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The evolution of synapses from early proto-synaptic protein complexes in unicellular eukaryotes to sophisticated machines comprising thousands of proteins parallels the emergence of finely tuned synaptic plasticity, a molecular correlate for memory and learning. Phenotypic change in organisms is ultimately the result of evolution of their genotype at the molecular level. Selection pressure is a measure of how changes in genome sequence that arise though naturally occurring processes in populations are fixed or eliminated in subsequent generations. Inferring phylogenetic information about proteins such as the variation of selection pressure across coding sequences can provide valuable information not only about the origin of proteins, but also the contribution of specific sites within proteins to their current roles within an organism. Recent evolutionary studies of synaptic proteins have generated attractive hypotheses about the emergence of finely-tuned regulatory mechanisms in the post-synaptic proteome related to learning, however, these analyses are relatively superficial. In this thesis, I establish a scalable molecular phylogenetic modelling framework based on three new inference methodologies to investigate temporal and spatial aspects of selection pressure changes for the whole human proteome using protein orthologs from up to 68 taxa. Temporal modelling of evolutionary selection pressure reveals informative features and patterns for the entire human proteome and identifies groups of proteins that share distinct diversification timelines. Multi-ontology enrichment analysis of these gene cohorts was used to aid biological interpretation, but these approaches are statistically under powered and do not capture a clear picture of the emergence of synaptic plasticity. Subsequent pathway-centric analysis of key synaptic pathways extends the interpretation of temporal data and allows for revision of previous hypotheses about the evolution of complex synaptic function. I proceed to integrate inferred selection pressure timeline information in the context of static protein-protein interaction data. A network analysis of the full human proteome reveals systematic patterns linking the temporal profile of proteins’ evolution and their topological role in the interaction graph. These graphs were used to test a mechanistic hypothesis that proposed a propagating diversification signal between interactors using the temporal modelling data and network analysis tools. Finally, I analyse the data of amino-acid level spatial modelling of selection pressure events in Arc, one of the master regulators of synaptic plasticity, and its interactors for which detailed experimental data is available. I use the Arc interactome as an example to discuss episodic and localised diversifying selection pressure events in tightly coupled complexes of protein and showcase potential for a similar systematic analysis of larger complexes of proteins using a pathway-centric approach. Through my work I revised our understanding of temporal evolutionary patterns that shaped contemporary synaptic function through profiling of emergence and refinement of proteins in multiple pathways of the nervous system. I also uncovered systematic effects linking dependencies between proteins with their active diversification, and hypothesised about their extension to domain level selection pressure events.

Lytopylus is species-rich genus of Agathidinae (Hymenoptera: Braconidae: Agathidinae), but limited information of the genus has been published. Morphological, molecular, and ecological data were compared to resolve the species limits of Lytopylus reared from caterpillars collected the Area de Conservación Guanacaste (ACG) in Costa Rica. Molecular data were initially used to hypothesize species limits, and morphological and host use data were employed to make a final decision when molecular data was indecisive, e.g., when the genetic difference between species was slight. Thirty-two new species are described with image plates of each species. Phylogenetic analyses of the barcode region of the cytochrome c oxidase subunit I (COI) mitochondrial gene was conducted using Neighbor-Joining (NJ) and the Maximum likelihood (ML) analysis. A concatenated COI+28S dataset was analyzed by ML analysis to elucidate evolutionary patterns in ecological characters.

The city, since the industrialization period, is no longer the product of a single mind. With bold and massive investment in infrastructure networks that followed this period, engineering professions gained unparallel social status and gained importance in municipality ranks. In parallel to this, social sciences have been very slow to pick up on the issue of mobility. The global neoliberal environment and more competitive one in which cities are confronted today, has resulted with local governments, public-private partnerships and new ways of augmenting chances of economical investments. Municipality documents used as a basis for the production and construction of urban environments are not equipped to deal with commercial and political motivated drawings and plans. There is a lack of communication between both languages that result in an unfiltered ‘laissez faire’ of aesthetics. Spatial design fields are capable of creating terminology that can properly address the serious issues concerning our networks of flows but are not enough by themselves considering the economical environment and the following self-generated urbanity inflicting our cities. Landscape architecture offers an open-ended perspective on small to large scale networks of infrastructures, thus possibly being able to bridge the gap between institutional planning mechanisms and actual design. The theoretical background generated from this research will be applied to a case scenario. Boulevard Taschereau (also called provincial road 134 at some parts) is among the most important and used arteries of the South Shore of Montréal, Québec (Canada). A contextual solution to boulevard Taschereau’s congestion issues will have to be generated in order for it to meet the expectations and social needs of its current and future users.