Process,correlation and parameter fitting in species distribution models: a response to Kriticos et al

In a recent article (Dormann et al., 2012, Journal of Biogeography, 39, 2119–2131), we compared different approaches to species distribution modelling and depicted modelling approaches along an axis from purely ‘correlative’ to ‘forward process‐based’ models. In their correspondence, Kriticos et al. (2013, Journal of Biogeography, doi: 10.1111/j.1365‐2699.2012.02791.x ) challenge this view, claiming that our continuum representation neglects differences among models and does not consider the ability of fitted process‐based models to combine the advantages of both process‐based and correlative modelling approaches. Here we clarify that the continuum view resulted from recognition of the manifold differences between models. We also reinforce the point that the current trend towards combining different modelling approaches may lead not only to the desired combination of the advantages but also to the accumulation of the disadvantages of those approaches. This point has not been made sufficiently clear previously.     

Temporal variability of ecological niches: a study on intertidal macrobenthic fauna

The determination of temporal niche dynamics under field conditions is an important component of a species’ ecology. Recent developments in niche mapping, and the possibility to account for spatial autocorrelation in species distributions, hold promise for the statistical approach explored here. Using species counts from a landscape‐scale benthic monitoring programme in the western Dutch Wadden Sea during 1997–2005 in combination with sediment characteristics and tidal height as explanatory variables, we statistically derive realised niches for two bivalves, two crustaceans and three polychaetes, encompassing predators, suspension and bottom feeding functional groups. Unsurprisingly, realized niches varied considerably between species. Intraspecific temporal variation was assessed as overlap between the year‐specific niche and the overall mean niche, and this analysis revealed considerable variation between years. The main functional groups represented by these species showed idiosyncratic and wide variability through the study period. There were no strong associations between niche characteristics and mean abundance or body size. Our assessment of intraspecific niche variability has ramifications for species distribution models in general and offers advances from previous methods. 1) By assessing species’ realized niches in the multivariate environmental space, analyses are independent from the relative availability of particular environments. Predicted realized niches present differences between years, rather than annual differences in environmental conditions. 2) Using spatially explicit models to predict species habitat preferences provide more precise and unbiased estimates of species–environment relationships. 3) Current niche models assume constant niches, whereas we illustrate how much these can vary over only a few generations. This emphasizes the potentially limited scope of global change studies with forecasts based on single‐time species distribution snapshots.     

A preliminary assessment of congruence between biodiversity patterns in Afrotropical forest birds and forest mammals

Burgess, N., de Klerk, H., Fjeldsá, J., Crowe, T. & Rahbek, R. 2000. A preliminary assessment of congruence between biodiversity patterns in Afrotropical forest birds and forest mammals. Ostrich 71 (1 & 2): 286–291.

Databases compiled for forest birds and forest mammals in the Afrotropics were tested for congruence of overall patterns and hotspots of species richness and endemism. We also looked at how well a near-minimum set of priority areas for one taxon catered for the second taxon. Overall species richness and richness hotspots of forest birds were significantly correlated with those of forest mammals, as was the case for overall endemism. Endemism hotspots for forest birds and mammals were not significantly correlated. The near-minimum set for forest birds represented 136 (76.5%) forest mammal species. The near-minimum set for forest mammals represented 350 (93.62%) forest bird species. However, to represent all forest mammals three times each, 51 grids were needed in addition to the 78 chosen as a near-minimum set for forest birds, and to represent all forest birds three times each, 43 more grids were needed in addition to the 80 selected for forest mammals. There is some congruence between the patterns of richness, endemism and near-minimum sets for forest birds and mammals in the Afrotropics, but the one taxon does not provide the ideal conservation solution for the other. Further refinement of the databases used in this paper would allow for more rigorous testing of congruence between these two groups.     

Visualizing the Beta Interferon Response in Mice during Infection with Influenza A Viruses Expressing or Lacking Nonstructural Protein 1

The innate host defense against influenza virus is largely dependent on the type I interferon (IFN) system. However, surprisingly little is known about the cellular source of IFN in the infected lung. To clarify this question, we employed a reporter mouse that contains the firefly luciferase gene in place of the IFN-β-coding region. IFN-β-producing cells were identified either by simultaneous immunostaining of lungs for luciferase and cellular markers or by generating conditional reporter mice that express luciferase exclusively in defined cell types. Two different strains of influenza A virus were employed that either do or do not code for nonstructural protein 1 (NS1), which strongly suppresses innate immune responses of infected cells. We found that epithelial cells and lung macrophages, which represent the prime host cells for influenza viruses, showed vigorous IFN-β responses which, however, were severely reduced and delayed if the infecting virus was able to produce NS1. Interestingly, CD11c⁺ cell populations that were either expressing or lacking macrophage markers produced the bulk of IFN-β at 48 h after infection with wild-type influenza A virus. Our results demonstrate that the virus-encoded IFN-antagonistic factor NS1 disarms specifically epithelial cells and lung macrophages, which otherwise would serve as main mediators of the early response against infection by influenza virus.     

Inhibition of Real-Time PCR in DNA Extracts from Aquifer Sediment

Variation in inhibition of real-time PCR was investigated with DNA extracts from 50 aquifer sediment core samples of 5 cm length collected through a 2.5 meter vertical profile across a landfill leachate plume. The inhibition was quantified using an internal control of the green fluorescent protein ( gfp ) gene, which was spiked into the real-time PCR reactions. The inhibition was investigated at two gfp gene concentrations: at 1.7 · 10 ⁷ gfp gene copies/g sediment (5.1 · 10 ⁴ gfp gene copies/PCR reaction) and at 1.7 · 10 ⁵ gfp gene copies/g sediment (5.1 · 10 ² gfp gene copies/PCR reaction). Despite the low TOC content of the sediment (average 0.4 mg C/g dw) the average real-time PCR response was partially inhibited, compared to a reference (pure water), at both high and low gfp concentrations. The relative amplification (reference = 1) was 0.85 ± 0.20 (high) and 0.66 ± 0.23 (low), showing significantly (P < 0.05) stronger inhibition at the lower target gene concentration. The inhibition of the real-time PCR did not show a systematic variation in the vertical profile related to plume position but variations were significant on a small scale of 5–15 cm depth intervals. One of the 50 samples failed to produce a signal with either concentration of the gfp internal control and three other samples inhibited real-time PCR at both high and low gfp concentration. These 4 samples, which were the samples with the highest inhibition, were the only DNA extracts with a visible brown colouration, indicating contents of humic-like substances. Elevated absorbance at 400 nm of these samples also indicated that humic-like substances were responsible for inhibition. However, other factors not associated with either absorbance or TOC may have contributed to the inhibition in less inhibited samples since the variation in real-time PCR response could not be sufficiently explained by absorbance or TOC. The results of this study suggest that an internal control is needed in real-time PCR reactions with DNA from environmental samples due to variation in inhibition to correctly quantify the number of target genes, especially at low target gene concentrations, when dilution of DNA extracts is not practical.     

Evidence for Benzylsuccinate Synthase Subtypes Obtained by Using Stable Isotope Tools

We studied the benzylsuccinate synthase (Bss) reaction mechanism with respect to the hydrogen-carbon bond cleavage at the methyl group of toluene by using different stable isotope tools. Λ values (slopes of linear regression curves for carbon and hydrogen discrimination) for two-dimensional compound-specific stable isotope analysis (2D-CSIA) of toluene activation by Bss-containing cell extracts (in vitro studies) were found to be similar to previously reported data from analogous experiments with whole cells (in vivo studies), proving that Λ values generated by whole cells are caused by Bss catalysis. The Bss enzymes of facultative anaerobic bacteria produced smaller Λ values than those of obligate anaerobes. In addition, a partial exchange of a single deuterium atom in benzylsuccinate with hydrogen was observed in experiments with deuterium-labeled toluene. In this study, the Bss enzymes of the tested facultative anaerobes showed 3- to 8-fold higher exchange probabilities than those for the enzymes of the tested obligate anaerobic bacteria. The phylogeny of the Bss variants, determined by sequence analyses of BssA, the gene product corresponding to the α subunit of Bss, correlated with the observed differences in Λ values and hydrogen exchange probabilities. In conclusion, our results suggest subtle differences in the reaction mechanisms of Bss isoenzymes of facultative and obligate anaerobes and show that the putative isoenzymes can be differentiated by 2D-CSIA.     

The Small Heat Shock Protein Hsp27 Affects Assembly Dynamics and?Structure of Keratin Intermediate Filament Networks

The mechanical properties of living cells are essential for many processes. They are defined by the cytoskeleton, a composite network of protein fibers. Thus, the precise control of its architecture is of paramount importance. Our knowledge about the molecular and physical mechanisms defining the network structure remains scarce, especially for the intermediate filament cytoskeleton. Here, we investigate the effect of small heat shock proteins on the keratin 8/18 intermediate filament cytoskeleton using a well-controlled model system of reconstituted keratin networks. We demonstrate that Hsp27 severely alters the structure of such networks by changing their assembly dynamics. Furthermore, the C-terminal tail domain of keratin 8 is shown to be essential for this effect. Combining results from fluorescence and electron microscopy with data from analytical ultracentrifugation reveals the crucial role of kinetic trapping in keratin network formation.