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.

Patterns and transitions in substance use among young Swiss men: a latent transition analysis approach

This study investigates the potential stages of drug use. Data from the longitudinal Cohort Study on Substance Use Risk Factors were used (N = 5,116). Drug use (alcohol, tobacco, and 16 illicit drugs) over the previous 12 months was assessed at two time points. Patterns and trajectories of drug use were studied using latent transition analysis (LTA). This study's substantive contributions are twofold. First, the pattern of drug use displayed the well-known sequence of drug involvement (licit drugs to cannabis to other illicit drugs), but with an added distinction between two kinds of illicit drugs ("middle-stage" drugs: uppers, hallucinogens, inhaled drugs; and "final-stage" drugs: heroin, ketamine, GHB/GBL, research chemicals, crystal meth, and spice). Second, subgroup membership was stable over time, as the most likely transition was remaining in the same latent class.

Benefits from ecological study methods to taxonomy of enchytraeids in southern Mata Atlântica

The objective of this work was to determine how taxonomy benefited from the ecological quantitative and site-based sampling methods in enchytraeids studies. Enchytraeids (small relatives of earthworms) were sampled in different phases of rain forest regeneration in the southern Mata Atlântica in Paraná, Brazil. The research combined ecological and taxonomic work, because enchytraeids are poorly studied and difficult to identify, and many new species were expected. The provision of large numbers of specimens enabled the test of species diagnoses by investigating the ranges of character variations in a larger series of specimens. Simplified species diagnoses adapted to the local conditions that allowed the identification of all specimens, juveniles included, were developed. Key characters and character states are presented for the three genera: Achaeta, Hemienchytraeus and Guaranidrilus. Among several new species, a rare species, possibly a remnant of the autochthonous forest fauna, was found and described.

Brittle to ductile transition in a fiber bundle with strong heterogeneity

We analyze the failure process of a two-component system with widely different fracture strength in the framework of a fiber bundle model with localized load sharing. A fraction 0≤α≤1 of the bundle is strong and it is represented by unbreakable fibers, while fibers of the weak component have randomly distributed failure strength. Computer simulations revealed that there exists a critical composition αc which separates two qualitatively different behaviors: Below the critical point, the failure of the bundle is brittle, characterized by an abrupt damage growth within the breakable part of the system. Above αc, however, the macroscopic response becomes ductile, providing stability during the entire breaking process. The transition occurs at an astonishingly low fraction of strong fibers which can have importance for applications. We show that in the ductile phase, the size distribution of breaking bursts has a power law functional form with an exponent μ=2 followed by an exponential cutoff. In the brittle phase, the power law also prevails but with a higher exponent μ=92. The transition between the two phases shows analogies to continuous phase transitions. Analyzing the microstructure of the damage, it was found that at the beginning of the fracture process cracks nucleate randomly, while later on growth and coalescence of cracks dominate, which give rise to power law distributed crack sizes.

Towards an ecological index for tropical soil quality based on soil macrofauna

The objective of this work was to construct a simple index based on the presence/absence of different groups of soil macrofauna to determine the ecological quality of soils. The index was tested with data from 20 sites in South and Central Tabasco, Mexico, and a positive relation between the model and the field observations was detected. The index showed that diverse agroforestry systems had the highest soil quality index (1.00), and monocrops without trees, such as pineapple, showed the lowest soil quality index (0.08). Further research is required to improve this model for natural systems that have very low earthworm biomass (<10 g m-2) and a high number of earthworm species (5-7), as it is in the tropical rain forest, whose soil quality index was medium (0.5). The application of this index will require an illustrated guide for its users. Further studies are required in order to test the use of this index by farmers.

Multidelayed random walks: Theory and application to the neolithic transition in Europe

We present a model in which particles (or individuals of a biological population) disperse with a rest time between consecutive motions (or migrations) which may take several possible values from a discrete set. Particles (or individuals) may also react (or reproduce). We derive a new equation for the effective rest time T˜ of the random walk. Application to the neolithic transition in Europe makes it possible to derive more realistic theoretical values for its wavefront speed than those following from the single-delayed framework presented previously [J. Fort and V. Méndez, Phys. Rev. Lett. 82, 867 (1999)]. The new results are consistent with the archaeological observations of this important historical process

Equilibrium curves and growth models to deal with forests in transition to uneven-aged structure : application in two sample stands

Abstract

A mixed ecologic-cohort comparison of physical activity & weight among young adults from five populations of African origin.

BACKGROUND: Examination of patterns and intensity of physical activity (PA) across cultures where obesity prevalence varies widely provides insight into one aspect of the ongoing epidemiologic transition. The primary hypothesis being addressed is whether low levels of PA are associated with excess weight and adiposity. METHODS: We recruited young adults from five countries (500 per country, 2500 total, ages 25-45 years), spanning the range of obesity prevalence. Men and women were recruited from a suburb of Chicago, Illinois, USA; urban Jamaica; rural Ghana; peri-urban South Africa; and the Seychelles. PA was measured using accelerometry and expressed as minutes per day of moderate-to-vigorous activity or sedentary behavior. RESULTS: Obesity (BMI ≥ 30) prevalence ranged from 1.4% (Ghanaian men) to 63.8% (US women). South African men were the most active, followed by Ghanaian men. Relatively small differences were observed across sites among women; however, women in Ghana accumulated the most activity. Within site-gender sub-groups, the correlation of activity with BMI and other measures of adiposity was inconsistent; the combined correlation across sites was -0.17 for men and -0.11 for women. In the ecological analysis time spent in moderate-to-vigorous activity was inversely associated with BMI (r = -0.71). CONCLUSION: These analyses suggest that persons with greater adiposity tend to engage in less PA, although the associations are weak and the direction of causality cannot be inferred because measurements are cross-sectional. Longitudinal data will be required to elucidate direction of association.

Integro-difference equations for interacting species and the Neolithic transition

We introduce a set of sequential integro-difference equations to analyze the dynamics of two interacting species. Firstly, we derive the speed of the fronts when a species invades a space previously occupied by a second species, and check its validity by means of numerical random-walk simulations. As an example, we consider the Neolithic transition: the predictions of the model are consistent with the archaeological data for the front speed, provided that the interaction parameter is low enough. Secondly, an equation for the coexistence time between the invasive and the invaded populations is obtained for the first time. It agrees well with the simulations, is consistent with observations of the Neolithic transition, and makes it possible to estimate the value of the interaction parameter between the incoming and the indigenous populations

Fronts from integrodifference equations and persistence effects on the Neolithic transition

We extend a previous model of the Neolithic transition in Europe [J. Fort and V. Méndez, Phys. Rev. Lett. 82, 867 (1999)] by taking two effects into account: (i) we do not use the diffusion approximation (which corresponds to second-order Taylor expansions), and (ii) we take proper care of the fact that parents do not migrate away from their children (we refer to this as a time-order effect, in the sense that it implies that children grow up with their parents, before they become adults and can survive and migrate). We also derive a time-ordered, second-order equation, which we call the sequential reaction-diffusion equation, and use it to show that effect (ii) is the most important one, and that both of them should in general be taken into account to derive accurate results. As an example, we consider the Neolithic transition: the model predictions agree with the observed front speed, and the corrections relative to previous models are important (up to 70%)

Nonequilibrium phase transition in a model for the propagation of innovations among economic agents

We characterize the different morphological phases that occur in a simple one-dimensional model of propagation of innovations among economic agents [X. Guardiola et al., Phys. Rev E 66, 026121 (2002)]. We show that the model can be regarded as a nonequilibrium surface growth model. This allows us to demonstrate the presence of a continuous roughening transition between a flat (system size independent fluctuations) and a rough phase (system size dependent fluctuations). Finite-size scaling studies at the transition strongly suggest that the dynamic critical transition does not belong to directed percolation and, in fact, critical exponents do not seem to fit in any of the known universality classes of nonequilibrium phase transitions. Finally, we present an explanation for the occurrence of the roughening transition and argue that avalanche driven dynamics is responsible for the novel critical behavior.