Reticulate Evolution: Symbiogenesis, Lateral Gene Transfer, Hybridization and Infectious heredity

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Molecular Tools for Species Identification and Population Assessment of Marine Organisms

Sessile or site attached marine species rely on the dispersal of their pelagic larvae to ensure the exchange of reproductive individuals within and among subpopulations. The resultant and continued mixing of genetic identities constitutes their population connectivity and can ensure resilience against disturbance, disease or local extinctions. Studies focusing on population connectivity in centers of high biodiversity are particularly needed to protect and sustain these ecosystems in light of global climate change and increasing anthropogenic impacts from growing coastal populations and fisheries. Coral reef organisms, like anemonefishes and their host sea anemones, are ideal candidates to study the dynamics of larval dispersal, as adults are site attached and adult migration therefore does not factor in genetic mixing. The overarching aim of this thesis is to develop, test and apply molecular markers in the study of different aspects of genetic and biological diversity in anemonefishes and their obligate symbiont sea anemone partners in the Indo-Malay Archipelago, adding to the body of scientific evidence needed to support biodiversity conservation in this â biodiversity hotspotâ . Specifically, the study furthers our understanding of connectivity in anemonefishes by presenting single species population genetic studies for, Amphiprion perideraion (Chapter I) and A. sandaracinos (Chapter II), where species specific structures are discussed in detail to highlight differences despite the highly similar life history and ecology of these fishes. This data is used as a basis for a multispecies approach to connectivity in anemonefishes by identifying and scaling regional barriers to geneflow among congeners (Amphiprion perideraion, A. sandaracinos, A. clarkii and A. ocellaris), making these results more accessible for application and implementation driven fields of research. By applying a comparative intergenomic (mitochondrial and nuclear markers) and an intrageneric (four species) approach, the mechanisms shaping genetic diversity in natural populations of anemonefishes are addressed and the variability in the system is explored.The impact of host specialization (generalist vs. specialist) and the length of the pelagic larval phase are tentatively discussed in light of the overall genetic structure that could be detected for each species. To heed the close association between anemonefishes and their sea anemone host, two mitochondrial and one nuclear marker are investigated as to their potential to delineate and identify species within the Actiniaria (Chapter III). Following a fourth research aim to study connectivity and diversity in host sea anemones, the attempted development of a set of polymorphic microsatellite loci is shown (Chapter IV)

Insights into Genome Functional Organisation through the Analysis of Interaction Networks

Using computational techniques to identify orthology and operon structure, it is possible to find functional interactions between genes, which, together, define the genetic interactome. These large networks contain information about the relationships between phenotypes in organisms as genes responsible for related abilities are often co-regulated and reasserting of these genes can be detected in the operon structure. However, these networks are too large to analyse by hand In order to practically analyse the networks, a computational tool, gisql, was developed and, using this tool, the connectivity patterns in the genetic interactome can be analysed to understand high-level organisation of the genome and to narrow the list of candidate genes for wet lab analysis. The many strains of Escherichia coli are interesting subjects as there are many sequenced strains and they show highly variable pathogenic abilities. Analysis shows that the pathogenic genes have a strong tendency to connect to genes ubiquitous in the E. coli pan-genome. The Rhizobiales, including Sinorhizobium meliloti and Ochrobactrum anthropi, are multi-chromosomal eukaryote-associated bacteria and a significant history of horizontal transfer. Regions of the pSymB megaplasmid of S. meliloti which cannot be deleted via transposon-targeted homologous recombination were shown to be significantly more connected to the main chromosome. Targets for functional complementation of deletions in pSymB in S. meliloti using genes from O. anthropi were identified and unusual connectivity patterns of orthologs were identified. Finally, a putative cytokinin receptor in the Rhizobiaceæ, likely involved in symbiosis with plant hosts, was identified. Thanks to the flexibility of gisql, these analyses were straight-forward and fast to develop

Rules of engagement : competitive coevolutionary dynamics in computational systems

Given that evolutionary biologists have considered coevolutionary interactions since the dawn of Darwinism, it is perhaps surprising that coevolution was largely overlooked during the formative years of evolutionary computing. It was not until the early 1990s that Hillis' seminal work thrust coevolution into the spotlight. Upon attempting to evolve fixed-length sorting networks, a problem with a long and competitive history, Hillis found that his standard evolutionary algorithm was producing sub-standard networks. In response, he decided to reciprocally evolve a population of testlists against the sorting network population; thus producing a coevolutionary system. The result was impressive; coevolution not only outperformed evolution, but the best network it discovered was only one comparison longer than the best-known solution. For the first time, a coevolutionary algorithm had been successfully applied to problem-solving. Pre-Hillis, the shortcomings of standard evolutionary algorithms had been understood for some time: whilst defining an adequate fitness function can be as challenging as the problem one is hoping to solve, once achieved, the accumulation of fitness-improving mutations can push a population towards local optima that are difficult to escape. Coevolution offers a solution. By allowing the fitness of each evolving individual to vary (through competition) with other reciprocally evolving individuals, coevolution removes the requirement of a fitness yardstick. In conjunction, the reciprocal adaptations of each individual begin to erode local optima as soon as they appear. However, coevolution is no panacea. As a problem-solving tool, coevolutionary algorithms suffer from some debilitating dynamics, each a result of the relative fitness assessment of individuals. In a single-, or multi-, population competitive system, coevolution may stabilize at a suboptimal equilibrium, or mediocre stable state; analogous to the traditional problem of local optima. Populations may become highly specialized in an unanticipated (and undesirable) manner; potentially resulting in brittle solutions that are fragile to perturbation. The system may cycle; producing dynamics similar to the children's game rock-paper-scissors. Disengagement may occur, whereby one population out-performs another to the extent that individuals cannot be discriminated on the basis of fitness alone; thus removing selection pressure and allowing populations to drift. Finally, coevolution's relative fitness assessment renders traditional visualization techniques (such as the graph of fitness over time) obsolete; thus exacerbating each of the above problems. This thesis attempts to better understand and address the problems of coevolution through the design and analysis of simple coevolutionary models. 'Reduced virulence' - a novel technique specifically designed to tackle disengagement - is developed. Empirical results demonstrate the ability of reduced virulence to combat disengagement both in simple and complex domains, whilst outperforming the only known competitors. Combining reduced virulence with diversity maintenance techniques is also shown to counteract mediocre stability and over-specialization. A critique of the CIAO plot - a visualization technique developed to detect coevolutionary cycling - highlights previously undocumented ambiguities; experimental evidence demonstrates the need for complementary visualizations. Extending the scope of visualization, a first exploration into coevolutionary steering is performed; a technique allowing the user to interact with a coevolutionary system during run-time. Using a simple model incorporating reduced virulence, the coevolutionary steering demonstration highlights the future potential of such tools for both research and education. The role of neutrality in coevolution is discussed in detail. Whilst much emphasis is placed upon neutral networks in the evolutionary computation literature, the nature of coevolutionary neutrality is generally overlooked. Preliminary ideas for modelling coevolutionary neutrality are presented. Finally, whilst this thesis is primarily aimed at a computing audience, strong reference to evolutionary biology is made throughout. Exemplifying potential crossover, the CIAO plot, a tool previously unused in biology, is applied to a simulation of E. Coli, with results con rming empirical observations of real bacteria.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Sociobiology, universal Darwinism and their transcendence: An investigation of the history, philosophy and critique of Darwinian paradigms, especially gene-Darwinism, process-Darwinism, and their types of reductionism towards a theory of the evolution of evolutionary processes, evolutionary freedom and ecological idealism

Based on a review of different Darwinian paradigms, particularly sociobiology, this work, both, historically and philosophically, develops a metaphysic of gene-Darwinism and process-Darwinism, and then criticises and transcends these Darwinian paradigms in order to achieve a truly evolutionary theory of evolution. Part I introduces essential aspects of current sociobiology as the original challenge to this investigation. The claim of some sociobiologists that ethics should become biologized in a gene-egoistic way, is shown to be tied to certain biological views, which ethically lead to problematic results. In part II a historical investigation into sociobiology and Darwinism in general provides us, as historical epistemology', with a deeper understanding of the structure and background of these approaches. Gene-Darwinism, which presently dominates sociobiology and is linked to Dawkins' selfish gene view of evolution, is compared to Darwin's Darwinism and the evolutionary' synthesis and becomes defined more strictly. An account of the external history of Darwinism and its subparadigms shows how cultural intellectual presuppositions, like Malthusianism or the Newtonian concept of the unchangeable laws of nature, also influenced biological theory' construction. In part III universal 'process-Darwinism' is elaborated based on the historical interaction of Darwinism with non-biological subject areas. Building blocks for this are found in psychology, the theory of science and economics. Additionally, a metaphysical argument for the universality of process- Darwinism, linked to Hume's and Popper's problem of induction, is proposed. In part IV gene-Darwinism and process-Darwinism are criticised. Gene-Darwinism—despite its merits—is challenged as being one-sided in advocating 'gene-atomism', 'germ-line reductionism' and 'process-monism'. My alternative proposals develop and try to unify different criticisms often found. In respect of gene-atomism I advocate a many-level approach, opposing the necessary radical selfishness of single genes. I develop the concept of higher-level genes, propose a concept of systemic selection, which may stabilise group properties, without relying on permanent group selection and extend the applicability of a certain group selectionist model generally to small open groups. Proposals of mine linked to the critique of germ-line reductionism are: 'exformation', phenotypes as evolutionary factors and a field theoretic understanding of causa formalis (resembling Aristotelian hylemorphism). Finally the process-monism of gene-Darwinism, process-Darwinism and, if defined strictly, Darwinism in general is criticised. 1 argue that our ontology and ethics would be improved by replacing the Newtoman-Paleyian deist metaphor of an eternal and unchangeable law of nature, which lies at tire very heart of Darwinism, by a truly evolutionary understanding of evolution where new processes may gain a certain autonomy. All this results in a view that I call 'ecological idealism', which, although still very much based on Darwinism, clearly transcends a Darwinian world view

Graph-based modeling and evolutionary analysis of microbial metabolism

Microbial organisms are responsible for most of the metabolic innovations on Earth. Understanding microbial metabolism helps shed the light on questions that are central to biology, biomedicine, energy and the environment. Graph-based modeling is a powerful tool that has been used extensively for elucidating the organising principles of microbial metabolism and the underlying evolutionary forces that act upon it. Nevertheless, various graph-theoretic representations and techniques have been applied to metabolic networks, rendering the modeling aspect ad hoc and highlighting the conflicting conclusions based on the different representations. The contribution of this dissertation is two-fold. In the first half, I revisit the modeling aspect of metabolic networks, and present novel techniques for their representation and analysis. In particular, I explore the limitations of standard graphs representations, and the utility of the more appropriate model---hypergraphs---for capturing metabolic network properties. Further, I address the task of metabolic pathway inference and the necessity to account for chemical symmetries and alternative tracings in this crucial task. In the second part of the dissertation, I focus on two evolutionary questions. First, I investigate the evolutionary underpinnings of the formation of communities in metabolic networks---a phenomenon that has been reported in the literature and implicated in an organism's adaptation to its environment. I find that the metabolome size better explains the observed community structures. Second, I correlate evolution at the genome level with emergent properties at the metabolic network level. In particular, I quantify the various evolutionary events (e.g., gene duplication, loss, transfer, fusion, and fission) in a group of proteobacteria, and analyze their role in shaping the metabolic networks and determining the organismal fitness. As metabolism gains an increasingly prominent role in biomedical, energy, and environmental research, understanding how to model this process and how it came about during evolution become more crucial. My dissertation provides important insights in both directions

MODELLING AND CONTROL OF MULTI-FINGERED ROBOT HAND USING INTELLIGENT TECHNIQUES

Research and development of robust multi-fingered robot hand (MFRH) have been going on for more than three decades. Yet few can be found in an industrial application. The difficulties stem from many factors, one of which is that the lack of general and effective control techniques for the manipulation of robot hand. In this research, a MFRH with five fingers has been proposed with intelligent control algorithms. Initially, mathematical modeling for the proposed MFRH has been derived to find the Forward Kinematic, Inverse Kinematic, Jacobian, Dynamics and the plant model. Thereafter, simulation of the MFRH using PID controller, Fuzzy Logic Controller, Fuzzy-PID controller and PID-PSO controller has been carried out to gauge the system performance based parameters such rise time, settling time and percent overshoot

Genomic and Transcriptomic Studies on Non-Model Organisms

As the advance in high-throughput sequencing enables the generation of large volumes of genomic information, it provides researchers the opportunity to study non-model organisms even in the absence of a fully sequenced genome. The hugely advantageous progress calls for powerful sequencing assembly algorithms as these technologies also raise challenging assembly problems: (1) Some RNA products are highly expressed but others may have much lower expression level. (2) Data cannot easily be represented as linear structure, due to post-transcriptional modification like alternative splicing. (3) Conserved sequences in domains in gene families can result in assembly errors, (4) Sequencing errors due to technique limitations. Useful assembly algorithms are required to overcome the difficulties above. In these studies, there is often a need to identify similar transcripts in non-model organisms to transcripts found in related organisms. The traditional approach to address this problem is to perform de novo transcriptome assemblies to obtain predicted transcripts for these organisms and then employ similarity comparison algorithms to identify them. I observe it is possible to obtain a more complete set of similar transcripts from transcriptome assembly by making use of evolutionary information. I apply new algorithms to study non-model organisms which play an important role in applied biology. Moreover, improvement of sequencing technologies and application of current algorithms also help to study interkingdom signals between blow flies and bacteria community. With current computational tools, I annotate genomes of Proteus mirabilis and Providencia stuartii, which play an important role in bacteria-insect interaction. The study shows significant features of these strains isolated, which provides useful information to develop and test hypothesis in related interactions in insects and bacteria