Please read the abstract (Summary)in the section 08summary of this document / Dissertation (MSc (Botany))--University of Pretoria, 2002. / Please note that Chapter 2 is removed due to sensitive information / Plant Science / MSc / Unrestricted

Monitoring the distribution, abundance and demography of species is vital to ensure that conservation efforts are appropriate and effective. Monitoring enables evaluation of responses to natural or human disturbance, highlights the need for management interventions and enables these interventions to be assessed and refined. The methods used largely depend on the specific aim of monitoring and behaviour of the target species, as well as the time and spatial scale that monitoring is required to cover. The European pine marten (Martes martes) is one of few remaining mammalian predators native to the UK. Since persecution in the early 19th century resulted in their near extinction, pine martens have recovered part of their former range in Scotland. Their recent recovery and an overlap in territory with vulnerable prey species such as the capercaillie (Tetrao urogallus) make the collection of accurate baseline data and subsequent monitoring of population trends vital for conservation efforts. Faecal counts have traditionally been used to provide a relative measure of population density for pine marten. In most cases, absolute measures of population density require individual identification. Non-invasive genotyping can provide this information but the quality of DNA from these samples is often poor. Here, the process is refined for pine marten faeces (scats) and hair samples. DNA degradation increased significantly for scats exposed to rainfall, with the rate of DNA amplification success reduced by 38% over a 16 day period. Success rates for hair samples were higher when more hair follicles were included in the analysis. Population densities were estimated for three forests in Scotland using a robust combination of non-invasive genotyping of hair samples and spatially explicit capture recapture modelling. Population density estimates of 0.07 (95% CI 0.03 - 0.16) to 0.38 km-2 (95% CI 0.11 - 1.07) were obtained which are within the range of previous estimates for forests elsewhere in Scotland. The first attempt to quantify the relationship between traditional scat counts and home range size was then conducted; a significant negative correlation exists but only when population density is relatively low. Previous studies suggest that pine martens in Western Europe are less forest dependent than those in Eastern Europe. Results from this thesis support this, with populations at the highest density found at sites with intermediate forest cover. This tolerance of lower forest cover is also apparent in the diet. Despite a preference for Myodes voles in populations in Eastern Europe, those in Western Europe show a strong preference for Microtus voles as well as a higher level of frugivory. We assess the autumn diet of four populations in Scotland assess the effect of forest cover and sex on the diet. There was no evidence of differential consumption of Microtus voles or birds between the sexes. Our analysis shows that frugivory is influenced by forest fragmentation, with a 5-fold increase in the occurrence of fruit (from 2% to 10%) as forest cover increased from 4% to 47%. Diversionary feeding has been suggested as a management technique to reduce the depredation of capercaillie by pine martens. This thesis presents the first attempt to quantify the success and cost-efficacy of diversionary feeding for a range of problems (crop damage, threatened safety, livestock depredation) across 30 experimental trials. The strategy proved more effective when targeted towards food-limited populations, and when aiming to alleviate habitat damage or risks to human safety rather than depredation. A novel decision-making framework was developed to aid managers with the initial planning of the strategy and its subsequent implementation within an adaptive format. Further to this, the feasibility of using diversionary feeding with a view to reduce the depredation of capercaillie by pine martens was assessed. Questionnaire responses were collected from people who have provided food for pine martens throughout Scotland. A positive reaction to food was observed, with 58% of respondents reporting that initial visits occurred within one week of placement and 46% reporting that subsequent visits were received daily. These results suggest that diversionary feeding may be a viable option for pine marten management, although testing of its impact on capercaillie productivity would be required.

The restoration of rivers and streams should be based on a strong conceptual framework. Streams are developing systems. As such, streams exhibit temporal behaviors that change with changing stream environments. Underlying the dynamic development of streams is potential capacity. Streams express this capacity as an array of habitats over time and across the landscape. Human land uses in the western United States have rapidly altered aquatic habitats as well as the processes that shape habitat. As a result, the diversity of native fishes and their habitats has been suppressed. Restoration is fundamentally about allowing stream systems to re-express their capacities. Four steps are provided to guide stream restoration activities. Key tasks include: identification of the historic patterns of habitat development; protection of the developmental diversity that remains; local application of specific knowledge about suppressive factors; classification of sensitive, critical or refugium habitats; release of anthropogenic suppression; and monitoring of biotic response to habitat change. Applying these concepts, I describe potential habitat refugia for aquatic organisms in the Joseph Creek basin in the Blue Mountains of northeast Oregon. Five valley segment classes, differing in valley corridor landforms, are described. Of these, low-gradient wide alluvial valleys have been most altered by human land use. Riparian vegetation has been extensively removed or altered in alluvial valleys. Currently, stream habitats are structurally depauperate, and warm to temperatures well above thermal tolerances of native salmonids. Potential refugia for native coldwater fishes in these valleys include patches of complex habitat within stream reaches. Reaches fenced to exclude domestic livestock exhibit narrower channels, more pools, and higher frequencies of stable vegetated banks than nearby unfenced reaches. During summer low flow periods, cold groundwater seeping into and accumulating in stream channels forms "cold pools". Cold pools provide potential seasonal refuge for coldwater fish at microhabitat scales. Cold pools are associated with channel complexity, and are more frequent in reaches with vigorous riparian vegetation. Seven classes of cold pools are described. Cold pool classes differ in minimum temperature, maximum depth and volume. Distributions of cold pool classes between valley segment classes suggest that valley geomorphology in addition to local channel form may influence development of certain cold pool types. Although refugia at the microhabitat to reach scales are important, the context within which remnant or refugium habitats and associated relict populations are maintained may ultimately determine the persistence of those species and habitats. In managed landscapes, protection and restoration of habitats at many scales may be necessary if we are to best insure the persistence of native species. / Graduation date: 1995

The fitness of female Pacific salmon (Oncorhynchus spp.) with respect to breeding behavior can be partitioned into at least four components: survival to reproduction, competition for breeding sites, success of egg incubation, and suitability of the local environment near breeding sites for early rearing of juveniles. Accordingly, breeding sites should exhibit predictable habitat features linked to these components. In this study, I evaluated the relative influences of habitat features linked to fitness components on selection of breeding sites by coho salmon (Oncorhynchus kisutch). I also evaluated associations between breeding site selection and additions of large wood, as the latter were introduced into the study system as a means of restoring habitat conditions to benefit coho salmon. I used a model selection approach to organize specific habitat features into groupings reflecting fitness components and influences of large wood. The relative likelihood of each of these models was then evaluated based on how coho salmon were observed to select breeding sites. Specific variables examined within these models included depth at the redd, width to depth ratio, stream network location, proximity to other redds, maximum depth, proximity to a pool tail, and the count of naturally occurring and artificially placed large wood. Results of this work suggest that female coho salmon most likely select breeding sites based on habitat features linked to all four hypothesized fitness components. Linkages between large wood and breeding site selection were less clear, likely due to mismatches between the scale at which availability was quantified relative to the geomorphic influences of wood, insufficient time for wood to have geomorphic influences on habitat, or the directionality in which geomorphic effects are currently manifested (i.e., upstream, downstream, or bi-directional influences). Future work focused on geomorphic processes in this system could reveal stronger linkages between instream wood and the habitat features that coho salmon select for breeding. / Graduation date: 2013

Thesis (M.S.)--University of Tennessee, Knoxville, 2009. / Title from title page screen (viewed on Mar. 8, 2009). Thesis advisor: Craig Harper. Vita. Includes bibliographical references.

Increased afforestation and protective legislation in the latter half of the 20th Century allowed the British pine marten Martes martes population to recover from near extinction. Although still largely confined to northern Scotland, the marten population is expanding its size and range by utlising coniferous plantation forests which have become increasingly available. However, little is known about the marten’s ecology in plantation forestry, and less about how they may adapt to changing silvicultural trends. This study investigated aspects of pine marten ecology within Morangie forest, a managed plantation in NE Scotland, with the ultimate aim of formulating management guidelines for modern plantation forests. During the course of the study 11 pine marten were radiotracked and their home ranges mapped to examine marten-habitat associations at several spatial scales. Compositional analysis of habitat based on dominant vegetation type showed that martens established their home ranges in areas dominated by mature forest, whilst showing relative avoidance for open heath moor and grazed pasture. Within home ranges, foraging martens utilised patches of graminoid vegetation, such as those typically associated with Microtus voles, in areas with little or no tree canopy cover. These findings provide unequivocal evidence that fine-scale patches of non-forested habitat provide crucial foraging resources for marten, and therefore ought to be provisioned for in forest management plans. To assist the implementation of these requirements in forest planning, a model was developed to predict the fine scale distribution of Microtus-rich foraging habitat for marten using GIS-based habitat variables that are routinely available to forest managers: topographic wetness index, stand tree height and stand basal area. Management recommendations of ways to improve wind-firm plantation forests as habitats for pine marten are provided. To augment the investigation of marten spatial ecology, the diet of martens was examined seasonally through the analysis of contents from c. 2450 scats, 86 % of which were genetically identified as being pine marten in origin. Marten diets displayed marked seasonality, but small mammals, berries and small birds were the principal foods consumed based on both frequency of occurrence and estimated weight of biomass ingested. Comparison of the relative composition of small mammal species in the diet with those available in the environment revealed that marten displayed an indisputable preference for Microtus voles. Such habits demonstrate that the niche of Scottish martens has diverged from those in mainland populations which predominantly prey upon Clethrionomys voles. A comparison of the marten’s winter diet with those found in studies at similar latitudes (58°N) demonstrated that the Scottish diet was more similar to diets at more southerly latitudes as they contained more fruit and fewer large mammals than typically boreal diets. Investigation of inter-annual variation of the marten’s spring diet from five successive years revealed that Microtus were consistently the most important prey species in the diet each year. Indirect evidence of the relative abundance of Microtus suggested that Microtus populations were non-cyclic. Findings are discussed with reference to the unique ecological circumstances confronting marten in the Scotland; typical of insular populations the UK has a depauperate native fauna in comparison with mainland Europe, in addition to this, mild climatic conditions, particularly over winter, and a historically fragmented landscape appear to have allowed the niche of the Scottish marten to diverge from that considered typical elsewhere in its range. The Scottish marten is dependent on both forested and open habitats, and is both a Microtus specialist and trophic generalist.

River restoration projects are being installed worldwide to rehabilitate degraded river habitat. Many of these projects focus on stream habitat improvement (SHI), and an estimated 60%of the 37,000 projects listed in the National River Restoration Science Synthesis Program focus on SHI for salmon and trout species. These projects frequently lack a sufficient monitoring program or account for the environmental costs associated with SHI. The present study used life cycle assessment (LCA) techniques and topographic effectiveness monitoring to quantify environmental costs on the basis of geomorphic change. This methodology was a novel approach to assessing the cost-benefit relationship of SHI. To test this methodology, two phases of the Lower Scotts Creek Floodplain and Habitat Enhancement Project (LSCR) were used as a case study. The LSCR was a SHI project installed along the northern coast of Santa Cruz County, California, USA. A limited scope LCA was used to quantify the life cycle impacts of raw material production, materials transportation, and on-site construction. Once these baseline results were produced, a topographic monitoring program was used to quantify the topographic diversity index (TDI) in pre- and post-project conditions. The TDI percent change was used to scale the baseline LCA results, which quantified the environmental impacts based on geomorphic change. Phase II outperformed phase I. Phase I had greater cumulative environmental impacts and experienced a 7.7 % TDI increase from pre- to post-project conditions. Phase II had 43% less cumulative environmental impacts and experienced a 7.9% TDI increase from pre- to post-project conditions. The impacts in phase I were greater because of the amount of material excavated to create off-channel features, which were a key feature of the LSCR. A scenario analysis also was conducted within the LCA component of this study. The scenario analysis suggests that life cycle impacts could be reduced by 30%-65% by using the accelerated recruitment method in place of importing materials to build large wood complexes. The results of this study suggest that managers may improve the environmental performance of SHI projects by: (1) using the accelerated recruitment method to introduce larger key pieces to the channel, reducing the need to import materials; (2) using nursery grown plants as opposed to excavating plants for revegetation; (3) minimizing fuel combustion in heavy equipment and haul trucks by ensuring clear access to the channel and streambank, using small engine equipment to clear access corridors during site preparation, running more fuel-efficient machinery or bio-fuel powered machinery, and by attempting to minimize haul distances by sourcing materials locally; and (4) utilizing a “franken-log” design (a ballasted LWC configuration with a rootwad fastened to the downstream end of a log) in LWCs which led to favorable TDI change. This study concluded that LCA could be a valuable tool for monitoring SHI and river restoration projects and that further research of the TDI analysis is justified.

Availability of suitable nesting habitat that is free of nest predators and provides access to adequate prey resources within commuting distance is a major factor limiting seabird populations. Caspian terns (Hydroprogne caspia) in western North America have shifted their breeding habitat from naturally occurring habitats in interior wetlands, lakes, and rivers to primarily human-created habitats in coastal bays and estuaries. This shift has brought Caspian terns into conflict with fisheries of conservation concern, in particular anadromous salmonids. Prior to the 2010 breeding season, three artificial islands were built in the Klamath Basin National Wildlife Refuge (NWR) Complex as alternative nesting habitat for Caspian terns currently nesting at the world's largest colony for the species, near the mouth of the Columbia River, Oregon. I investigated the efficacy of habitat creation (island building) and social attraction (decoys and recorded vocalizations) for establishing new breeding colonies in the Upper Klamath Basin, California. In 2010, approximately 258 pairs of Caspian terns attempted to nest on the new islands and raised an average of 0.65 fledglings/breeding pair; in 2011, 222 pairs attempted to nest and raised an average of 0.11 fledglings/breeding pair. Competition with California and ring-billed gulls (Larus californicus and L. delawarensis) for nesting space, gull predation on Caspian tern eggs and chicks, low water levels, and depredation by great horned owls (Bubo virginianus) were the primary factors limiting colony development and productivity, especially in 2011. The immediate response by Caspian terns to habitat creation and social attraction in the Upper Klamath Basin demonstrates that these can be effective restoration techniques to establish new breeding colonies where nesting habitat is a major limiting factor; however, continued management of other limiting factors (e.g., control of on-colony predators and competitors) will likely be necessary to promote the development of established, self-sustaining breeding colonies on these artificial islands. Efforts to conserve and restore seabird colonies can be compromised by low prey availability within foraging distance of the breeding colony. I used GPS telemetry to study the fine-scale foraging behavior of Caspian terns nesting at two newly established colonies and cluster analysis to discriminate behavioral states based on movement characteristics. Terns breeding at the Sheepy Lake colony spent less time at the colony (52% of the day) than terns breeding at the Tule Lake colony (74%). Caspian terns breeding at Sheepy Lake foraged more extensively than terns breeding at Tule Lake; the foraging trips of Sheepy Lake terns lasted longer (median = 186 min) and were longer-distance (27 km) compared to those of Tule Lake terns (55 min and 6 km, respectively). Between-colony differences in foraging behavior corresponded to 5% lower average body mass of breeding adults and significantly lower size-adjusted body mass of chicks at the Sheepy Lake colony compared to the Tule Lake colony. Proximity to high-quality foraging areas influenced the foraging behavior and parental care of breeding Caspian terns, which in turn had effects on nesting success. The successful use of GPS telemetry to study the fine-scale foraging behavior of Caspian terns represents a significant advance in our ability to investigate the foraging ecology of this species and other moderate-sized seabirds. / Graduation date: 2013

Le modèle input-output régional environnementalisé développé dans la thèse de M. Cordier suggère qu’il serait possible de restaurer 25% des surfaces naturelles de nourriceries de poissons détruites dans l’estuaire de la Seine entre 1834 et 2004. Le modèle suggère que la mesure de restauration pourrait augmenter de 15% à 23% la biomasse de soles produite dans l’estuaire par rapport à une situation sans mesure. Quant à l’effet des coûts de restauration sur les agrégats macroéconomiques (PIB, emploi, etc.), il génère une diminution qui ne dépasse pas 0,5% par rapport à une situation sans mesure. Le modèle montre cependant que trois secteurs sont particulièrement touchés par la mesure, leur bénéfice étant considérablement réduit. Cela indique le compromis à réaliser entre les objectifs écologiques à long terme et les objectifs économiques sectoriels à court terme. La quantification des compromis par le modèle constitue un atout utile aux processus de décision participatifs multicritère / The regional green input-output model developed in Mateo Cordier's PhD shows that it seems possible to restore 25% of the natural areas of fish nurseries destroyed in the Seine estuary between 1834 and 2004. The model suggests that the restoration measure could increase between 15% and 23% the biomass of sole generated by the estuary compared to a situation without measure. Regarding the impact of restoration costs on macro-economic indicators (GDP, employment, etc.), it generates a decrease that does not exceed 0,5% compared to a situation without measure. However, the model shows that three sectors are particularly impacted by the measure. Their benefits are considerably reduced. This shows the trade-off that occurs between ecological targets on the long run and economic targets on the short run. The quantification of such trade-offs in the model is particularly useful to public participation in decision-making. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

I evaluated effects of 5 intensive pine plantation establishment regimes during years 1 – 5 post-establishment on vegetation communities, loblolly pine (Pinus taeda) growth, nutritional carrying capacity for white-tailed deer (Odocoileus virginianus), habitat values for northern bobwhite (Colinus virginianus), and projected financial viability in the Lower Coastal Plain of Mississippi. Treatments were combinations of mechanical site preparation (MSP), chemical site preparation (CSP), and herbaceous weed control (HWC) designed to reflect the range of operational intensities on industrial forest lands in the southeastern U.S. Results should inform plantation management decisions throughout the region. Pine growth increased with greater treatment intensity. At age 5, trees in the most intensively managed treatment were 1.5 m taller than those in the least intensive treatment. Mechanical site preparation improved growth by alleviating soil physical problems. Growth and yield projections indicated that increased fiber yield may not justify investment in more intensive regimes; financial analysis favored the least expensive treatment, though all regimes produced potential internal rates of return > 9% when managed to financial maturity. Use of MSP with banded HWC yielded abundant low-quality deer forage sufficient for body maintenance; nutritional needs for lactating does were better served by CSP with banded HWC. Broadcast HWC reduced biomass of high-quality forbs. In this region of limited soil nutrients and abundant low-quality forages, the optimal combination of maintenance-level and lactation-level nutrition was provided by CSP or CSP and MSP combined with banded HWC. I evaluated vegetation communities for nesting, loafing, brood-rearing, and fall and winter food suitability for northern bobwhite. No treatment provided brood-rearing habitat due to combined lack of bare ground and forb coverage. Fall and winter feeding, nesting, and loafing cover were best produced by MSP and CSP combined with banded HWC. However, lack of brood-rearing cover may reduce or eliminate usable space in all treatments. Differences between vegetation communities were caused by use of CSP, which eliminated many residual woody and vine species, and by differences in broadcast versus banded HWC. Herbicide use decreased plant diversity and species richness, and impacted successional trajectory. Community differences persisted through year 5.