A comprehensive literature classification of simulation optimisation methods

Simulation Optimization (SO) provides a structured approach to the system design and configuration when analytical expressions for input/output relationships are unavailable. Several excellent surveys have been written on this topic. Each survey concentrates on only few classification criteria. This paper presents a literature survey with all classification criteria on techniques for SO according to the problem of characteristics such as shape of the response surface (global as compared to local optimization), objective functions (single or multiple objectives) and parameter spaces (discrete or continuous parameters). The survey focuses specifically on the SO problem that involves single per-formance measureSimulation Optimization, classification methods, literature survey

The origin of alternative phenotypes in fishes

A basic aim of evolutionary biology is to explain the enormous diversity among animal and plant species. But also within species there is often large genetic and phenotypic variation, and such variation is necessary for evolution to create new reproductively isolated species. The present thesis is directed to explain differentiation within populations highlighting and discussing the significance of phenotypic plasticity as an evolutionary process that leads to the expression of alternative phenotypes within a species. Such phenotypic expressions are particularly interesting, because the process by which new species are formed typically involves a temporary stage within the splitting species, that is, different heritable and distinct types that coexist within the same population. Such phenotypes may be raw material for full species formation, and the study of alternative-phenotype species should therefore be particularly worthwhile in speciation research. When alternative phenotypes are not entirely genetic they may arise as a result of developmental plasticity, when organisms develop in accordance with local abiotic and biotic conditions. Subject to developmental plasticity, alternative phenotypes, take different developmental routes depending on the local selection pressures, or depending on the environmental conditions experienced during development. Here, laboratory experiments showed that three-spined sticklebacks exhibit alternative phenotypes as a plastic response to physical environment and diet, demonstrating and supporting the idea that environmental inputs modulate the expression of traits through phenotypic plasticity during ontogeny. When, morphological differences arise, discrete morphological characteristics are originated and may be reinforced by the continuous presence of same environmental conditions. Here is demonstrated that these discrete morphological characteristics lead the individuals to specialise on specific prey or habitat types. Moreover, it is showed that plasticity may also play a role in the final stages of species formation, when reproductive isolation completes the speciation process. It is shown that diet-induced morphology has an important influence in mate preferences representing a strong potential to generate reproductive isolation via assortative mating, and this mate preferences may be highly efficient to maintaining isolation, thus the hypothesis of ecological speciation is supported. Finally, in this study, two alternative-phenotype lakes are described. It is suggested that the origin of the segregated alternative phenotypes in both lakes is a consequence of ecological traits divergences; however in one of the lakes the alternative phenotypes arose from a founder population, meanwhile in the second lake the alternative phenotypes may arose by the ecological adaptation of the forms in allopatry

Parallel surrogate-assisted global optimization with expensive functions – a survey

Surrogate assisted global optimization is gaining popularity. Similarly, modern advances in computing power increasingly rely on parallelization rather than faster processors. This paper examines some of the methods used to take advantage of parallelization in surrogate based global optimization. A key issue focused on in this review is how different algorithms balance exploration and exploitation. Most of the papers surveyed are adaptive samplers that employ Gaussian Process or Kriging surrogates. These allow sophisticated approaches for balancing exploration and exploitation and even allow to develop algorithms with calculable rate of convergence as function of the number of parallel processors. In addition to optimization based on adaptive sampling, surrogate assisted parallel evolutionary algorithms are also surveyed. Beyond a review of the present state of the art, the paper also argues that methods that provide easy parallelization, like multiple parallel runs, or methods that rely on population of designs for diversity deserve more attention.United States. Dept. of Energy (National Nuclear Security Administration. Advanced Simulation and Computing Program. Cooperative Agreement under the Predictive Academic Alliance Program. DE-NA0002378

Assessing primate skull shape variation in relation to habitat: a 3D geometric morphometric approach

The advancement of digital imaging and open-source geometric morphometric (GM) software is positively impacting the way we understand morphological adaptation as an evolutionary response. Shape-space data and multivariate statistics quantify shape variation patterning and, therefore, consolidate hominoid systematic procedures. This thesis identifies ecomorphological patterns of variation within extant primates. Through a comparative, multivariate and geometric morphometric approach, this research provides a better understanding of the effects of the environment on craniomandibular form in early hominins. In this study, 107 cranial and 108 mandible specimens of 9 modern primate species were 3D imaged, and geometric morphometrics statistics were used to quantify and assess the patterns of variation between intra- and interspecific datasets concerning habitat type. Results were visualised through Principal Component scatter plots and Thin-plate Spline deformation warps, which identified critical morphological high-to-low-energy bending areas. This application addressed the questions: • to what extent does ecology influence craniomandibular morphology? • what are the main environmental pressures that encourage morphological variance in hominins? The main methodological aims sought to a) create accurate 3D digital renderings of primate skull specimens and b) define a reproducible geometric morphometric technique, which could be used as a valid and precise statistical procedure for future studies regarding hominin ecomorphology. This was achieved by pilot testing laser scanning hardware, digitising cranial and mandibular specimen, testing 3D scanning accuracy, and the best practice for capturing accurate 3D imagery, e.g. environment, lighting and meshing multiple scans. The pilot phase of this thesis also tested statistical programming toolkits capable of carrying out the finalised geometric morphometric methodology. This was achieved through trials of landmarking and statistical procedures on various data processing software, e.g. Checkpoint, TINA, and MeshLabs. Ultimately, the R Project software and accompanying IDE, R Studio, was used to collect, process and analyse the specimen shape data. This thesis contributes to the study of hominin ecomorphological patterning through a comparative approach investigating primate skull adaptation. The main findings showed habitat type as having statistical significance on the cranium's morphology but quantifiably more so in the mandible, which reported 63.71% of the overall variance observed in the first two Principal Components. This was an increase of 10.44% compared to the interspecific cranial dataset and was supported by Two-block Partial Least Squares and Procrustes ANOVA analysis. The geometric morphometric results showed significant environmental influence on the morphology of the primate cranium, most notably concerned with locomotive functions and visualises a distinction between primates who are more arboreally inclined versus those whose primary form of locomotion is terrestrial. The study also found that dietary specialisations are particularly distinguished by patterns of variation between highly folivorous versus more frugivorous species in both inter-and intraspecific groups

THE ECOLOGICAL CAUSES AND CONSEQUENCES OF PREY CHOICE AND ONTOGENETIC NICHE SHIFTS IN THE COMMON GOBY

Foraging behaviour of the common goby, Pomatoschistus microps was investigated in both the United Kingdom and Sweden, with the aim of establishing causes and consequences of prey choice and ontogenetic shifts in diet. Goby life-cycle could be clearly divided into two stages, where prey choice changed abruptly from meio- to macrofauna at a standard length of 30 mm. This diet-shift maximised net energy intake rates, as illustrated by a quantitatively validated optimal foraging model. Intrinsic mechanisms were of greater importance than extrinsic factors in driving this shift. Metabolism, the primary prey choice determinant, revealed canalised and predictable diet shifts in the face of variable prey availability. This was in strong contrast to the more usual determinants such as gape limitation or extrinsic factors, such as habitat shift, prey availability and predation risk. Post diet-shift gobies consumed a range of benthic macrofauna dependent on availability. This plasticity in prey choice suggested that foraging efficiency was at some level below that expected for specialist foragers. Translocation experiments provided support for the general assertion that learning and experience are mechanisms through which generalist foragers could improve their foraging efficiency. Ontogenetic changes in prey choice did not result in a trade-off between foraging efficiency and other ecological parameters, leading to a prediction, upheld by geometric morphometries, that there would be no change in morphology associated with this change in diet. Conditions precluding diet shifts, and the resulting consequences, were explored using mesocosm manipulations. Adult gobies prevented from feeding on macrofauna suffered reduced condition and fitness. Pomatoschistus microps is an ideal species for investigations into foraging behaviour and has provided valuable support for current foraging paradigms as well as novel insights into the causes and consequences of prey choice

Getting its feet on the ground : elucidating Paralouatta's semi-terrestriality using the virtual morpho-functional toolbox

Altres ajuts: CERCA Programme/Generalitat de CatalunyaCurrently, there are no living platyrrhine primates inhabiting the main Caribbean islands. Nevertheless, the fossil record of this area has provided outstanding findings of different New World monkeys that were part of a diverse radiation exhibiting remarkably unusual morphologies. Among these, the Cuban genus Paralouatta corresponds to one of the most enigmatic primates ever found in the Greater Antilles. Some researchers have argued that Paralouatta's post-cranium shows evidence of semi-terrestriality, a locomotor adaptation that is unusual, if not unique, in platyrrhine evolutionary history. Whether or not Paralouatta was truly semi-terrestrial remains uncertain, however, due to a lack of more sophisticated functional analyses on its morphology. Using novel virtual morpho-functional techniques on a comparative sample of 3D talar models belonging to diverse primate species representing three substrate preferences, this study aims to further evaluate whether Paralouatta was a semi-terrestrial genus or not. Geometric morphometrics and finite element analysis were used to empirically assess shape and biomechanical performance, respectively, and then several machine-learning (ML) classification algorithms were trained using both morphometric and biomechanical data to elucidate the substrate preference of the fossils. The ML algorithms categorized the Paralouatta specimens as either arboreal or as species commonly active on both ground and in trees. These mixed results are suggestive of some level of semi-terrestriality, thus representing the only known example of this locomotor behavior in platyrrhine evolutionary history