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  • 1
    Keywords: Biological systems--Computer simulation--Congresses. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (921 pages)
    Edition: 1st ed.
    ISBN: 9783540394327
    Series Statement: Lecture Notes in Computer Science Series ; v.2801
    DDC: 570.11300000000006
    Language: English
    Note: Lecture Notes in Artificial Intelligence 2801 -- Advances in Artificial Life -- Copyright -- Preface -- Organization -- Table of Contents -- A Universal Framework for Self-Replication -- Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting -- How to Program Artificial Chemistries -- Artificial Life as an Aid to Astrobiology: Testing Life Seeking Techniques -- Molecularly Accessible Permutations -- Simulating Evolution's First Steps -- Cellular Evolution in a 3D Lattice Artificial Chemistry -- Evolution of Rewriting Rule Sets Using String-Based Tierra -- Models for the Conservation of Genetic Information with String-Based Artificial Chemistry -- Interaction Based Evolution of Self-Replicating Loop Structures -- Architectural Design for the Survival Optimization of Panicking Fleeing Victims -- Meta-evolutionary Game Dynamics for Mathematical Modelling of Rules Dynamics -- Preventing Bluff Agent Invasions in Honest Societies -- Effects of Group Composition and Level of Selection in the Evolution of Cooperation in Artificial Ants -- Effects of Learning to Interact on the Evolution of Social Behavior of Agents in Continuous Predators-Prey Pursuit Problem -- War and Peace among Artificial Nations - A Model and Simulation Based on a Two-Layered Multi-agent System -- Developmental Neural Networks for Agents -- Revisiting Idiotypic Immune Networks -- Production of Gliders by Collisions in Rule 110 -- A Computational Model of Neocortical-Hippocampal Cooperation and Its Application to Self-Localization -- Fascinating Rhythms by Chaotic Hopfield Networks -- Solving a Delayed Response Task with Spiking and McCulloch-Pitts Agents -- First Steps in Evolving Path Integration in Simulation -- On the Dynamics of an Artificial Regulatory Network -- Evolution and Growth of Virtual Plants. , Evolvability of the Genotype-Phenotype Relation in Populations of Self-Replicating Digital Organisms in a Tierra-Like System -- An Evolutionary Approach to Damage Recovery of Robot Motion with Muscles -- Evolving Developmental Programs for Adaptation, Morphogenesis, and Self-Repair -- Evolving Embodied Genetic Regulatory Network-Driven Control Systems -- Evolution of Fault-Tolerant Self-Replicating Structures -- Evolving the Ability of Limited Growth and Self-Repair for Artificial Embryos -- Caring versus Sharing: How to Maintain Engagement and Diversity in Coevolving Populations -- Culture and the Baldwin Effect -- Evolutionary Network Minimization: Adaptive Implicit Pruning of Successful Agents -- Population Dynamics under Spatially and Temporally Heterogenous Resource Limitations in Multi-Agent Networks -- Adaptive Coupling and Intersubjectivity in Simulated Turn-Taking Behaviour -- Distributed Genetic Algorithm: Learning by Direct Exchange of Chromosomes -- An Approach to Describe the Tierra Instruction Set Using Microopcrations: The First Result -- Critical Values in Asynchronous Random Boolean Networks -- Artificial Organisms That Sleep -- Visualizing Evolutionary Dynamics of Self-Replicators Using Graph-Based Genealogy -- The Baldwin Effect Revisited: Three Steps Characterized by the Quantitative Evolution of Phenotypic Plasticity -- Does the Red Queen Reign in the Kingdom of Digital Organisms? -- Conditions for Stable Vowel Systems in a Population -- Piep Piep Piep - Ich Hab' Dich Lieb1 : Rhythm as an Indicator of Mate Quality -- Evolving Agent Societies with VUScape -- Why Synonymy Is Rare: Fitness Is in the Speaker -- A Noisy Way to Evolve Signaling Behaviour -- Language Games with Mixed Populations -- Artificial Agents and Natural Determiners -- Coevolution of Birdsong Grammar without Imitation. , Systemic Architecture for Audio Signal Processing -- Semantic Generalisation and the Inference of Meaning -- Language Evolution in Populations: Extending the Iterated Learning Model -- Learning Biases for the Evolution of Linguistic Structure: An Associative Network Model -- The Learning and Emergence of Mildly Context Sensitive Languages -- THSim v3.2: The Talking Heads Simulation Tool -- Grounded Lexicon Formation without Explicit Reference Transfer: Who's Talking to Who? -- Optimal Communication in a Noisy and Heterogeneous Environment -- A Clustering Algorithm Based on the Ants Self-Assembly Behavior -- A Multi-agent Based Approach to Modelling and Rendering of 3D Tree Bark Textures -- Measuring the Dynamics of Artificial Evolution1 -- Pattern Recognition in a Bucket -- Discovering Clusters in Spatial Data Using Swarm Intelligence -- When Can We Call a System Self-Organizing? -- Contextual Random Boolean Networks -- Representation of Genotype and Phenotype in a Coherent Framework Based on Extended L-Systems -- Integrated-Adaptive Genetic Algorithms -- Simulating the Evolution of Ant Behaviour in Evaluating Nest Sites -- Evolving Evolutionary Algorithms Using Multi Expression Programming -- Modelling Artificial Ecosystem Selection: A Preliminary Investigation -- Measuring Self-Organization via Observers -- General Framework for Evolutionary Activity -- Developing and Testing Methods for Microarray Data Analysis Using an Artificial Life Framework -- Approaching Virtual Organism by PheGe -- Robustness to Damage of Biological and Synthetic Networks -- An Agent-Based Approach to Routing in Communications Networks with Swarm Intelligence -- Biomorphs Implemented as a Data and Signals Cellular Automaton -- Analyzing the Performance of "Winner-Take-All" and "Voting-Based" Action Selection Policies within the Two-Resource Problem. , Are There Representations in Embodied Evolved Agents? Taking Measures -- Evolving Fractal Gene Regulatory Networks for Robot Control -- Explorations of Task-Dependent Visual Morphologies in Competitive Co-evolutionary Experiments -- Optimal Morphology of a Biologically-Inspired Whisker Array on an Obstacle-Avoiding Robot -- Phase Transitions in Self-Organising Sensor Networks -- Artificial Metabolism: Towards True Energetic Autonomy in Artificial Life -- An Imitation Game for Emerging Action Categories -- Multi-agent Model of Biological Swarming -- Visually Guided Physically Simulated Agents with Evolved Morphologies -- The Robot in the Swarm: An Investigation into Agent Embodiment within Virtual Robotic Swarms -- Building a Hybrid Society of Mind Using Components from Ten Different Authors -- Requirements for Getting a Robot to Grow up -- Coevolving Communication and Cooperation for Lattice Formation Tasks -- Evolving Aggregation Behaviors in a Swarm of Robots -- Low-Level Visual Homing -- Controlling a Simulated Khepera with an XCS Classifier System with Memory -- Collective Decision-Making and Behaviour Transitions in Distributed Ad Hoc Wireless Networks of Mobile Robots: Target-Hunting -- Author Index.
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  • 2
    ISSN: 1432-1432
    Keywords: Key words: MADS-box genes — Transcription factors — Homeotic genes — Multigene family — Gene phylogeny — Body plans — Link between development and evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The MADS-box encodes a novel type of DNA-binding domain found so far in a diverse group of transcription factors from yeast, animals, and seed plants. Here, our first aim was to evaluate the primary structure of the MADS-box. Compilation of the 107 currently available MADS-domain sequences resulted in a signature which can strictly discriminate between genes possessing or lacking a MADS-domain and allowed a classification of MADS-domain proteins into several distinct subfamilies. A comprehensive phylogenetic analysis of known eukaryotic MADS-box genes, which is the first comprising animal as well as fungal and plant homologs, showed that the vast majority of subfamily members appear on distinct subtrees of phylogenetic trees, suggesting that subfamilies represent monophyletic gene clades and providing the proposed classification scheme with a sound evolutionary basis. A reconstruction of the history of the MADS-box gene subfamilies based on the taxonomic distribution of contemporary subfamily members revealed that each subfamily comprises highly conserved putative orthologs and recent paralogs. Some subfamilies must be very old (1,000 MY or more), while others are more recent. In general, subfamily members tend to share highly similar sequences, expression patterns, and related functions. The defined species distribution, specific function, and strong evolutionary conservation of the members of most subfamilies suggest that the establishment of different subfamilies was followed by rapid fixation and was thus highly advantageous during eukaryotic evolution. These gene subfamilies may have been essential prerequisites for the establishment of several complex eukaryotic body structures, such as muscles in animals and certain reproductive structures in higher plants, and of some signal transduction pathways. Phylogenetic trees indicate that after establishment of different subfamilies, additional gene duplications led to a further increase in the number of MADS-box genes. However, several molecular mechanisms of MADS-box gene diversification were used to a quite different extent during animal and plant evolution. Known plant MADS-domain sequences diverged much faster than those of animals, and gene duplication and sequence diversification were extensively used for the creation of new genes during plant evolution, resulting in a relatively large number of interacting genes. In contrast, the available data on animal genes suggest that increase in gene number was only moderate in the lineage leading to mammals, but in the case of MEF2-like gene products, heterodimerization between different splice variants may have increased the combinatorial possibilities of interactions considerably. These observations demonstrate that in metazoan and plant evolution, increased combinatorial possibilities of MADS-box gene product interactions correlated with the evolution of increasingly complex body plans.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1432-1432
    Keywords: MADS-box genes ; Transcription factors ; Homeotic genes ; Multigene family ; Gene phylogeny ; Body plans ; Link between development and evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The MADS-box encodes a novel type of DNA-binding domain found so far in a diverse group of transcription factors from yeast, animals, and seed plants. Here, our first aim was to evaluate the primary structure of the MADS-box. Compilation of the 107 currently available MADS-domain sequences resulted in a signature which can strictly discriminate between genes possessing or lacking a MADS-domain and allowed a classification of MADS-domain proteins into several distinct subfamilies. A comprehensive phylogenetic analysis of known eukaryotic MADS-box genes, which is the first comprising animal as well as fungal and plant homologs, showed that the vast majority of subfamily members appear on distinct subtrees of phylogenetic trees, suggesting that subfamilies represent monophyletic gene clades and providing the proposed classification scheme with a sound evolutionary basis. A reconstruction of the history of the MADS-box gene subfamilies based on the taxonomic distribution of contemporary subfamily members revealed that each subfamily comprises highly conserved putative orthologs and recent paralogs. Some subfamilies must be very old (1,000 MY or more), while others are more recent. In general, subfamily members tend to share highly similar sequences, expression patterns, and related functions. The defined species distribution, specific function, and strong evolutionary conservation of the members of most subfamilies suggest that the establishment of different subfamilies was followed by rapid fixation and was thus highly advantageous during eukaryotic evolution. These gene subfamilies may have been essential prerequisites for the establishment of several complex eukaryotic body structures, such as muscles in animals and certain reproductive structures in higher plants, and of some signal transduction pathways. Phylogenetic trees indicate that after establishment of different subfamilies, additional gene duplications led to a further increase in the number of MADS-box genes. However, several molecular mechanisms of MADS-box gene diversification were used to a quite different extent during animal and plant evolution. Known plant MADS-domain sequences diverged much faster than those of animals, and gene duplication and sequence diversification were extensively used for the creation of new genes during plant evolution, resulting in a relatively large number of interacting genes. In contrast, the available data on animal genes suggest that increase in gene number was only moderate in the lineage leading to mammals, but in the case of MEF2-like gene products, heterodimerization between different splice variants may have increased the combinatorial possibilities of interactions considerably. These observations demonstrate that in metazoan and plant evolution, increased combinatorial possibilities of MADS-box gene product interactions correlated with the evolution of increasingly complex body plans.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1573-5028
    Keywords: angiosperm ; development ; evolution ; fern ; gymnosperm ; MADS-box gene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Evolutionary developmental genetics (evodevotics) is a novel scientific endeavor which assumes that changes in developmental control genes are a major aspect of evolutionary changes in morphology. Understanding the phylogeny of developmental control genes may thus help us to understand the evolution of plant and animal form. The principles of evodevotics are exemplified by outlining the role of MADS-box genes in the evolution of plant reproductive structures. In extant eudicotyledonous flowering plants, MADS-box genes act as homeotic selector genes determining floral organ identity and as floral meristem identity genes. By reviewing current knowledge about MADS-box genes in ferns, gymnosperms and different types of angiosperms, we demonstrate that the phylogeny of MADS-box genes was strongly correlated with the origin and evolution of plant reproductive structures such as ovules and flowers. It seems likely, therefore, that changes in MADS-box gene structure, expression and function have been a major cause for innovations in reproductive development during land plant evolution, such as seed, flower and fruit formation.
    Type of Medium: Electronic Resource
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