Macroinvertebrate communities and habitat structure in least-impacted hill streams of central Portugal

We surveyed macroinvertebrate communities in 31 hill streams in the Vouga River and Mondego River catchments in central Portugal. Despite applying a "least-impacted" criterion, channel and bank management was common, with 38% of streams demonstrating channel modification (damming) and 80% with evidence of bank modification. Principal component analysis (PCA) at the family and species level related the macroinvertebrates to habitat variables derived at three spatial scales -- site (20 m), reach (200 m), and catchment. Variation in community structure between sites was similar at the species and family level and was statistically related to pH, conductivity, temperature, flow, shade, and substrate size at the site scale; channel and bank habitat and riparian vegetation and land-use at the reach scale; and altitude and slope at the catchment scale. While the effects of river management were apparent in various ecologically important habitat features at the site and reach scale, a direct relationship with macroinvertebrate assemblages was only apparent between the extent of walled banks and the secondary PCA axis described by species data. The strong relationship between catchment scale variables and descriptors of physical structure at the reach and site scale suggests that catchment-scale parameters are valuable predicators of macroinvertebrate community structure in these streams despite the anthropogenic modifications of the natural habitat.

Scale and ecosystem services: how do observation, management, and analysis shift with scale212;lessons from Québec

Ecosystem service assessment and management are shaped by the scale at which they are conducted; however, there has been little systematic investigation of the scales associated with ecosystem service processes, such as production, benefit distribution, and management. We examined how social-ecological spatial scale impacts ecosystem service assessment by comparing how ecosystem service distribution, trade-offs, and bundles shift across spatial scales. We used a case study in Québec, Canada, to analyze the scales of production, consumption, and management of 12 ecosystem services and to analyze how interactions among 7 of these ecosystem services change across 3 scales of observation (1, 9, and 75 km²). We found that ecosystem service patterns and interactions were relatively robust across scales of observation; however, we identified 4 different types of scale mismatches among ecosystem service production, consumption, and management. Based on this analysis, we have proposed 4 aspects of scale that ecosystem service assessments should consider.

Effects of protected area downsizing on habitat fragmentation in Yosemite National Park (USA), 1864 211; 2014

Protected area downgrading, downsizing, and degazettement (PADDD) has been documented worldwide, but its impacts on biodiversity are poorly understood. To fill this knowledge gap, we reviewed historical documents to identify legal changes that altered the boundaries of Yosemite National Park. We identified two downsizes and five additions between 1905 and 1937 that reduced the size of Yosemite National Park by 30%. To examine the effects of these downsizing events on habitat fragmentation by roads, we compared protected, never-protected, and downsized lands at three spatial scales using four habitat fragmentation metrics: road density, fragment (land surrounded by roads) area-to-perimeter ratio, fragment area, and fragment density. In general, lands that were removed from protection, e.g., downsized, were more highly fragmented than protected lands and indistinguishable from never-protected lands. Lands where downsizes were reversed were less fragmented than lands where downsizes were not reversed. These results suggest that protected area downsizing may exacerbate habitat fragmentation, a key contributor to biodiversity loss globally. Furthermore, the case study in Yosemite National Park demonstrates that iconic protected areas in developed countries are not immune to downsizing. These findings underscore the need to account for PADDD and governance histories in ecological research, monitoring, and evaluation. As we move toward more evidence-based conservation policy, a rigorous understanding of PADDD is essential to ensure that protected areas fulfill their promise as a strategy for conserving global biodiversity.

Catch and effort from a recreational trolling fishery in a large lake

Over recent decades recreational fisheries have grown substantially throughout the world. Despite this increase, catches from recreational fisheries have often been ignored in fisheries management, although this is now being remedied. Monitoring recreational fisheries can be expensive, and the primary means used for monitoring is angler (creel) surveys, typically funded from sales of fishing licences. The studies presented in this thesis examine different approaches to monitoring recreational trolling fisheries’ catch and effort, where fishing licenses are not required and there are no reporting requirements. I present results from a complemented roving/mail-in survey undertaken during 2013-2014 to estimate recreational effort and catch of Atlantic salmon (Salmo salar) and brown trout (S. trutta) in the largest lake in the European Union, Lake Vänern, Sweden. I also evaluate different angler catch reporting methods (mail-in, tournament reports and face-to-face interviews) and compare catch rates within and among spring and fall fishing periods. In addition, mail-in survey data are examined for recall bias.   I estimate that 28.7 tonnes of salmon and trout combined were harvested by the recreational trolling fishery in 2014, more than the commercial and subsistence fisheries combined. Seasonal differences in both recreational effort and catch were observed. Effort, in boat hours, was significantly higher in spring than in fall. Catch rates of trout were higher in fall than in spring, but there were no seasonal differences in catches of salmon. Harvest per boat day did not differ significantly among catch reporting methods, indicating that all three methods could be useful for managers interested in harvest rates. In contrast, total and released catch per boat day differed among reporting methods, with tournament anglers catching more fish in total. Finally, there was little evidence for recall bias in mail-in surveys, indicating that mail-in surveys are useful for collecting unbiased catch data. My study is the most comprehensive angler survey to date for Lake Vänern, and my results should be of immediate use to local fisheries managers and should also be of interest to researchers and managers interested in estimating catch and effort for fisheries at large spatial scales.

Variation in composition of macro-benthic invertebrates as an indication of water quality status in three bays in Lake Victoria

Knowledge of how biota can be used to monitor ecosystem health and assess impacts by human alterations such as land use and management measures taken at different spatial scales is critical for improving the ecological quality of aquatic ecosystems. This knowledge in Uganda is very limited or unavailable yet it is needed to better understand the relationship between environmental factors at different spatial scales, assemblage structure and taxon richness of aquatic ecosystems. In this study, benthic invertebrate community patterns were sampled between June 2001 and April 2002 and analysed in relation to water quality and catchment land use patterns from three shallow near-shore bays characterized by three major land uses patterns: urban (Murchison Bay); semi-urban (Fielding Bay); rural (Hannington Bay). Variations in density and guild composition of benthic macro-invertebrates communities were evaluated using GIS techniques along an urban-rural gradient of land use and differences in community composition were related to dissolved oxygen and conductivity variation. Based on numerical abundance and tolerance values, Hilsenhoff's Biotic Index ofthe invertebrates was determined in order to evaluate the relative importance of water quality in the three bays. Murchison Bay supported a relatively taxa-poor invertebrate assemblage mainly comprising stenotopic and eurytopic populations of pollution-tolerant groups such as worms and Chironomus sp. with an overall depression in species diversity. On the contrary, the communities in Fielding and Hannington bays were quite similar and supported distinct and diverse assemblages including pollution-intolerant forms such as Ephemeroptera (mayflies), Odonata (dragonflies). The Hilsenhoff Biotic Index in Murchison Bay was 6.53. (indicating poor water quality) compared to 6.34 for Fielding Bay and 5.78 for Hannington Bay (both indicating fair water quality). The characterization of maximum taxa richness balanced among taxa groups with good representation of intolerant individuals in Hannington Bay relative to Fielding and Murchison bays concludes that the bay is the cleanest in terms of water quality. Contrary, the dominance of few taxa with many tolerant iqdividuals present in Murchison Bay indicates that the bay is degraded in terms of water quality. These result are ofimportance when planning conservation and management measures, implementing large-scale biomonitoring programs, and predicting how human alterations (e.g nutrient loading) affect water ecosystems. Therefore, analysis of water quality in relation to macro-invertebrate community composition patterns as bio-indicators can lead to further understanding of their responses to environmental manipulations and perturbations.

Iron mineral structure, reactivity, and isotopic composition in a South Pacific Gyre ferromanganese nodule over 4 Ma

Deep-sea ferromanganese nodules accumulate trace elements from seawater and underlying sediment porewaters during the growth of concentric mineral layers over millions of years. These trace elements have the potential to record past ocean geochemical conditions. The goal of this study was to determine whether Fe mineral alteration occurs and how the speciation of trace elements responds to alteration over ∼3.7 Ma of marine ferromanganese nodule (MFN) formation, a timeline constrained by estimates from 9Be/10Be concentrations in the nodule material. We determined Fe-bearing phases and Fe isotope composition in a South Pacific Gyre (SPG) nodule. Specifically, the distribution patterns and speciation of trace element uptake by these Fe phases were investigated. The time interval covered by the growth of our sample of the nodule was derived from 9Be/10Be accelerator mass spectrometry (AMS). The composition and distribution of major and trace elements were mapped at various spatial scales, using micro-X-ray fluorescence (μXRF), electron microprobe analysis (EMPA), and inductively coupled plasma mass spectrometry (ICP-MS). Fe phases were characterized by micro-extended X-ray absorption fine structure (μEXAFS) spectroscopy and micro-X-ray diffraction (μXRD). Speciation of Ti and V, associated with Fe, was measured using micro-X-ray absorption near edge structure (μXANES) spectroscopy. Iron isotope composition (δ56/54Fe) in subsamples of 1-3 mm increments along the radius of the nodule was determined with multiple-collector ICP-MS (MC-ICP-MS). The SPG nodule formed through primarily hydrogeneous inputs at a rate of 4.0 ± 0.4 mm/Ma. The nodule exhibited a high diversity of Fe mineral phases: feroxyhite (δ-FeOOH), goethite (α-FeOOH), lepidocrocite (γ-FeOOH), and poorly ordered ferrihydrite-like phases. These findings provide evidence that Fe oxyhydroxides within the nodule undergo alteration to more stable phases over millions of years. Trace Ti and V were spatially correlated with Fe and found to be adsorbed to Fe-bearing minerals. Ti/Fe and V/Fe ratios, and Ti and V speciation, did not vary along the nodule radius. The δ56/54Fe values, when averaged over sample increments representing 0.25 to 0.75 Ma, were homogeneous within uncertainty along the nodule radius, at -0.12 ± 0.07 ‰ (2sd, n=10). Our results indicate that the Fe isotope composition of the nodule remained constant during nodule growth and that mineral alteration did not affect the primary Fe isotope composition of the nodule. Furthermore, the average δ56/54Fe value of -0.12 ‰ we find is consistent with Fe sourced from continental eolian particles (dust). Despite mineral alteration, the trace element partitioning of Ti and V, and Fe isotope composition, do not appear to change within the sensitivity of our measurements. These findings suggest that Fe oxyhydroxides within hydrogenetic ferromanganese nodules are out of geochemical contact with seawater once they are covered by subsequent concentric mineral layers. Even though Fe-bearing minerals are altered, trace element ratios, speciation and Fe isotope composition are preserved within the nodule.

Phylodynamic modelling of foot-and-mouth disease virus sequence data

The under-reporting of cases of infectious diseases is a substantial impediment to the control and management of infectious diseases in both epidemic and endemic contexts. Information about infectious disease dynamics can be recovered from sequence data using time-varying coalescent approaches, and phylodynamic models have been developed in order to reconstruct demographic changes of the numbers of infected hosts through time. In this study I have demonstrated the general concordance between empirically observed epidemiological incidence data and viral demography inferred through analysis of foot-and-mouth disease virus VP1 coding sequences belonging to the CATHAY topotype over large temporal and spatial scales. However a more precise and robust relationship between the effective population size (

Seafloor heterogeneity influences the biodiversity–ecosystem functioning relationships in the deep sea

Theoretical ecology predicts that heterogeneous habitats allow more species to co-exist in a given area. In the deep sea, biodiversity is positively linked with ecosystem functioning, suggesting that deep-seabed heterogeneity could influence ecosystem functions and the relationships between biodiversity and ecosystem functioning (BEF). To shed light on the BEF relationships in a heterogeneous deep seabed, we investigated variations in meiofaunal biodiversity, biomass and ecosystem efficiency within and among different seabed morphologies (e.g., furrows, erosional troughs, sediment waves and other depositional structures, landslide scars and deposits) in a narrow geo-morphologically articulated sector of the Adriatic Sea. We show that distinct seafloor morphologies are characterized by highly diverse nematode assemblages, whereas areas sharing similar seabed morphologies host similar nematode assemblages. BEF relationships are consistently positive across the entire region, but different seabed morphologies are characterised by different slope coefficients of the relationship. Our results suggest that seafloor heterogeneity, allowing diversified assemblages across different habitats, increases diversity and influence ecosystem processes at the regional scale, and BEF relationships at smaller spatial scales. We conclude that high-resolution seabed mapping and a detailed analysis of the species distribution at the habitat scale are crucial for improving management of goods and services delivered by deep-sea ecosystems.

Development of new analytical procedures of isotope geochemistry by mass spectrometry. Application to the study of high-pressure metamorphic rocks from the Iberian Massif

319 p.

POSITIVE FILTERED P_N METHOD FOR LINEAR TRANSPORT EQUATIONS AND THE ASSOCIATED OPTIMIZATION ALGORITHM

We propose a positive, accurate moment closure for linear kinetic transport equations based on a filtered spherical harmonic (FP_N) expansion in the angular variable. The FP_N moment equations are accurate approximations to linear kinetic equations, but they are known to suffer from the occurrence of unphysical, negative particle concentrations. The new positive filtered P_N (FP_N+) closure is developed to address this issue. The FP_N+ closure approximates the kinetic distribution by a spherical harmonic expansion that is non-negative on a finite, predetermined set of quadrature points. With an appropriate numerical PDE solver, the FP_N+ closure generates particle concentrations that are guaranteed to be non-negative. Under an additional, mild regularity assumption, we prove that as the moment order tends to infinity, the FP_N+ approximation converges, in the L2 sense, at the same rate as the FP_N approximation; numerical tests suggest that this assumption may not be necessary. By numerical experiments on the challenging line source benchmark problem, we confirm that the FP_N+ method indeed produces accurate and non-negative solutions. To apply the FP_N+ closure on problems at large temporal-spatial scales, we develop a positive asymptotic preserving (AP) numerical PDE solver. We prove that the propose AP scheme maintains stability and accuracy with standard mesh sizes at large temporal-spatial scales, while, for generic numerical schemes, excessive refinements on temporal-spatial meshes are required. We also show that the proposed scheme preserves positivity of the particle concentration, under some time step restriction. Numerical results confirm that the proposed AP scheme is capable for solving linear transport equations at large temporal-spatial scales, for which a generic scheme could fail. Constrained optimization problems are involved in the formulation of the FP_N+ closure to enforce non-negativity of the FP_N+ approximation on the set of quadrature points. These optimization problems can be written as strictly convex quadratic programs (CQPs) with a large number of inequality constraints. To efficiently solve the CQPs, we propose a constraint-reduced variant of a Mehrotra-predictor-corrector algorithm, with a novel constraint selection rule. We prove that, under appropriate assumptions, the proposed optimization algorithm converges globally to the solution at a locally q-quadratic rate. We test the algorithm on randomly generated problems, and the numerical results indicate that the combination of the proposed algorithm and the constraint selection rule outperforms other compared constraint-reduced algorithms, especially for problems with many more inequality constraints than variables.

Stable spike clusters for the one-dimensional Gierer-Meinhardt system

We consider the Gierer-Meinhardt system with precursor inhomogeneity in a one-dimensional interval. A spike cluster is the combination of several spikes which all approach the same point in the singular limit of small activator diffusivity. We rigorously prove the existence of a steady-state spike cluster consisting of N spikes near a non-degenerate local minimum point of the smooth inhomogeneity, where N is an arbitrary positive integer. Further, we show that this solution is linearly stable. We explicitly compute all eigenvalues, both large (of order O(1)) and small (of order o(1)). The main features of studying the Gierer-Meinhardt system in this setting are as follows: (i) it is biologically relevant since it models a hierarchical process (pattern formation of small-scale structures induced by a pre-existing large-scale inhomogeneity), (ii) it contains three different spatial scales two of which are small. (iii) all the expressions can be made explicit and often have a particularly simple form.

Large-scale neural dynamics: simple and complex

We review the use of neural field models for modelling the brain at the large scales necessary for interpreting EEG, fMRI, MEG and optical imaging data. Albeit a framework that is limited to coarse-grained or mean-field activity, neural field models provide a framework for unifying data from different imaging modalities. Starting with a description of neural mass models we build to spatially extended cortical models of layered two-dimensional sheets with long range axonal connections mediating synaptic interactions. Reformulations of the fundamental non-local mathematical model in terms of more familiar local differential (brain wave) equations are described. Techniques for the analysis of such models, including how to determine the onset of spatio-temporal pattern forming instabilities, are reviewed. Extensions of the basic formalism to treat refractoriness, adaptive feedback and inhomogeneous connectivity are described along with open challenges for the development of multi-scale models that can integrate macroscopic models at large spatial scales with models at the microscopic scale.

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species.

Does Landscape Context Affect Habitat Value? The Importance of Seascape Ecology in Back-reef Systems

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.

The role of agriculture and food consumption in tropical conservation

A growing human population, shifting human dietary habits, and climate change are negatively affecting global ecosystems on a massive scale. Expanding agricultural areas to feed a growing population drives extensive habitat loss, and climate change compounds stresses on both food security and ecosystems. Understanding the negative effects of human diet and climate change on agricultural and natural ecosystems provides a context within which potential technological and behavioral solutions can be proposed to help maximize conservation. The purpose of this research was to (1) examine the potential effects of climate change on the suitability of areas for commercial banana plantations in Latin America in the 2050s and how shifts in growing areas could affect protected areas; (2) test the ability of small unmanned aerial vehicles (UAVs) to map productivity of banana plantations as a potential tool for increasing yields and decreasing future plantation expansions; (3) project the effects on biodiversity of increasing rates of animal product consumption in developing megadiverse countries; and (4) estimate the capacity of global pasture biomass production and Fischer-Tropsch hydrocarbon synthesis (IGCC-FT) processing to meet electricity, gasoline and diesel needs. The results indicate that (1) the overall extent of areas suitable for conventional banana cultivation is predicted to decrease by 19% by 2050 because of a hotter and drier climate, but all current banana exporting countries are predicted to maintain some suitable areas with no effects on protected areas; (2) Spatial patterns of NDVI and ENDVI were significantly positively correlated with several metrics of fruit yield and quality, indicating that UAV systems can be used in banana plantations to map spatial patterns of fruit yield; (3) Livestock production is the single largest driver of habitat loss, and both livestock and feedstock production are increasing in developing biodiverse tropical countries. Reducing global animal product consumption should therefore be at the forefront of strategies aimed at reducing biodiversity loss; (4) Removing livestock from global pasture lands and instead utilizing the biomass production could produce enough energy to meet 100% of the electricity, gasoline, and diesel needs of over 40 countries with extensive grassland ecosystems, primarily in tropical developing countries.^