Modelling ecological niches with support vector machines

1. The ecological niche is a fundamental biological concept. Modelling species' niches is central to numerous ecological applications, including predicting species invasions, identifying reservoirs for disease, nature reserve design and forecasting the effects of anthropogenic and natural climate change on species' ranges. 2. A computational analogue of Hutchinson's ecological niche concept (the multidimensional hyperspace of species' environmental requirements) is the support of the distribution of environments in which the species persist. Recently developed machine-learning algorithms can estimate the support of such high-dimensional distributions. We show how support vector machines can be used to map ecological niches using only observations of species presence to train distribution models for 106 species of woody plants and trees in a montane environment using up to nine environmental covariates. 3. We compared the accuracy of three methods that differ in their approaches to reducing model complexity. We tested models with independent observations of both species presence and species absence. We found that the simplest procedure, which uses all available variables and no pre-processing to reduce correlation, was best overall. Ecological niche models based on support vector machines are theoretically superior to models that rely on simulating pseudo-absence data and are comparable in empirical tests. 4. Synthesis and applications. Accurate species distribution models are crucial for effective environmental planning, management and conservation, and for unravelling the role of the environment in human health and welfare. Models based on distribution estimation rather than classification overcome theoretical and practical obstacles that pervade species distribution modelling. In particular, ecological niche models based on machine-learning algorithms for estimating the support of a statistical distribution provide a promising new approach to identifying species' potential distributions and to project changes in these distributions as a result of climate change, land use and landscape alteration.

Impact of model complexity on cross-temporal transferability in Maxent species distribution models: An assessment using paleobotanical data

Maximum entropy modeling (Maxent) is a widely used algorithm for predicting species distributions across space and time. Properly assessing the uncertainty in such predictions is non-trivial and requires validation with independent datasets. Notably, model complexity (number of model parameters) remains a major concern in relation to overfitting and, hence, transferability of Maxent models. An emerging approach is to validate the cross-temporal transferability of model predictions using paleoecological data. In this study, we assess the effect of model complexity on the performance of Maxent projections across time using two European plant species (Alnus giutinosa (L.) Gaertn. and Corylus avellana L) with an extensive late Quaternary fossil record in Spain as a study case. We fit 110 models with different levels of complexity under present time and tested model performance using AUC (area under the receiver operating characteristic curve) and AlCc (corrected Akaike Information Criterion) through the standard procedure of randomly partitioning current occurrence data. We then compared these results to an independent validation by projecting the models to mid-Holocene (6000 years before present) climatic conditions in Spain to assess their ability to predict fossil pollen presence-absence and abundance. We find that calibrating Maxent models with default settings result in the generation of overly complex models. While model performance increased with model complexity when predicting current distributions, it was higher with intermediate complexity when predicting mid-Holocene distributions. Hence, models of intermediate complexity resulted in the best trade-off to predict species distributions across time. Reliable temporal model transferability is especially relevant for forecasting species distributions under future climate change. Consequently, species-specific model tuning should be used to find the best modeling settings to control for complexity, notably with paleoecological data to independently validate model projections. For cross-temporal projections of species distributions for which paleoecological data is not available, models of intermediate complexity should be selected.

Predicted decrease in global climate suitability masks regional complexity of invasive fruit fly species response to climate change

Climate change affects the rate of insect invasions as well as the abundance, distribution and impacts of such invasions on a global scale. Among the principal analytical approaches to predicting and understanding future impacts of biological invasions are Species Distribution Models (SDMs), typically in the form of correlative Ecological Niche Models (ENMs). An underlying assumption of ENMs is that species-environment relationships remain preserved during extrapolations in space and time, although this is widely criticised. The semi-mechanistic modelling platform, CLIMEX, employs a top-down approach using species ecophysiological traits and is able to avoid some of the issues of extrapolation, making it highly applicable to investigating biological invasions in the context of climate change. The tephritid fruit flies (Diptera: Tephritidae) comprise some of the most successful invasive species and serious economic pests around the world. Here we project 12 tephritid species CLIMEX models into future climate scenarios to examine overall patterns of climate suitability and forecast potential distributional changes for this group. We further compare the aggregate response of the group against species-specific responses. We then consider additional drivers of biological invasions to examine how invasion potential is influenced by climate, fruit production and trade indices. Considering the group of tephritid species examined here, climate change is predicted to decrease global climate suitability and to shift the cumulative distribution poleward. However, when examining species-level patterns, the predominant directionality of range shifts for 11 of the 12 species is eastward. Most notably, management will need to consider regional changes in fruit fly species invasion potential where high fruit production, trade indices and predicted distributions of these flies overlap.

The importance of sward architectural complexity in structuring predatory and phytophagous invertebrate assemblages

1. Although the importance of plant community assemblages in structuring invertebrate assemblages is well known, the role that architectural complexity plays is less well understood. In particular, direct empirical data for a range of invertebrate taxa showing how functional groups respond to plant architecture is largely absent from the literature. 2. The significance of sward architectural complexity in determining the species richness of predatory and phytophagous functional groups of spiders, beetles, and true bugs, sampled from 135 field margin plots over 2 years was tested. The present study compares the relative importance of sward architectural complexity to that of plant community assemblage. 3. Sward architectural complexity was found to be a determinant of species richness for all phytophagous and predatory functional groups. When individual species responses were investigated, 62.5% of the spider and beetle species, and 50.0% of the true bugs responded to sward architectural complexity. 4. Interactions between sward architectural complexity and plant community assemblage indicate that the number of invertebrate species supported by the plant community alone could be increased by modification of sward architecture. Management practices could therefore play a key role in diversifying the architectural structure of existing floral assemblages for the benefit of invertebrate assemblages. 5. The contrasting effects of sward architecture on invertebrate functional groups characterised by either direct (phytophagous species) or indirect (predatory species) dependence on plant communities is discussed. It is suggested that for phytophagous taxa, plant community assemblage alone is likely to be insufficient to ensure successful species colonisation or persistence without appropriate development of sward architecture.

Latitudinal gradients in intraspecific ecological diversity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The effects of habitat complexity and hydraulic conditions on the establishment of benthic stream macroalgae

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Accounting for uncertainty in ecological analysis: the strengths and limitations of hierarchical statistical modeling

Analyses of ecological data should account for the uncertainty in the process(es) that generated the data. However, accounting for these uncertainties is a difficult task, since ecology is known for its complexity. Measurement and/or process errors are often the only sources of uncertainty modeled when addressing complex ecological problems, yet analyses should also account for uncertainty in sampling design, in model specification, in parameters governing the specified model, and in initial and boundary conditions. Only then can we be confident in the scientific inferences and forecasts made from an analysis. Probability and statistics provide a framework that accounts for multiple sources of uncertainty. Given the complexities of ecological studies, the hierarchical statistical model is an invaluable tool. This approach is not new in ecology, and there are many examples (both Bayesian and non-Bayesian) in the literature illustrating the benefits of this approach. In this article, we provide a baseline for concepts, notation, and methods, from which discussion on hierarchical statistical modeling in ecology can proceed. We have also planted some seeds for discussion and tried to show where the practical difficulties lie. Our thesis is that hierarchical statistical modeling is a powerful way of approaching ecological analysis in the presence of inevitable but quantifiable uncertainties, even if practical issues sometimes require pragmatic compromises.

ECOLOGICAL CONTROL OF BIRD HAZARD TO AIRCRAFT

The Canadian Wildlife Service has had twenty-five years experience with the problem caused by bird contacts with aircraft. I experienced my first bird strike, while flying as an observer on a waterfowl survey in August, 1940. Officers of the Service investigated bird problems at airports at Yarmouth, Nova Scotia, and Cartierville, Quebec, in the late 1940's. Those incidents involving gulls and low speed piston-engined aircraft caused minor damage to the aircraft but considerable disturbance to the operators. As aircraft speeds increased and airports became more numerous and busier the problem increased in extent and complexity. By 1960 it was apparent that the problem would grow worse and that work should be directed toward reducing the number of incidents. In 1960 an electra aircraft crashed at Boston, Massachusetts, killing 61 passengers. Starlings were involved in the engine malfunction which preceded the crash. In November, 1962 a viscount aircraft was damaged by collision with two swans between Baltimore and Washington and crashed with a loss of 17 lives. Those incidents focused attention on the bird hazard problem in the United States.

Long-term stasis in ecological assemblages: Evidence from the fossil record

Studies of plant and animal assemblages from both the terrestrial and the marine fossil records reveal persistence for extensive periods of geological time, sometimes millions of years. Persistence does not require lack of change or the absence of variation from one occurrence of the assemblage to the next in geological time. It does, however, imply that assemblage composition is bounded and that variation occurs within those bounds. The principal cause for these patterns appears to be species-, and perhaps clade-level, environmental fidelity that results in long-term tracking of physical conditions. Other factors that influence persistent recurrence of assemblages are historical, biogeographic effects, the law of large numbers, niche differentiation, and biotic interactions. Much research needs to be done in this area, and greater uniformity is needed in the approaches to studying the problem. However, great potential also exists for enhanced interaction between paleoecology and neoecology in understanding spatiotemporal complexity of ecological dynamics.

Úton egy fenntartható gazdasági paradigma felé – A komplexitás befogadása a hálózati elméleteken keresztül (Towards a sustainable economic paradigm – Acceptance of the complexity through network theories)

Mára elkerülhetetlennek tűnik a gondolati váltás a gazdaságtudományok területén annak érdekében, hogy közelebb kerüljünk a hármas (gazdasági, társadalmi, környezeti) válságot előidéző problémák megoldásaihoz. A szerzők cikkükben amellett érvelnek, hogy a komplexitás befogadása kezdeti törekvésként értelmezhető azon az úton, amely a mindennapokban érzékelhető társadalmi és ökológiai problémák megoldásához vezet. Már léteznek olyan gazdaság- és vállalatelméletek, amelyek kezdik megkérdőjelezni az eddigi főáramú koncepciókat, és készek arra, hogy elveiket, elméleteiket a működési környezet bonyolultságát elfogadva alakítsák ki, és így találjanak mindennapos megoldásokat a gazdasági működésben. Ilyen például – a cikkben szereplő – IMP (Industrial Marketing and Purchasing) csoport hálózatelmélete. A szerzők azt kívánják bemutatni, hogy az ilyen hálózatelméletek alkalmasak arra, hogy a vállalatközi szférán túl is befolyásolják azt, ahogyan a vállalatok döntéseiket meghozzák és kapcsolataikat kezelik. ______ Today, it seems inevitable change of thought in the field of economics in order to get closer to solutions of problems which induced the triple (economic, social, environmental) crisis. In their article, the authors argue that the reception of complexity can be interpreted as an initial effort on the path that leads to the solutions of the everyday perceived social and ecological problems. The authors aim to present that the IMP (Industrial Marketing and Purchasing) group network theory is able to influence beyond the sphere of inter-company, that companies take their decisions and their relationships are treated.

Comparison of different space indexing methods for ecological evaluation of urban openspaces

Nowadays we meet many different evaluation methods regarding the ecological performance of green surfaces and parks. All these methods are extremely valuable in determining how well a green surface performs from ecological aspect and to what extent the environment were damaged if these sites would be built or would be developed any other way causing reduction of green surfaces. The goal of the article is to clarify the differences between two evaluation methods (GSI – Green Space Intensity, BARC – Biological Activity Rate Calculation) suitable for urban green infrastructure analysis and to see if any significant difference can be observed evaluating the same site by these methods. Our research sites are in Budapest and their sizes vary between 2,5-8 acres. The most important aspects of site analysis are the following: size and boundaries of the park, existence or lack of water features, the characteristics of their surfaces and the complexity of vegetation. We summarize the data of the site analysis in tables, make a summarizing diagram for visual representation and draw conclusions from the results. As a final step, we evaluate how these two evaluation systems relate to urban open space developments.

Phylogenetic and ecological significance in the evolution of Cetacean tonal sounds

Cetaceans are aquatic mammals that rely primarily on sound for most daily tasks. A compendium of sounds is emitted for orientation, prey detection, and predator avoidance, and to communicate. Communicative sounds are among the most studied Cetacean signals, particularly those referred to as tonal sounds. Because tonal sounds have been studied especially well in social dolphins, it has been assumed these sounds evolved as a social adaptation. However, whistles have been reported in ‘solitary’ species and have been secondarily lost three times in social lineages. Clearly, therefore, it is necessary to examine closely the association, if any, between whistles and sociality instead of merely assuming it. Several hypotheses have been proposed to explain the evolutionary history of Cetacean tonal sounds. The main goal of this dissertation is to cast light on the evolutionary history of tonal sounds by testing these hypotheses by combining comparative phylogenetic and field methods. This dissertation provides the first species-level phylogeny of Cetacea and phylogenetic tests of evolutionary hypotheses of cetacean communicative signals. Tonal sounds evolution is complex in that has likely been shaped by a combination of factors that may influence different aspects of their acoustical structure. At the inter-specific level, these results suggest that only tonal sound minimum frequency is constrained by body size. Group size also influences tonal sound minimum frequency. Species that live in large groups tend to produce higher frequency tonal sounds. The evolutionary history of tonal sounds and sociality may be intertwined, but in a complex manner rejecting simplistic views such as the hypothesis that tonal sounds evolved ‘for’ social communication in dolphins. Levels of social and tonal sound complexity nevertheless correlate indicating the importance of tonal sounds in social communication. At the intraspecific level, tonal sound variation in frequency and temporal parameters may be product of genetic isolation and local levels of underwater noise. This dissertation provides one of the first insights into the evolution of Cetacean tonal sounds in a phylogenetic context, and points out key species where future studies would be valuable to enrich our understanding of other factors also playing a role in tonal sound evolution. ^

Phylogenetic and Ecological Significance in the Evolution of Cetacean Tonal Sounds

Cetaceans are aquatic mammals that rely primarily on sound for most daily tasks. A compendium of sounds is emitted for orientation, prey detection, and predator avoidance, and to communicate. Communicative sounds are among the most studied Cetacean signals, particularly those referred to as tonal sounds. Because tonal sounds have been studied especially well in social dolphins, it has been assumed these sounds evolved as a social adaptation. However, whistles have been reported in ‘solitary’ species and have been secondarily lost three times in social lineages. Clearly, therefore, it is necessary to examine closely the association, if any, between whistles and sociality instead of merely assuming it. Several hypotheses have been proposed to explain the evolutionary history of Cetacean tonal sounds. The main goal of this dissertation is to cast light on the evolutionary history of tonal sounds by testing these hypotheses by combining comparative phylogenetic and field methods. This dissertation provides the first species-level phylogeny of Cetacea and phylogenetic tests of evolutionary hypotheses of cetacean communicative signals. Tonal sounds evolution is complex in that has likely been shaped by a combination of factors that may influence different aspects of their acoustical structure. At the inter-specific level, these results suggest that only tonal sound minimum frequency is constrained by body size. Group size also influences tonal sound minimum frequency. Species that live in large groups tend to produce higher frequency tonal sounds. The evolutionary history of tonal sounds and sociality may be intertwined, but in a complex manner rejecting simplistic views such as the hypothesis that tonal sounds evolved ‘for’ social communication in dolphins. Levels of social and tonal sound complexity nevertheless correlate indicating the importance of tonal sounds in social communication. At the intraspecific level, tonal sound variation in frequency and temporal parameters may be product of genetic isolation and local levels of underwater noise. This dissertation provides one of the first insights into the evolution of Cetacean tonal sounds in a phylogenetic context, and points out key species where future studies would be valuable to enrich our understanding of other factors also playing a role in tonal sound evolution.

Building resilience for social-ecological sustainability in Atlantic Europe

This thesis argues that complex adaptive social–ecological systems (SES) theory has important implications for the design of integrated ocean and coastal governance in the EU. Traditional systems of governance have struggled to deal with the global changes, complexity and uncertainties that challenge a transition towards sustainability in Europe’s maritime macro-regions. There is an apparent disconnect between governance strategies for sustainability in Europe’s maritime macro-regions and a sound theoretical basis for them. My premise is that the design of governance architecture for maritime regional sustainability should be informed by SES theory. Therefore, the aim of this research was to gain insight into a multilevel adaptive governance architecture that combines notions of sustainability and development in the context of the Atlantic Europe maritime macro-region. The central research question asked whether it is possible to achieve this insight by using a SES as a framework and analytical tool. This research adopted social ecology and sustainability science as a foundation for understanding society–nature relations. Concepts from complex adaptive systems, SES and resilience theories were integrated into a conceptual framework that guided the investigation and analysis. A study was conducted to conceptualise the European Atlantic social–ecological system (EASES). This was used to represent and understand the Atlantic Europe macro-region as a SES. The study examined the proposition that governance can be focused on building SES resilience to help achieve maritime regional sustainability. A workbook method was developed and used to elicit expert opinion regarding EASES. The study identified sources of resilience and resilience dynamics that require management in the context of multilevel adaptive governance. This research found that the Atlantic Europe macro-region is a key focal level for multilevel adaptive governance architecture. The majority of the findings are specific to Atlantic Europe and not generalisable to other maritime macro-regions in Europe.

Physiological and ecological variables measured at the high and low pCO2 reef sections

Experiments have shown that ocean acidification due to rising atmospheric carbon dioxide concentrations has deleterious effects on the performance of many marine organisms. However, few empirical or modelling studies have addressed the long-term consequences of ocean acidification for marine ecosystems. Here we show that as pH declines from 8.1 to 7.8 (the change expected if atmospheric carbon dioxide concentrations increase from 390 to 750 ppm, consistent with some scenarios for the end of this century) some organisms benefit, but many more lose out. We investigated coral reefs, seagrasses and sediments that are acclimatized to low pH at three cool and shallow volcanic carbon dioxide seeps in Papua New Guinea. At reduced pH, we observed reductions in coral diversity, recruitment and abundances of structurally complex framework builders, and shifts in competitive interactions between taxa. However, coral cover remained constant between pH 8.1 and ~7.8, because massive Porites corals established dominance over structural corals, despite low rates of calcification. Reef development ceased below pH 7.7. Our empirical data from this unique field setting confirm model predictions that ocean acidification, together with temperature stress, will probably lead to severely reduced diversity, structural complexity and resilience of Indo-Pacific coral reefs within this century.