency against fenhexamid, iprodione and benomyl varied, with the highest levels of resistance present against benomyl and low levels of resistance seen towards iprodione and fenhexamid. In conclusion, this study has shown that there exist within the studied populations of B. cinerea, obtained from rooibos nurseries and pear orchards, an adaptive capacity to overcome current means of control. The use of population genetics to further our understanding of how plant pathogens interact and spread throughout a given environment is of cardinal importance in aiding the development of sustainable and integrated management strategies. Knowledge of the dispersal of B. cinerea in the two studied cropping systems has shed light on the inherent risk that it poses, and this together with knowledge of the levels of resistance that occurs should serve as an early warning to help divert possible loss of control in future. / AFRIKAANSE OPSOMMING: Botrytis cinerea Pers. Fr. [teleomorf Botryotinia fuckeliana (de Bary) Whetzel] veroorsaak ernstige verliese van meer as 200 gewasse wêreldwyd, insluitende rooibossaailinge en pere. Hierdie patogeen word deur morfologiese, fisiologiese, asook genetiese diversiteit gekenmerk. Die genetiese diversiteit en populasie-struktuur van B. cinerea populasies wat in Suid-Afrika voorkom, is nog nie ondersoek nie. Botrytis cinerea verkryg vanaf rooibossaailinge en in peerboorde in die Wes-Kaap van Suid-Afrika is ondersoek. Hierdie studie is met behulp van mikrosatellietmerkers, amplifikasie van die twee paringstipe gene (MAT1-1 en MAT1-2), asook die bepaling van weerstandsvlakke teenoor verskeie swamdoders, uitgevoer. Populasie-dinamika is afgelei en ‘n soortgelyke tendens is in beide produksie-sisteme waargeneem. Botrytis cinerea veroorsaak jaarliks ernstige verliese van rooibossaailinge (Aspalathus linearis) in kwekerye in die Clanwilliam-area. Monsters is in vyf kwekerye versamel en die kriptiese spesiestatus van die verkrygde isolate is deur restriksie-ensiemvertering van die Bc-hch geen bepaal. Almal behalwe een (206 uit 207) isolaat het aan Groep II of B. cinerea ‘sensu stricto’ behoort. Analise van die B. cinerea Groep II populasie, deur middel van sewe mikrosatellietmerkers, is uitgevoer om die genetiese populasiestruktuur te bepaal. Totale geendiversiteit (H) was hoog, met ‘n gemiddelde van 0.67. Alhoewel twee van die kwekerye se monstergrootte erg ingeperk is ná kloonverwydering, is daar nogtans 100 genotipes onder die 206 isolate wat geïsoleer is, waargeneem. Die persentasie van maksimale genotipiese diversiteit (G) het tussen 16 en 68, vir die vyf populasies, gewissel, met ‘n totaal van 17 vir die 100 genotipes. Een genotipe, verteenwoordig deur 27 klone, is uit vier kwekerye geïsoleer. Relatief lae dog noemenswaardige populasie-differensiasie is in totaal tussen kwekerye waargeneem (gem. FST = 0.030, P = 0.001). Die verspreiding van die twee paringstipes (MAT1-1 en MAT1-2) het beduidend verskil van ‘n 1:1 verhouding vir die totale populasie, asook twee van die kwekerye se populasies. Die drie oorblywende kwekerye se populasies het egter ‘n gelyke verdeling van die twee paringstipes getoon. Die indeks van assosiasie (IA) analises toon dat die populasies ongeslagtelik voortplant. Analise van molekulêre variasie (AMOVA) het aangedui dat 97% van die totale genetiese variasie binne die subpopulasies versprei is. Hoogs variërende vlakke van weerstand tussen die vyf kwekerye teenoor die swamdoder iprodioon, is vir die 198 isolate wat getoets is, gevind. Die totale gemiddelde frekwensie van weerstand teenoor iprodioon was 43%, wat tussen 0% en 81% vir die vyf kwekerye gevarieer het. Fondasie-vlak-sensitiwiteit vir pyrimethanil het ‘n gemiddelde EC50 waarde van 0.096 mg/L opgelewer. Botrytis cinerea isolate is ook vanuit peerbloeisels (Pyrus communis L.) vanuit vier boorde versamel, twee uit elk van die Ceres- en Grabouw-areas. In totaal is 181 isolate vanuit die vier boorde versamel. Die frekwensie van bloeiselinfeksie het tussen 3% en 17% gewissel. Oor die algemeen was daar ‘n hoë frekwensie van isolate wat slegs die Boty transponeerbare element teenwoordig gehad het (74%) in vergelyking met dié wat tegelykertyd beide (Boty en Flipper) teenwoordig gehad het. Een isolaat het slegs die Flipper element gehad. Bepaling van die kriptiese spesiestatus met behulp van restriksie-ensiemvertering van die Bc-hch geen het aangedui dat alle versamelde isolate tot Groep II of B. cinerea ‘sensu stricto’ behoort het. Analise van die Groep II populasie, deur middel van sewe mikrosatellietmerkers, is uitgevoer om genetiese populasie-struktuur te bepaal. Totale geendiversiteit (H) was hoog, met ‘n gemiddelde van 0.69 oor alle populasies. Alhoewel twee subpopulasies ‘n hoë klonale fraksie getoon het, is 91 genotipes tussen die 181 isolate wat verkry is, onderskei. Die persentasie van maksimale genotipiese diversiteit (G) het tussen 18 en 33 vir die vier populasies gewissel, met ‘n totale waarde van 14 vir die 91 genotipes. Een genotipe, verteenwoordig deur 27 klone, was in al vier boorde teenwoordig. Gematigde dog beduidende populasie differensiasie was in totaal tussen boorde teenwoordig (gem. FST = 0.118, P = 0.001). Die verspreiding van die paringstipes (MAT1-1 en MAT1-2) het nie betekenisvol van ‘n 1:1 verhouding vir die totale populasie, insluitende die subpopulasies, verskil nie. Indeks van assosiasie (IA) analises het egter aangedui dat die populasies ongeslagtelik voortplant. Analise van molekulêre variasie (AMOVA) het aangedui dat 88% van die totale genetiese variasie in subpopulasies te vinde was, 9% tussen subpopulasies en slegs 3% tussen produksie-areas. Frekwensie van swamdoder weerstandbiedendheid vir fenhexamid, iprodioon en benomyl het gewissel, met die hoogste vlakke teenoor benomyl waargeneem, maar baie lae vlakke teenoor fenhexamid en iprodioon. Samevattend het hierdie studie getoon dat die populasies van B. cinerea wat in hierdie twee produksie-sisteme, op rooibossaailinge en in peer boorde, ondersoek is, ‘n aanpasbaarheid toon om huidige metodes van beheer te oorkom. Die gebruik van populasiegenetika as ‘n hulpmiddel om ons kennis van patogeen-interaksies en -verspreiding te verbreed, is van kardinale belang in die ontwikkeling van geïntegreerde en volhoubare beheermaatreëls. Kennis van die verspreiding van B. cinerea in die bestudeerde gewasproduksiestelsels, werp lig op die inherente risiko wat dié patogeen inhou. Dít, tesame met kennis van die weerstandsvlakke wat voorkom, kan as ‘n vroegtydige waarskuwing dien ten einde moontlike verlies van beheer in die toekoms te help teenwerk.

Inbreeding occurs when relatives mate and have offspring. Inbreeding depression is hypothesized to have influenced the evolution of mating systems and behavioural mechanisms of inbreeding avoidance in the animal kingdom. Inbreeding in the wild is difficult to measure, as in order to build a pedigree allowing us to identify matings between relatives, the identity of as many as possible members of a population needs to be known. For a long time, the main source of knowledge about inbreeding depression was based on laboratory and agricultural studies, which did not reflect the array of environmental pressures wild populations have to cope with. In consequence, the deleterious consequences of inbreeding have often been underestimated. This is problematic because accurate estimates of the effect size of inbreeding depression are needed to study the strength of selection on inbreeding avoidance mechanisms, and are also of importance to conservation genetics. The aim of this thesis was to use pedigree data to infer the occurrence and effects of inbreeding using over forty years of breeding events of the great tit Parus major from Wytham Woods, Oxfordshire. The effects of inbreeding on fitness were investigated across a life-history continuum, and across environments. I found that close inbreeding (f=0.25) resulted in pronounced inbreeding depression, which acted independently on hatching success, fledging success, and recruitment success, and reduced the number of fledged grand-offspring by 55%. My results therefore suggest that estimates of fitness costs of inbreeding must focus on the entire life cycle. I also show that the variation in the strength of inbreeding depression varies across environments, particularly so the more the environmental variable considered is linked to fitness. These results emphasise the need of using relevant environmental contrasts when investigating inbreeding by environment interactions. I further asked whether individuals involved in matings with relatives differed relative to individuals mating with unrelated partners. I did not find any evidence for clear predictors of inbreeding, and I show that inbreeding depression in our population is entirely independent of any tendency for low quality parental genotypes, or phenotypes, to inbreed. Neither did I find any evidence for active inbreeding avoidance: great tits did not mate less often with kin than expected based on several scenarios of random mating, nor did I find increased rates of extra-pair paternity among birds breeding with relatives. In fact, I observed quite the contrary, as birds mating with kin exhibited a higher than average rate of close inbreeding relative to all scenarios of random mating investigated, showed lower rates of extra-pair paternity and divorce than birds mated to unrelated partners. I hypothesise that cases of occasional inbreeding in this population may result from mis-imprinting or a related process whereby some birds develop particularly strong bonds that are at odds with all predictions of avoiding inbreeding. Finally, I asked to what extent natal dispersal, a behaviour that is often hypothesized to play an important role in avoiding inbreeding, indeed reduces the likelihood of inbreeding. I found that male and female individuals breeding with a relative dispersed over several-fold shorter distances than those outbreeding. This led to a 3.4 fold increase (2.3-5, 95% CI) in the likelihood of close inbreeding relative to the population average when individuals dispersed less than 200m. This thesis demonstrates that inbreeding has deleterious effects on a wild population of birds, occurring throughout an individual’s life, and is of varying strength across environments. My findings strongly support the theory that natal dispersal should be considered as a mechanism of prime importance for inbreeding avoidance.

Résumé indisponible. / In this thesis we have concerned ourselves with university timetabling problems both course timetabling and examination timetabling problems. Most of the timetabling problems are computationally NP-complete problems, which means that the amount of computation required to find solutions increases exponentially with problem size. These are idiosyncratic nature problems, for example different universities have their own set of constraints, their own definition of good timetable, feasible timetable and their own choice about the use of constraint type (as a soft or hard constraint). Unfortunately, it is often the case that a problem solving approach which is successfully applied for one specific problem may not become suitable for others. This is a motivation, we propose a generalized problem which covers many constraints used in different universities or never used in literature. Many university timetabling problems are sub problems of this generalized problem. Our proposed algorithms can solve these sub problems easily, moreover constraints can be used according to the desire of user easily because these constraints can be used as reference to penalty attached with them as well. It means that give more penalty value to hard constraints than soft constraint. Thus more penalty value constraints are dealt as a hard constraint by algorithm. Our algorithms can also solve a problem in two phases with little modification, where in first phase hard constraints are solved. In this work we have preferred and used two phase technique to solve timetabling problems because by using this approach algorithms have broader search space in first phase to satisfy hard constraints while not considering soft constraints at all. Two types of algorithms are used in literature to solve university timetabling problem, exact algorithms and approximation algorithms. Exact algorithms are able to find optimal solution, however in university timetabling problems exact algorithms constitute brute-force style procedures. And because these problems have the exponential growth rates of the search spaces, thus these kinds of algorithms can be applied for small size problems. On the other side, approximation algorithms may construct optimal solution or not but they can produce good practically useable solutions. Thus due to these factors we have proposed approximation algorithms to solve university timetabling problem. We have proposed metaheuristic based techniques to solve timetabling problem, thus we have mostly discussed metaheuristic based algorithms such as evolutionary algorithms, simulated annealing, tabu search, ant colony optimization and honey bee algorithms. These algorithms have been used to solve many other combinatorial optimization problems other than timetabling problem by modifying a general purpose algorithmic framework. We also have presented a bibliography of linear integer programming techniques used to solve timetabling problem because we have formulated linear integer programming formulations for our course and examination timetabling problems. We have proposed two stage algorithms where hard constraints are satisfied in first phase and soft constraints in second phase. The main purpose to use this two stage technique is that in first phase hard constraints satisfaction can use more relax search space because in first phase it does not consider soft constraints. In second phase it tries to satisfy soft constraints when maintaining hard constraints satisfaction which are already done in first phase. (...)

La gorgone rouge, Paramuricea clavata (Cnidaire, Octocoralliaire), est une espèce sessile, longévive à faible croissance dont les populations présentent une lente dynamique. Cette espèce est caractérisée par une phase larvaire pélagique qui représente l’unique phase de dispersion potentielle au cours du cycle de vie de cette espèce. P. clavata est une espèce clé des assemblages à coralligène de Méditerranée, qui subit les effets combinés des activités de plongée sous-marine et du changement climatique. Dans ce contexte, il était donc fondamental d’approfondir les connaissances sur les traits d’histoire de vie, la biologie et l’écologie de cette espèce. L’objectif de ce travail était d’étudier, à l’aide d’une approche génétique, les facteurs biologiques et écologiques clés qui devraient être importants pour la réponse de l’espèce aux changements environnementaux. Parmi ces facteurs, la dispersion larvaire joue un rôle fondamental dans la dynamique et la connectivité des populations marines. Dans le contexte actuel des fortes pressions anthropiques, la compréhension des degrés de connectivité entre les populations est primordiale pour évaluer le devenir des populations, face au changement climatique, et pour mettre en place des plans de conservation et des réseaux d’aires marines protégées. / The red gorgonian, Paramuricea clavata (Cnidaria, Octocorallia), is a sessile, long-lived and slow growing species which displays slow population dynamics. This species is characterized by a pelagic larval phase that represents the sole potential phase of dispersal during the life cycle of this species. P. clavata is a key species of coralligenous assemblages of the Mediterranean Sea which undergoes the combined effects of diving activities and climate change. In this context, extending the knowledge about life history traits, biology and ecology of the red gorgonian was of fundamental importance. Using a genetic approach, the goal of this work was to study some key biological and ecological factors which should be important for the response of this species to environmental changes. Among these factors, larval dispersal plays a major role in driving marine population dynamics and connectivity. In the current context of strong anthropic pressures, understanding the level of population connectivity is primordial to evaluate population outcome, facing climate change, and to develop conservation plans as well as to design marine reservenetworks.

Bottlenose dolphins exhibit fission-fusion social systems in which group size and composition change fluidly throughout the day. Societies are typically sexually segregated, and the quality and patterning of individual relationships in this social species shape the social structure of a population. Female dolphins usually have a large network of associates with whom they form recurring moderate bonds, while male associations are highly variable due to their mating strategies. Males employ one of two strategies; males may be solitary, and encounter and herd females individually, while others may form strong bonds with one to two other males and cooperatively herd individual females in the shape of a first-order alliance. Second-order alliances are more uncommon and have only been observed in Shark Bay, Australia, and more recently within the St. Johns River (SJR), Jacksonville, Florida. Given the inter-population variation in male mating strategies, greater documentation of social structure in neighboring populations along the Atlantic coast is needed. Therefore, chapter one documents the social structure of the Indian River Lagoon (IRL) estuarine system where dolphins have experienced recurrent cetacean morbillivirus (CeMV) epizootics. Although environmental disturbances can affect both social and mating systems, IRL dolphin sociality does not seem to be affected by the 2008 CeMV mass mortality event. Additionally, males only form first-order alliances within this population. Because multi-level alliances are unique to the SJR in this region, chapter two analyzes the stability and function of SJR alliances. Both first- and second-order alliances exhibited variation in stability, while alliance association appears dependent on female presence. Thus, SJR alliances likely function within a reproductive context. Together, this work provides insight into the social and mating systems of bottlenose dolphins, as well as the function of multi-level alliances at a relatively new study site.

In nest-building species, offspring survival and reproductive success of parental individuals are strongly influenced by nest location and quality. Thus, quantifying the influence of abiotic conditions on nest integrity is important to predict the effects that weather variability may have on offspring survival and parental reproductive success. Here we investigated how rainfall affects nest integrity and how nest integrity influences male attractiveness and nest tenure. Our study species was the harvestman Quindina limbata, in which males build cup-like mud nests on fallen logs and protect the eggs against predators and fungi infestation. Our dataset is based on 12 months of regular inspections of over 150 nests in a tropical rainforest from Costa Rica. We found that 43% of the nests were destroyed by rainfall. The drag force promoted by rainfall running on the log surface negatively affected nest integrity by decreasing the wall perimeter and the floor area. The intensity of fungi cover was not explained by nest position or by precipitation. No matter the body size of the owner males, nests with high integrity received more eggs than nests with low integrity. Curiously, nests with high values of fungi cover received more eggs. Finally, nest integrity and fungi cover did not affect nest tenure, but the probability of males abandoning their nests increased with time they did not receive eggs. Considering that intense rainfall occurs all year long in tropical forests, the best males can do to decrease the chances of nest destruction is to select protected places to build their nests. Protected sites may keep nest structure better preserved, improve offspring survival, attract more females, and ultimately increase male reproductive success / Em espécies que constroem ninhos, a sobrevivência da prole e o sucesso reprodutivo dos indivíduos parentais são fortemente influenciados pela localização e qualidade dos ninhos. Portanto, quantificar a influência das condições abióticas sobre a integridade dos ninhos é importante para prever os efeitos que a variabilidade climática pode ter na sobrevivência da prole e no sucesso reprodutivo dos pais. Neste estudo, investigamos como a chuva influencia a integridade dos ninhos e como a integridade dos ninhos influencia a atratividade masculina e o tempo de posse do ninho. Nossa espécie de estudo foi o opilião Quindina limbata, em que os machos constroem ninhos de barro em troncos caídos e protegem os ovos contra predadores e infestação por fungos. Nosso conjunto de dados é baseado em 12 meses de inspeções regulares de mais de 150 ninhos em uma floresta tropical na Costa Rica. Descobrimos que 43% dos ninhos foram destruídos pela chuva. A força de arrasto promovida pela chuva na superfície dos troncos caídos influenciou negativamente a integridade dos ninhos, diminuindo o perímetro da parede e a área do piso. A intensidade de cobertura de fungos não foi explicada pela posição do ninho ou pela precipitação. O tamanho corporal dos machos não influenciou o ganho de ovos, mas ninhos com alta integridade receberam mais ovos do que ninhos com baixa integridade. Curiosamente, ninhos com altos valores de cobertura de fungos receberam mais ovos. Por fim, a integridade dos ninhos e a cobertura de fungos não influenciaram o tempo de posse do ninho, mas a probabilidade de os machos abandonarem seus ninhos aumentou com o tempo em que não receberam ovos em seus ninhos. Considerando que temporais ocorrem durante todo o ano em florestas tropicais, os melhores machos devem selecionar locais protegidos para construção dos seus ninhos a fim de diminuir as chances de destruição promovida pela chuva. Locais protegidos podem manter a estrutura do ninho melhor preservada, melhorar a sobrevivência da prole, atrair mais fêmeas e, finalmente, aumentar o sucesso reprodutivo dos machos

The availability of reproductive sites is a major factor shaping the behavior of males and females in species with resource-based mating systems. Using a meta-analytic approach, we tested five predictions directly or indirectly derived from the mating system theory. We expected that reproductive site limitation would lead to: (1) intense male-male competition for resource possession; (2) high variance in male reproductive success, generating high values of opportunity for sexual selection; (3) high intensity of selection on male traits related to resource possession; (4) high sperm competition risk; and (5) low quality of paternal care. We compiled information from observational and experimental studies that compared the reproductive behavior of individuals of the same species under low and high reproductive site limitation. We found that, when reproductive sites are limited, there is a slight increase in male-male competition, with higher rates of nest takeover and agonistic interactions, and a slight increase in the selection gradient on male traits, with successful males tending to be larger than unsuccessful males. Reproductive site limitation has no consistent effect on the opportunity for sexual selection and on the sperm competition risk. However, territorial males invest more in gonads and lose less paternity when reproductive sites are limited. There is also no clear effect of reproductive site limitation on the quality of paternal care, but few studies have addressed this subject. Taken together, our findings indicate that predictions on how reproductive site limitation affects several aspects of resource-based mating systems have weak empirical support. These predictions do not consider the plasticity in the mating tactics of males and females, which make them too simplistic. Moreover, since the original proposition of the mating system theory, our understanding of sperm competition increased a lot. We now know that accurate predictions on the intensity and direction of sexual selection should take into account both pre- and post-copulatory processes. Finally, the interplay between sexual selection and parental care is complex, and the original framework of mating system theory does not provide sufficient elements to derive clear and taxonomically broad predictions / A disponibilidade de sítios reprodutivos influencia tanto o comportamento de machos quanto de fêmeas em espécies cujo sistema de acasalamento depende da defesa de recursos. Usando uma abordagem meta-analítica, testamos cinco previsões direta ou indiretamente relacionadas à teoria de sistemas de acasalamento. Esperávamos que a limitação de sítios reprodutivos promoveria: (1) aumento na competição masculina pela posse de recursos; (2) aumento na variância do sucesso reprodutivo dos machos, gerando valores alto de oportunidade para a seleção sexual; (3) aumento da intensidade da seleção sobre características masculinas relacionadas à posse de recursos; (4) aumento no risco de competição espermática e (5) diminuição da qualidade do cuidado paternal. Compilamos informações de estudos observacionais e experimentais que compararam o comportamento reprodutivo de indivíduos da mesma espécie em situação de alta e baixa disponibilidade de sítios reprodutivos. Encontramos que, quando os sítios reprodutivos são escassos, há um ligeiro aumento na competição masculina, com maiores taxas de roubo de ninhos e interações agonísticas, e um ligeiro aumento no gradiente de seleção sobre características masculinas, com machos bem sucedidos tendendo a ser maiores do que machos mal sucedidos em monopolizar recursos. A disponibilidade de sítios reprodutivos não teve nenhum efeito consistente sobre a oportunidade para a seleção sexual e o risco de competição espermática. Entretanto, machos territoriais investiram mais em gônadas e perderam menos paternidade quando os sítios reprodutivos eram escassos. Não encontramos nenhum efeito da disponibilidade de sítios reprodutivos sobre a qualidade do cuidado paternal. Em conjunto, nossos resultados indicam que as previsões sobre como a disponibilidade de sítios reprodutivos influencia diversos aspectos de sistemas de acasalamento baseados na defesa de recursos têm fraco respaldo empírico. Tais previsões não consideram a plasticidade nas táticas de acasalamento de machos e fêmeas, tornando-as demasiadamente simplistas. Adicionalmente, desde a formulação original da teoria de sistemas de acasalamento, nossa compreensão sobre competição espermática aumentou. Sabemos atualmente que previsões acuradas sobre a intensidade e direção da seleção sexual devem levar em consideração processos pré- e pós-copulatórios. Finalmente, a interconexão entre seleção sexual e cuidado parental é complexa e a teoria original de sistemas de acasalamento não provê elementos suficientes para a construção de previsões claras e de amplo escopo taxonômico