Thesis (Ph. D.)--Drexel University, 2004. / Includes abstract and vita. Includes bibliographical references (leaves 192-199).

Assessment of the “health” of an ecosystem is often of great interest to those interested in monitoring and conservation of ecosystems. Traditionally, scientists have quantified the health of an ecosystem using multimetric indices that are semi-qualitative. Recently, a statistical-based index called the Latent Health Factor Index (LHFI) was devised to address many inadequacies of the conventional indices. Relying on standard modelling procedures, unlike the conventional indices, accords the LHFI many advantages: the LHFI is less arbitrary, and it allows for straightforward model inference and for formal statistical prediction of health for a new site (using only supplementary environmental covariates). In contrast, with conventional indices, formal statistical prediction does not exist, meaning that proper estimation of health for a new site requires benthic data which are expensive and time-consuming to gather. As the LHFI modelling methodology is a relatively new concept, it has so far only been demonstrated (and validated) on freshwater ecosystems. The goal of this thesis is to apply the LHFI modelling methodology to estuarine ecosystems, particularly to the previously unassessed system in Richibucto, New Brunswick. Specifically, the aims of this thesis are threefold: firstly, to investigate whether the LHFI is even applicable to estuarine systems since estuarine and freshwater metrics, or indicators of health, are quite different; secondly, to determine the appropriate form that the LHFI model if the technique is applicable; and thirdly, to assess the health of the Richibucto system. Note that the second objective includes determining which covariates may have a significant impact on estuarine health. As scientists have previously used the AZTI Marine Biotic Index (AMBI) and the Infaunal Trophic Index (ITI) as measurements of estuarine ecosystem health, this thesis investigates LHFI models using metrics from these two indices simultaneously. Two sets of models were considered in a Bayesian framework and implemented using Markov chain Monte Carlo techniques, the first using only metrics from AMBI, and the second using metrics from both AMBI and ITI. Both sets of LHFI models were successful in that they were able to make distinctions between health levels at different sites.

Assessment of the “health” of an ecosystem is often of great interest to those interested in monitoring and conservation of ecosystems. Traditionally, scientists have quantified the health of an ecosystem using multimetric indices that are semi-qualitative. Recently, a statistical-based index called the Latent Health Factor Index (LHFI) was devised to address many inadequacies of the conventional indices. Relying on standard modelling procedures, unlike the conventional indices, accords the LHFI many advantages: the LHFI is less arbitrary, and it allows for straightforward model inference and for formal statistical prediction of health for a new site (using only supplementary environmental covariates). In contrast, with conventional indices, formal statistical prediction does not exist, meaning that proper estimation of health for a new site requires benthic data which are expensive and time-consuming to gather. As the LHFI modelling methodology is a relatively new concept, it has so far only been demonstrated (and validated) on freshwater ecosystems. The goal of this thesis is to apply the LHFI modelling methodology to estuarine ecosystems, particularly to the previously unassessed system in Richibucto, New Brunswick. Specifically, the aims of this thesis are threefold: firstly, to investigate whether the LHFI is even applicable to estuarine systems since estuarine and freshwater metrics, or indicators of health, are quite different; secondly, to determine the appropriate form that the LHFI model if the technique is applicable; and thirdly, to assess the health of the Richibucto system. Note that the second objective includes determining which covariates may have a significant impact on estuarine health. As scientists have previously used the AZTI Marine Biotic Index (AMBI) and the Infaunal Trophic Index (ITI) as measurements of estuarine ecosystem health, this thesis investigates LHFI models using metrics from these two indices simultaneously. Two sets of models were considered in a Bayesian framework and implemented using Markov chain Monte Carlo techniques, the first using only metrics from AMBI, and the second using metrics from both AMBI and ITI. Both sets of LHFI models were successful in that they were able to make distinctions between health levels at different sites.

Excessive sedimentation is a major stressor to ecosystem health in freshwater systems globally. Benthic macroinvertebrates are excellent bioindicators of ecosystem health because they have a range of environmental tolerances and are typically associated with certain substrate types. This study tested the hypothesis that sedimentation is a driver of benthic macroinvertebrate communities by determining their responses to increased deposited sediment levels in the Northern Great Plains using both experimental and survey approaches. In both approaches, the effects of deposited sediment were isolated, the responses of specific indicator invertebrates were characterized and finally, indices that commonly respond to deposited sediment were analyzed for their sensitivity. At the community level, the overall multivariate redundancy model was not significant and deposited sediment accounted for only 0.2% of the total variation in species composition in the river survey. Indicator species analysis identified taxa that were associated with sediment impairment classes in both studies. Index sensitivities indicated that Percent Swimmers responded to sediment and can potentially be used as an index of deposited sediment in this region, however this index was not sensitive to sediment in the landscape-scale survey. Although individual taxa that responded to sediment deposition may be used as bioindicators of sediment impairment in further studies, the relatively small effect of sediment at the community level and on univariate composition metrics suggests benthic macroinvertebrate communities are adapted to deposited sediment in the Northern Great Plains.

Aim: This series of studies assessed the influence that digenean parasites exert on a host population beyond the initial cost of infection. It aimed to address the discrepancy between the exclusion of parasites from most ecological studies, and their functional importance within the wider free-living community. It also assessed methodologies that utilise the diversity of the parasite community as well as the phenotypic effects of parasitism, as potential tools for ecology and palaeoecology. Results: From 2004-2007, in excess of 53,000 snails were dissected during the course of these studies. Making it one of the most detailed parasitological studies undertaken on a single host parasite interaction in this field. Community studies - Parasite diversity was found to be influenced by local scale abiotic, as well as large scale environmental patterns. Parasite diversity correlates with the distribution of definitive avian hosts, which in turn correlates with intertidal benthic communities. These correlations provide an effective methodology for monitoring ecosystem health. Behavioural studies - A critical assessment of parasite mediated behavioural change revealed the indirect cost of gigantism in the host population to be a side effect, and that differences in behaviours were often a result of size rather than infection. Growth/Morphometric studies - Gigantism was revealed as both infection and environment driven. Finally, morphometric analysis revealed conchiometric markers that provide tools for reconstructing past environments and infection prevalence. Main conclusions: The functional importance of digenean parasitism within the intermediate host snail Hydrobia ulvae, extends far beyond the individual. Digeneans directly and indirectly manipulate the host population, in turn affecting wider community structure. Environmental, abiotic and biotic factors can leave observable imprints on the infected and uninfected host population. Such markers can provide tools and methodologies for furthering our understanding of both extinct and extant host-parasite populations.

Thesis--Auburn University, 2009. / Abstract. Includes bibliographical references (p. 125-131).

Thesis (Ph. D.)--Oregon State University, 2001. / Typescript (photocopy). Includes bibliographical references. Also available on the World Wide Web.

Thesis (Ph.D.)--University of Waikato, 2006. / Includes bibliographical references (leaves 135-150)

Context: Since the beginnings of software engineering, metrics (such as SLOCs) and practices have been used in an attempt to measure and improve the features of software development projects, their process, or their contributors. Measuring and enhancing software ecosystem features brings a new complexity level because a software ecosystem comprises several interrelated software projects. Over the past two decades, software ecosystems have gained considerable attention, and researchers have proposed various metrics and practices to measure and improve software ecosystems' health. Objective: This thesis presents a systematic literature review that aims to build comprehensive taxonomies for software ecosystem health metrics and practices. These taxonomies synthesize the results of previous categorizations and update them with newer metrics and practices proposed since then. This study also aims to collect and synthesize all the definitions, metrics, and practices proposed to define, measure, and improve software ecosystem health in the literature. Method: I conducted a systematic literature review and identified 40 primary studies related to defining and measuring software ecosystem health. I extracted the definitions, metrics, and practices for software ecosystem health from the primary studies, and then I categorized the metrics and practices to build the taxonomies. Results: I identified a total of 7 different definitions for software ecosystem health, 142 different metrics, and 174 various practices for software ecosystem health. Our taxonomies for software ecosystem health metrics and practices have three categories (niche creation, productivity, and robustness). Each of these categories has several sub-categories of metrics and practices. Conclusion: Software ecosystems have a wide range of stakeholders that have different perspectives regarding software ecosystem health. To satisfy this spectrum, researchers have proposed various metrics and practices to measure and improve software ecosystems' health. To improve unifying contrasting opinions, I conducted this study. The metrics and practices proposed are diverse in both purpose and the data required to compute them. Some metrics are presented along with a method on how to compute them. In contrast, others are defined abstractly without an operational approach to calculate them, and some are mentioned without a clear rationale. Furthermore, the same metric or practice is often proposed in more than one publication using different names. This thesis addresses these alignment problems. / Graduate

Increasing urbanisation is one of the biggest pressures to vegetation in the City of Cape Town. The growth of the city dramatically reduced the area under indigenous Fynbos vegetation, which remains in isolated fragments. These are subject to a number of threats including atmospheric deposition, atypical fire cycles and invasion by exotic plant and animal species. Especially the Port Jackson willow (Acacia saligna) extensively suppresses the indigenous Fynbos vegetation with its rapid growth. The main objective of this study was to investigate indicators for a quick and early prediction of the health of the remaining Fynbos fragments in the City of Cape Town with help of remote sensing. First, the productivity of the vegetation in response to rainfall was determined. For this purpose, the Enhanced Vegetation Index (EVI), derived from Terra MODIS data with a spatial resolution of 250m, and precipitation data of 19 rainfall stations for the period from 2000 till 2008 were used. Within the scope of a flexible regression between the EVI data and the precipitation data, different lags of the vegetation response to rainfall were analysed. Furthermore, residual trends (RESTREND) were calculated, which result from the difference between observed EVI and the one predicted by precipitation. Negative trends may suggest a degradation of the habitats. In addition, the so-called Rain-use Efficiency (RUE) was tested in this context. It is defined as the ratio between net primary production (NPP) – represented by the annual sum of EVI – and the annual rainfall sum. These indicators were analysed for their suitability to determine the health of the indigenous Fynbos vegetation. Furthermore, the degree of dispersal of invasive species especially the Acacia saligna was investigated. With the specific characteristics of the tested indicators and the spectral signature of Acacia saligna, i.e. its unique reflectance over the course of the year, the dispersal was estimated. Since the growth of invasive species dramatically reduces the biodiversity of the fragments, their presence is an important factor for the condition of ecosystem health. This work focused on 11 test sites with an average size of 200ha, distributed over the whole area of the City of Cape Town. Five of these fragments are under conservation and the others shall be protected in the near future, too, which makes them of special interest. In January 2010, fieldwork was undertaken in order to investigate the state and composition of the local vegetation. The results show promising indicators for the assessment of ecosystem health. The coefficients of determination of the EVI-rainfall regression for Fynbos are minor, because the reaction of this vegetation type to rainfall is considerably lower than the one of the invasive species. Thus, a good distinction between indigenous and alien vegetation is possible on the basis of this regression. On the other hand, the RESTREND method, for which the regression forms the basis, is only of limited use, since the significance of these trends is not given for Fynbos vegetation. Furthermore, the RUE has considerable potential for the assessment of ecosystem health in the study area. The Port Jackson willow has an explicitly higher EVI than the Fynbos vegetation and thus its RUE is more efficient for a similar amount of rainfall. However, it has to be used with caution, because local and temporal variability cannot be extinguished in the study area over the rather short MODIS time series. These results display that the interpretation of the indicators has to be conducted differently from the literature, because the element of invasive species was not considered in most of the previous papers. An increase in productivity is not necessarily equivalent with an improvement in health of the fragment, but can indicate a dispersal of Acacia saligna. This shows the general problem of the term ‘degradation’ which in most publications so far is only measured by productivity and other factors like invasive species are disregarded. On the basis of the EVI-rainfall regression and statistical measures of the EVI, the distribution of invasive species could be delineated. Generally, a strong invasion of the Port Jackson willow was discovered on the test sites. The results display that a reasoned and sustainable management of the fragments is essential in order to prevent the suppression of the indigenous Fynbos vegetation by Acacia saligna. For this purpose, remote sensing can give an indication which areas changed so that specific field surveys can be undertaken and subsequent management measures can be determined. / Zunehmende Urbanisierung stellt eine der größten Bedrohungen für die Vegetation im Großraum Kapstadt dar. Durch das schnelle Wachstum der Stadt bleibt immer weniger der ursprünglichen Vegetation in isolierten Fragmenten zurück. Diese sind in ihrer Funktion als Lebensraum für Flora und Fauna unter Anderem durch Luftverschmutzung, untypische Feuerzyklen und das Eindringen fremder Arten gefährdet. Besonders die Weidenblatt-Akazie (Acacia Saligna) verdrängt die einheimische Fynbos-Vegetation großflächig durch ihr schnelles Wachstum. Hauptziel dieser Arbeit war es, mit Hilfe der Fernerkundung Indikatoren zu finden, um eine schnelle und frühzeitige Aussage über die Gesundheit der verbliebenen natürlichen Vegetationsfragmente im Großraum Kapstadt zu ermöglichen. Zunächst wurde die Produktivität der Vegetation und deren Reaktion auf Niederschlag analysiert. Zu diesem Zweck wurden der Enhanced Vegetation Index (EVI) aus Terra-MODIS-Daten mit einer räumlichen Auflösung von 250m und Niederschlagsdaten von 19 Wetterstationen aus dem Zeitraum 2000 bis 2008 verwendet. Im Rahmen einer flexiblen Regression zwischen EVI und Niederschlagsdaten wurden verschiedene Verzögerungen der Reaktion der Vegetation auf den Niederschlag getestet. Des Weiteren wurden residuale Trends (RESTREND) berechnet, die sich aus der Differenz zwischen beobachtetem EVI und dem aus dem Niederschlag vorhergesagten EVI ergeben. Zusätzlich wurde die sogenannte Rain-use Efficiency (RUE) getestet. Diese ist definiert durch das Verhältnis zwischen Nettoprimärproduktion, repräsentiert durch die Jahressumme des EVI, und der Jahressumme des Niederschlags. Die angewandten Indikatoren wurden darauf untersucht, ob sie eine Aussage über die Gesundheit der einheimischen Fynbos-Vegetation ermöglichen. Des Weiteren wurde der Verbreitungsgrad invasiver Arten, besonders der der Weidenblatt-Akazie bestimmt. Auf Basis der spezifischen Charakteristika der getesteten Indikatoren und der spektralen Signatur von Acacia saligna, also ihrer besonderen Reflexion über den Jahresverlauf, wurde die Verbreitung ermittelt. Da das ungehinderte Wachstum invasiver Arten die Biodiversität der Fragmente stark verringert, ist ihre Anwesenheit ein wichtiger Faktor für die Gesundheit von Ökosystemen. Diese Arbeit konzentrierte sich auf 11 Testflächen mit einer durchschnittlichen Größe von 200ha, die über die gesamte Fläche des Großraums Kapstadt verteilt sind. Fünf dieser Fragmente stehen bereits unter Schutz, während die anderen in absehbarer Zeit folgen sollen; dies macht sie von besonderem Interesse. Im Januar 2010 wurden Geländearbeiten durchgeführt um den Zustand und die Zusammensetzung der Vegetation vor Ort festzustellen. Die Ergebnisse weisen aussichtsreiche Indikatoren zur Abschätzung der Ökosystemgesundheit auf. Die Werte des Bestimmtheitsmaßes der EVI-Niederschlags-Regression sind niedrig für Fynbos, da die Reaktion dieses Vegetationstyps auf Niederschlag wesentlich geringer ist als die der invasiven Arten. Daher ist auf Basis dieser Regression eine gute Unterscheidung zwischen einheimischer und invasiver Vegetation möglich. Auf der anderen Seite ist die RESTREND-Methode, für die diese Regression die Grundlage bildet, nur begrenzt von Nutzen, da die Signifikanzen dieser Trends für Fynbos-Vegetation nicht gegeben sind. Des Weiteren weist die RUE Potential für die Abschätzung von Ökosystemgesundheit im Testgebiet auf. Die Weidenblatt-Akazie hat einen wesentlichen höheren EVI als die Fynbos-Vegetation und daher ist deren RUE bei vergleichbarer Niederschlagsmenge effizienter. Dennoch muss diese mit Vorsicht angewandt werden, da die hohe lokale und temporale Variabilität der RUE im Testgebiet über die relativ kurze MODIS-Zeitserie nicht eliminiert werden kann. Die Ergebnisse verdeutlichen zudem, dass die Interpretation der Indikatoren anders als in der Literatur durchgeführt werden muss, da das Element der invasiven Vegetation in den meisten der vorangegangenen Arbeiten nicht berücksichtigt wurde. Ein Anstieg der Produktivität ist hier nicht gleichzusetzen mit einer Verbesserung der Gesundheit eines Fragments, sondern deutet viel mehr auf eine Verbreitung der Weidenblatt-Akazie hin. Dies verdeutlicht das generelle Problem des Begriffs ‚Degradation‘, welche in den meisten Veröffentlichungen nur über die Produktivität der Vegetation bestimmt wird während andere Faktoren wie zum Beispiel invasive Arten unberücksichtigt bleiben. Auf Basis der EVI-Niederschlags-Regression und der statistischen Messgrößen des EVI konnte die Verbreitung der invasiven Arten abgegrenzt werden. Generell wurde ein starker Befall der Testflächen durch die Weidenblatt-Akazie festgestellt. Die Ergebnisse machen deutlich, dass ein durchdachtes und nachhaltiges Management der Fragmente notwendig ist um die Verdrängung der einheimischen Fynbos-Vegetation durch Acacia saligna zu verhindern. Die Fernerkundung kann zu diesem Zweck Hinweise liefern, welche Flächen sich verändert haben um anschließend gezielte Begehungen vorzunehmen und Maßnahmen einzuleiten.