Animal space use: distinguishing a two‐level superposition of scale‐specific walks from scale‐free Lévy walk

How to differentiate between scale‐free space use like Lévy walk and a two‐level scale‐specific process like composite random walk (mixture of intra‐ and inter‐patch habitat movement) is surrounded by controversy. Composite random walk may under some parameter conditions appear Lévy walk‐like from the perspective of the path’s distribution of step lengths due to superabundance of very long steps relative to the expectation from a classic (single‐level) random walk. However, a more explicit focus on the qualitative differences between studying movement at a high resolution mechanistic (behavioral) level and the more coarse‐grained statistical mechanical level may contribute to resolving both this and other issues related to scaling complexity. Specifically, a re‐sampling of a composite random walk at larger time lags than the micro‐level unit time step for the simulation makes a Lévy‐look‐alike step length distribution re‐shaping towards a Brownian motion‐like pattern. Conversely, a true Levy walk maintains its scaling characteristics upon re‐sampling. This result illustrates how a confusing pattern at the mechanistic level may be resolved by changing observational scale from the micro level to the coarser statistical mechanical meso‐ or macro‐scale. The instability of the composite random walk pattern under rescaling is a consequence of influence of the central limit theorem. I propose that a coarse‐graining test – studying simulated animal paths at a coarsened temporal scale by re‐sampling a series – should be routinely performed prior to comparing theoretical results with those patterns generated from GPS data describing animal movement paths. Fixes from terrestrial mammals are often collected at hourly intervals or larger, and such a priori coarse‐grained series may thus comply better with the statistical mechanical meso‐ or macro‐level of analysis than the behavioral mechanics observed at finer resolutions typically in the range of seconds and minutes. If fixes of real animals are collected at this high frequency, coarse graining both the simulated and real series is advised in order to bring the analysis into a temporal scale domain where analytical methods from statistical mechanics can be applied.     

Plant species richness and environmental heterogeneity in a mountain landscape: effects of variability and spatial configuration

The loss of biodiversity has become a matter of urgent concern and a better understanding of local drivers is crucial for conservation. Although environmental heterogeneity is recognized as an important determinant of biodiversity, this has rarely been tested using field data at management scale. We propose and provide evidence for the simple hypothesis that local species diversity is related to spatial environmental heterogeneity. Species partition the environment into habitats. Biodiversity is therefore expected to be influenced by two aspects of spatial heterogeneity: 1) the variability of environmental conditions, which will affect the number of types of habitat, and 2) the spatial configuration of habitats, which will affect the rates of ecological processes, such as dispersal or competition. Earlier, simulation experiments predicted that both aspects of heterogeneity will influence plant species richness at a particular site. For the first time, these predictions were tested for plant communities using field data, which we collected in a wooded pasture in the Swiss Jura mountains using a four-level hierarchical sampling design. Richness generally increased with increasing environmental variability and roughness (i.e. decreasing spatial aggregation). Effects occurred at all scales, but the nature of the effect changed with scale, suggesting a change in the underlying mechanisms, which will need to be taken into account if scaling up to larger landscapes. Although we found significant effects of environmental heterogeneity, other factors such as history could also be important determinants. If a relationship between environmental heterogeneity and species richness can be shown to be general, recently available high-resolution environmental data can be used to complement the assessment of patterns of local richness and improve the prediction of the effects of land use change based on mean site conditions or land use history.     

The local‐regional species richness relationship: new perspectives on the null‐hypothesis

Despite considerable criticism in recent years, the use of local (SL) and regional species richness (SR) plots has a long tradition to test for community saturation. The traditional approach has been to compare linear and polynomial regression models of untransformed measures of SL and SR with a statistically significant linear or polynomial model indicating unsaturated and saturated communities, respectively. This approach has been the target of much controversy owing to statistical issues, the confounding effects of the arbitrary choice for the size of the local and regional area, and the difficulty in attributing ecological processes to the underlying SL SR pattern. The statistical issues and effects of scale stem from the lack of statistical independence and induced correlation between SL SR arising from the mathematical constraint, SL<SR. However, by removing this mathematical constraint by means of a logratio transformation, SL SR relationships can be calculated using ordinary linear regression and with a logical and definitive null‐hypothesis based solely on the presence of a statistically significant slope, which provides a quantitative measure of curvature. Simulations of SL SR relationships with varying curvature and SL:SR ratio demonstrate that the logratio model can accurately measure curvature independent of the SL:SR ratio. Therefore, the tendency for studies with high local:regional area ratio to result in linear SL SR trends when analysed by traditional regression methods may be mitigated by reanalysis by the logratio model. By alleviating the effects of scale, the logratio model offers a more statistically sound assessment of the SL SR relationship, which in turn can serve as an effective tool to complement emerging process‐based models.     

Relationship between species richness and spatial and temporal distance from seed source in semi‐natural grassland

Question: How do traditional management practices of field margins maintain the biodiversity of native grassland species? Location: Semi‐natural grassland on the field margins of traditional and consolidated agricultural fields on Awaji Island, central Japan. Methods: The distance to the nearest traditional field margin to the study sites was determined because the traditional field was considered as a seed source of native vegetation to the semi‐natural grasslands under study. We selected field margins in consolidated fields of different ages and distances from seed sources. Indicator species for both field types were sought. Regression analysis and detrended correspondence analysis (DCA) were used to determine the effect of spatial and temporal distances on the species composition of native vegetation. Results: Species richness differed significantly between the margin of traditional and consolidated fields. We identified significant indicator species of traditional fields, but not of consolidated fields. In consolidated fields, species richness increased significantly with age and decreased significantly with increasing distance to the source. At younger sites, species richness decreased faster with distance to the source because of strong negative correlation, but not at older sites. DCA ordination plots similarly indicated that similarities of vegetation composition in consolidated and traditional fields decreased with distance, and the effect of distance decreased with age. Conclusions: The species composition of the grassland margins of consolidated field was more similar to the margins of traditional fields if the consolidated fields were older, and/or closer to traditional fields. This pattern suggests that dispersal may play a role in the establishment of species on field margins.     

Fine‐scale spatial variability in anatoxin‐a and homoanatoxin‐a concentrations in benthic cyanobacterial mats: implication for monitoring and management

Aims: The purpose of this study was to determine the variability in anatoxin‐a (ATX) and homoanatoxin‐a (HTX) concentrations in benthic cyanobacterial mats within sampling sites and to assess the applicability of using a PCR‐based approach to determine ATX‐ and HTX‐production potential. Methods and Results: ATX and HTX variability was investigated by collecting 15 samples from 10 × 10 m grids in seven rivers. ATX and HTX concentrations were determined using liquid chromatography–mass spectrometry (LC–MS). Samples from two sites contained no ATX or HTX and at one site ATX and HTX were detected in all samples. At four sites, both toxic and nontoxic samples co‐occurred and these samples were sometimes spaced less than 1 m apart. PCR amplification of a region of a polyketide synthase (ks2, putatively involved in the biosynthetic pathway of ATX and HTX) successfully distinguished ATX‐and‐HTX‐ and non‐ATX‐and‐HTX‐producing cultured Phormidium strains. Results from environmental samples were more variable, and the results were in congruence with the LC–MS data in only 58% of samples. Conclusions: Fine‐scale spatial variability in ATX and HTX concentrations occurs among benthic cyanobacterial mats. Significance and Impact of the Study: Multiple benthic cyanobacterial mat samples must be collected at a sampling site to provide an accurate assessment of ATX and HTX concentrations at that location. The PCR‐based technique offers the potential to be a useful early warning technique.     

Species–area relationships of butterflies in Europe and species richness forecasting

Species–area relationships (SARs) of European butterfly species (Rhopalocera) appear to follow power functions with Mediterranean butterflies having a much higher slope value (z=0.49) compared to the slope for the northern and eastern European countries (z=0.10). A simulated process of species extinction by a stepwise density dependent random elimination of species affected species–area patterns differently. For Mediterranean countries SAR slopes decreased, for other European countries slopes increased during the extinction process. Comparisons of species numbers before and after extinction with those predicted by a classical SAR approach differed widely and revealed that SARs are not able to predict future species numbers at local scales. For Mediterranean countries the classical SAR approach underestimated the number of species remaining after simulated extinction, for all other European countries SARs highly overestimated species numbers. These contrasting patterns indicate that changes in SAR patterns do not unequivocally point to changes in species diversity or community structure as assumed by current theory. On the other hand, the results strongly indicate that simplified applications of SARs for forecasting might give misimpressions about species loss and future biodiversity if the initial community structure, especially relative densities and numbers of species with restricted range size, are not taken into account.     

Production and scale‐up of a monoclonal antibody against 17‐hydroxyprogesterone

The hybridoma 192 was used to produce a monoclonal antibody (MAb) against 17‐hydroxyprogesterone (17‐OHP), for possible use in screening for congenital adrenal hyperplasia (CAH). The factors influencing the MAb production were screened and optimized in a 2 L stirred bioreactor. The production was then scaled up to a 20 L bioreactor. All of the screened factors (aeration rate, stirring speed, dissolved oxygen concentration, pH, and temperature) were found to significantly affect production. Optimization using the response surface methodology identified the following optimal production conditions: 36.8°C, pH 7.4, stirring speed of 100 rpm, 30% dissolved oxygen concentration, and an aeration rate of 0.09 vvm. Under these conditions, the maximum viable cell density achieved was 1.34 ± 0.21 × 10⁶ cells mL^?1 and the specific growth rate was 0.036 ± 0.004 h^?1. The maximum MAb titer was 11.94 ± 4.81 μg mL^?1 with an average specific MAb production rate of 0.273 ± 0.135 pg cell^?1 h^?1. A constant impeller tip speed criterion was used for the scale‐up. The specific growth rate (0.040 h^?1) and the maximum viable cell density (1.89 × 10⁶ cells mL^?1) at the larger scale were better than the values achieved at the small scale, but the MAb titer in the 20 L bioreactor was 18% lower than in the smaller bioreactor. A change in the culture environment from the static conditions of a T‐flask to the stirred bioreactor culture did not affect the specificity of the MAb toward its antigen (17‐OHP) and did not compromise the structural integrity of the MAb. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013     

Area‐sensitivity by forest songbirds: theoretical and practical implications of scale‐dependency

Songbird presence is often associated with the area of suitable habitat in the surrounding landscape. However, the size of landscape for which this association is maximized is generally unknown, likely to vary among species, and may affect our ability to incorporate songbirds in landscape management. We measured the occurrence and the persistence of forest songbirds in relation to the amount of habitat measured at several scales: local (100, 200 m radius), neighborhood (400, 800 m), landscape (1.6, 3.2, 6.4 km) and regional (12–24 km), based on data from Ontario's Forest Bird Monitoring Program (1987–2005). Songbird occurrence was obtained from point count sites distributed across southern Ontario and each revisited in multiple years (mean=5.8 yr). Presence of each species at a site was associated with forest habitat area measures that account for differences in preferred forest cover types among species. Area of coniferous, deciduous and mixed forest was derived from Landsat TM imagery. Thirty‐two of the 35 species studied were area‐sensitive, and area‐sensitivity was apparent for 13–25 species at each spatial scale. For 24 species, the strength of area‐sensitivity varied with scale, suggesting the importance of local, neighborhood, landscape and regional habitat for 3, 5, 5, and 11 species respectively. As a result, the list of the five most area‐sensitive species varied depending on the scale at which habitat was described. We conclude that area‐sensitivity can occur at a broader set of scales than generally assumed, and is most pronounced at the regional scale. We suggest that a broad set of scales should be examined before taking conservation decisions based on avian area‐sensitivity.     

Individual species–area relationships and spatial patterns of species diversity in a Great Basin,semi‐arid shrubland

Traditional biodiversity metrics operate at the level of a plant community but do not capture spatial variation in diversity from a ‘plant's‐eye view’ of a community. Recently‐developed statistics consider the spatial patterns of plants as well as the number and distribution of species in local plant neighborhoods to quantitatively assess multispecies spatial patterns from a ‘plant's‐eye view’. We used one such statistic, the individual species area relationship (ISAR), to assess spatial patterns of species diversity in a Great Basin (USA) semi‐arid shrubland through an analysis of a spatial dataset on shrub species and locations. In conjunction with appropriate null models, the ISAR blends species area relationships with second‐order spatial statistics to measure the expected species richness in local neighborhoods of variable size around the individuals of a focal species within a community. We found that, contrary to a previous analysis using more traditional methods, the community was well‐mixed with a typical shrub surrounded on average by 4.9 shrub neighbors of 2.1 species at a neighborhood scale of 1.0 m. We also found statistically significant fine‐scale variation in diversity patterns, such that neighborhoods of two species were more diverse than expected by a heterogeneous Poisson null model that accounted for larger‐scale habitat heterogeneity. However, this effect was caused by intraspecific aggregation of these species and was not due to positive interspecific association. Contrary to previous findings in other semi‐arid shrublands, our analysis suggests that the spatial pattern of the shrub community was not significantly structured by interspecific facilitation. This result supports growing evidence for balanced species patterns of adult plants in multispecies communities. Our approach may be used in other communities to describe complex multispecies spatial patterns, quantify species‐specific associations with diversity patterns, and to generate hypotheses regarding relationships between patterns and community‐structuring processes.     

Mimic of a large‐scale diafiltration process by using ultra scale‐down rotating disc filter

Ultra scale‐down (USD) approach is a powerful tool to predict large‐scale process performance by using very small amounts of material. In this article, we present a method to mimic flux and transmission performance in a labscale crossflow operation by an USD rotating disc filter (RDF). The Pellicon 2 labscale system used for evaluation of the mimic can readily be related to small pilot and industrial scale. Adopted from the pulsed sample injection technique by Ghosh and Cui (J Membr Sci. 2000;175:5‐84), the RDF has been modified by building in inserts to allow the flexibility of the chamber volume, so that only 1.5 mL of processing material is required for each diafiltration experiment. The reported method enjoys the simplicity of dead‐end mode operation with accurate control of operation conditions that can mimic well the crossflow operation in large scale. Wall shear rate correlations have been established for both the labscale cassette and the USD device, and a mimic has been developed by operating both scales under conditions with equivalent averaged shear rates. The studies using E. coli lysate show that the flux vs. transmembrane pressure profile follows a first‐order model, and the transmission of antibody fragment (Fab′) is independent of transmembrane pressure. Predicted flux and transmission data agreed well with the experimental results of a labscale diafiltration where the cassette resistance was considered. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Actinomycetes scale‐up for the production of the antibacterial,nocathiacin

An Amycolatopsis fastidiosa culture, which produces the nocathiacin class of antibacterial compounds, was scaled up to the 15,000 L working volume. Lower volume pilot fermentations (600, 900, and 1,500 L scale) were conducted to determine process feasibility at the 15,000 L scale. The effects of inoculum volume, impeller tip speed, volumetric gas flow rate, superficial gas velocity, backpressure, and sterilization heat stress were examined to determine optimal scale‐up operating conditions. Inoculum volume (6 vs. 2 vol %) and medium sterilization (R_o of 68 vs. 92 min^?1) had no effect on productivity or titer, and higher impeller tip speeds (2.1 vs. 2.9 m/s) had a slight effect (20% decrease). In contrast, higher backpressure, incorporating increased head pressure at the 15,000 L scale (1.2 vs. 0.7 kg/cm²) and low gas flow rates (0.25 vs. 0.8 vvm), appeared to be problematic (40–50% decrease). High off‐gas CO₂ levels were likely reasons for observed lower productivity. Consequently, air flow rate for this 25‐fold scale‐up (600–15,000 L) was controlled to match off‐gas CO₂ profiles of acceptable smaller scale batches to maintain levels below 0.5%. The 15,000 L‐scale fermentation achieved an expected nocathiacin I titer of 310 mg/L after 7 days. Other on‐line data (i.e., pH, oxygen uptake rate, and CO₂ evolution rate) and off‐line data (i.e., analog production, glucose utilization, ammonium production, and dry cell weight) at the 15,000 L scale also tracked similarly to the smaller scale, demonstrating successful fermentation scale‐up. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Opposite effects of environmental variability and species richness on temporal turnover of species in a complex habitat mosaic

Species are continuously lost and added to a local community. Dynamics of this process in a complex habitat mosaic (multiple habitats in a landscape), particularly of its rates (species turnover) are of primary concern for biodiversity conservation. Various studies suggest that species traits such as habitat specialization should affect species turnover. In communities where habitat specialization is a function of abiotic constraints, habitat specialists should respond faster to changing environment than generalists. We thus predicted a higher temporal turnover for specialists than for generalists in the presence of environmental variability (EV). In addition, we predicted that temporal turnover should decrease with increasing species richness of the communities they live in. We tested these predictions in a model system of 49 natural rock pools inhabited by 70 invertebrate species for which long-term (9 years) environmental and population dynamics data are available. We computed standard deviation of salinity measurements to represent EV for each pool. We further obtained the number of combined colonization and extinction events weighted by the number of years a species was recorded as a temporal turnover for each species in individual pools. We found that EV induced greater temporal turnover, however, the turnover depended on the species habitat traits (habitat specialization)—it has been higher in specialists but that relationship between EV and temporal turnover dissolved with increasing niche breadth (generalists). We further found that for some species, temporal turnover decreased with higher species richness and for other species, temporal turnover increased with higher species richness. The effect of species richness on temporal turnover was unrelated to species traits. This study suggests that whenever habitat is complex and heterogeneous and species pool diversified, local community dynamics becomes a composite of differential responses.     

Seasonal and spatial hydrological variability drives aquatic biodiversity in a flood‐pulsed,sub‐tropical wetland

1. Flood‐pulsed wetlands make vital contributions to local and global biodiversity. However, the patterns and controls of spatial and temporal variation in aquatic biodiversity in flood‐pulsed wetlands are not well understood. We analysed the relationship between variation in hydrological regime and the patterns of aquatic biodiversity in a large pristine flood‐pulsed wetland, the Okavango Delta, Botswana. 2. Surveys of water chemistry, diatoms and macroinvertebrates were conducted over the seasonal phases of the flood pulse. Hydrological variables of flood frequency and hydroperiod class were collated from 16 years of satellite images. Multivariate regression trees and generalised least squares regression were used to determine the chief controls of community composition and taxon richness. 3. Hydroperiod class, phase of the flood and conductivity explained 32% and 43% of the variation in diatom and invertebrate taxon richness, respectively. There was a negative relationship between hydroperiod class and invertebrate taxon richness on the rising, peak and receding flood, whereas at low flood there was no significant relationship. Multivariate regression tree analysis revealed hydroperiod class, phase of the flood and conductivity as the dominant forces shaping invertebrate and diatom community composition. 4. Seasonal and spatial variation in hydrological conditions are the principal drivers of variation in aquatic biodiversity in flood‐pulsed wetlands. In pristine flood‐pulsed wetlands, increased productivity caused by the arrival of the flood waters appears to override disturbance and connectivity in shaping taxon richness and community composition. Thus, these data suggest that the maintenance of a rich mosaic of habitats covering a broad range of hydroperiod is the key to preserving aquatic biodiversity and natural ecosystem function in flood‐pulsed wetlands.     

Ultra scale‐down approaches for clarification of mammalian cell culture broths in disc‐stack centrifuges

Ultra‐scale down (USD) methodology developed by University College London for cell broth clarification with industrial centrifuges was applied to two common cell lines (NS0 and GS‐CHO) expressing various therapeutic monoclonal antibodies. A number of centrifuges at various scales were used with shear devices operating either by high speed rotation or flow‐through narrow channels. The USD methodology was found effective in accounting for both gravitational and shear effects on clarification performance with three continuous centrifuges at pilot and manufacturing scales. Different shear responses were observed with the two different cell lines and even with the same cell line expressing different products. Separate particle size analysis of the treated broths seems consistent with the shear results. Filterability of the centrifuged solutions was also evaluated to assess the utility of the USD approach for this part of the clarification operation. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Development and scale‐up of a commercial fed batch refolding process for an anti‐CD22 two chain immunotoxin

We describe the development and scale‐up of a novel two chain immunotoxin refolding process. This work provides a case study comparing a clinical manufacturing process and the commercial process developed to replace it. While the clinical process produced high quality material, it suffered from low yield and high yield variability. A systematic approach to process development and understanding led to a number of improvements that were implemented in the commercial process. These include a shorter inclusion body recovery process, limiting the formation of an undesired deamidated species and the implementation of fed batch dilution refolding for increased refold titers. The use of a combination of urea, arginine and DTT for capture column cleaning restored the binding capacity of the capture step column and resulted in consistent capture step yields compared to the clinical process. Scalability is shown with data from 250 L and 950 L scale refolding processes. Compared to the clinical process it replaces, the commercial process demonstrated a greater than fivefold improvement in volumetric productivity at the 950 L refolding scale. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1380–1389, 2014     

EstimateS turns 20: statistical estimation of species richness and shared species from samples,with non‐parametric extrapolation

EstimateS offers statistical tools for analyzing and comparing the diversity and composition of species assemblages, based on sampling data. The latest version computes a wide range of biodiversity statistics for both sample‐based and individual‐based data, including analytical rarefaction and non‐parametric extrapolation, estimators of asymptotic species richness, diversity indices, Hill numbers, and (for sample‐based data) measures of compositional similarity among assemblages. In the first 20 yr of its existence, EstimateS has been downloaded more than 70 000 times by users in 140 countries, who have cited it in 5000 publications in studies of taxa from microbes to mammals in every biome.     

Latitudinal gradients of species richness: a test of the geographic area hypothesis at two ecological scales

The geographic area hypothesis advances area as the primary cause of latitudinal gradients in diversity. The greater area of tropical zones, it suggests, stimulates speciation, inhibits extinction, and leads to increased species richness compared to the situation in smaller temperate and boreal zones. Because bats exhibit exceptionally strong latitudinal gradients of richness at multiple spatial scales in the New World, they are an appropriate system with which to test the geographic area hypothesis. We used range maps for 250 species of New World bats to estimate species richness in biogeographic zones at two hierarchical spatial scales: biome types and provinces. We then conducted a series of regression analyses to evaluate the ability of area to account for latitudinal gradients in species richness. However, spillover (zonal bleeding) of tropical species into extra-tropical zones may mask the species-area relationship and alter perceptions of the latitudinal gradient. To address this issue, we conducted additional analyses excluding tropical species, using a series of increasingly inclusive definitions of tropical ranges. Ecogeographic zones of the New World are not larger at tropical versus extra-tropical latitudes. Moreover, spillover of tropical species into ecogeographic zones within extra-tropical regions generally does not diminish the association between richness and area. Nonetheless, the latitudinal gradient of species richness is strong and significant at both ecogeographic scales. Clearly, area does not drive the latitudinal gradient of bat species richness in the New World. In fact, area represents a source of noise rather than a dominant signal at the focal scale of biome types and provinces in the Western Hemisphere.