Molecular Mechanisms of Sexual Dimorphism in Threespine Stickleback

Sexual dimorphism is commonly understood as differences in external features, such as morphological features or coloration. However, it can more broadly encompass behavior and physiology and at the core of these differences is the genetic mechanism – mRNA and protein expression. How, and which, molecular mechanisms influence sexually dimorphic features is not well understood thus far. DNA, RNA and proteins are the template required to create the phenotype of an individual, and they are connected to each other via processes of transcription and translation. As the genome of males and females are almost identical with the exception of the few genes on the sex chromosome or the sex-determining alleles (in the case of organisms without sex chromosomes), it is likely that many of the downstream processes resulting in sexual dimorphism are produced by changes in gene regulation and result from a regulatory cascade and not from a vastly different gene composition. Thus, in this thesis a systems biology approach is used to understand sexual dimorphism at all molecular levels and how different genomic features, e.g. sex chromosome evolution, can affect the interplay of these molecules. The threespine stickleback, Gasterosteus aculeatus, is used as the model to investigate molecular mechanisms of sexual dimorphism. It has well-characterized ecology and behavior, especially in the breeding season when sexual dimorphism is high. Moreover, threespine stickleback has a recently evolved Y chromosome in the early stages of sex chromosome evolution, characterized by a lack of recombination leading to degeneration (i.e. gene loss). The aim of my thesis is to investigate how the genotype links to the molecular phenotype and relates to differences in molecular expression between males and females. Based on previous research on sex differences in mRNA expression, I investigated sex-biased protein expression in adult fish outside the breeding season to see if differences persisted after translation. As sex-biased expression also prevailed in the proteome and previous transcription expression seemed to be related to the sex chromosomes, I investigated the genome level with a particular focus on the sex-chromosomes. I characterized the status of Y chromosome degeneration in the threespine stickleback and its effects on gene function. Furthermore, since the degeneration process leaves genes in a single copy in males, I examined whether the resulting dosage difference of messenger RNA for hemizygous genes is compensated as it is in other organisms. In addition, threespine sticklebacks have wellcharacterized behavioral differences related to the male’s social status during the breeding season. To understand the connection between the genotype and behavior, I examined gene expression patterns related to breeding behavior using dominant and subordinate males as well as female

Nested Rollout Policy Adaptation for optimizing vehicle selection in complex VRPs

The goal of Vehicle Routing Problems (VRP) and their variations is to transport a set of orders with the minimum number of vehicles at least cost. Most approaches are designed to solve specific problem variations independently, whereas in real world applications, different constraints are handled concurrently. This research extends solutions obtained for the traveling salesman problem with time windows to a much wider class of route planning problems in logistics. The work describes a novel approach that:  supports a heterogeneous fleet of vehicles  dynamically reduces the number of vehicles  respects individual capacity restrictions  satisfies pickup and delivery constraints  takes Hamiltonian paths (rather than cycles) The proposed approach uses Monte-Carlo Tree Search and in particular Nested Rollout Policy Adaptation. For the evaluation of the work, real data from the industry was obtained and tested and the results are reported.

The molecular mechanisms and evolutionary significance of plumage colour variation in pied flycatchers (Ficedula hypoleuca)

A common feature of natural populations is that individuals differ in morphology, physiologyand behavior (i.e .phenotype). A thorough understanding of the molecular mechanisms and evolutionary forces behind this phenotypic variation is a prerequisite for understanding evolution.This thesis examines the molecular mechanism and the roles of the different evolutionary forces in plumage colour variation in pied flycatchers (Ficedulahypoleuca). Malepied flycatchers exhibit marked variation in both pigmentary and structural plumage colourand the trait has repeatedly been suggested to be of adaptive significance. An examination of plumage colour variation on reproductive output trevealed that structural colouration, and more specifically the degree of ultraviolet (UV) reflectance had an effect on number of young sired. Paternity analyses of breeding males revealed that males that had been cuckolded by their social mate tended to be less UV reflectant than males that had not been cuckolded.Neither pigment-based norstructural colouration was found to affect the probability of siring young in other nests. Phenotypic differentiation was found to be markedly greater than differentiation at neutralgenetic markers across the pied flycatcher breeding range. Furthermore patterns of differentiationin phenotypes and selectively neutral genes were not uniform. Outlier tests searching for genomic footprints of selection revealed elevated levels of genetic divergence in a gene associated with feather development (and thus potentially structural colouration) and ultraviolet vision. Th eobserved differentiation in allelic frequencies was particularly pronounced in the Spanish piedflycatcher populations. Examining gene expression during feather development indicated that the TYRP1 gene (known to be involved in the production of black pigment) may be relevant in generating phenotypic variation in pied flycatcher plumage. Also, energy homeostasis related genesfeatured prominently among the genes found to be expressed in one extreme phenotype but not the other. This is of particular interest in light of what is known about the pleiotropy ofthe melanocortin system which underlies brown-black pigment production. The melanocortinsystem is also associated with energy homeostasis (among a number of other physiological functions) and thus the results could be pointing to the signalling function of brown-blackplumage. Plumage colour variation in pied flycatchers, both structural and pigmentary, can thus beconcluded to be exhibiting signals of non-neutral evolution. Structural colouration was found to play a role in sexual selection and putative signals of selection were further detected in acandidate gene for this trait. Evidence for non-neutral evolution of pigmentary colouration was also detected. These findings, together with the fact that preliminary evidence for an energy balance associated signalling function for plumage was found, present good starting points for further investigations into the meaning and mechanisms of plumage colour variation in piedflycatchers.

International research partnerships: establishing partner selection criteria in the university-university context

The main objective of the study was to identify and evaluate criteria for international partner selection in university-university context. This study attempted at promoting better understanding of how universities should proceed in selecting partners for producing joint research publications. Thus, the aim of the study was to gain an understanding of how research collaborations can be developed and how partners can be selected. The choice of a right partner has been identified as a precondition for partnership success. In international research collaborations partnering scientists with different skills and backgrounds bring together complementary knowledge into research projects, which in most cases results in a higher quality output. Therefore, prior to selecting a partner, the set of criteria should be established. This research examined twelve Russian universities with the status of national research university as potential partners for Lappeenranta University of Technology, and selected the most appropriate universities based on established set of criteria. Potential partners’ evaluation was done using secondary sources by tracking partners’ academic success during the period 2005 – 2010. Based on established criteria, the study calculated the partnership index for each university. The results of the research reveal that among twelve examined universities there are four potential partners who have been rather active in publishing scientific articles during 2005 – 2010.

Host Parasite Interactions in Damselflies. From Individuals to Populations

The main goal of this thesis is to increase understanding on evolutionary and ecological factors that have contributed to differences in parasite numbers in insects. Furthermore, the thesis addresses the effects of parasites on their hosts. The most important findings were: The Northern damselfly’s (Coenagrion hastulatum) immune response to artificial pathogen increased with increasing parasite numbers (Article I). Marginal, more isolated C. hastulatum populations on the edge of distribution have fewer parasites when compared to distribution’s core populations (Article II). The Banded damselfly Calopteryx splendens individuals with higher homozygosity have more parasites, however, the rate of homozygosity did not differ between populations (Article III). Parasite prevalence was affected by whether the host species occurred in allopatric or sympatric population: sympatric C. splendens populations with sister species the Beautiful damselfly Calopteryx virgo harbored more parasites (Article IV). Parasites were associated with the wing spot size, an ornament under sexual selection, and thus may play an important role in character displacement, i.e. the size of the wing spot (Article V). To conclude with, this thesis brings about new information on the parasite infection patterns in insects, proposing several factors to contribute to these patters, as well as it addresses the effects of parasites on their hosts, from individual to population level.