Towards computer-automated mechatronic design and optimization using linear graphs and evolutionary computing

A comparison of literature between the linear graph (LG) and bond graph (BG) approaches shows that the surpassing of BGs to LGs in applications related to the modeling of mechatronic systems is driven primarily by a lack of available LG-based software. As a result, a robust software toolbox called LGtheory has been developed for automating the evaluation of LG models in the MATLAB programming environment. This thesis details the development of LGtheory, and the algorithms and procedures employed for the evaluation of LG models. In addition, demonstrations of this toolbox to a process for automating the design of electronic filter circuits, as well as, the modeling and simulation of the dynamics of a mobile robotic system are presented. The results of these demonstrations validate the accuracy of the LGtheory toolbox for modeling complex multi-domain systems, and provides the methodological basis for the automated design of mechatronic systems using LGs

Vessel noise affects routine swimming and escape response of a coral reef fish

An increasing number of studies have shown that anthropogenic noise can negatively affect aspects of the anti-predator behaviour of reef fishes, potentially affecting fitness and survival. However, it has been suggested that effects could differ among noise sources. The present study compared two common sources of anthropogenic noise and investigated its effects on behavioural traits critical for fish survival. In a tank-based experiment we examined the effects of noise from 4-stroke motorboats and ships (bulk carriers > 50,000 tonnes) on the routine swimming and escape response of a coral reef fish, the whitetail damselfish (Pomacentrus chrysurus). Both 4-stroke boat and ship noise playbacks affected the fast-start response and routine swimming of whitetail damselfish, however the magnitude of the effects differed. Fish exposed to ship noise moved shorter distances and responded more slowly (higher response latency) to the startle stimulus compared to individuals under the 4-stroke noise treatment. Our study suggests that 4-stroke and ship noise can affect activity and escape response of individuals to a simulated predation threat, potentially compromising their anti-predator behaviour

Habitat degradation and predators have independent trait-mediated effects on prey

Coral reefs are degrading globally leading to a catastrophic loss of biodiversity. While shifts in the species composition of communities have been well documented associated with habitat change, the mechanisms that underlie change are often poorly understood. Our study experimentally examines the effects of coral degradation on the trait-mediated effects of predators on the morphology, behaviour and performance of a juvenile coral reef fish. Juvenile damselfish were exposed to predators or controls (omnivore or nothing) in seawater that had flowed over either live or dead-degraded coral over a 45d period. No interaction between water source and predator exposure was found. However, fish exposed to degraded water had larger false eyespots relative to the size of their true eyes, and were more active, both of which may lead to a survival advantage. Non-consumptive effects of predators on prey occurred regardless of water source and included longer and deeper bodies, large false eyespots that may distract predator strikes away from the vulnerable head region, and shorter latencies in their response to a simulated predator strike. Research underscores that phenotypic plasticity may assist fishes in coping with habitat degradation and promote greater resilience to habitat change than may otherwise be predicted

Relative influence of environmental factors on the timing and occurrence of multi-species coral reef fish aggregations

Reef configuration and hydrodynamics were identified as the principle physical drivers behind coral reef fish aggregations on a mid-shelf patch reef in the northern section of the Great Barrier Reef (-16.845°, 146.23°). The study was carried out over a six-year period at a large reef pass on the oceanic margin of the northern Great Barrier Reef. Over this period (February 2006 –December 2012) tidal state, moon phase and surface seawater temperature were monitored. The timing of sampling was organised to assess variation in physical environment at daily, monthly, seasonal and annual time scales. Over these time scales, temporal patterns of occurrence of 10 species of coral reef fish from 5 families representing 5 defined trophic groups were monitored. The study incorporated 1,357 underwater visual census counts involving 402,370 fish and these estimates were collated with data on tidal state, water temperature, lunar and seasonal periodicity. Aggregated boosted regression trees analysed the univariate responses of fish abundance and species richness to the variation in the physical environment of the reef pass. Flood tides or when water flows from open water through the pass and into the Moore Reef lagoon had 2.3 times as many fish and 1.75 times as many species compared to counts made on ebb tides. Fish abundance was highest in late winter and spring months (Austral calendar), but notably when water temperatures were below the long-term mean of 27°C. Multivariate regression trees and Dufrêne-Legendre indicator predicted 4 out of 10 times the occurrence of all 10 species at any temporal scale ranging from hours to years. Flood tides were the principle driver underlying the occurrence of all 10 species regardless of their trophic classification and produced distinct seasonal assemblages, indicative of fishes aggregating to forage and reproduce

Reduced swimming performance repeatedly evolves on loss of migration in landlocked populations of alewife

Author Posting. © University of Chicago, 2018. This article is posted here by permission of University of Chicago Press for personal use, not for redistribution. The definitive version was published in Physiological and Biochemical Zoology 91 (2018):814–825, doi:10.1086/696877.Whole-organism performance tasks are accomplished by the integration of morphological traits and physiological functions. Understanding how evolutionary change in morphology and physiology influences whole-organism performance will yield insight into the factors that shape its own evolution. We demonstrate that nonmigratory populations of alewife (Alosa pseudoharengus) have evolved reduced swimming performance in parallel, compared with their migratory ancestor. In contrast to theoretically and empirically based predictions, poor swimming among nonmigratory populations is unrelated to the evolution of osmoregulation and occurs despite the fact that nonmigratory alewives have a more fusiform (torpedo-like) body shape than their ancestor. Our results suggest that elimination of long-distance migration from the life cycle has shaped performance more than changes in body shape and physiological regulatory capacity.Funding was provided by the University of Connecticut’s Department of Ecology and Evolutionary Biology and El Muy Viejo.2019-01-3

Reduced swimming performance repeatedly evolves on loss of migration in landlocked populations of alewife

Author Posting. © University of Chicago, 2018. This article is posted here by permission of University of Chicago Press for personal use, not for redistribution. The definitive version was published in Physiological and Biochemical Zoology 91 (2018):814–825, doi:10.1086/696877.Whole-organism performance tasks are accomplished by the integration of morphological traits and physiological functions. Understanding how evolutionary change in morphology and physiology influences whole-organism performance will yield insight into the factors that shape its own evolution. We demonstrate that nonmigratory populations of alewife (Alosa pseudoharengus) have evolved reduced swimming performance in parallel, compared with their migratory ancestor. In contrast to theoretically and empirically based predictions, poor swimming among nonmigratory populations is unrelated to the evolution of osmoregulation and occurs despite the fact that nonmigratory alewives have a more fusiform (torpedo-like) body shape than their ancestor. Our results suggest that elimination of long-distance migration from the life cycle has shaped performance more than changes in body shape and physiological regulatory capacity.Funding was provided by the University of Connecticut’s Department of Ecology and Evolutionary Biology and El Muy Viejo.2019-01-3

Identification of supraoptimal temperatures in juvenile blueback herring (\u3cem\u3eAlosa aestivalis\u3c/em\u3e) using survival, growth rate and scaled energy reserves

For young fishes, growth of somatic tissues and energy reserves are critical steps for survival and progressing to subsequent life stages. When thermal regimes become supraoptimal, routine metabolic rates increase and leave less energy for young fish to maintain fitness-based activities and, in the case of anadromous fishes, less energy to prepare for emigration to coastal habitats. Thus, understanding how energy allocation strategies are affected by thermal regimes in young anadromous fish will help to inform climate-ready management of vulnerable species and their habitat. Blueback herring (Alosa aestivalis) are an anadromous fish species that remain at historically low population levels and are undergoing southern edge-range contraction, possibly due to climate change. We examined the effects of temperature (21°C, 24°C, 27°C, 30°C, 33°C) on survival, growth rate and energy reserves of juveniles collected from the mid-geographic range of the species. We identified a strong negative relationship between temperature and growth rate, resulting in smaller juveniles at high temperatures. We observed reduced survival at both 21°C and 33°C, increased fat and lean mass-at-length at high temperatures, but no difference in energy density. Juveniles were both smaller and contained greater scaled energy reserves at higher temperatures, indicating growth in length is more sensitive to temperature than growth of energy reserves. Currently, mid-geographic range juvenile blueback herring populations may be well suited for local thermal regimes, but continued warming could decrease survival and growth rates. Blueback herring populations may benefit from mitigation actions that maximize juvenile energy resources by increasing the availability of cold refugia and food-rich habitats, as well as reducing other stressors such as hypoxic zones

Living in mixed species groups promotes predator learning in degraded habitats

Living in mix-species aggregations provides animals with substantive anti-predator, foraging and locomotory advantages while simultaneously exposing them to costs, including increased competition and pathogen exposure. Given each species possess unique morphology, competitive ability, parasite vulnerability and predator defences, we can surmise that each species in mixed groups will experience a unique set of trade-offs. In addition to this unique balance, each species must also contend with anthropogenic changes, a relatively new, and rapidly increasing phenomenon, that adds further complexity to any system. This complex balance of biotic and abiotic factors is on full display in the exceptionally diverse, yet anthropogenically degraded, Great Barrier Reef of Australia. One such example within this intricate ecosystem is the inability of some damselfish to utilize their own chemical alarm cues within degraded habitats, leaving them exposed to increased predation risk. These cues, which are released when the skin is damaged, warn nearby individuals of increased predation risk and act as a crucial associative learning tool. Normally, a single exposure of alarm cues paired with an unknown predator odour facilitates learning of that new odour as dangerous. Here, we show that Ambon damselfish, Pomacentrus amboinensis, a species with impaired alarm responses in degraded habitats, failed to learn a novel predator odour as risky when associated with chemical alarm cues. However, in the same degraded habitats, the same species learned to recognize a novel predator as risky when the predator odour was paired with alarm cues of the closely related, and co-occurring, whitetail damselfish, Pomacentrus chrysurus. The importance of this learning opportunity was underscored in a survival experiment which demonstrated that fish in degraded habitats trained with heterospecific alarm cues, had higher survival than those we tried to train with conspecific alarm cues. From these data, we conclude that redundancy in learning mechanisms among prey guild members may lead to increased stability in rapidly changing environments