Primal Eukaryogenesis:On the Communal Nature of Precellular States, Ancestral to Modern Life

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution—leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other

The coevolution of the firm and the supply network : a complex systems perspective

A complex adaptive systems approach has been permeating organizational studies and the field of supply network management helping to describe and explain supply network dynamics and emergent inter-firm structures. This has improved our theoretical knowledge of the nature of supply networks transforming raw materials into products, within a constantly changing environment. From the early days of simple structures, describing bi-lateral, local arrangements between firms for the creation of relatively simple products, we are now in an environment of various supply network archetypes, describing different global sourcing regimes of highly integrated, sophisticated products within multi-tier networks. This thesis is a study of the coevolution of the firm and supply network in the commercial aerospace manufacturing sector producing jetliners of 100 or more seats. One of the contributions of this research is to demonstrate how the holistic approach of complexity science can be applied to describe, understand and gain new insight into the coevolution of the firm and the supply network. Based on the findings of multiple interviews and questionnaires in eight global aerospace firms across multiple supply chain tiers, this research finds high-performing clusters of inter-firm characteristics, plus the aspects of structure and integration which deliver the supply network performance. Practitioners can use these specific results to examine their own firms and the new coevolutionary conceptual framework developed in the thesis may aid future research studies of complex adaptive systems in practice. The simple survey design and analysis method used in the final research stage of this research, has the potential for use in other industries, markets and other complex adaptive systems generally to examine performance outcomes and the effects of having or adopting new inter-firm characteristics. Finally, implications for policy include the potential to legitimize supply networks in order to stimulate competition and innovation in the economy.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

The role of visual adaptation in cichlid fish speciation

D. Shane Wright (1) , Ole Seehausen (2), Ton G.G. Groothuis (1), Martine E. Maan (1) (1) University of Groningen; GELIFES; EGDB(2) Department of Fish Ecology & Evolution, EAWAG Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum AND Institute of Ecology and Evolution, Aquatic Ecology, University of Bern.In less than 15,000 years, Lake Victoria cichlid fishes have radiated into as many as 500 different species. Ecological and sexual sel ection are thought to contribute to this ongoing speciation process, but genetic differentiation remains low. However, recent work in visual pigment genes, opsins, has shown more diversity. Unlike neighboring Lakes Malawi and Tanganyika, Lake Victoria is highly turbid, resulting in a long wavelength shift in the light spectrum with increasing depth, providing an environmental gradient for exploring divergent coevolution in sensory systems and colour signals via sensory drive. Pundamilia pundamila and Pundamilia nyererei are two sympatric species found at rocky islands across southern portions of Lake Victoria, differing in male colouration and the depth they reside. Previous work has shown species differentiation in colour discrimination, corresponding to divergent female preferences for conspecific male colouration. A mechanistic link between colour vision and preference would provide a rapid route to reproductive isolation between divergently adapting populations. This link is tested by experimental manip ulation of colour vision - raising both species and their hybrids under light conditions mimicking shallow and deep habitats. We quantify the expression of retinal opsins and test behaviours important for speciation: mate choice, habitat preference, and fo raging performance

Coalition Formation For Distributed Constraint Optimization Problems

This dissertation presents our research on coalition formation for Distributed Constraint Optimization Problems (DCOP). In a DCOP, a problem is broken up into many disjoint sub-problems, each controlled by an autonomous agent and together the system of agents have a joint goal of maximizing a global utility function. In particular, we study the use of coalitions for solving distributed k-coloring problems using iterative approximate algorithms, which do not guarantee optimal results, but provide fast and economic solutions in resource constrained environments. The challenge in forming coalitions using iterative approximate algorithms is in identifying constraint dependencies between agents that allow for effective coalitions to form. We first present the Virtual Structure Reduction (VSR) Algorithm and its integration with a modified version of an iterative approximate solver. The VSR algorithm is the first distributed approach for finding structural relationships, called strict frozen pairs, between agents that allows for effective coalition formation. Using coalition structures allows for both more efficient search and higher overall utility in the solutions. Secondly, we relax the assumption of strict frozen pairs and allow coalitions to form under a probabilistic relationship. We identify probabilistic frozen pairs by calculating the propensity between two agents, or the joint probability of two agents in a k-coloring problem having the same value in all satisfiable instances. Using propensity, we form coalitions in sparse graphs where strict frozen pairs may not exist, but there is still benefit to forming coalitions. Lastly, we present a cooperative game theoretic approach where agents search for Nash stable coalitions under the conditions of additively separable and symmetric value functions

Multiscale Simulation and Analysis of Structured Ribonucleic Acids

I present the results of three projects in the course of my scientific work in the context of native structure-based models (SBMs) for regulatory RNA. They comprise a new and openly accessible software implementation of native structure-based model generation and evaluation, a study that employs a multiscale model to investigate cotranscriptional riboswitch folding and advances to a novel approach in the field of RNA tertiary structure prediction

MITOCHONDRIAL AND NUCLEAR PATTERNS OF CONFLICT AND CONCORDANCE AT THE GENE, GENOME, AND BEHAVIORAL SCALES IN \u3cem\u3eDESMOGNATHUS\u3c/em\u3e SALAMANDERS

Advancements in molecular sequencing have revealed unexpected cryptic genetic diversity and contrasting evolutionary histories within genes and between genomes of many organisms; often in disagreement with recognized taxonomy. Incongruent patterns between the mitochondrial and nuclear evolutionary history can have several plausible explanations, but widespread systematic conflict inevitably challenges our conceptions of species boundaries when there is discordance between coevolving and coinherited genomes. It is unknown to what degree mitonuclear conflict drives the process of divergence, or how ubiquitous these patterns are across the tree of life. To understand the evolutionary relevance of intergenomic discordance we must identify the conflicting patterns that exist in natural systems by generating robust estimates of the underlying species history, quantify support for alternative hypotheses of lineage formation, and describe patterns of genetic variation present in robust nuclear genomic datasets. Empirically testing correlations between mitonuclear genomic conflict and reduced gene flow at the organism level will contribute toward a better understanding of lineage boundaries and how intergenomic interactions shape the process of divergence. Mitochondrial introgression has been inferred in many salamander systems with limited perspective from nuclear sequence data. Within dusky salamanders (Desmognathus), these patterns have been observed between morphologically and geographically disparate populations. I sequenced regions throughout the nuclear genome to reconstruct species trees, performed population-level analyses testing concordance between the mitochondrial, nuclear datasets, and nuclear genes with mitochondrial functions with the expectation that coevolutionary interactions among genomes are more likely to manifest in these regions. I also estimated migration rates between populations that may have experienced historical mitochondrial introgression to evaluate phylogeographic patterns. Using these data we definitively reject species models in which genetic boundaries are based solely on mitochondrial data, favoring geographic models instead. Furthermore, analyses soundly reject current taxonomic models based on morphological characteristics, suggesting there is greater lineage diversity than is currently recognized. I also used empirical assays of pre-zygotic reproductive mating behavior within and among populations containing diverse mitochondrial lineages to test metrics of reproductive isolation, and to determine if introgression shapes the evolution of complex traits directly influencing rates of divergence. These results may explain incongruent patterns observed between the mitochondrial and nuclear data as a function of inheritance and population dynamics rather than directly functioning to suppress nuclear gene flow. This research builds upon recent studies suggesting that speciation is a highly complex and often non-bifurcating process in which introgression can have a profound and lasting signature on the nuclear evolutionary history. Mechanisms responsible for divergence with gene flow challenge evolutionary biologists to reevaluate our notions and definitions of species boundaries to accommodate seemingly conflicted genomic patterns within and between genomes

Module hierarchy and centralisation in the anatomy and dynamics of human cortex

Systems neuroscience has recently unveiled numerous fundamental features of the macroscopic architecture of the human brain, the connectome, and we are beginning to understand how characteristics of brain dynamics emerge from the underlying anatomical connectivity. The current work utilises complex network analysis on a high-resolution structural connectivity of the human cortex to identify generic organisation principles, such as centralised, modular and hierarchical properties, as well as specific areas that are pivotal in shaping cortical dynamics and function. After confirming its small-world and modular architecture, we characterise the cortex’ multilevel modular hierarchy, which appears to be reasonably centralised towards the brain’s strong global structural core. The potential functional importance of the core and hub regions is assessed by various complex network metrics, such as integration measures, network vulnerability and motif spectrum analysis. Dynamics facilitated by the large-scale cortical topology is explored by simulating coupled oscillators on the anatomical connectivity. The results indicate that cortical connectivity appears to favour high dynamical complexity over high synchronizability. Taking the ability to entrain other brain regions as a proxy for the threat posed by a potential epileptic focus in a given region, we also show that epileptic foci in topologically more central areas should pose a higher epileptic threat than foci in more peripheral areas. To assess the influence of macroscopic brain anatomy in shaping global resting state dynamics on slower time scales, we compare empirically obtained functional connectivity data with data from simulating dynamics on the structural connectivity. Despite considerable micro-scale variability between the two functional connectivities, our simulations are able to approximate the profile of the empirical functional connectivity. Our results outline the combined characteristics a hierarchically modular and reasonably centralised macroscopic architecture of the human cerebral cortex, which, through these topological attributes, appears to facilitate highly complex dynamics and fundamentally shape brain function