A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar

Pattern and process are inextricably linked in biogeographic analyses, though we can observe pattern, we must infer process. Inferences of process are often based on ad hoc comparisons using a single spatial predictor. Here, we present an alternative approach that uses mixed-spatial models to measure the predictive potential of combinations of hypotheses. Biodiversity patterns are estimated from 8,362 occurrence records from 745 species of Malagasy amphibians and reptiles. By incorporating 18 spatially explicit predictions of 12 major biogeographic hypotheses, we show that mixed models greatly improve our ability to explain the observed biodiversity patterns. We conclude that patterns are influenced by a combination of diversification processes rather than by a single predominant mechanism. A ‘one-size-fits-all’ model does not exist. By developing a novel method for examining and synthesizing spatial parameters such as species richness, endemism and community similarity, we demonstrate the potential of these analyses for understanding the diversification history of Madagascar’s biota.

Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F(CT) = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F(CT) range 0.275-0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.

Spacing abstraction: capitalism, law and the metropolis

In considering contemporary accounts of the interrelations of economic, legal and urban forms of social relations in the emergence of a global capitalist modernity, this paper argues that politico-juridical imaginaries of new forms of transnational universality have tended to be limited by virtue of both an anachronistic recourse to spatial models of the polis and a failure to confront the ineliminability of abstraction to any idea of global social interconnectivity. In such terms, it argues, Lefebvre’s famous call for a ‘right to the city’ needs to be reinscribed as a properly modern right to the metropolis; one that would allow us to conceive of the possibility of new kinds of relation between individual and collective subjectivity and the development of abstract social forms.

GLS Detrending, Efficient Unit Root Tests and Structural Change

We extend the class of M-tests for a unit root analyzed by Perron and Ng (1996) and Ng and Perron (1997) to the case where a change in the trend function is allowed to occur at an unknown time. These tests M(GLS) adopt the GLS detrending approach of Dufour and King (1991) and Elliott, Rothenberg and Stock (1996) (ERS). Following Perron (1989), we consider two models : one allowing for a change in slope and the other for both a change in intercept and slope. We derive the asymptotic distribution of the tests as well as that of the feasible point optimal tests PT(GLS) suggested by ERS. The asymptotic critical values of the tests are tabulated. Also, we compute the non-centrality parameter used for the local GLS detrending that permits the tests to have 50% asymptotic power at that value. We show that the M(GLS) and PT(GLS) tests have an asymptotic power function close to the power envelope. An extensive simulation study analyzes the size and power in finite samples under various methods to select the truncation lag for the autoregressive spectral density estimator. An empirical application is also provided.

Simulation-Based Finite-and Large-sample Inference Methods in Multivariate Regressions and Seemingly Unrelated Regressions

In the context of multivariate regression (MLR) and seemingly unrelated regressions (SURE) models, it is well known that commonly employed asymptotic test criteria are seriously biased towards overrejection. in this paper, we propose finite-and large-sample likelihood-based test procedures for possibly non-linear hypotheses on the coefficients of MLR and SURE systems.

The FCLT with Dependent Errors: an Helicopter Tour of the Quality of the Approximation

This note investigates the adequacy of the finite-sample approximation provided by the Functional Central Limit Theorem (FCLT) when the errors are allowed to be dependent. We compare the distribution of the scaled partial sums of some data with the distribution of the Wiener process to which it converges. Our setup is purposely very simple in that it considers data generated from an ARMA(1,1) process. Yet, this is sufficient to bring out interesting conclusions about the particular elements which cause the approximations to be inadequate in even quite large sample sizes.

Tests multiples simulés et tests de normalité basés sur plusieurs moments dans les modèles de régression

Cet article illustre l’applicabilité des méthodes de rééchantillonnage dans le cadre des tests multiples (simultanés), pour divers problèmes économétriques. Les hypothèses simultanées sont une conséquence habituelle de la théorie économique, de sorte que le contrôle de la probabilité de rejet de combinaisons de tests est un problème que l’on rencontre fréquemment dans divers contextes économétriques et statistiques. À ce sujet, on sait que le fait d’ignorer le caractère conjoint des hypothèses multiples peut faire en sorte que le niveau de la procédure globale dépasse considérablement le niveau désiré. Alors que la plupart des méthodes d’inférence multiple sont conservatrices en présence de statistiques non-indépendantes, les tests que nous proposons visent à contrôler exactement le niveau de signification. Pour ce faire, nous considérons des critères de test combinés proposés initialement pour des statistiques indépendantes. En appliquant la méthode des tests de Monte Carlo, nous montrons comment ces méthodes de combinaison de tests peuvent s’appliquer à de tels cas, sans recours à des approximations asymptotiques. Après avoir passé en revue les résultats antérieurs sur ce sujet, nous montrons comment une telle méthodologie peut être utilisée pour construire des tests de normalité basés sur plusieurs moments pour les erreurs de modèles de régression linéaires. Pour ce problème, nous proposons une généralisation valide à distance finie du test asymptotique proposé par Kiefer et Salmon (1983) ainsi que des tests combinés suivant les méthodes de Tippett et de Pearson-Fisher. Nous observons empiriquement que les procédures de test corrigées par la méthode des tests de Monte Carlo ne souffrent pas du problème de biais (ou sous-rejet) souvent rapporté dans cette littérature – notamment contre les lois platikurtiques – et permettent des gains sensibles de puissance par rapport aux méthodes combinées usuelles.

Simulating urban growth in a developing nation's region using a cellular automata-based model

Urbanization is one of the most evident global changes. Research in the field of urban growth modelling has generated models that explore for drivers and components of the urban growth dynamics. Cellular automata (CA) modeling is one of the recent advances, and a number of CA-based models of urban growth have produced satisfactory simulations of spatial urban expansion over time. Most application and test of CA-based models of urban growth which provide likely and reliable simulations has been developed in urban regions of developed nations; urban regions in the United States, in particular. This is because most of the models were developed in universities and research centers of developed nations, and these regions have the required data, which is extensive. Most of the population growth in the world, however, occurs in the developing world. While some European countries show signs of stabilization of their population, in less developed countries, such as India, population still grows exponentially. And this growth is normally uncoordinated, which results in serious environmental and social problems in urban areas. Therefore, the use of existing dynamic–spatial models of urban growth in regions of developing nations could be a means to assist planners and decision makers of these regions to understand and simulate the process of urban growth and test the results of different development strategies. The pattern of growth of urban regions of developing nations, however, seems to be different of the pattern of developed countries. The former use to be more dense and centralized, normally expanding outwards from consolidated urban areas; while the second is normally more fragmented and sparse. The present paper aims to investigate to how extent existing CA-based urban growth models tested in developed nations can also be applied to a developing country urban area. The urban growth model was applied to Porto Alegre City, Brazil. An expected contiguous expansion from existing urban areas has been obtained as following the historical trends of growth of the region. Moreover, the model was sensitive and able to portray different pattern of growth in the study area by changing the value of its parameters.

Fire Hazard in Coconino County, Arizona

Fire is a major management issue in the southwestern United States. Three spatial models of fire risk for Coconino County, Northern Arizona. These models were generated using thematic data layers depicting vegetation, elevation, wind speed and direction, and precipitation for January (winter), June (summer), and July (start of monsoon season). ArcGIS 9.0 was used to weight attributes in raster layers to reflect their influence on fire risk and to interpolate raster data layers from point data. Final models were generated using the raster calculator in the Spatial Analyst extension of ArcGIS 9.0. Ultimately, the unique combinations of variables resulted in three different models illustrating the change in fire risk during the year.

Análise da incidência de casos de dengue na área urbana de Belém – PA: uma aplicação de modelos espaciais e temporais

Neste trabalho, foi realizado um estudo de mapeamento de áreas de incidência e previsões para os casos de dengue na área urbana de Belém. Para as previsões foi utilizada à incidência de dengue com a precipitação pluviométrica a partir de modelos estatísticos, baseados na metodologia de Box e Jenkins de series temporais. O período do estudo foi de 05 anos (2007-2011). Na pesquisa temos métodos multivariados de series temporais, com uso de função de transferência e modelos espaciais, em que se analisou a existência de autocorrelações espaciais na variável em estudo. Os resultados das análises dos dados de incidência de casos de dengue e precipitação mostraram que, o aumento no número de casos de dengue acompanha o aumento na precipitação, demonstrando a relação direta entre o número de casos de dengue e a precipitação nos anos em estudo. O modelo de previsão construído para a incidência de casos de dengue apresentou um bom ajuste com resultados satisfatórios podendo, neste caso, ser utilizado na previsão da dengue. Em relação à análise espacial, foi possível uma visualização da incidência de casos na área urbana de Belém, com as respectivas áreas de incidência, mostrando os níveis de significância em porcentagem. Para o período estudado observou-se o comportamento e as variações dos casos de dengue, com destaque para quatro bairros: Marco, Guamá, Pedreira e Tapanã, com possíveis influências destes bairros nas áreas (bairros) vizinhas. Portanto, o presente estudo evidencia a contribuição para o planejamento das ações de controle da dengue, ao servir de instrumento no apoio às decisões na área de saúde pública.

Quantitative and qualitative dynamics of exotic and native blowflies ( Diptera: Calliphoridae) with migrations among municipalities

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

Um Modelo Espacial para a Resposta Imunológica Adaptativa da Hepatite B

This paper proposed a two-dimensional spatial model to describe the adaptive immune response for viral hepatitis B. This model considered six populations: healthy hepatocytes T, infected hepatocytes Y , hepatitis B virus V , innate immune system I, active immune system X and memory cells, X. First, a compartmental model was constructed and its equilibrium solutions and also the threshold values related to the stability of each solution were obtained. Using this model, we was able to reproduce the different trends observed for the disease, which are: individuals that eliminate the infection without forming immune response, patients with acute and chronic carriers. By including dispersion of defense cells of the immune system and virus (spatial model), we analyze two situations: homogeneous model, in which the model parameters are the same at all points of the network, and heterogeneous model, which characterizes cells more permeable and less permeable to virus invasion. For the two spatial models (homogeneous and heterogeneous) the times relatead to the viral erradication and/or virus invasion and persistence becoming smaller in relation to the compartmental model. The results also showed that for the set of values used in the simulations and if the two diffusion rates are different from zero, the model is sensitive to variations in the rate of viral spread and not dependent on the dispersion of memory cells. Finally, the heterogeneous model when compared to the homogeneous model shows that the infection can be spatially limited depending on the type of the cell involved in the infection process

Seeking a Second Opinion: Uncertainty in Disease Ecology

Analytical methods accounting for imperfect detection are often used to facilitate reliable inference in population and community ecology. We contend that similar approaches are needed in disease ecology because these complicated systems are inherently difficult to observe without error. For example, wildlife disease studies often designate individuals, populations, or spatial units to states (e.g., susceptible, infected, post-infected), but the uncertainty associated with these state assignments remains largely ignored or unaccounted for. We demonstrate how recent developments incorporating observation error through repeated sampling extend quite naturally to hierarchical spatial models of disease effects, prevalence, and dynamics in natural systems. A highly pathogenic strain of avian influenza virus in migratory waterfowl and a pathogenic fungus recently implicated in the global loss of amphibian biodiversity are used as motivating examples. Both show that relatively simple modifications to study designs can greatly improve our understanding of complex spatio-temporal disease dynamics by rigorously accounting for uncertainty at each level of the hierarchy.

Landscape and forest structure at moose mortality sites on Isle Royale National Park. A LiDAR based assessment

Landscape structure and heterogeneity play a potentially important, but little understood role in predator-prey interactions and behaviourally-mediated habitat selection. For example, habitat complexity may either reduce or enhance the efficiency of a predator's efforts to search, track, capture, kill and consume prey. For prey, structural heterogeneity may affect predator detection, avoidance and defense, escape tactics, and the ability to exploit refuges. This study, investigates whether and how vegetation and topographic structure influence the spatial patterns and distribution of moose (Alces alces) mortality due to predation and malnutrition at the local and landscape levels on Isle Royale National Park. 230 locations where wolves (Canis lupus) killed moose during the winters between 2002 and 2010, and 182 moose starvation death sites for the period 1996-2010, were selected from the extensive Isle Royale Wolf-Moose Project carcass database. A variety of LiDAR-derived metrics were generated and used in an algorithm model (Random Forest) to identify, characterize, and classify three-dimensional variables significant to each of the mortality classes. Furthermore, spatial models to predict and assess the likelihood at the landscape scale of moose mortality were developed. This research found that the patterns of moose mortality by predation and malnutrition across the landscape are non-random, have a high degree of spatial variability, and that both mechanisms operate in contexts of comparable physiographic and vegetation structure. Wolf winter hunting locations on Isle Royale are more likely to be a result of its prey habitat selection, although they seem to prioritize the overall areas with higher moose density in the winter. Furthermore, the findings suggest that the distribution of moose mortality by predation is habitat-specific to moose, and not to wolves. In addition, moose sex, age, and health condition also affect mortality site selection, as revealed by subtle differences between sites in vegetation heights, vegetation density, and topography. Vegetation density in particular appears to differentiate mortality locations for distinct classes of moose. The results also emphasize the significance of fine-scale landscape and habitat features when addressing predator-prey interactions. These finer scale findings would be easily missed if analyses were limited to the broader landscape scale alone.

Design of the blood group AB glycotope

Although the nature of the blood groups A and B has been comprehensively studied for a long time, it is still unclear as to what exactly is the epitope that is recognized by antibodies having AB specificity, i.e. monoclonal and polyclonal antibodies which are capable of interacting equally well with the antigens GalNAcalpha 1-3(Fucalpha 1-2)Gal (A trisaccharide) and Galalpha 1-3(Fucalpha 1-2)Gal (B trisaccharide), but do not react with their common fragment Fucalpha 1-2Gal. We have supposed that besides Fucalpha 1-2Gal, A and B antigens have one more shared epitope. The trisaccharides A and B are practically identical from the conformational point of view, the only difference being situated at position 2 of Galalpha residue, i.e. trisaccharide A has a NHAc group, whereas trisaccharide B has a hydroxyl group (see formulas). We have hypothesized that the AB-epitope should be situated in the part of the molecule that is opposite to the NHAc group of GalNAc residue. In order to test this hypothesis we have synthesized a polymeric conjugate in such a way that de-N-acetylated A-trisaccharide is attached to a polymer via the nitrogen in position C-2 of the galactosamine residue. In this conjugate the supposed AB-epitope should be maximally accessible for antibodies from the solution, whereas the discrimination site of antigens A and B by the antibodies should be maximally hidden due to the close proximity of the polymer. Interaction with several anti-AB monoclonal antibodies revealed that a part of them really interacted with the synthetic AB-glycotope, thus confirming our hypothesis. Moreover, similar antibodies were revealed in the blood of healthy blood group 0 donors. Analysis of spatial models was performed in addition to identify the hydroxyl groups of Fuc, Galalpha, and Galbeta residues, which are particularly involved in the composition of the AB-glycotope.