A new method for dealing with residual spatial autocorrelation in species distribution models

Species distribution modelling (SDM) is a widely used tool and has many applications in ecology and conservation biology. Spatial autocorrelation (SAC), a pattern in which observations are related to one another by their geographic distance, is common in georeferenced ecological data. SAC in the residuals of SDMs violates the ‘independent errors’ assumption required to justify the use of statistical models in modelling species’ distributions. The autologistic modelling approach accounts for SAC by including an additional term (the autocovariate) representing the similarity between the value of the response variable at a location and neighbouring locations. However, autologistic models have been found to introduce bias in the estimation of parameters describing the influence of explanatory variables on habitat occupancy. To address this problem we developed an extension to the autologistic approach by calculating the autocovariate on SAC in residuals (the RAC approach). Performance of the new approach was tested on simulated data with a known spatial structure and on strongly autocorrelated mangrove species’ distribution data collected in northern Australia. The RAC approach was implemented as generalized linear models (GLMs) and boosted regression tree (BRT) models. We found that the BRT models with only environmental explanatory variables can account for some SAC, but applying the standard autologistic or RAC approaches further reduced SAC in model residuals and substantially improved model predictive performance. The RAC approach showed stronger inferential performance than the standard autologistic approach, as parameter estimates were more accurate and statistically significant variables were accurately identified. The new RAC approach presented here has the potential to account for spatial autocorrelation while maintaining strong predictive and inferential performance, and can be implemented across a range of modelling approaches.     

Differences in fungal and bacterial physiology alter soil carbon and nitrogen cycling: insights from meta‐analysis and theoretical models

Since fungi and bacteria are the dominant decomposers in soil, their distinct physiologies are likely to differentially influence rates of ecosystem carbon (C) and nitrogen (N) cycling. We used meta‐analysis and an enzyme‐driven biogeochemical model to explore the drivers and biogeochemical consequences of changes in the fungal‐to‐bacterial ratio (F : B). In our meta‐analysis data set, F : B increased with soil C : N ratio (R² = 0.224, P < 0.001), a relationship predicted by our model. We found that differences in biomass turnover rates influenced F : B under conditions of C limitation, while differences in biomass stoichiometry set the upper bounds on F : B once a nutrient limitation threshold was reached. Ecological interactions between the two groups shifted along a gradient of resource stoichiometry. At intermediate substrate C : N, fungal N mineralisation fuelled bacterial growth, increasing total microbial biomass and decreasing net N mineralisation. Therefore, we conclude that differences in bacterial and fungal physiology may have large consequences for ecosystem‐scale C and N cycling.     

In Vitro Assembly of Alphavirus Cores by Using Nucleocapsid Protein Expressed in Escherichia coli

The production of the alphavirus virion is a multistep event requiring the assembly of the nucleocapsid core in the cytoplasm and the maturation of the glycoproteins in the endoplasmic reticulum and the Golgi apparatus. These components associate during the budding process to produce the mature virion. The nucleocapsid proteins of Sindbis virus and Ross River virus have been produced in a T7-based Escherichia coli expression system and purified. In the presence of single-stranded but not double-stranded nucleic acid, the proteins oligomerize in vitro into core-like particles which resemble the native viral nucleocapsid cores. Despite their similarities, Sindbis virus and Ross River virus capsid proteins do not form mixed core-like particles. Truncated forms of the Sindbis capsid protein were used to establish amino acid requirements for assembly. A capsid protein starting at residue 19 [CP(19-264)] was fully competent for in vitro assembly, whereas proteins with further N-terminal truncations could not support assembly. However, a capsid protein starting at residue 32 or 81 was able to incorporate into particles in the presence of CP(19-264) or could inhibit assembly if its molar ratio relative to CP(19-264) was greater than 1:1. This system provides a basis for the molecular dissection of alphavirus core assembly.     

Epidermal growth factor inhibits cytokine-induced apoptosis of primary human trophoblasts

In the placenta, as in other organs, the development and maintenance of the differentiated phenotype depend on a balance between cell proliferation, maturation, and death. We are interested in the mechanisms that regulate the survival and differentiation of placental trophoblasts and have recently demonstrated that the inflammatory cytokines tumor necrosis factor alpha (TNFα) and gamma interferon (IFNγ) act in concert to induce apoptotic cell death in normal cytotrophoblasts in culture. In this report we show that exposure to epidermal growth factor (EGF), a 6,700 dalton polypeptide that is abundantly expressed in maternal and fetal tissues, blocks the in vitro TNF/IFN-induced cytotoxicity of human cytotrophoblasts and syncytiotrophoblasts from normal term placentas. This antagonistic effect is dose-related (10⁻¹⁰ M EGF, half-maximal) and proceeds via the interruption of an early step in the cytokine-induced apoptotic response. These observations suggest a novel role for EGF in normal placental development and indicate that the interplay between EGF, TNFα, and IFNγ may determine the rate of trophoblast growth and renewal during gestation. © 1996 Wiley-Liss, Inc.     

Systems ecology,people ecology,and the anthropology of fishing communities

Ecological approaches within maritime anthropology are reviewed, particularly those concerned with resource management in fisheries and characterized by certain assumptions of systems ecology. The systems ecology approach used in anthropology exhibits certain problems, including the assumption of equilibria, the tendency to restrict analyses to immediate and natural environmental relations, and the reification of analytical systems. Under the rubric of people ecology, data from research among commercial fishermen of Fogo Island, Newfoundland, are used to explore an alternative that emphasizes people rather than systems as starting points for study, and underscores the role of larger social and political processes in affecting local man — environment relations.     

Worlds of Talk: The Presentation of Self in Everyday Conversation

Worlds of Talk: The Presentation of Self in Everyday Conversation. Martin J. Malone. Maiden, MA: Blackwell Publishers. 1997.182pp.