Organic carbon sources and their transfer in a gulf of Mexico coral reef ecosystem

Coral reefs face unprecedented threats throughout most of their range. Poorly planned coastal development has contributed increased nutrients and sewage contamination to coastal waters, smothering some corals and contributing to overgrowth by macroalgae. My approach to assessing the degree to which coral reef ecosystems have been influenced by terrestrial and anthropogenic organic carbon inputs is through the use of carbon (C) and nitrogen (N) stable isotopes and lipid biomarkers in a marine protected area, the Coral Reef System of Veracruz: Parque Nacional Sistema Arrecifal Veracruzano (PNSAV) in the southwest Gulf of Mexico. Firstly, I used a C and N stable isotope mixing model and a calculated fatty acid (FA) retention factor to reveal the primary producer sources that fuel the coral reef food web. Secondly, I used lipid classes, FA and sterol biomarkers to determine production of terrestrial and marine biogenic material of nutritional quality to pelagic and benthic organisms. Finally, I used coprostanol to determine pollutant loading from sewage in the suspended particulate matter. Results indicate that phytoplankton is the major source of essential metabolite FA for marine fish and that dietary energy from terrestrial sources such as mangroves are transferred to juvenile fish, while seagrass non-essential FA are transferred to the entire food web mainly in the rainy season. Sea urchins may be the main consumers of brown macroalgae, especially in the dry season, while surgeon fish prefer red algae in both dry and rainy seasons. C and N isotopic values and the ratio C:N suggest that fertilizer is the principal source of nitrogen to macroalgae. Thus nitrogen supply also favored phytoplankton and seagrass growth leading to a better nutritional condition and high retention of organic carbon in the food web members during the rainy season when river influence increases. However, the great star coral Montastrea cavernosa nutritional condition decreased significantly in the rainy season. The nearest river to the PNSAV was polluted in the dry season; however, a dilution effect was detected in the rainy season, when some coral reefs were contaminated. In 2013, a new treatment plant started working in the area. I would suggest monitoring δ¹⁵N and the C: N ratio in macroalgae as indicators of the nitrogen input and coprostanol as an indicator of human feces pollution in order to verify the efficiency of the new treatment plant as part of the management program of the PNSAV.

Using Bird Distributions to Assess Extinction Risk and Identify Conservation Priorities in Biodiversity Hotspots

Habitat loss, fragmentation, and degradation threaten the World’s ecosystems and species. These, and other threats, will likely be exacerbated by climate change. Due to a limited budget for conservation, we are forced to prioritize a few areas over others. These places are selected based on their uniqueness and vulnerability. One of the most famous examples is the biodiversity hotspots: areas where large quantities of endemic species meet alarming rates of habitat loss. Most of these places are in the tropics, where species have smaller ranges, diversity is higher, and ecosystems are most threatened.

Species distributions are useful to understand ecological theory and evaluate extinction risk. Small-ranged species, or those endemic to one place, are more vulnerable to extinction than widely distributed species. However, current range maps often overestimate the distribution of species, including areas that are not within the suitable elevation or habitat for a species. Consequently, assessment of extinction risk using these maps could underestimate vulnerability.

In order to be effective in our quest to conserve the World’s most important places we must: 1) Translate global and national priorities into practical local actions, 2) Find synergies between biodiversity conservation and human welfare, 3) Evaluate the different dimensions of threats, in order to design effective conservation measures and prepare for future threats, and 4) Improve the methods used to evaluate species’ extinction risk and prioritize areas for conservation. The purpose of this dissertation is to address these points in Colombia and other global biodiversity hotspots.

In Chapter 2, I identified the global, strategic conservation priorities and then downscaled to practical local actions within the selected priorities in Colombia. I used existing range maps of 171 bird species to identify priority conservation areas that would protect the greatest number of species at risk in Colombia (endemic and small-ranged species). The Western Andes had the highest concentrations of such species—100 in total—but the lowest densities of national parks. I then adjusted the priorities for this region by refining these species ranges by selecting only areas of suitable elevation and remaining habitat. The estimated ranges of these species shrank by 18–100% after accounting for habitat and suitable elevation. Setting conservation priorities on the basis of currently available range maps excluded priority areas in the Western Andes and, by extension, likely elsewhere and for other taxa. By incorporating detailed maps of remaining natural habitats, I made practical recommendations for conservation actions. One recommendation was to restore forest connections to a patch of cloud forest about to become isolated from the main Andes.

For Chapter 3, I identified areas where bird conservation met ecosystem service protection in the Central Andes of Colombia. Inspired by the November 11th (2011) landslide event near Manizales, and the current poor results of Colombia’s Article 111 of Law 99 of 1993 as a conservation measure in this country, I set out to prioritize conservation and restoration areas where landslide prevention would complement bird conservation in the Central Andes. This area is one of the most biodiverse places on Earth, but also one of the most threatened. Using the case of the Rio Blanco Reserve, near Manizales, I identified areas for conservation where endemic and small-range bird diversity was high, and where landslide risk was also high. I further prioritized restoration areas by overlapping these conservation priorities with a forest cover map. Restoring forests in bare areas of high landslide risk and important bird diversity yields benefits for both biodiversity and people. I developed a simple landslide susceptibility model using slope, forest cover, aspect, and stream proximity. Using publicly available bird range maps, refined by elevation, I mapped concentrations of endemic and small-range bird species. I identified 1.54 km2 of potential restoration areas in the Rio Blanco Reserve, and 886 km2 in the Central Andes region. By prioritizing these areas, I facilitate the application of Article 111 which requires local and regional governments to invest in land purchases for the conservation of watersheds.

Chapter 4 dealt with elevational ranges of montane birds and the impact of lowland deforestation on their ranges in the Western Andes of Colombia, an important biodiversity hotspot. Using point counts and mist-nets, I surveyed six altitudinal transects spanning 2200 to 2800m. Three transects were forested from 2200 to 2800m, and three were partially deforested with forest cover only above 2400m. I compared abundance-weighted mean elevation, minimum elevation, and elevational range width. In addition to analyzing the effect of deforestation on 134 species, I tested its impact within trophic guilds and habitat preference groups. Abundance-weighted mean and minimum elevations were not significantly different between forested and partially deforested transects. Range width was marginally different: as expected, ranges were larger in forested transects. Species in different trophic guilds and habitat preference categories showed different trends. These results suggest that deforestation may affect species’ elevational ranges, even within the forest that remains. Climate change will likely exacerbate harmful impacts of deforestation on species’ elevational distributions. Future conservation strategies need to account for this by protecting connected forest tracts across a wide range of elevations.

In Chapter 5, I refine the ranges of 726 species from six biodiversity hotspots by suitable elevation and habitat. This set of 172 bird species for the Atlantic Forest, 138 for Central America, 100 for the Western Andes of Colombia, 57 for Madagascar, 102 for Sumatra, and 157 for Southeast Asia met the criteria for range size, endemism, threat, and forest use. Of these 586 species, the Red List deems 108 to be threatened: 15 critically endangered, 29 endangered, and 64 vulnerable. When ranges are refined by elevational limits and remaining forest cover, 10 of those critically endangered species have ranges < 100km2, but then so do 2 endangered species, seven vulnerable, and eight non-threatened ones. Similarly, 4 critically endangered species, 20 endangered, and 12 vulnerable species have refined ranges < 5000km2, but so do 66 non-threatened species. A striking 89% of these species I have classified in higher threat categories have <50% of their refined ranges inside protected areas. I find that for 43% of the species I assessed, refined range sizes fall within thresholds that typically have higher threat categories than their current assignments. I recommend these species for closer inspection by those who assess risk. These assessments are not only important on a species-by-species basis, but by combining distributions of threatened species, I create maps of conservation priorities. They differ significantly from those created from unrefined ranges.

Molecular docking and geographical information systems as tools to assess the potential impact of veterinary medicines on non-target organisms and the environment

Veterinary medicines (VMs) from agricultural industry can enter the environment in a number of ways. This includes direct exposure through aquaculture, accidental spillage and disposal, and indirect entry by leaching from manure or runoff after treatment. Many compounds used in animal treatments have ecotoxic properties that may have chronic or sometimes lethal effects when they come into contact with non-target organisms. VMs enter the environment in mixtures, potentially having additive effects. Traditional ecotoxicology tests are used to determine the lethal and sometimes reproductive effects on freshwater and terrestrial organisms. However, organisms used in ecotoxicology tests can be unrepresentative of the populations that are likely to be exposed to the compound in the environment. Most often the tests are on single compound toxicity but mixture effects may be significant and should be included in ecotoxicology testing. This work investigates the use, measured environmental concentrations (MECs) and potential impact of sea lice treatments on salmon farms in Scotland. Alternative methods for ecotoxicology testing including mixture toxicity, and the use of in silico techniques to predict the chronic impact of VMs on different species of aquatic organisms were also investigated. The Scottish Environmental Protection Agency (SEPA) provided information on the use of five sea lice treatments from 2008-2011 on Scottish salmon farms. This information was combined with the recently available data on sediment MECs for the years 2009-2012 provided by SEPA using ArcGIS 10.1. In depth analysis of this data showed that from a total of 55 sites, 30 sites had a MEC higher than the maximum allowable concentration (MAC) as set out by SEPA for emamectin benzoate and 7 sites had a higher MEC than MAC for teflubenzuron. A number of sites that were up to 16 km away from the nearest salmon farm reported as using either emamectin benzoate or teflubenzuron measured positive for the two treatments. There was no relationship between current direction and the distribution of the sea lice treatments, nor was there any evidence for alternative sources of the compounds e.g. land treatments. The sites that had MECs higher than the MAC could pose a risk to non-target organisms and disrupt the species dynamics of the area. There was evidence that some marine protected sites might be at risk of exposure to these compounds. To complement this work, effects on acute mixture toxicity of the 5 sea lice treatments, plus one major metabolite 3-phenoxybenzoic acid (3PBA), were measured using an assay using the bioluminescent bacteria Aliivibrio fischeri. When exposed to the 5 sea lice treatments and 3PBA A. fischeri showed a response to 3PBA, emamectin benzoate and azamethiphos as well as combinations of the three. In order to establish any additive effect of the sea lice treatments, the efficacy of two mixture prediction equations, concentration addition (CA) and independent action ii(IA) were tested using the results from single compound dose response curves. In this instance IA was the more effective prediction method with a linear regression confidence interval of 82.6% compared with 22.6% of CA. In silico molecular docking was carried out to predict the chronic effects of 15 VMs (including the five used as sea lice control). Molecular docking has been proposed as an alternative screening method for the chronic effects of large animal treatments on non-target organisms. Oestrogen receptor alpha (ERα) of 7 non-target bony fish and the African clawed frog Xenopus laevis were modelled using SwissModel. These models were then ‘docked’ to oestradiol, the synthetic oestrogen ethinylestradiol, two known xenoestrogens dichlorodiphenyltrichloroethane (DDT) and bisphenol A (BPA), the antioestrogen breast cancer treatment tamoxifen and 15 VMs using Auto Dock 4. Based on the results of this work, four VMs were identified as being possible xenoestrogens or anti-oestrogens; these were cypermethrin, deltamethrin, fenbendazole and teflubenzuron. Further investigation, using in vitro assays, into these four VMs has been suggested as future work. A modified recombinant yeast oestrogen screen (YES) was attempted using the cDNA of the ERα of the zebrafish Danio rerio and the rainbow trout Oncorhynchus mykiss. Due to time and difficulties in cloning protocols this work was unable to be completed. Use of such in vitro assays would allow for further investigation of the highlighted VMs into their oestrogenic potential. In conclusion, VMs used as sea lice treatments, such as teflubenzuron and emamectin benzoate may be more persistent and have a wider range in the environment than previously thought. Mixtures of sea lice treatments have been found to persist together in the environment, and effects of these mixtures on the bacteria A. fischeri can be predicted using the IA equation. Finally, molecular docking may be a suitable tool to predict chronic endocrine disrupting effects and identify varying degrees of impact on the ERα of nine species of aquatic organisms.

Examples of “land stewarship” in Brazil. The “Projecto Sempre Viva” (Mucugê-Bahia)

In recent years the concept of "Land Stewardship" has gained a great importance. In short, it means that local entities and individuals can protect enclave of high ecological and cultural value. This vision has been effective in some places in the world with success. For example, the “Projeto Sempre Viva”, created in the town of Mucugê, a place located in one of Brazil´s most renowned Natural Protected Areas: the Chapada Diamantina (State of Bahia). We had looked over the available information about this project on the Internet, as well as a personal visit that was made to the site to know it and to have the possibility to talk to their managers. On this basis, it has been reached to the conclusion that this project, born to protect a Sempre Viva´s endemic species in danger of extinction, has turned into an important site for tourism and environmental education, completed with the preservation of the cultural identity of this region which is linked to diamond mining.

Deep Corals, Deep Learning: Moving the Deep Net Towards Real-Time Image Annotation

The mismatch between human capacity and the acquisition of Big Data such as Earth imagery undermines commitments to Convention on Biological Diversity (CBD) and Aichi targets. Artificial intelligence (AI) solutions to Big Data issues are urgently needed as these could prove to be faster, more accurate, and cheaper. Reducing costs of managing protected areas in remote deep waters and in the High Seas is of great importance, and this is a realm where autonomous technology will be transformative.

Extractivism and the de jure and de facto ethno-territorial rights in Latin America: How important are the constitutions? : Extractivismo y derechos étnico-territoriales de jure y de facto en Latinoamérica: ¿Cuán importantes son las constituciones?

A growing number of Latin American rural groups have attained extended ethno-territorial rights, and sizeable territories were safeguarded by progressive constitutions. This trend was the product of extended cycles of protest at local, national and transnational levels; social movements struggle, with broader collective South-South collaboration. Nonetheless, the continent simultaneously experienced a resource extraction boom. Commonly, the extractivism takes place in protected areas and/or indigenous territories. Accordingly, economic interests clash with the safeguarding and recognition of constitutional rights. Through the analysis of selected illustrative cases across Latin America, this study analyses the (de jure) rights on paper versus the (de facto) rights in practice. 

Macroinvertebrate Diversity in Urban and Rural Ponds: Implications for Freshwater Biodiversity Conservation

Ponds are among the most biodiverse freshwater ecosystems, yet face significant threats from removal, habitat degradation and a lack of legislative protection globally. Information regarding the habitat quality and biodiversity of ponds across a range of land uses is vital for the long term conservation and management of ecological resources. In this study we examine the biodiversity and conservation value of macroinvertebrates from 91 lowland ponds across 3 land use types (35 floodplain meadow, 15 arable and 41 urban ponds). A total of 224 macroinvertebrate taxa were recorded across all ponds, with urban ponds and floodplain ponds supporting a greater richness than arable ponds at the landscape scale. However, at the alpha scale, urban ponds supported lower faunal diversity (mean: 22 taxa) than floodplain (mean: 32 taxa) or arable ponds (mean: 30 taxa). Floodplain ponds were found to support taxonomically distinct communities compared to arable and urban ponds. A total of 13 macroinvertebrate taxa with a national conservation designation were recorded across the study area and 12 ponds (11 floodplain and 1 arable pond) supported assemblages of high or very high conservation value. Pond conservation currently relies on the designation of individual ponds based on very high biodiversity or the presence of taxa with specific conservation designations. However, this site specific approach fails to acknowledge the contribution of ponds to freshwater biodiversity at the landscape scale. Ponds are highly appropriate sites outside of protected areas (urban/arable), with which the general public are already familiar, for local and landscape scale conservation of freshwater habitats.

Creating restoration landscapes: partnerships in large-scale conservation in the UK

It is increasingly recognized that ecological restoration demands conservation action beyond the borders of existing protected areas. This requires the coordination of land uses and management over a larger area, usually with a range of partners, which presents novel institutional challenges for conservation planners. Interviews were undertaken with managers of a purposive sample of large-scale conservation areas in the UK. Interviews were open-ended and analyzed using standard qualitative methods. Results show a wide variety of organizations are involved in large-scale conservation projects, and that partnerships take time to create and demand resilience in the face of different organizational practices, staff turnover, and short-term funding. Successful partnerships with local communities depend on the establishment of trust and the availability of external funds to support conservation land uses. We conclude that there is no single institutional model for large-scale conservation: success depends on finding institutional strategies that secure long-term conservation outcomes, and ensure that conservation gains are not reversed when funding runs out, private owners change priorities, or land changes hands.

Conservation narratives in Peru: envisioning biodiversity in sustainable development

In the mega-diverse country Peru, a resource intensive development model collides with the interest of conserving biodiversity. Peruvian biodiversity experts have developed different lines of argumentation as to how to integrate conservation into the sustainable development of their country. Applying grounded theory, I define five groups of conservation narratives based on the analysis of 72 qualitative interviews with experts working in areas of biodiversity conservation. I have labeled them: biodiversity protectionists, biodiversity traditionalists, biodiversity localists, biodiversity pragmatists, and biodiversity capitalists. These groups are each discussed in connection with what they have to say about biodiversity in relation to human life, valuation and knowledge systems, participation and leadership, substitutability of natural capital, and its predominant political strategy. In a second step, a comparative analysis of the dominant and diverging political perspectives is made. I argue that by deconstructing underlying premises and ideologies, common ground and possible opportunities for collaboration can be identified. Moreover, although the presented results can serve as a discussion scaffold to organize conservation debates in Peru, this example demonstrates how the terms biodiversity and sustainability are operationalized in conservation narratives.

Espaços especiais em Natal (moradia e meio ambiente): um necessário diálogo entre direitos e espaços na perspectiva de proteção aos direitos fundamentais na cidade contemporânea

Some protected special spaces on behalf of fundamental rights to the environment and the housing at the city of Natal are fragile by facing actions and attempts to suppress and changing (or omission in the implementation) of standards in furtherance of those rights at the local level, which seems to reflect a situation that goes beyond the context of the city. Based on integrated approach of the housing rights and the environment and its protection of special spaces on the field of fundamental rights, the thesis seeks to understand the weaknesses that affect the legal state duty under the realization/implementation of fundamental rights to the environment and housing in cities, focusing on the issues of flexibility of the founding legislation of special spaces to the detriment of the attributes they protected and the lack of implementation of the legal system that allows their effectiveness. So, it looks initially to understand the environment and housing rights and their special protected areas in the brazilian legal system, looking forward the evolution of its legal protection, as well as the weaknesses that emerge in the field of their effectiveness. Analyzing the trajectory of the environment and housing rights and their special protected areas in Natal, considering its standards, attributes, protection indicators, weaknesses and negative evidence within its legal protections and their enforcement by state entity, this thesis proposes to verify the existence of forms to confronting the weaknesses founded in the maintenance of legal protection and its implementation. At this point it discusses the legal basis and safeguard instruments of protection, especially within the juridical field, as part of a (re)discussion about issues of legislative and administrative discretion in the face of objective legal state duty to realization/implementation of fundamental rights in the urban space. With all these issues together the thesis does not ignore the scenario where the dividing line between public and private (economic) are becoming ever more tenuous in the field of state action and where the city stands as a special commodity to the reproduction of real estate, according to the interests of capitalist logic

Comunidades tradicionais em áreas protegidas: convergências e lacunas da Política Urbana e Ambiental na Reserva de Desenvolvimento Sustentável Estadual Ponta do Tubarão/RN

This work presents a reflection on possibilities and boundaries of consolidation and expansion of human settlements characterized as traditional communities that are located within protected areas, using as study reference the State Sustainable Development Reserve Ponta do Tubarão, at Rio Grande do Norte state. The main topics highlight the conflict between the right to housing and the prevalence of fundamental rights of traditional populations, opposed to the diffuse right to environment, according to the regulatory framework of the Brazilian Urban and Environmental Policies. At the same time that these settlements, historically built, are substantiated by the principles of recognition of rights to traditional populations, they are in a condition of complexity to the resolution of conflicts in its urban dimension and lead to an impairment of natural sites. This work questions how the instruments of land use and occupation are defined and relate to environmental planning, especially considering that the settlements are located in Permanent Preservation Areas (APP). It aims to further the discussion of the urban dimension in settlements, characterizing its formation and growth process, to identify the gaps and convergences between the Urban and Environmental Policy, under the foundations of a socio-environmental approach. The results spotlights the conflicts between occupation and natural areas, inferring that the definition of Urban Policies instruments and its integration with Environmental Policies instruments account for essential and priority actions to the achievement to the rights to a sustainable city, as determined in the Cities Statute and environmental protection goals, defined for the Conservation Units

Small-scale variability of the current in the Strait of Bonifacio

Current dynamics in the Strait of Bonifacio (south Corsica) were investigated at a small scale during the STELLAMARE1 multidisciplinary cruise in summer 2012, using in situ measurements and modeling data. The Strait of Bonifacio is a particularly sensitive marine area in which specific conservation measures have been taken to preserve the natural environment and wild species. Good knowledge of the hydrodynamics in this area is essential to optimize the Marine Protected Area's management rules. Therefore, we used a high-resolution model (400 m) based on the MARS3D code to investigate the main flux exchanges and to formulate certain hypotheses about the formation of possible eddy structures. The aim of the present paper is first to synthetize the results obtained by combining Acoustic Doppler Current Profiler data, hydrological parameters, Lagrangian drifter data, and satellite observations such as MODIS OC5 chlorophyll a data or Metop-A AVHRR Sea Surface Temperature (SST) data. These elements are then used to validate the presence of the mesoscale eddies simulated by the model and their recurrence outside the cruise period. To complete the analysis, the response of the 3D hydrodynamical model was evaluated under two opposing wind systems and certain biases were detected. Strong velocities up to 1 m s(-1) were recorded in the east part due to the Venturi effect; a complementary system of vortices governed by Coriolis effect and west wind was observed in the west part, and horizontal stratification in the central part has been identified under typical wind condition.

O pedestrianismo como instrumento de valorização ecoturística dos sítios da Rede Natura 2000, nas ilhas de São Miguel e Flores

Tese de Doutoramento, Ciências do Ambiente (Ecologia), 30 de Julho de 2013, Universidade dos Açores.

Minería de oro en el marco de la inseguridad normativa, los grupos de interés y las zonas de exclusión

En este artículo se aborda el tema de la minería en zonas excluibles, por medio de una revisión bibliográfica de la legislación vigente, y se ejemplifican dos casos icono que se han presentado en Colombia en relación con la minería de oro en áreas de protección: el Parque Nacional Yaigojé-Apaporis y el Páramo de Santurbán. En ambos casos se evidencia la falta de coordinación entre las autoridades mineras y ambientales, y el vacío legislativo especialmente en la fase exploratoria, que, además de causar serios impactos ambientales y vulnerar los derechos de minorías étnicas y la población en general, crea inseguridad normativa y grandes costos a las empresas mineras. En un primer momento se describe el panorama jurídico que rige la explotación minera en Colombia, seguido de un contexto técnico del ciclo minero y de las implicaciones desde el punto de vista jurídico de este tipo de explotaciones en áreas protegidas. Luego, se presenta una cronología de los estudios de caso de la minería en un área protegida del sistema de Parques Nacionales y otra de carácter regional, concluyendo que la falta de coordinación entre instituciones deja al sector en un limbo jurídico.

Caracterização ecológica dos peixes recifais do Atol das Rocas

The present work was carried out at the Atol das Rocas (3º 51 S; 33º 49 W), the only atoll of the South Atlantic and the first Brazilian marine protected area. It was guided by the following hypothesis: the composition of the fish communities varies in agreement with the position of the pools; in other words, with or without permanent ocean connection. To test the validity of this hypothesis, the fish abundance was estimated in the connected pools (Barretinha/Barreta Falsa) and unconnected ones (Cemiteriozinho/Âncoras), carrying an ecological characterization of the fishes that inhabit these pools. Additionally, the structural complexity of the sampled places was also evaluated intending to verify the variations of the abundance and diversity of fishes in function to this factor. By the fact of this research was being carried out through the limits of a conservation unit, the samples was realized using visual census techniques. The results generated through uni and multivariate analytic techniques allowed the evidence that decisive factor in the density, richness and diversity variations of fishes are linked to the substratum type (Hard / Soft bottom) and not by the fact that the pool are or are not connected permanently to the ocean. In relation to the structural complexity; 58% of the variations in the diversity of fishes were attributed to changes in the structural complexity, while 12% of the variations in the abundance were attributed to the structural complexity