Evolutionary rates play a central role in connecting micro- and macroevolution. All evolutionary rate estimates, including of molecular evolution, trait lineage diversification, share similar scaling pattern with time: The highest are those measured over the shortest time interval. This creates disconnect between macroevolution, although is opposite what some might expect: Patterns change short...

We tell the story of BrilliAnt, the winner of the Ant Wars contest organized within GECCO’2007, Genetic and Evolutionary Computation Conference. The task for the AntWars contestants was to evolve a controller for a virtual ant that collects food in a square toroidal grid environment in the presence of a competing ant. BrilliAnt, submitted to the contest by our team, has been evolved through com...

The neural controller of anguilliform swimming in lampreys is particularly well studied because of its relative robustness and simplicity. In this chapter we look at connectionist models of the controller – in which populations of similar neurons are represented by abstract, differential-equation-based models – and describe the use of evolutionary computation techniques for investigating the sp...

The history of biological systematics documents a continuing tension between classifications in terms of nested hierarchies congruent with branching diagrams (the ‘Tree of Life’) versus reticulated relations. The recognition of conflicting character distribution led to the dissolution of the scala naturae into reticulated systems, which were then transformed into phylogenetic trees by the addit...

Evolutionary programs (EPs) and evolutionary pattern search algorithms (EPSAs) are two general classes of evolutionary methods for optimizing on continuous domains. The relative performance of these methods has been evaluated on standard global optimization test functions, and these results suggest that EPSAs more robustly converge to near-optimal solutions than EPs. In this paper we evaluate t...

A common assumption in comparative sequence analysis is that the sequences have evolved with the same pattern of nucleotide substitution (homogeneity of the evolutionary process). Violation of this assumption is known to adversely impact the accuracy of phylogenetic inference and tests of evolutionary hypotheses. Here we propose a disparity index, ID, which measures the observed difference in e...

We describe in this paper a new hybrid approach for optimization combining Particle Swarm Optimization (PSO) and Genetic Algorithms (GAs) using Fuzzy Logic to integrate the results. The new evolutionary method combines the advantages of PSO and GA to give us an improved FPSO+FGA hybrid method. Fuzzy Logic is used to combine the results of the PSO and GA in the best way possible. The new hybrid ...

A recent advance in the phylogenetic comparative analysis of continuous traits has been explicit, model-based measurement of "phylogenetic signal" in data sets composed of observations collected from species related by a phylogenetic tree. Phylogenetic signal is a measure of the statistical dependence among species' trait values due to their phylogenetic relationships. Although phylogenetic sig...

The divergence in phenotype and habitat preference within the crested newt Triturus cristatus superspecies, examined across different ontogenetic stages, provides an excellent setting to explore the pattern of adaptive radiation. The crested newts form a well-supported monophyletic clade for which at least the full mitochondrial DNA phylogeny is resolved. Here we summarise studies that explored...