The application of artificial neural networks to the interpretation and classification of freshwater benthic invertebrate communities

This thesis presents a thorough and principled investigation into the application of artificial neural networks to the biological monitoring of freshwater. It contains original ideas on the classification and interpretation of benthic macroinvertebrates, and aims to demonstrate their superiority over the biotic systems currently used in the UK to report river water quality. The conceptual basis of a new biological classification system is described, and a full review and analysis of a number of river data sets is presented. The biological classification is compared to the common biotic systems using data from the Upper Trent catchment. This data contained 292 expertly classified invertebrate samples identified to mixed taxonomic levels. The neural network experimental work concentrates on the classification of the invertebrate samples into biological class, where only a subset of the sample is used to form the classification. Other experimentation is conducted into the identification of novel input samples, the classification of samples from different biotopes and the use of prior information in the neural network models. The biological classification is shown to provide an intuitive interpretation of a graphical representation, generated without reference to the class labels, of the Upper Trent data. The selection of key indicator taxa is considered using three different approaches; one novel, one from information theory and one from classical statistical methods. Good indicators of quality class based on these analyses are found to be in good agreement with those chosen by a domain expert. The change in information associated with different levels of identification and enumeration of taxa is quantified. The feasibility of using neural network classifiers and predictors to develop numeric criteria for the biological assessment of sediment contamination in the Great Lakes is also investigated.

Knowledge-based systems and engineering software

The work described was carried out as part of a collaborative Alvey software engineering project (project number SE057). The project collaborators were the Inter-Disciplinary Higher Degrees Scheme of the University of Aston in Birmingham, BIS Applied Systems Ltd. (BIS) and the British Steel Corporation. The aim of the project was to investigate the potential application of knowledge-based systems (KBSs) to the design of commercial data processing (DP) systems. The work was primarily concerned with BIS's Structured Systems Design (SSD) methodology for DP systems development and how users of this methodology could be supported using KBS tools. The problems encountered by users of SSD are discussed and potential forms of computer-based support for inexpert designers are identified. The architecture for a support environment for SSD is proposed based on the integration of KBS and non-KBS tools for individual design tasks within SSD - The Intellipse system. The Intellipse system has two modes of operation - Advisor and Designer. The design, implementation and user-evaluation of Advisor are discussed. The results of a Designer feasibility study, the aim of which was to analyse major design tasks in SSD to assess their suitability for KBS support, are reported. The potential role of KBS tools in the domain of database design is discussed. The project involved extensive knowledge engineering sessions with expert DP systems designers. Some practical lessons in relation to KBS development are derived from this experience. The nature of the expertise possessed by expert designers is discussed. The need for operational KBSs to be built to the same standards as other commercial and industrial software is identified. A comparison between current KBS and conventional DP systems development is made. On the basis of this analysis, a structured development method for KBSs in proposed - the POLITE model. Some initial results of applying this method to KBS development are discussed. Several areas for further research and development are identified.

User interface design support for the development of knowledge-based systems

The present scarcity of operational knowledge-based systems (KBS) has been attributed, in part, to an inadequate consideration shown to user interface design during development. From a human factors perspective the problem has stemmed from an overall lack of user-centred design principles. Consequently the integration of human factors principles and techniques is seen as a necessary and important precursor to ensuring the implementation of KBS which are useful to, and usable by, the end-users for whom they are intended. Focussing upon KBS work taking place within commercial and industrial environments, this research set out to assess both the extent to which human factors support was presently being utilised within development, and the future path for human factors integration. The assessment consisted of interviews conducted with a number of commercial and industrial organisations involved in KBS development; and a set of three detailed case studies of individual KBS projects. Two of the studies were carried out within a collaborative Alvey project, involving the Interdisciplinary Higher Degrees Scheme (IHD) at the University of Aston in Birmingham, BIS Applied Systems Ltd (BIS), and the British Steel Corporation. This project, which had provided the initial basis and funding for the research, was concerned with the application of KBS to the design of commercial data processing (DP) systems. The third study stemmed from involvement on a KBS project being carried out by the Technology Division of the Trustees Saving Bank Group plc. The preliminary research highlighted poor human factors integration. In particular, there was a lack of early consideration of end-user requirements definition and user-centred evaluation. Instead concentration was given to the construction of the knowledge base and prototype evaluation with the expert(s). In response to this identified problem, a set of methods was developed that was aimed at encouraging developers to consider user interface requirements early on in a project. These methods were then applied in the two further projects, and their uptake within the overall development process was monitored. Experience from the two studies demonstrated that early consideration of user interface requirements was both feasible, and instructive for guiding future development work. In particular, it was shown a user interface prototype could be used as a basis for capturing requirements at the functional (task) level, and at the interface dialogue level. Extrapolating from this experience, a KBS life-cycle model is proposed which incorporates user interface design (and within that, user evaluation) as a largely parallel, rather than subsequent, activity to knowledge base construction. Further to this, there is a discussion of several key elements which can be seen as inhibiting the integration of human factors within KBS development. These elements stem from characteristics of present KBS development practice; from constraints within the commercial and industrial development environments; and from the state of existing human factors support.

Industrial Discharges of Metals in Kigali, Rwanda, and the Impact on Drinking Water Quality

Rwanda is a landlocked country located in Africa's Central-East Great Lakes region. It has a population of 7.5 million which occupies 26,338 km'. Its population density (285/km') is one of the highest in the world and has prompted fear of a rapid degradation of the ecosystem. There are no central sewer systems in Rwanda. The use of pit latrines and septic tanks is common in urban and rural areas. People still defecate in the fields (World Bank, 1989). Less than half of the urban population is served by a central water supply. The majority of people get their water untreated from rivers that have been polluted by chemicals and human excreta. In and around the capital city of Kigali, there is a concentration of people, farms, and industries which discharge wastewater into the Nyabarongo River and its tributaries. The Nyabarongo River, a tributary of the Nile, empties into the Akagera River which flows into Lake Victoria. Nyabarongo River water is used for drinking water, cooking, bathing, and agriculture in the Kigali area. There has been very little monitoring of the water quality of the Nyabarongo River and of industrial outfalls located on tributaries of the Nyabarongo River. As a first step in understanding the water quality of the Nyabarongo River, wastewater samples were collected in 1993 from industrial outfalls located on tributaries of the Nyabarongo River. Most of the facilities sampled had no wastewater treatment. The impact of these discharges on the water quality of the Nyabarongo River was evaluated.

Age determinations and stable isotope records of four sediment profiles off Nova Scotia

Continental margin sediments off Nova Scotia accumulate at high rates (up to 360 cm/kyr) and contain a history of millennial-scale environmental changes which are dominated by the proximity of the Laurentide ice sheet during the latest Quaternary. Using stable isotope ratios of oxygen, accelerator mass spectrometer radiocarbon dating, micropaleontology, and sedimentology, we document these changes in six piston cores ranging in water depth from ab. 450 to ab. 4300 m. We find that maximum d18O in N. pachyderma occurred about 15 ka and preceded the maximum abundance of this species in these cores by ab. 1000 years. Between 13 and 14 ka we find a second peak in abundance of N. pachyderma, minimum d18O, and two pulses of ice rafting. The sediment lithology supports terrestrial studies which indicate that there was a general withdrawal of ice beyond the upper Paleozoic and Mesozoic red beds by 14 ka in southeastern Canada, so the ice rafting events between 13 and 14 ka probably reflect ice stream activity in the St. Lawrence valley. The Younger Dryas event is recognized as a peak in abundance of N. pachyderma and ice rafting (dated as ab. 11.3 ka), but meltwater discharge to the Gulf of St. Lawrence was either too small or occurred over too long a time to leave a distinct d18O minimum off Nova Scotia. At 7.1 ka, in the middle of Holocene warming, we find a third peak in abundance of N. pachyderma and another d18O minimum but no ice rafting. We interpret these data as evidence of a late-occurring meltwater event which, if correct, could have originated in the Great Lakes, in the Labrador-Ungava region, or in both. The final millennial-scale phenomenon off Nova Scotia is the onset of "Neoglaciation," marked by increased ice rafting and increased % N. pachyderma beginning about 5 kyr ago.

Quantifying avian relative abundance and ecosystem service value to identify conservation opportunities in the Midwestern U.S.

Grassland birds are highly imperiled because of historical habitat loss and ongoing conversion of grasslands to agricultural and urban land uses. Therefore, prioritizing and further justifying conservation action in remaining grasslands is critical to protecting what remains. Grassland bird conservation has focused on identifying and protecting large grassland complexes referred to as Grassland Bird Conservation Areas (GBCAs). We identified and classified GBCAs in a region highly impacted by both agricultural and urban land conversion using previously developed methods. Then, we extended the analysis to include estimated relative abundance of five grassland focal species in each GBCA. Models of relative abundance were built using eight years of monitoring data collected by citizen scientists. Finally, we quantified the value of ecosystem services provided by each GBCA. There were nearly 55,000 ha of grassland habitats in the Chicago Metropolitan Region that met GBCA criteria, 33% (18,415 ha) of which were protected. Proportion of abundance in protected versus unprotected areas was similar for Bobolink (Dolichonyx oryzivorus; 46%), Grasshopper Sparrow (Ammodramus savannarum; 52%), and Sedge Wren (Cistothorus platensis; 48%), whereas, Henslow’s Sparrow (Ammodramus henslowii; 75%) had a higher proportion of relative abundance in protected GBCAs and Eastern Meadowlark (Sturnella magna) had lower proportions (37%). GBCAs provisioned just under $900 million annually in ecosystem services, 73% of which is because of flood control. Outputs of this comprehensive approach will inform grassland bird conservation by providing detailed information about the value for birds and people of grassland habitats.

(Table 1, page 204), Minor element concentrations in nodules of lake Ontario at Glenola, Bay of Quinte

Spark source mass spectroscopy was used to analyze 61 elements in ten ferromanganese nodules found near Glenora in the Bay of Quinte at the eastern end of Lake Ontario. Most minor elements, including As, Pb, and Hg, have concentrations between 1-100 µg/g. F, S, Co, Zn, and La have concentrations in 100 µg/g range. Ba and Sr are present at levels of 1% and 0.1% respectively. Compared to similar measurements on nodules found in the Great Lakes and in other parts of the globe, values reported here are generally lower. Compared to their marine equivalents, lake nodules appear to be inferior scavengers of minor elements. Examination of all available data corroborates the postulate that marine biological material is an important source of minor elements found in oceanic nodules.

Biological Impacts and Uses of Black Bass Competitive Fishing Tournaments on Large Lake Systems

Recreational fisheries in North America are valued between $47.3 billion and $56.8 billion. Fisheries managers must make strategic decisions based on sound science and knowledge of population ecology, to effectively conserve populations. Competitive fishing, in the form of tournaments, has become an important part of recreational fisheries, and is common on large waterbodies including the Great Lakes. Black Bass, Micropterus spp., are top predators and among the most sought after species in competitive catch-and-release tournaments. This study investigated catch-and-release tournaments as an assessment tool through mark-recapture for Largemouth Bass (>305mm) populations in the Tri Lakes, and Bay of Quinte, part of the eastern basin of Lake Ontario. The population in the Tri Lakes (1999-2002) was estimated to be stable between 21,928-29,780, and the population in the Bay of Quinte (2012-2015) was estimated to be between 31,825-54,029 fish. Survival in the Tri Lakes varied throughout the study period, from 31%-54%; while survival in the Bay of Quinte remained stable at 63%. Differences in survival may be due to differences in fishing pressure, as 34-46% of the Largemouth Bass population on the Tri Lakes is harvested annually and only 19% of catch was attributed to tournament angling. Many biological issues still surround catch-and-release tournaments, particularly concerning displacement from initial capture sites. In the past, the majority of studies have focused on small inland lakes and coastal areas, displacing bass relatively short distances. My study displaced Largemouth and Smallmouth Bass up to 100km, and found very low rates of return; only 1 of 18 Largemouth Bass returned 15 km and 1 of 18 Smallmouth Bass returned 135 km. Both species remained near the release sites for an average of approximately 2 weeks prior to dispersing. Tournament organizers should consider the use of satellite release locations to facilitate dispersal and prevent stockpiling at the release site. Catch-and-release tournaments proved to be a valuable tool in assessing population variables and the effects of long distance displacement through the use of mark recapture and acoustic telemetry on large lake systems.

Molecular Characterization of Three Novel Phospholipase A2 Proteins from the Venom of Atheris chlorechis, Atheris nitschei and Atheris squamigera

Secretory phospholipase A2 (sPLA2) is known as a major component of snake venoms and displays higher-order catalytic hydrolysis functions as well as a wide range of pathological effects. Atheris is not a notoriously dangerous genus of snakes although there are some reports of fatal cases after envenomation due to the effects of coagulation disturbances and hemorrhaging. Molecular characterization of Atheris venom enzymes is incomplete and there are only a few reports in the literature. Here, we report, for the first time, the cloning and characterization of three novel cDNAs encoding phospholipase A2 precursors (one each) from the venoms of the Western bush viper (Atheris chlorechis), the Great Lakes bush viper (Atheris nitschei) and the Variable bush viper (Atheris squamigera), using a “shotgun cloning” strategy. Open-reading frames of respective cloned cDNAs contained putative 16 residue signal peptides and mature proteins composed of 121 to 123 amino acid residues. Alignment of mature protein sequences revealed high degrees of structural conservation and identity with Group II venom PLA2 proteins from other taxa within the Viperidae. Reverse-phase High Performance Liquid Chromatography (HPLC) profiles of these three snake venoms were obtained separately and chromatographic fractions were assessed for phospholipase activity using an egg yolk suspension assay. The molecular masses of mature proteins were all identified as approximately 14 kDa. Mass spectrometric analyses of the fractionated oligopeptides arising from tryptic digestion of intact venom proteins, was performed for further structural characterization.

Génomique des populations et association génotype-phénotype des écotypes de touladi du Lac Supérieur

L’apparition et le maintien d’écotypes adaptés à différentes niches écologiques, en situation de sympatrie, est régit par une multitude de facteurs. Ceux-ci sont essentiels pour la compréhension des processus évolutifs impliqués mais aussi pour la gestion et la conservation des populations en question. Le touladi (Salvelinus namaycush) est un salmonidé reconnu pour la présence d’écotypes liée à l’utilisation des ressources et de l’habitat à travers l’Amérique du Nord. Un total de quatre écotypes a été décrit vivant dans le lac Supérieur, se différenciant par l’habitat utilisé, l’alimentation, la morphologie ainsi que l’ostéologie. L’objectif principal de la présente étude était de quantifier l’étendue de la différentiation génétique entre les différents sites d’échantillonnage ainsi qu’entre les différents écotypes. Un second objectif était d’identifier des marqueurs potentiellement sous sélection entre les différents écotypes reflétant de possibles adaptations locales. Pour ce faire, un total de 486 individus, représentant les quatre écotypes pour chacun des quatre sites d’échantillonnages, a été génotypé à 6822 SNPs (polymorphisme de nucléotide simple). De plus, des analyses morphométriques ont été effectuées afin de caractériser l’ampleur de la divergence morphologique entre les écotypes à chacun des sites. Les résultats ont montré une différentiation génétique, bien que faible, plus prononcée entre les sites d’échantillonnage qu’entre les écotypes à chacun de ces sites. Des indices indiquant la présence de sélection divergente ont aussi été décelés entre les écotypes ou en association avec des variations morphologiques, dont certains marqueurs représentant des traits importants dans la divergence des différents écotypes. Les résultats de cette étude permettront une meilleure gestion et conservation des populations de touladi du lac Supérieur en plus d’éclairer le choix possible de populations sources pour l’ensemencement des autres Grands Lacs.

The bioaccumulation of persistent contaminants by zebra mussels and their effects on state-endangered common terns

Common terns currently are listed as endangered or threatened in many states, including Illinois, Vermont, Pennsylvania, Ohio, Wisconsin, Michigan, and New York, and a species of special concern by the U.S. Fish and Wildlife Service (USFWS, 2002). The sole remaining nesting colony in Illinois is located at the Naval Station Great Lakes (NSGL) in Lake County where intensive management by the Illinois Department of Natural Resources has reduced nest predation and increased the number of eggs that hatch. However, the overall reproductive success (the number of young successfully reaching independence) has not improved. Observations of gross deformities in hatchlings (i.e. compromised feather development and cross-bill), lethargic behavior of young birds, and lesions, suggested the influence of environmental contaminants (Jablonski et al., 2005). I investigated if there were significant levels of environmental contaminants in eggs and nestlings of common terns. While there were minimal concentration of selenium, mercury, lead, and cadmium, there were large concentration of polychlorinated biphenyls (PCBs) in both the eggs and nestlings. The greater amounts of PCBs in older chicks than younger chicks suggest local contamination. In order to potentially manage the factors responsible for exposing the terns to PCBs I investigated the pathway by which PCBs were exposed to terns. The two most likely biological pathways as determined by research on Great Lake fishes were investigated. The first pathway is through atmospheric deposition of PCBs and resuspension of PCB-ladel sediment which are subsequently acquired by filter-feeding fish (e.g. alewives, Alosa pseudoharengus) and then pelagic fish (e.g. lake trout, Salvelinus namaychus) or in this case terns. The second pathway explored was via the biodeposits of zebra mussels which are consumed by round gobies (Neogobius melanostromus) and ultimately littoral fish (e.g. small-mouthed bass, Micropterus dolomieui) or terns. Because common terns breed in near-shore sites where concentrations of zebra mussels are found, as well as forage in more pelagic environments it is possible that either or both pathways may be contributing to their PCB exposure. Field experiments and stable isotope analyses demonstrated that the most likely pathway by which terns are exposed to PCBs is via alewives, similar to how apex predators such as lake trout acquire PCBs. Biodeposits from zebra mussels do not appear to be a significant factor in PCB accumulation in terns. The impact of PCB exposure on birds can vary widely, however in this situation we choise to investigate one specific behavior often affected by PCB exposure, parental attentiveness. PCBs are known to cause endocrine disruption which ultimately results in reduced brooding of young and incubation of eggs. I used temperature sensors to quantify nest temperatures and parental attentiveness during incubation. High concentrations of PCBs in our study population appear to be leading to poor parental attentiveness, and extended periods of absence during incubation and brooding, ultimately leading to poor reproductive success. Common terns are perilously close to being extirpated in Illinois and management of PCB exposure will be difficult. I propose that additional testing should be conducted to locate a site with less PCB contamination and then to move the tern colony to this location, possibly using social cues as has been done with other tern species in Illinois. PCBs are having a profound impact on common tern populations in Illinois and without moving the colony it is likely that the population will continue to decline.

The effect of ecological changes in Lake Victoria on the present trophic characteristics of Oreochromis niloticus in relation to the species' role as a stabilizing factor of biomanipulation

The Lake Victoria ecosystem has experienced such a profound ecological change that Oreochromis niloticus - an introduced species, is the only important cichlid (out of the original 250 + spp) left in the lake. It is the basis of an important commercial fishery which is intensely exploited by sophisticated methods. An investigation of its feeding habits at present indicates that the species could also playa major role in the energy flux of the lake. Fisheries management in Lake Victoria will thus require multi-disciplinary studies which reflect a total ecosystem approach.

The future prospects for the Lake Victoria fishery

The annual fish yields from Lake Victoria have been increasing when the species diversity was dramatically declining. The new fishery is dominated by the introduced predator (Lates niloticus Linne), the exotic herbivore (Oreochromis niloticus Linne) and an indigenous zooplanktivore (Rastrineobola argentea Pellegrin). While the three predominant fish species could sustain the high catch levels, the future viability for the fishery will depend on prudent exploitation regimes and effective management and conservation strategies.

The state and known impacts of fish species transferred to or within continental Africa

Fish introductions have been made from small fish ponds to the largest lakes in Africa. The primary intent of these introductions has been to sustain or increase fish production, although some introductions have been made to develop sport fisheries and to control unwanted organisms. Some of these introductions have fulfilled their objective in the short term, but several of these "successful" introductions have created uncertainties about their long term sustainability. Lates niloticus, Oreochromis niloticus, O. leucostictus, Tilapia melanopleura and T. zilli were introduced into lakes Victoria and Kyoga in 1950s and early 1960s. By the 1980s O. niloticus and O. niloticus dominated the fisheries of these lakes, virtually eliminating a number of endemic fish species. The loss of genetic diversity of the fish in the worlds second largest lake has also been accompanied by a loss of trophic diversity. The transformation of the fish community has, in Lake Victoria coincided with a profound eutrophication (algal blooms, fish kills, hypolimnetic anoxia) which might be related to alterations of the lake's food-web structure. In contrast, the introduction of a planktivore, Limnothrissa miodon into Lake Kivu and the Kariba reservoir has established highly successful fisheries with little documented effect on the pre-existing fish community or trophic ecology of the lakes. The highly endemised species-rich African Great lakes may be particularly sensitive to species introductions and require special consideration and caution when introductions are contemplated because species extinctions, introgressive hybridization and ecosystem alterations may occur following fish introductions.