Yes / Lichenicolous (lichen-dwelling) fungi have been extensively researched taxonomically over many years, and phylogenetically in recent years, but the biology of the relationship between the invading fungus and the lichen host has received limited attention, as has the effects on the chemistry of the host, being difficult to examine in situ. Raman spectroscopy is an established method for the characterization of chemicals in situ, and this technique is applied to a lichenicolous fungus here for the first time. Xanthoriicola physciae occurs in the apothecia of Xanthoria parietina, producing conidia at the hymenium surface. Raman spectroscopy of apothecial sections revealed that parietin and carotenoids were destroyed in infected apothecia. Those compounds protect healthy tissues of the lichen from extreme insolation and their removal may contribute to the deterioration of the apothecia. Scytonemin was also detected, but was most probably derived from associated cyanobacteria. This work shows that Raman spectroscopy has potential for investigating changes in the chemistry of a lichen by an invading lichenicolous fungus. / This work was completed while D.L.H. was in receipt of an award from the Ministerio de Economica y Competitividad of Spain (Proyectos CGL 2014-55542-P).

Fiskar kan drabbas av många olika parasiter tillhörande ett brett spektrum av organismgrupper. Parasiter kan påverka värdens fysiologi, morfologi och beteende, vilket kan ha negativa effekter på värden.  Den starkt hotade flodpärlmusslan (Margaritifera margaritifera) parasiterar under sitt tidiga liv som glochidielarver på fiskgälar, i Sverige främst på öringen (Salmo trutta). I tidigare studier har man sett såväl negativa som inga effekter av parasiteringen på värdfisken. Syftet med min studie var att undersöka effekten av musslans parasitering på öringens rörelse, habitatval och tillväxt i Älgån i Arvika kommun, Värmland. Resultaten visade att höginfekterad öring förflyttade sig längre sträckor och hade lägre tillväxt än låginfekterad öring. Det var ingen skillnad mellan hög- och låginfekterade öringars habitatval med avseende på djup, vattenhastighet eller substrat. Sammanfattningsvis kan höginfekterade öringar ha högre mortalitetsrisk än låginfekterade, lägre tillväxt och sämre konkurrensförmåga, vilket kan ha negativa konsekvenser för musslans rekryteringsframgång. / Fish are affected by various parasites, belonging to many different taxonomic groups. Parasites can affect the host’s physiology, morphology, and behaviour, which may have negative effects for the host. The critically endangered freshwater pearl mussel (Margaritifera margaritifera) lives parasitically as glochidia larvae on the gills of fish, and in Sweden this occurs mainly in the gills of brown trout (Salmo trutta). During their parasitic stage, which lasts for almost one year, the mussel grows up to four or five times their initial size.  Previous studies have reported both negative and no effects of the parasite on the host fish. The aim of my study was to analyse the effect of the freshwater pearl mussel parasitation on the brown trout’s movement, habitat choice, and growth in the stream Älgån in Arvika municipalty, Värmland. The results show that highly infected brown trout moved greater distances and had lower growth than less infected trout. There was no difference in habitat choice in terms of depth, velocity, or substrate between high or low infected trout. In summary, highly infected trout may have high energy costs, low growth, and poor competitive ability, which can have negative consequences for the mussel’s recruitment.

Doctor of Philosophy / Department of Biology / Ari M. Jumpponen / Dark septate endophytes (DSE) are darkly pigmented microfungal ascomycetes commonly observed in the healthy plant roots. Studying the functional roles of DSE is challenging as fundamental information about their identity, nutritional requirements, host range or host preference are lacking. Objective 1: root colonizing fungi were isolated from Konza plants roots and DSE fungi were identified by testing Koch’s postulates using leek plants. Periconia macrospinosa and Microdochium sp., were identified as DSE as they produced microsclerotia and chlamydospores in the root cortex. Select DSE were tested for their enzymatic capabilities and ability to utilize nitrogen sources: fungi tested positive for amylase, cellulase, polyphenol oxidases and gelatinase. Periconia isolates utilized organic and inorganic nitrogen suggesting facultative biotrophic and saprotrophic habits. Objective 2: a Microdochium isolate and three Periconia isolates were screened on 16 plant species (six native grasses and forbs, four crops) in a resynthesis system to test host range. DSE colonized all plant species, albeit to varying degrees. Host biomass and nutritional levels to DSE colonization varied within and among host species confirming the broad host range. Based on % responsiveness to DSE colonization, a metric similar to ‘mycorrhizal dependency’, grasses responded positively, while forbs and crops responded negatively. To test this observed ‘host preference’ under natural conditions, Konza roots from seven grass and nine forb species were surveyed for DSE colonization. Grasses hosted 50% greater DSE than forbs, supporting the broad host range and host preference of DSE fungi. Objective 3: three conspecific Arabidopsis ecotypes, Col-0, Cvi-0 and Kin-1 were inoculated with 25 P. macrospinosa isolates in resynthesis system. The three ecotypes responded differently to inoculation: Col-0 and Cvi-0 responded negatively, while Kin-1 response was neutral. Despite the negative or neutral response, each ecotype responded positively to one or two isolates. The outcomes were along the mutualism-parasitism continuum precluding an unambiguous assignment to any particular life-style. This study shows that the outcomes along this continuum are dictated by host and fungal genotypes. However, the more important question about their function remains. Additional studies with Arabidopsis microarrays are likely to provide unique insights into the potential roles of DSE.

Many zoonotic pathogens of concern to human and veterinary health are maintained in the environment within small mammal reservoirs and vectored to new hosts by ectoparasitic arthropods. While the ecological relationships among small mammals, ectoparasites, and disease-causing symbiotic microorganisms are important to these dynamics, little is known about them across much of North America. The sylvatic cycle of Borrelia burgdorferi, the etiologic agent of Lyme disease, is of particular interest because Lyme disease is the most common vector-borne disease of humans in the United States. However, cases of Lyme disease are primarily confined to the northeastern and Midwestern United States, with only sporadic cases extending into the southeast. As a result, much of what is known of the ecology of Lyme disease comes from studies conducted in those regions. The goal of this study was to examine the ecological dynamics of the B. burgdorferi/vector/reservoir system in south-central Kentucky and gain insight into the relative paucity of Lyme disease in Kentucky. Small mammals were captured using live traps in three 200x50 m trapping grids within Western Kentucky University’s Green River Preserve from November 2014-October 2015. Captured small mammals were identified to species and standard measurements were recorded. Ectoparasites were removed and retained for identification. Collected blood and tissue were examined for B. burgdorferi DNA by polymerase chain reaction with primers specific to the OspA gene. The Bray-Curtis dissimilarity index, Schnabel population estimates, and the Shannon-Wiener diversity index were used to assess the structure of the small mammal communities. Parasite infestation was low but was affected by age and sex of the host, site, and season in different parasite taxa. Infestation by Ixodes scapularis, the primary vector for B. burgdorferi, was uncommon and prevalence of B. burgdorferi in blood was similar to the lowest prevalence previously observed in the Lyme disease endemic regions. We found that life history characteristics of hosts and ectoparasites drive their associations. We also suggest that the lack of an efficient vector for B. burgdorferi is the likely explanation for the few reported cases of Lyme disease in Kentucky.

Two separate phylogenetic studies were performed for two different taxonomic levels within Hymenoptera. The first study examined the utility of expressed sequence tags for resolving relationships among hymenopteran superfamilies. Transcripts were assembled from 14,000 sequenced clones for 6 disparate Hymenopteran taxa, averaging over 660 unique contigs per species. Orthology and gene determination were performed using modifications to a previously developed computerized pipeline and compared against annotated insect genomes. Sequences from additional taxa were added from public databases with a final dataset of 24 genes for 16 taxa. The concatenated dataset recovered a robust and well-supported topology; however, there was extreme incongruity among individual gene trees. Analyses of sequences indicated strong compositional and transition biases, particularly in the third codon positions. The use of filtered supernetworks aided visualization of the existing congruent phylogenetic signal that existed across the individual gene trees. Additionally, treeness triangle plots indicated a strong residual signal in several gene trees and across codon positions in the concatenated dataset. However, most analyses of the concatenated dataset recovered expected relationships, known from other independent analyses. Thus, ESTs provide a powerful source of information for phylogenetic analysis, but results are sensitive to low taxonomic sampling and missing data. The second study examined subfamilial relationships within the parasitoid family Braconidae, using over 4kb of sequence data for 139 taxa. Bayesian inference of the concatenated dataset recovered a robust phylogeny, particularly for early divergences within the family. There was strong evidence supporting two independent lineages within the family: one leading to the noncyclostomes and one leading to the cyclostomes. Ancestral state reconstructions were performed to test the theory of ectoparasitism as the ancestral condition for all taxa within the family. Results indicated an endoparasitic ancestor for the family and for the non-cyclostome lineage, with an early transition to ectoparasitism for the cyclostome lineage. However, reconstructions of some nodes were sensitive to outgroup coding and will also be impacted with increased biological knowledge.

Gastrointestinal parasitism in grazing lambs adversely affects animal performance and welfare, causing significant production losses for the sheep industry. Control of gastrointestinal parasitism using chemotherapeutic treatment is under threat due to the emergence of anthelmintic resistance, thus stimulating research into alternative control strategies. Whilst investigating control strategies experimentally can be costly and time consuming, using a mathematical modelling approach can reduce such constraints. A previously developed model which describes the impact of host nutrition, genotype and gastrointestinal parasitism in a growing lamb, provided an appropriate starting point to explore control strategies and their impact on host-parasite interactions. Two contrasting mechanisms have previously been proposed to account for the occurrence of anorexia during parasitism. These were reductions in either intrinsic growth rate or relative food intake. Thus, the existing individual lamb model was modified to evaluate these mechanisms by exploring the relationship between anorexia and food composition (Chapter 2). For foods that did not constrain food intake, published data was found to be consistent with the predictions that arose from anorexia being modelled as a reduction in relative food intake. Reported genetic parameter estimates for resistance and performance traits appear to vary under differing production environments. In order to explore the impact of epidemiological effects and anthelmintic input on genetic parameter estimates the model was extended to simulate a population of lambs in a grazing scenario (Chapter 3). Whilst estimates of heritabilities and genetic correlations for drenched lambs remained constant, for lambs given no anthelmintic treatment, the heritability of empty body weight (EBW) reduced and the genetic correlation between faecal egg count (FEC) and EBW became increasingly negative with increasing exposure to infective larvae. Thus differences in anthelmintic input and pasture larval contamination (PC) may provide plausible causes for the variation in genetic parameter estimates previously reported. To investigate the interactions between host resistance and epidemiology (Chapter 4) a population of 10,000 lambs were simulated and FEC predictions used to assign the 1,000 lambs with the highest and lowest predicted FEC to ‘susceptible’ (S) and ‘resistant’ (R) groups, respectively. R and S groups were then simulated to graze separate pastures over 3 grazing seasons. The average FEC and PC predictions of these groups diverged during the first 2 grazing seasons and stabilised during the third, such that the difference in FEC predictions between R and S groups were double those predicted when grazed with the population. This was found to be consistent with experimental data. Further, anthelmintic treatment and grazing strategies were predicted to have no impact on the EBW of resistant lambs, suggesting that control strategies should be targeted towards susceptible animals. Targeted selective anthelmintic treatment (TST) has been proposed to reduce risks of anthelmintic resistance with minimal impacts on performance. To describe the short- and long-term impacts of TST and drenching frequency on sheep production and the emergence of anthelmintic resistance, the model was extended to include a description of anthelmintic resistance genotypes within the nematode population (Chapter 5). Reducing the proportion of treated animals was predicted to increase the duration of anthelmintic efficacy, whilst reducing the drenching frequency increased the long-term benefits of anthelmintic on sheep production. Various determinant criteria for use in TST regimes were compared (Chapter 5) including performance traits such as live weight and growth rate, and parasitological traits such as FEC. Using FEC as the TST criterion was predicted to allow the greatest reduction in the number of anthelmintic treatments administered whilst maintaining the highest average EBW, whilst live weight and growth rate were predicted to give little to no improvement in comparison to selecting animals at random for TST. Using estimated breeding values (EBVs) for FEC as the determinant criterion for TST regimes was compared to using measured FEC (Chapter 6). The EBV for true FEC across the entire growth period, akin to perfect genomic selection, was predicted to be a better criterion than measured time-specific FEC (including a sampling error) for a TST regime. EBVs calculated using measured time-specific FEC showed little benefit compared to measured FEC. The information gained from these simulation studies increases our understanding of control strategies and their impact on host-parasite interactions under various scenarios that may not have been possible using experimental methods. It is important to remember that the aim of alternative or complimentary control strategies is to maintain the sustainability of sheep production systems, and as such the production gain of any control strategy needs to be weighed against the financial, labour and time costs involved in implementation.

Mating behavior has a profound impact on reproductive success and the resulting genetic structure of offspring. Extra-pair copulation is a widely observed behavior within avian species. This study explored the genetic effects of mating behaviors of Prothonotary warblers, Protonotaria citrea (Parulidae), using co-dominant microsatellite markers. Prothonotary warblers are migratory songbirds that build nests in cavities, commonly found in wetland habitats. A set of artificial nest boxes were initiated by Dr Robert Reilly in 2002 in Dutch Gap, Chesterfield County Virginia, USA, a tidal tributary off the James River. From this population, 28 nest boxes were surveyed yielding 47 adults and 110 offspring. All individuals were genotyped and the multilocus genotypes were used to identify parentage. Using paternity exclusion, 27.2% of offspring were identified as resulting from extra-pair mating. Surprisingly, an additional 11.8% of offspring were classified as genetically unrelated to the resident female, being presumably the result of an egg dumping from a female not caught at the nest box. The vast majority of nest boxes, 82.1% in this study, had at least one offspring that was a result of a mating behavior outside of the social pair. There was also positive spatial autocorrelation in extra-pair paternity suggesting that these matings are not randomly distributed across the sampling landscape. These data show that Protonotaria citrea engage in both extra-pair copulations and nest parasitism. Whether this is normal mating behavior for the species, or something that is unique to this population is unknown.

L’insertion du contrat dans la vie sociale a mis en lumière des conflits d’intérêts entre d’une part les parties contractantes, qui souhaitent que leurs prévisions contractuelles se réalisent et d’autre part, les tiers, qui ne veulent pas voir leur liberté limitée par un contrat auquel ils n’ont pas consenti. La théorie de l’opposabilité, assurant une fonction préférentielle, tranche le conflit d’intérêts antagonistes en réservant aux parties contractantes une exclusivité, la connaissance étant alors le critère d’attribution de cette situation préférentielle. Dès lors tout tiers qui avec connaissance incite ou aide un débiteur à violer son obligation contractuelle engage sa responsabilité à l’égard du créancier de cette obligation. Dans un contexte concurrentiel, l’opposabilité du contrat (ou du droit subjectif) va aboutir à créer une zone d’exclusivité en faveur des parties (ou détenteurs de droits) et étouffer la liberté concurrentielle des tiers. Le droit va alors délimiter une zone d’activité pour chacun. Nos travaux de recherches visent à étudier le phénomène d’opposabilité, entendu comme l’effet d’un acte ou fait juridique sur les tiers, dans un contexte concurrentiel ; et le mécanisme de conciliation qu’est l’action en concurrence déloyale. Après l’étude des solutions existantes, nous tenterons de dégager un critère du comportement déloyal permettant une appréhension globale et contextuelle de l’effet de l’acte concurrentiel sur un marché, afin d’ajuster le degré d’opposabilité suffisant à la protection des uns et à la préservation de la liberté concurrentielle des autres. / Law rules relations between individuals. From an economic angle, it defines an activity range for each operator. Our research work aims at studying the french concept of “opposabilité” in a competitive background. The question is about analysing the effects of a contract or an exclusive right regarding third competitors; and the reconciliation proceeding that is the action on unfair competition. We will attempt to draw a criterion from unfair behaviour that enables a better analysis of the effect of competitive action on a market and therefore on this market's own operators, to adapt the “opposabilié” degree to allow protection of some and preservation of freedom for others.

The release of the seed eating beetle Sulcobruchus subsuturalis for biological control of Caesalpinia decapetala in South Africa has been ongoing since 2000. This is the first post release evaluation of the efficacy of the agent against the weed. The study assessed the phenology of C. decapetala and S. subsuturalis at two sites and included determining the establishment of the beetle on the target weed at 25 study sites. In addition, the effects of S. subsuturalis on seed densities as well as seed germination and seedling recruitment were examined. Furthermore predation by native ants and attacks by native parasitoids were also examined at two release sites. Mature filled pods were available on the tree from September (spring) to March (summer) when the beetle is expected to be reproductively active. The majority of beetle releases by Working for water took place in summer. However the proportion of beetle infested seeds, which were only recovered inside pods in the tree canopy at study sites, was low (0 to 15.5%). Consequently high seed densities and seedling recruitment were observed in the field. In the laboratory, S. subsuturalis did not lay eggs on buried seeds, however seed infestation levels were generally high. Only 8.3% of the seeds containing adults germinated and 6.3% emerged into seedlings. Of the seeds containing larvae, only 14.6% germinated and 2.1% emerged into seedlings. Thus far, S. subsuturalis has failed to maintain high populations on the target weed, possibly due to egg predation by native ants (Crematogaster species, Pheidole megacephala, Messor natalensis and Tetramorium avium) and attacks by native parasitoids. Egg predation reached 100% within 10 days. Egg parasitism by unknown parasitoids ranged between 80 and 93.1% in Limpopo. The parasitic wasp Dinarmus altifrons was recovered once developing inside a C. decapetala seed infested with S. subsuturalis. Further investigations regarding attacks by indigenous parasitoids on S. subsuturalis are required to determine the extent of this problem. Meanwhile releases of S. subsuturalis against C. decapetala should continue. However release efforts need to be improved by (a) using inundative rather than inoculative releases (b) Releasing every year between September and March (summer) and (c) involving land owners, farmers and nature reserve authorities in release activities. Ultimately an additional agent should be sought for release against C. decapetala as the weed may not be the preferred host for S. subsuturalis.

As abelhas sem ferrão exercem importante papel ecológico como polinizadores de muitas espécies vegetais das regiões tropicais e tem significativo potencial para uso na polinização de culturas agrícolas. Contudo, com a contínua degradação de habitats, as populações de inúmeras espécies tem se tornado cada vez menores e separadas umas das outras por grandes distâncias. A criação de espécies de abelhas é um componente essencial para a conservação da biodiversidade, além de uma alternativa de fonte de renda. Para tanto, esforços de conservação e programas de criação em escala comercial requerem uma combinação de fatores, como o conhecimento biológico mais amplo, principalmente os relacionados à produção de sexuados e à diversidade genética necessária para manter a viabilidade de pequenas populações destas abelhas. Nesse contexto, os principais objetivos desta tese foram avaliar a variabilidade genética em populações manejadas, sob condições de isolamento genético ou não, e a produção de machos e rainhas nessas populações e o papel na reprodução. Para isso estudamos duas populações de Melipona scutellaris mantidas em regiões geográficas distintas, uma no município de Igarassu (PE; 7°50S 34°54W), onde a espécie ocorre naturalmente e outra no município de São Simão (SP; 21°26 47°34W), onde a população foi iniciada com duas colônias e criada por mais de 10 anos, quando chegou, a partir de sucessivas multiplicações, a 55 ninhos. Assim, embora a população de S. Simão tivesse maior redução na diversidade alélica e maior frequência de machos diplóides, quando comparada à mantida em Igarassu, ela foi criada com sucesso por um extenso período (ca. 10 anos). Provavelmente o baixo número de alelos sexuais em S. Simão, e a conseqüente produção de machos diplóides, foi a principal explicação para a freqüência significativamente maior de sexuados criados nessa população. Como contraponto à alta produção de machos diplóides, as substituições das rainhas-mãe foram mais frequentes e as colônias produziram mais rainhas. Além disso, a alta produção de machos e rainhas também pode ser entendida em termos de benefícios reprodutivos individuais. Tanto as rainhas fisogástricas como as operárias poedeiras foram responsáveis pela maternidade de machos haplóides. Contudo, 80% dos machos filhos de operárias foram produzidos por operárias filhas da rainha-mãe substituída, indicando que essas operárias especiais tem sobrevida maior que as demais e parasitam reprodutivamente a força de trabalho da geração seguinte, que são menos relacionadas a elas. Quanto à super-produção de rainhas, detectou-se que 25% das colônias órfãs, após a perda da rainha-mãe, eram invadidas por rainhas que foram produzidas e vieram de colônias próximas. Nessas colônias não-natais, elas iniciaram suas atividades de postura. Este importante resultado muda as bases para melhoramento genético destas abelhas estabelecidas até o momento. Outro estudo relacionado à alta produção de rainhas foi realizado em colônia poligínica de M. quadrifasciata, em que oito rainhas fisogástricas co-existiam. Ao contrário da hipótese de que alguma das rainhas poderia ter vindo de outro ninho, todas eram irmãs completas. Isto sugere novas estratégias reprodutivas ainda desconhecidas para as abelhas do gênero Melipona. / Stingless bees play an important ecological role as pollinators of many wild plant species in the tropics and have significant potential for the pollination of agricultural crops. However, as a consequence of habit degradation, populations of a number of bee species have became increasingly small and separated from one another by large distances. Thus, stingless beekeeping is an essential component of biodiversity conservation, as well as a profitable business. Therefore, conservation efforts and breeding programme on a large scale require a combination of factors, including a broader biological knowledge, especially those related to production of sexuals and to the genetic diversity needed to maintain the viability of small population. In this context, the main goals were to evaluate the genetic variability in managed populations under or not genetic isolation and the production of males and queens. Two Melipona scutellaris populations were studied and they were kept in different geographic regions, one in Igarassu (PE; 7°50\'S 34°54\'W), in the species natural area of occurrence, and the other in São Simão (SP; 21°26 47°34W), where the population was started from only two foundress colonies and which after a breeding programme of ten years increased to about 55. Despite a great reduction in the number of alleles and an increased frequency of diploid males in the S. Simão population, it could be successfully bred and maintained for a prolonged period (ca. 10 years). Probably the low number of sex alleles in S. Simão population, leading to production of diploid males, was the main reason for the highest level of sexual production. To counter-balance the high production of diploid males, the replacement of mother queen was more frequent leading to higher levels of queen production by the colonies. Furthermore, the high production of males and queens can also be explained by the individual fitness benefits. Queen and reproductive workers were haploid males mothers. However, 80% of the workers sons had genotypes that were compatible with them being the sons of workers that were the offspring of a superseded queen, indicating that these workers greatly outlive all other workers and reproductively parasitize the next-generation workforce, that are less related individuals. Related to queen overproduction, 25% of all queenless colonies were invaded by unrelated queens that fly in from unrelated hives nearby. In these non-natal colonies, the alien queens started their egg laying activities. Another study related to the high queen production was conducted in a polygyne colony of M. quadrifasciata, where eight physogastric queens coexisted. Contrary to the hypothesis that some of these queens could be an alien queen, it was confirmed that they were full-sisters. This suggests new reproductive strategies that are unknown for Melipona bees.