Data to Decision in a Dynamic Ocean: Robust Species Distribution Models and Spatial Decision Frameworks

Human use of the oceans is increasingly in conflict with conservation of endangered species. Methods for managing the spatial and temporal placement of industries such as military, fishing, transportation and offshore energy, have historically been post hoc; i.e. the time and place of human activity is often already determined before assessment of environmental impacts. In this dissertation, I build robust species distribution models in two case study areas, US Atlantic (Best et al. 2012) and British Columbia (Best et al. 2015), predicting presence and abundance respectively, from scientific surveys. These models are then applied to novel decision frameworks for preemptively suggesting optimal placement of human activities in space and time to minimize ecological impacts: siting for offshore wind energy development, and routing ships to minimize risk of striking whales. Both decision frameworks relate the tradeoff between conservation risk and industry profit with synchronized variable and map views as online spatial decision support systems.

For siting offshore wind energy development (OWED) in the U.S. Atlantic (chapter 4), bird density maps are combined across species with weights of OWED sensitivity to collision and displacement and 10 km2 sites are compared against OWED profitability based on average annual wind speed at 90m hub heights and distance to transmission grid. A spatial decision support system enables toggling between the map and tradeoff plot views by site. A selected site can be inspected for sensitivity to a cetaceans throughout the year, so as to capture months of the year which minimize episodic impacts of pre-operational activities such as seismic airgun surveying and pile driving.

Routing ships to avoid whale strikes (chapter 5) can be similarly viewed as a tradeoff, but is a different problem spatially. A cumulative cost surface is generated from density surface maps and conservation status of cetaceans, before applying as a resistance surface to calculate least-cost routes between start and end locations, i.e. ports and entrance locations to study areas. Varying a multiplier to the cost surface enables calculation of multiple routes with different costs to conservation of cetaceans versus cost to transportation industry, measured as distance. Similar to the siting chapter, a spatial decisions support system enables toggling between the map and tradeoff plot view of proposed routes. The user can also input arbitrary start and end locations to calculate the tradeoff on the fly.

Essential to the input of these decision frameworks are distributions of the species. The two preceding chapters comprise species distribution models from two case study areas, U.S. Atlantic (chapter 2) and British Columbia (chapter 3), predicting presence and density, respectively. Although density is preferred to estimate potential biological removal, per Marine Mammal Protection Act requirements in the U.S., all the necessary parameters, especially distance and angle of observation, are less readily available across publicly mined datasets.

In the case of predicting cetacean presence in the U.S. Atlantic (chapter 2), I extracted datasets from the online OBIS-SEAMAP geo-database, and integrated scientific surveys conducted by ship (n=36) and aircraft (n=16), weighting a Generalized Additive Model by minutes surveyed within space-time grid cells to harmonize effort between the two survey platforms. For each of 16 cetacean species guilds, I predicted the probability of occurrence from static environmental variables (water depth, distance to shore, distance to continental shelf break) and time-varying conditions (monthly sea-surface temperature). To generate maps of presence vs. absence, Receiver Operator Characteristic (ROC) curves were used to define the optimal threshold that minimizes false positive and false negative error rates. I integrated model outputs, including tables (species in guilds, input surveys) and plots (fit of environmental variables, ROC curve), into an online spatial decision support system, allowing for easy navigation of models by taxon, region, season, and data provider.

For predicting cetacean density within the inner waters of British Columbia (chapter 3), I calculated density from systematic, line-transect marine mammal surveys over multiple years and seasons (summer 2004, 2005, 2008, and spring/autumn 2007) conducted by Raincoast Conservation Foundation. Abundance estimates were calculated using two different methods: Conventional Distance Sampling (CDS) and Density Surface Modelling (DSM). CDS generates a single density estimate for each stratum, whereas DSM explicitly models spatial variation and offers potential for greater precision by incorporating environmental predictors. Although DSM yields a more relevant product for the purposes of marine spatial planning, CDS has proven to be useful in cases where there are fewer observations available for seasonal and inter-annual comparison, particularly for the scarcely observed elephant seal. Abundance estimates are provided on a stratum-specific basis. Steller sea lions and harbour seals are further differentiated by ‘hauled out’ and ‘in water’. This analysis updates previous estimates (Williams & Thomas 2007) by including additional years of effort, providing greater spatial precision with the DSM method over CDS, novel reporting for spring and autumn seasons (rather than summer alone), and providing new abundance estimates for Steller sea lion and northern elephant seal. In addition to providing a baseline of marine mammal abundance and distribution, against which future changes can be compared, this information offers the opportunity to assess the risks posed to marine mammals by existing and emerging threats, such as fisheries bycatch, ship strikes, and increased oil spill and ocean noise issues associated with increases of container ship and oil tanker traffic in British Columbia’s continental shelf waters.

Starting with marine animal observations at specific coordinates and times, I combine these data with environmental data, often satellite derived, to produce seascape predictions generalizable in space and time. These habitat-based models enable prediction of encounter rates and, in the case of density surface models, abundance that can then be applied to management scenarios. Specific human activities, OWED and shipping, are then compared within a tradeoff decision support framework, enabling interchangeable map and tradeoff plot views. These products make complex processes transparent for gaming conservation, industry and stakeholders towards optimal marine spatial management, fundamental to the tenets of marine spatial planning, ecosystem-based management and dynamic ocean management.

An assessment of the influence of the industry distribution chain on the oxygen levels in commercial modified atmosphere packaged cheddar cheese using non-destructive oxygen sensor technology

The establishment and control of oxygen levels in packs of oxygen-sensitive food products such as cheese is imperative in order to maintain product quality over a determined shelf life. Oxygen sensors quantify oxygen concentrations within packaging using a reversible optical measurement process, and this non-destructive nature ensures the entire supply chain can be monitored and can assist in pinpointing negative issues pertaining to product packaging. This study was carried out in a commercial cheese packaging plant and involved the insertion of 768 sensors into 384 flow-wrapped cheese packs (two sensors per pack) that were flushed with 100% carbon dioxide prior to sealing. The cheese blocks were randomly assigned to two different storage groups to assess the effects of package quality, packaging process efficiency, and handling and distribution on package containment. Results demonstrated that oxygen levels increased in both experimental groups examined over the 30-day assessment period. The group subjected to a simulated industrial distribution route and handling procedures of commercial retailed cheese exhibited the highest level of oxygen detected on every day examined and experienced the highest rate of package failure. The study concluded that fluctuating storage conditions, product movement associated with distribution activities, and the possible presence of cheese-derived contaminants such as calcium lactate crystals were chief contributors to package failure.

San Francisco Coastal System grain size and geochemical data for sand provenance study

Over 150 million cubic meter of sand-sized sediment has disappeared from the central region of the San Francisco Bay Coastal System during the last half century. This enormous loss may reflect numerous anthropogenic influences, such as watershed damming, bay-fill development, aggregate mining, and dredging. The reduction in Bay sediment also appears to be linked to a reduction in sediment supply and recent widespread erosion of adjacent beaches, wetlands, and submarine environments. A unique, multi-faceted provenance study was performed to definitively establish the primary sources, sinks, and transport pathways of beach sized-sand in the region, thereby identifying the activities and processes that directly limit supply to the outer coast. This integrative program is based on comprehensive surficial sediment sampling of the San Francisco Bay Coastal System, including the seabed, Bay floor, area beaches, adjacent rock units, and major drainages. Analyses of sample morphometrics and biological composition (e.g., Foraminifera) were then integrated with a suite of tracers including 87Sr/86Sr and 143Nd/144Nd isotopes, rare earth elements, semi-quantitative X-ray diffraction mineralogy, and heavy minerals, and with process-based numerical modeling, in situ current measurements, and bedform asymmetry to robustly determine the provenance of beach-sized sand in the region.

Distribution of surface sediment properties along the Portuguese western margin

Organic matter contained in surface sediments from four regions on the western Portuguese shelf, which are influenced by coastal upwelling and fluvial input, was analysed with respect to elemental organic carbon (Corg) and nitrogen (Ntotal) content and isotopic carbon and nitrogen ratios (d13Corg, d15N). Corg/Ntotal weight ratios and d13Corg values are interpreted in terms of terrigenous or marine organic matter sources, supported by CaCO3 content. Organic matter in the shelf sediments is mainly of marine origin, with increasing terrigenous components only close to rivers and estuaries. In the northern shelf region the data indicates significant terrigenous supply by the Douro River. North of the Nazaré Canyon organic matter composition implies a mainly marine origin, with a higher terrestrial influence close to the canyon head. Organic matter composition in the central shelf region, which is dominated by the Tagus Estuary and the Tagus prodelta, reveals a change from a continental-type signature within the estuary to a more marine-type signature further to the west and south of the estuary mouth. In the southern region near Cape Sines the geochemical properties clearly reflect the marine origin of sedimentary organic matter. Sedimentary d15N values are interpreted to reflect various degrees of assimilation of seasonally upwelled nitrate, in relation to the upwelling centres. In the estuarine environment, inputs of agriculturally influenced dissolved inorganic nitrogen are reflected in the sediments. No evidence for N2-fixation or denitrification is found. On the central shelf north of the Nazaré canyon, sedimentary d15N values are close to marine d15NO3- and thus indicate a complete NO3- assimilation and N-limitation of marine production. Light d15N values in distal sediments off the Douro River mouth and in samples south of C. Sines reflect high NO3- supply and a close proximity to the seasonal upwelling centres. Particularly in sediments form the Sines region, light d15N values in southern samples reflect stronger upwelling further south.

Vegetation community and geochemistry in the Uummannaq District, West Greenland

Beach and salt marsh vegetation of the Uummannaq District, northern West Greenland (c. 70°15' N - 72° N, 49° W - 54° W) was studied 1998 according to the Braun-Blanquet phytosociological approach. Habitat analyses included soil chemistry. Such vegetation locally occurs and is not developed over extensive areas. On gravely stony beaches a Mertensia maritima ssp. maritima community occurs, while a Honckenya peploides var. diffusa community is confined to sandy beaches. The association Honckenyo diffusae-Elymetum mollis Thannh. 1975 is confined to sandy shore walls and low dunes. All vegetation types are assigned to the alliance Honckenyo- Elymion arenariae Tx. 1966, which again is a unit of the order Honckenyo- Elymetalia arenariae Tx. 1966, which is sub ordered to the class Honckenyo-Elymetea arenariae Tx. 1966. On fine sediments along sheltered coasts salt marsh vegetation is locally developed mainly on fiord deltas and outwash plains of small rivers and streams. A distinct zonation pattern in vegetation can be observed from the lower to upper salt marsh: Puccinellietum phryganodis Hadac 1946 association, Caricetum subspathaceae Hadac 1946 association, Caricetum ursinae Hadac 1946 association (all assigned to the alliance Puccinellion phryganodis Hadac 1946) and Festuco-Caricetum glareosae Nordh. 1954 association (assigned to the alliance Armerion maritimae Br.-Bl. et de Leeuw 1936). Both alliances are units of the order Glauco- Puccinellietalia Beeftink et Westhoff in Beeftink 1965, which is assigned to the class Asteretea tripolii Westhoff et Beeftink in Beeftink 1962. TWINSPAN and CCA support the vegetation classification and the CCA with soil chemistry parameters shows that salinity (related to position above MHW) and Ncontent are strongly correlated with the floristical differentiation of the vegetation of the Honckenyo-Elymetea class. In the Asteretea tripolii class, position above MHW (negatively correlated with pH, conductivity and Clcontent) and fresh water supply are likely the main factors, which affect vegetation differentiation. A synoptic survey of vegetation types from Greenland based on published phytosociological tables is presented and distribution of the vegetation types is addressed, just as their position in a circumpolar context. Moreover a Cochlearia groenlandica-Melandrium triflorum community is described as a new vegetation type, occurring on shallow soil on cliffs influenced by salt spray.

Wind Resource Mapping Using Landscape Roughness and Spatial Interpolation Methods

Energy saving, reduction of greenhouse gasses and increased use of renewables are key policies to achieve the European 2020 targets. In particular, distributed renewable energy sources, integrated with spatial planning, require novel methods to optimise supply and demand. In contrast with large scale wind turbines, small and medium wind turbines (SMWTs) have a less extensive impact on the use of space and the power system, nevertheless, a significant spatial footprint is still present and the need for good spatial planning is a necessity. To optimise the location of SMWTs, detailed knowledge of the spatial distribution of the average wind speed is essential, hence, in this article, wind measurements and roughness maps were used to create a reliable annual mean wind speed map of Flanders at 10 m above the Earth’s surface. Via roughness transformation, the surface wind speed measurements were converted into meso- and macroscale wind data. The data were further processed by using seven different spatial interpolation methods in order to develop regional wind resource maps. Based on statistical analysis, it was found that the transformation into mesoscale wind, in combination with Simple Kriging, was the most adequate method to create reliable maps for decision-making on optimal production sites for SMWTs in Flanders (Belgium).

The influence of balanced and imbalanced resource supply on biodiversity – functioning relationship across ecosystems

Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity-ecosystem functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity-ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns of diversity-productivity relationships with respect to available resources. Meta-analysis was used to summarize the findings across ecosystem types ranging from aquatic ecosystems to grasslands and forests. As hypothesized, resource supply increased realized productivity and richness, but we found significant differences between ecosystems and study types. Increased richness was associated with increased productivity, although this effect was not seen in experiments. More even communities had lower productivity, indicating that biomass production is often maintained by a few dominant species, and reduced dominance generally reduced ecosystem productivity. This synthesis, which integrates observational and experimental studies in a variety of ecosystems and geographical regions, exposes common patterns and differences in biodiversity-functioning relationships, and increases the mechanistic understanding of changes in ecosystems productivity.

The influence of balanced and imbalanced resource supply on biodiversity – functioning relationship across ecosystems

Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity-ecosystem functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity-ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns of diversity-productivity relationships with respect to available resources. Meta-analysis was used to summarize the findings across ecosystem types ranging from aquatic ecosystems to grasslands and forests. As hypothesized, resource supply increased realized productivity and richness, but we found significant differences between ecosystems and study types. Increased richness was associated with increased productivity, although this effect was not seen in experiments. More even communities had lower productivity, indicating that biomass production is often maintained by a few dominant species, and reduced dominance generally reduced ecosystem productivity. This synthesis, which integrates observational and experimental studies in a variety of ecosystems and geographical regions, exposes common patterns and differences in biodiversity-functioning relationships, and increases the mechanistic understanding of changes in ecosystems productivity.

Assessing the resilience of water supply systems in Oman

Water systems in the Sultanate of Oman are inevitably exposed to varied threats and hazards due to both natural and man-made hazards. Natural disasters, especially tropical cyclone Gonu in 2007, cause immense damage to water supply systems in Oman. At the same time water loss from leaks is a major operational problem. This research developed an integrated approach to identify and rank the risks to the water sources, transmission pipelines and distribution networks in Oman and suggests appropriate mitigation measures. The system resilience was evaluated and an emergency response plan for the water supplies developed. The methodology involved mining the data held by the water supply utility for risk and resilience determination and operational data to support calculations of non-revenue water. Risk factors were identified, ranked and scored at a stakeholder workshop and the operational information required was principally gathered from interviews. Finally, an emergency response plan was developed by evaluating the risk and resilience factors. The risk analysis and assessment used a Coarse Risk Analysis (CRA) approach and risk scores were generated using a simple risk matrix based on WHO recommendations. The likelihoods and consequences of a wide range of hazardous events were identified through a key workshop and subsequent questionnaires. The thesis proposes a method of translating the detailed risk evaluations into resilience scores through a methodology used in transportation networks. A water audit indicated that the percentage of NRW in Oman is greater than 35% which is similar to other Gulf countries but high internationally. The principal strategy for managing NRW used in the research was the AWWA water audit method which includes free to use software and was found to be easy to apply in Oman. The research showed that risks to the main desalination processes can be controlled but the risk due to feed water quality might remain high even after implementing mitigation measures because the intake is close to an oil port with a significant risk of oil contamination and algal blooms. The most severe risks to transmission mains were found to be associated with pipe rather than pump failure. The systems in Oman were found to be moderately resilient, the resilience of desalination plants reasonably high but the transmission mains and pumping stations are very vulnerable. The integrated strategy developed in this study has a wide applicability, particularly in the Gulf area, which may have risks from exceptional events and will be experiencing NRW. Other developing countries may also experience such risks but with different magnitudes and the risk evaluation tables could provide a useful format for further work.

Sweet cherry: composition, postharvest preservation, processing and trends for its future use

Background Sweet cherries (Prunus avium L.) are a nutritious fruit which are rich in polyphenols and have high antioxidant potential. Most sweet cherries are consumed fresh and a small proportion of the total sweet cherries production is value added to make processed food products. Sweet cherries are highly perishable fruit with a short harvest season, therefore extensive preservation and processing methods have been developed for the extension of their shelf-life and distribution of their products. Scope and Approach In this review, the main physicochemical properties of sweet cherries, as well as bioactive components and their determination methods are described. The study emphasises the recent progress of postharvest technology, such as controlled/modified atmosphere storage, edible coatings, irradiation, and biological control agents, to maintain sweet cherries for the fresh market. Valorisations of second-grade sweet cherries, as well as trends for the diversification of cherry products for future studies are also discussed. Key Findings and Conclusions Sweet cherry fruit have a short harvest period and marketing window. The major loss in quality after harvest include moisture loss, softening, decay and stem browning. Without compromising their eating quality, the extension in fruit quality and shelf-life for sweet cherries is feasible by means of combination of good handling practice and applications of appropriate postharvest technology. With the drive of health-food sector, the potential of using second class cherries including cherry stems as a source of bioactive compound extraction is high, as cherry fruit is well-known for being rich in health-promoting components.

Marketing de cinema : a supply chain do sector cinematografico português

Mestrado em Marketing

Spatio-temporal patterns of herbage availability and livestock movements: A cross-border analysis in the Chinese-Mongolian Altay

Due to increasing population and the recent implementation of policies to intensify the use of land and water resources, the transhumant pastoral systems in the Chinese-Mongolian Altay-Dzungarian region are rapidly changing, leading to modifications of herd size, herd composition and spatial distribution of livestock grazing. This may have major consequences for the supply and quality of rangeland biomass. Despite similar topographic settings, the socio-political framework for Chinese and Mongolian pastoralists differs significantly, leading to differences in rangeland utilization. To substantiate these claims, the long-distance transhumance routes, frequency of pasture changes, daily grazing itineraries and size of pastures were recorded by means of GPS tracking of cattle and goats on 1,535 (China) and 1,396 (Mongolia) observation days. The status quo of the main seasonal pastures was captured by measuring the herbage offer and its nutritive value in 869 sampling spots. In the Altay-Dzungarian region, small ruminant herds covered up to 412 km (Mongolia) and grazed on up to nine pastures per year (China). In Mongolia, the herds’ average duration of stay at an individual pasture was longer than in China, particularly in spring and autumn. Herbage allowance at the onset of a grazing period (kg dry matter per sheep unit and day) ranged from 34/17 to 91/95 (China/Mongolia). Comparing crude protein and phosphorous concentrations of herbage, in China, the highest concentrations were measured for spring and summer pastures, whereas in Mongolia, the highest concentrations were determined for autumn and winter pastures. Based on our data, we conclude that regulation of animal numbers and access to pastures seemingly maintained pasture productivity in China, especially at high altitudes. However, this policy may prohibit flexible adaptation to sudden environmental constraints. In contrast, high stocking densities and grazing of pastures before flowering of herbaceous plants negatively affected rangeland productivity in Mongolia, especially for spring and summer pastures.

Lusitanian Amphorae in Carthago Nova (Cartagena, Spain): Distribution and Research Questions

The presence of Lusitanian amphorae in the region of Carthago Nova (Cartagena, Spain) has been known for a few years, and yet it has never been the subject of a monographic study. Integrated in the commercial networks of the western Mediterranean, these products circulated within the harbour system of this city between the 1st and the 5th century AD. This paper aims to present a synthesised review of the main Lusitanian imports that were detected: Dressel 14 and Almagro 50, Almagro 51a-b and Almagro 51c. The difficulty in identifying the ceramic fabrics and the scarce documentation regarding some finds pose complex problems. This study extends to the hinterland of the colony and to other nearby settlements, such as Portmán and Puerto de Mazarrón.

Mobilizing Greater Crop and Land Potentials Sustainably

The supply side of the food security engine is the way we farm. The current engine of conventional tillage farming is faltering and needs to be replaced. This presentation will address supply side issues of agriculture to meet future agricultural demands for food and industry using the alternate no-till Conservation Agriculture (CA) paradigm (involving no-till farming with mulch soil cover and diversified cropping) that is able to raise productivity sustainably and efficiently, reduce inputs, regenerate degraded land, minimise soil erosion, and harness the flow of ecosystem services. CA is an ecosystems approach to farming capable of enhancing not only the economic and environmental performance of crop production and land management, but also promotes a mindset change for producing ‘more from less’, the key attitude towards sustainable production intensification. CA is now spreading globally in all continents at an annual rate of 10 Mha and covers some 157 Mha of cropland. Today global agriculture produces enough food to feed three times the current population of 7.21 billion. In 1976, when the world population was 4.15 billion, world food production far exceeded the amount necessary to feed that population. However, our urban and industrialised lifestyle leads to wastage of food of some 30%-40%, as well as waste of enormous amount of energy and protein while transforming crop-based food into animal-derived food; we have a higher proportion of people than ever before who are obese; we continue to degrade our ecosystems including much of our agricultural land of which some 400 Mha is reported to be abandoned due to severe soil and land degradation; and yields of staple cereals appear to have stagnated. These are signs of unsustainability at the structural level in the society, and it is at the structural level, for both supply side and demand side, that we need transformed mind sets about production, consumption and distribution. CA not only provides the possibility of increased crop yields for the low input smallholder farmer, it also provides a pro-poor rural and agricultural development model to support agricultural intensification in an affordable manner. For the high output farmer, it offers greater efficiency (productivity) and profit, resilience and stewardship. For farming anywhere, it addresses the root causes of agricultural land degradation, sub-optimal ecological crop and land potentials or yield ceilings, and poor crop phenotypic expressions or yield gaps. As national economies expand and diversify, more people become integrated into the economy and are able to access food. However, for those whose livelihoods continue to depend on agriculture to feed themselves and the rest of the world population, the challenge is for agriculture to produce the needed food and raw material for industry with minimum harm to the environment and the society, and to produce it with maximum efficiency and resilience against abiotic and biotic stresses, including those arising from climate change. There is growing empirical and scientific evidence worldwide that the future global supplies of food and agricultural raw materials can be assured sustainably at much lower environmental and economic cost by shifting away from conventional tillage-based food and agriculture systems to no-till CA-based food and agriculture systems. To achieve this goal will require effective national and global policy and institutional support (including research and education).