Since 1982, the state of Illinois has afforested over 100,000 acres of abandoned or marginal cropland. Afforestation, the planting of trees on land not in forest cover, is a sustainable forest management practice that has been shown to store carbon, increase plant diversity, improve soil and water quality, and assist in flood abatement. Our research seeks to develop practical soil and vegetative indicators that can be used by researchers and land managers alike to accurately assess changes to ecosystem function following land use shifts. To assess forest restoration success in terms of ecological function, seven ecological indicators were measured across a chronosequence of 50 afforested sites and 20 mature forested sites. Soil indicators: bulk density, aggregate stability, total nitrogen, total carbon, and labile carbon, and vegetation indicators: forest productivity and stocking density were assessed for each site. Additional sampling was completed on 25 nearby agriculture fields for each of the five soil indicators. Our data were analyzed using an analysis of variance test with multiple comparisons to examine differences among indicator values by land use category. Overall, soil indicator bulk density significantly decreased across afforested sites with stand age, whereas indicators aggregate stability, labile carbon, and total carbon significantly increased across afforested sites with stand age. Linear regression analyses were used to assess the change in indicator values with stand age. Additional linear regression analyses were used to assess the change in indicator values with site index, and significant results were recorded for 3 out of the 5 soil indicators. Indicator bulk density displayed a significant negative relationship with site index, and indicators aggregate stability and total carbon displayed a significant positive relationship with site index. Overall, our results indicated that four out of the five soil parameters measured were successful indicators of restored ecological function in afforested sites. Furthermore, we believe that the inclusion of vegetation indices forest productivity and stocking density provides vital information into forest succession and a better understanding of how productive sites benefit soil quality.

Over the last 30 years, Crab Orchard National Wildlife Refuge in Southern Illinois has made a strong and well-documented effort to convert agricultural lands to forest to further their mission of wildlife and habitat conservation. Our research seeks to assess the influence that this land use conversion has on ecological function and to establish ecological indicators of successful restoration. We examined five potential soil-based indicators of ecological function across a chronosequence of afforested sites at the refuge and compared them to nearby row crop agricultural sites and mature forest sites with similar soils and landscape positions. Collected soil samples were analyzed for total carbon, total nitrogen, labile carbon, aggregate stability, and bulk density. Soil texture analysis was also conducted to validate comparisons among sites. The data were analyzed using a multivariate analysis of variance comparing land uses as well as linear regression analyses looking at the influence of age since restoration on an index value created by subtracting the soil indicator value of the nearby agricultural site from that of the forested site. The index value was used as the dependent variable in order to control for variation among sites and isolate the influence of age. Aggregate stability and labile carbon were positively correlated with age since restoration and bulk density was negatively correlated with age since restoration. These three soil parameters were promising indicators of restored ecological function in afforested sites. Target values for these indicators were proposed. Our results help to determine the timeframe in which these ecological functions return following restoration and can be used to assess the success of current and future afforestation projects.

There is growing concern that human access into areas of wildlife habitat and the management of that access has become one of the most significant issues in sustaining wildlife populations worldwide. Although access management is recommended throughout primary wildlife research and provincial land management plans as a means of wildlife management, limited research has been conducted on measuring the status of access or on access management strategies. Based on a review of the literature on resource management plans and provincial management strategies, this thesis identifies and describes fifteen potential ecological indicators for measuring and monitoring access and access management. Five key findings are summarized from this review. (1) Meaning and implementation of the term `access management' remains vague and ambiguous. (2) Measures of human access are often tied to large mammal management and studies. (3) Access management is a big question, encompassing cumulative impacts, and when viewed from a systems approach should consider ecological indicators across multiple levels of biological organization. (4) Attention is brought to two sub-types of indicators to monitor access management, land use indicators and wildlife use indicators. (5) Ecological indicators of access and access management share one similar data layer, GIS access infrastructure data.

Fishes are widely used by biologist as ecological indicators that measure key elements of complex systems, without having to capture the full complexity of a specific system. The Vaal River in South Africa is classified as Africa’s hardest working river and is home to, two yellowfish species that are socially and economically important. Both these yellowfish species are considered to be sensitive to changes in water quantity and quality, habitat destruction and utilisation pressure and are often used as ecological indicators to manage aquatic ecosystems. Very little however, is known about their movement, response to changing environmental variables and interspecies habitat preferences. This study therefore aims to use radio telemetry as a method to characterise and evaluate how yellowfish behaviour is influenced by changing environmental variables. To characterise the behavioural ecology of the Vaal-Orange River yellowfish species in lentic and lotic ecosystems, Labeobarbus aeneus (n=18) and L. kimberleyensis (n=3) were fitted with externally attached radio transmitters in Boskop Dam (L. aeneus, n=4) and the Vaal River (L. aeneus, n=14) (L. kimberleyensis, n=3). Various methods were used to collect yellowfish species including: gill nets, to target mobile individuals, in deep habitats, electro-fishing (electro-narcosis) to collect yellowfish in shallow habitats and angling techniques in a wide variety of habitats. Thereafter yellowfish species were sedated and tagged with externally attached radio transmitters, before being released back into the system. Yellowfish were monitored for eleven months using a remote monitoring system together with manual monitoring surveys. Analyses of data collected showed that L. aeneus follows distinct behavioural patterns, with some individual variations in behaviour. Labeobarbus aeneus exhibited higher movement that are associated with deeper water during daylight hours (04:00-16:00). During nocturnal periods (20:00-04:00) L. aeneus showed a decrease in movement activity and preferred shallower water compared to daytime. However, L. aeneus in the Vaal River seems to be less influenced by bright daylight and this might be due to the turbidity of the river water. Labeobarbus aeneus in Boskop Dam showed higher movement counts during full moon phases whereas L. aeneus in the Vaal River showed higher movement counts during new moon phases. All tagged fishes in Boskop Dam and in the Vaal River preferred deeper water during full moon phases than during new moon phases. Movement were significantly higher (P<0.05) with increased temperatures and shallower water in summer whereas movement significantly decreased (P<0.05) with a decrease in temperature and increased depth in autumn and winter. Seasonal movement data were, however, limited. This study confirms that radio telemetry methods can be used to characterise the behavioural ecology of yellowfish species. In addition, the study has improved the knowledge of how environmental variables may affect the behaviour of yellowfish species. However, due to limited data and our understanding of these species, it is still uncertain how behaviour of yellowfish species can be applied as an ecological indicator of aquatic ecosystems. / Thesis (MSc (Zoology))--North-West University, Potchefstroom Campus, 2013

Fishes are widely used by biologist as ecological indicators that measure key elements of complex systems, without having to capture the full complexity of a specific system. The Vaal River in South Africa is classified as Africa’s hardest working river and is home to, two yellowfish species that are socially and economically important. Both these yellowfish species are considered to be sensitive to changes in water quantity and quality, habitat destruction and utilisation pressure and are often used as ecological indicators to manage aquatic ecosystems. Very little however, is known about their movement, response to changing environmental variables and interspecies habitat preferences. This study therefore aims to use radio telemetry as a method to characterise and evaluate how yellowfish behaviour is influenced by changing environmental variables. To characterise the behavioural ecology of the Vaal-Orange River yellowfish species in lentic and lotic ecosystems, Labeobarbus aeneus (n=18) and L. kimberleyensis (n=3) were fitted with externally attached radio transmitters in Boskop Dam (L. aeneus, n=4) and the Vaal River (L. aeneus, n=14) (L. kimberleyensis, n=3). Various methods were used to collect yellowfish species including: gill nets, to target mobile individuals, in deep habitats, electro-fishing (electro-narcosis) to collect yellowfish in shallow habitats and angling techniques in a wide variety of habitats. Thereafter yellowfish species were sedated and tagged with externally attached radio transmitters, before being released back into the system. Yellowfish were monitored for eleven months using a remote monitoring system together with manual monitoring surveys. Analyses of data collected showed that L. aeneus follows distinct behavioural patterns, with some individual variations in behaviour. Labeobarbus aeneus exhibited higher movement that are associated with deeper water during daylight hours (04:00-16:00). During nocturnal periods (20:00-04:00) L. aeneus showed a decrease in movement activity and preferred shallower water compared to daytime. However, L. aeneus in the Vaal River seems to be less influenced by bright daylight and this might be due to the turbidity of the river water. Labeobarbus aeneus in Boskop Dam showed higher movement counts during full moon phases whereas L. aeneus in the Vaal River showed higher movement counts during new moon phases. All tagged fishes in Boskop Dam and in the Vaal River preferred deeper water during full moon phases than during new moon phases. Movement were significantly higher (P<0.05) with increased temperatures and shallower water in summer whereas movement significantly decreased (P<0.05) with a decrease in temperature and increased depth in autumn and winter. Seasonal movement data were, however, limited. This study confirms that radio telemetry methods can be used to characterise the behavioural ecology of yellowfish species. In addition, the study has improved the knowledge of how environmental variables may affect the behaviour of yellowfish species. However, due to limited data and our understanding of these species, it is still uncertain how behaviour of yellowfish species can be applied as an ecological indicator of aquatic ecosystems. / Thesis (MSc (Zoology))--North-West University, Potchefstroom Campus, 2013

Marine reserves are promising tools for fisheries management, and are especially suited for complex, multi-species fisheries. Recent work has focused on the design of reserves to achieve particular management objectives and on defining appropriate indicators for monitoring to determine whether these objectives are being met. In principle, there should be a strong correlation between biological, social and economic indicators that are all correlated with fish abundance and ecosystem health. In practice, different indicators are often inconsistent, and it is common for researchers and fishers to have conflicting opinions on how well reserves are meeting management goals. I suggest that these discrepancies are not necessarily due to conflicting opinions regarding management objectives, but rather that the inherent biases in different sampling schemes may cause different measures of the same parameter to be uncorrelated. For example, scientists tend to sample only snapshots in time and space in randomly chosen locations, while fishers sample over much greater temporal and spatial scales but in non-random locations. Furthermore, marine ecosystems are extremely complex, and failing to account for the full extent of this complexity may lead to erroneous measurement of biological trends. The purpose of this dissertation is to determine the causes of discrepancies between different types of indicators using a multidisciplinary approach. A detailed study of the Glover’s Reef Marine Reserve (GRMR) in Belize provides a basis for comparison. Chapters 2 to 4 of the dissertation focus on understanding how the GRMR has functioned to produce fisheries benefits, and elucidating some of the factors responsible for variation in species’ responses to reserve protection. Chapters 5 to 7 of the dissertation focus on comparisons of different indicators of changes in fish abundances, and explain the circumstances under which indicators may disagree. With a better understanding of the functioning of the GRMR based on both scientific and local knowledge, efforts can be made to develop more appropriate indicators, and these indicators can then be tested for use in other coral reef reserves worldwide.

Ecological indicators are defined as quantifiable metrics that can be used to monitor the state of ecosystems and their response to environmental perturbations. In the global oceans, commonly used indicators are typically based on the presence and distribution of phytoplankton (as indexed by the concentration of chlorophyll-a [Chl-a]), which form the base of oceanic food webs. Phytoplankton phenology (the timing of phytoplankton growth) and phytoplankton size structure are particularly important ecological indicators that can be derived via ocean colour remote sensing. Phytoplankton phenology has a direct control on food availability, which subsequently impacts the survival of higher trophic levels and the structure of marine ecosystems. Meanwhile, phytoplankton size structure can be used to define the major functional groups that ultimately influence marine food web structure, biogeochemical cycling and carbon export. The Red Sea is a relatively unexplored tropical marine ecosystem, particularly in relation to its large-scale biological dynamics. In light of recent evidence of rapid regional warming, the need to monitor the response of the Red Sea to potential future ecosystem modifications is becoming more imminent. Using a combination of contemporary oceanographic tools, with an emphasis on ocean colour remote sensing, this PhD thesis attempts to validate the retrieval of phytoplankton ecological indicators in the Red Sea - specifically phytoplankton abundance, phenology and size structure. The interannual variability of both indicators and their linkages with the regional physical environment are also explored.

We describe a case study evaluating the ecological impact of Bromus tectorum L. (cheatgrass) invasion following fire disturbance and the effectiveness of revegetation in improving ecological integrity in a degraded semi-arid shrub steppe system. The effectiveness of rehabilitation efforts was assessed from measurements of arthropod richness, vegetation and arthropod community composition, and ground cover characteristics in three habitats: undisturbed, burned and weed-infested (B. tectorum), and burned and rehabilitated with native and non-native vegetation. Arthropods were collected in each habitat using pitfall traps. Differences in arthropod richness were compared using rarefaction curves. Non-metric multidimensional scaling, and non-parametric multivariate statistical procedures including analysis of similarity and similarity percentages routines were used to compare arthropod and vegetation community composition and ground cover characteristics between habitats. Arthropod communities in the rehabilitated habitat were distinct from and intermediate to those observed in the undisturbed and weed-infested habitats. Rehabilitation in this instance resulted in an improvement in ecological integrity and perhaps an intermediate step on the way complete restoration. Arthropod richness, arthropod and vegetation community composition, and ground cover characteristics were all useful indicators of ecological integrity, but returned slightly different results. Assessing multiple variables yielded the most complete understanding of the habitats studied.

Apesar da importância, a restauração dos remanescentes florestais degradados em paisagens fragmentadas ainda carece de avanços técnico-científicos para que seja incluída na agenda da restauração ecológica. Atualmente, não existem métodos de restauração comprovados, e nem protocolos de avaliação e monitoramento da regeneração natural e da restauração ecológica em fragmentos florestais degradados. Na Floresta Estacional Semidecidual degradada é comum, em áreas de clareiras e com efeito de borda, a hiperabundância de algumas espécies de trepadeiras, que sufocam árvores, inibindo a regeneração de outras espécies. Nessas áreas, o corte de trepadeiras e o plantio de mudas de espécies arbóreas têm sido propostos como técnicas de restauração, entretanto, carecem de investigação quanto à sua eficácia ao longo do tempo. Do mesmo modo, pouco sabemos se de fato essa restauração se faz necessária, pois pouco sabemos se e como as áreas degradadas e sem cobertura de dossel se recuperam ao longo do tempo. A fim de analisar a efetividade do corte de trepadeiras e de plantios de árvores nativas sobre a regeneração da comunidade arbórea em fragmentos florestais degradados, avaliamos a trajetória de cobertura de dossel em um período de 22 anos, e de indicadores ecológicos de restauração florestal em uma cronossequência de 16 anos, em um remanescente de Floresta Estacional Semidecidual localizado na Mata de Santa Genebra, Campinas-SP. Para a avaliação da trajetória de cobertura de dossel, fotografias aéreas de 1994, 2005 e 2016 foram analisadas visualmente e suas clareiras vetorizadas manualmente, permitindo inferir se áreas de clareira se recuperaram ao logo do tempo e se a recuperação do dossel se deu de modo mais efetivo em áreas de borda submetidas a práticas de restauração. O percentual de áreas sem dossel arbóreo (clareiras e áreas cobertas por trepadeiras) aumentou ao longo dos anos, indo de 2,95% em 1994 a 10,71% em 2016. Boa parte das áreas se recupera naturalmente ao longo do tempo, sem interferência, mas outras clareiras surgem, em área maior, elevando as áreas sem dossel arbóreo. Nas bordas, o dossel se restabeleceu em 58,3% das áreas abandonadas e em 85,6% das áreas submetidas à restauração florestal, sugerindo que as práticas de restauração aceleram o restabelecimento do dossel. O corte de trepadeiras e o plantio de mudas de espécies arbóreas reduziram a infestação da copa das árvores por trepadeiras e aumentaram a riqueza e a área basal de árvores nativas ao longo do tempo. Além disso, todas as áreas submetidas às práticas de restauração florestal, independentemente da idade, apresentaram menor densidade e área basal de trepadeiras do que bordas degradadas. Por outro lado, a densidade de regenerantes arbóreos nativos é bastante inferior à densidade encontrada nas bordas conservadas usadas como referências, mesmo na restauração com 16 anos, sugerindo que embora as práticas de restauração florestal melhorem aspectos da estrutura e riqueza das bordas florestais degradadas, para alguns indicadores as áreas em restauração ainda não se equivalem às bordas conservadas. / Despite its importance, the restoration of degraded forest remnants in fragmented landscapes still lacks technical and scientific advances to be included in the agenda of ecological restoration. Currently, there are no consolidated restoration methods, nor protocols for evaluation and monitoring of natural regeneration and ecological restoration in degraded forest fragments. In the degraded Seasonal Semideciduous Forest of the Brazilian Atlantic Forest, some lianas became dominant, especially in treefall gaps and forest edges, suffocating trees and inhibiting the regeneration of other species. In these areas, lianas cutting and tree seedling plantings have been proposed as restoration techniques. However, we lack investigation on the effectiveness over time of those techniques. Besides, we even do not know if the restoration of degraded forest areas is indeed necessary, as we know little if and how degraded areas without canopy cover recover over time. Thus, in order to analyze the effectiveness of lianas cutting and tree seedling plantings on the regeneration of the tree community in degraded forest fragments, we evaluated the canopy cover trajectory over a period of 22 years. In addition, we evaluated ecological indicators in a 16-year chronosequence of forest restoration, in a degraded Semidecidual Seasonal Forest located in Campinas-SP, southeastern Brazil. For the assessment of the canopy cover trajectory, aerial photographs of 1994, 2005 and 2016 were visually analyzed and their canopy gaps manually vectored, allowing inferring if gaps areas recovered over time and if the canopy recovery occurred more effective in edge submitted to forest restoration practices. The percentage of areas without tree canopy (gaps and areas covered by lianas) has increased over the years, going from 2.95% in 1994 to 10.71% in 2016. Most of the areas recover naturally over time without human interference, but other gaps arised, and in a larger area, raising the areas without tree canopy. At the edges, tree canopy was reestablished in 58.3% of the abandoned areas and in 85.6% of the areas undergoing forest restoration, suggesting that restoration practices accelerate tree canopy restoration. Cutting tree and planting tree seedlings reduced treetop infestation by lianas, and increased tree richness and basal area over time. In addition, all areas submitted to forest restoration practices, regardless of age, presented lower lianas density and basal area than degraded forest edges. On the other hand, the density of trees in the natural regeneration is well below the density found on conserved edges used as references, even in the 16-year-old restoration. Our results suggest that although forest restoration practices improve the structure and richness of degraded forest edges, some indicators in the restoration areas are still far from being similar to the levels found in conserved edges.

Saltwater intrusion alters the natural salinity and phosphorus (P) gradients in the oligotrophic, freshwater wetlands located near coastlines of the Caribbean Basin with important consequences to the structure and function of key ecosystem components, including plants, soil microbes, and periphyton. Periphyton communities, particularly diatoms, are extremely sensitive to water quality changes and can serve as excellent bioindicators; however, little is known about their use in detecting novel rates of saltwater intrusion into coastal, freshwater wetlands. I examined the individual and combined effects of elevated salinity and P on periphyton functional processes and diatom composition by conducting transect surveys along salinity and P gradients in the southern Everglades, as well as through mesocosm studies in which salinity and P were experimental manipulated. I demonstrated that conductivity (a proxy for salinity) and P gradients drive spatial patterns in diatom assemblage structure in the southern Everglades and that these assemblages have relatively low conductivity (2 mS cm-1) and total P thresholds (82 µg g-1). These findings were supported by the experimental work which showed that monthly pulses of elevated salinity only ~1 ppt above ambient was sufficient to cause significant shifts in periphytic diatom assemblages along with reduced periphyton productivity, total carbon, and nutrient content. The addition of P to freshwater and salt-treated periphyton significantly elevated mat total P, underscoring the P-uptake efficiency of periphyton. Surprisingly, addition of P to freshwater periphyton did not elicit significant functional or compositional responses, although chlorophyll-aconcentrations and accumulation rates tended to be higher with P. Similar chlorophyll-atrends were observed for salt-treated mats with added P, but these mats also exhibited significantly higher gross primary productivity and net ecosystem productivity compared to all other treatments and a diatom assemblage distinct from any other treatment. This research provides new and valuable information regarding periphyton dynamics in response to changing water sources that will allow us to extend the use of periphyton, and their diatom assemblages, as tools for environmental assessments related to saltwater intrusion in the southern Everglades and other karstic, freshwater wetlands.