The geographical structure of British bird distributions:diversity, spatial turnover and scale

1. Using data on the spatial distribution of the British avifauna, we address three basic questions about the spatial structure of assemblages: (i) Is there a relationship between species richness (alpha diversity) and spatial turnover of species (beta diversity)? (ii) Do high richness locations have fewer species in common with neighbouring areas than low richness locations?, and (iii) Are any such relationships contingent on spatial scale (resolution or quadrat area), and do they reflect the operation of a particular kind of species-area relationship (SAR)?

2. For all measures of spatial turnover, we found a negative relationship with species richness. This held across all scales, with the exception of turnover measured as beta (sim).

3. Higher richness areas were found to have more species in common with neighbouring areas.

4. The logarithmic SAR fitted better than the power SAR overall, and fitted significantly better in areas with low richness and high turnover.

5. Spatial patterns of both turnover and richness vary with scale. The finest scale richness pattern (10 km) and the coarse scale richness pattern (90 km) are statistically unrelated. The same is true of the turnover patterns.

6. With coarsening scale, locations of the most species-rich quadrats move north. This observed sensitivity of richness 'hotspot' location to spatial scale has implications for conservation biology, e.g. the location of a reserve selected on the basis of maximum richness may change considerably with reserve size or scale of analysis.

7. Average turnover measured using indices declined with coarsening scale, but the average number of species gained or lost between neighbouring quadrats was essentially scale invariant at 10-13 species, despite mean richness rising from 80 to 146 species (across an 81-fold area increase). We show that this kind of scale invariance is consistent with the logarithmic SAR.

A species invasion mediated through habitat structure, intraguild predation and parasitism.

With field, laboratory, and modeling approaches, we examined the interplay among habitat structure, intraguild predation (IGP), and parasitism in an ongoing species invasion. Native Gammarus duebeni celticus (Crustacea: Amphipoda) are often, but not always, replaced by the invader Gammarus pulex through differential IGP. The muscle-wasting microsporidian parasite Pleistophora mulleri infects the native but not the invader. We found a highly variable prevalence of P. mulleri in uninvaded rivers, with 0–91% of hosts parasitized per sample. In addition, unparasitized natives dominated fast-flowing riffle patches of river, whereas parasitized individuals dominated slower- flowing, pooled patches. We examined the survivorship of invader and native in single and mixed-species microcosms with high, intermediate, and zero parasite prevalence. G. pulex survivorship was high in all treatments, whereas G. duebeni subsp. celticus survivorship was significantly lower in the presence of the invader. Further, parasitized G. duebeni subsp. celticus experienced near-total elimination. Models of the species replacement process implied that parasite-enhanced IGP would make invasion by G. pulex more likely, regardless of habitat and parasite spatial structure. However, where heterogeneity in parasite prevalence creates a landscape of patches with different susceptibilities to invasion, G. pulex may succeed in cases where invasion would not be possible if patches were equivalent. The different responses of parasitized and unparasitized G. duebeni subsp. celticus to environmental heterogeneity potentially link landscape patterns to the success or failure of the invasion process.

The effects of dispersal mode on the spatial distribution patterns of intertidal molluscs.

1. As many species of marine benthic invertebrates have a limited capacity for movement as adults, dispersal mode is often considered as a determinant of geographical ranges, genetic structure and evolutionary history. Species that reproduce without a larval stage can only disperse by floating or rafting. It is proposed that the colonization processes associated with such direct developing species result in spatial distributions that show relatively greater fine scale patchiness than the distributions of species with a larval dispersal stage. This hypothesis was tested by collecting molluscs at different spatial scales in the Isle of Man. 2. Spatial distribution patterns supported the predictions based on dispersal mode. Estimated variance components for species with larval dispersal suggested that the majority of the spatial variation was associated with variation between shores. In comparison, there was relatively more variability within shores for abundance counts of species with direct development. 3. Multivariate analyses reflected the univariate results. An assemblage of direct developers provided a better discrimination between sites (100 m separation) but the group of species with larval dispersal gave a clearer separation of shores (separated by several km). 4. The fine scale spatial structure of direct developing species was reflected in higher average species diversity within quadrats. Species richness also reflected dispersal mode, with a higher fraction of the regional species pool present for direct developers in comparison to species with larval dispersal. This may reflect the improved local persistence of taxa that avoid the larval dispersal stage.

Appearance of the frequency-doubling stimulus at threshold.

PURPOSE. It has been argued that the threshold for detecting frequency-doubling (FD) technology perimeter stimuli differs from the threshold for perceiving spatial structure (pattern) in the same targets. Thresholds for perceiving spatial structure have typically been assessed using orientation-identification experiments. The authors investigated the influence of orientation, edge profile, and psychophysical method on the origin of the reported differences in detection and orientation-identification thresholds for FD gratings.

METHODS. Detection and orientation-identification thresholds were determined in 12 observers with the use of FD stimuli (0.25 cyc/deg, 25 Hz) presented centrally and at 15° eccentricity. Edge profile (square- and Gaussian-windowed) and orientation (horizontal, vertical, and oblique) were independently modified. Detection thresholds were also measured for spatially uniform flickering targets (25 Hz). Orientation-identification thresholds using a two-alternative forced choice (2-AFC) and a two-interval forced choice (2-IFC) method were also compared in five experienced observers.

RESULTS. Orientation-identification and detection thresholds did not significantly differ under any condition tested. Orientation-identification thresholds obtained with 2-AFC were not significantly different from those obtained with 2-IFC. Thresholds for spatially uniform flicker were significantly lower than for FD stimuli.

CONCLUSIONS. The authors found that orientation-identification and detection thresholds for FD gratings did not differ and argue that recent findings to the contrary arise from the inappropriate use of spatially uniform flicker targets as alternatives in 2-IFC experiments.

A photospheric bright point model

Aims. A magneto-hydrostatic model is constructed with spectropolarimetric properties close to those of solar photospheric magnetic bright points.
Methods. Results of solar radiative magneto-convection simulations are used to produce the spatial structure of the vertical component of the magnetic field. The horizontal component of magnetic field is reconstructed using the self-similarity condition, while the magneto-hydrostatic equilibrium condition is applied to the standard photospheric model with the magnetic field embedded. Partial ionisation processes are found to be necessary for reconstructing the correct temperature structure of the model.
Results. The structures obtained are in good agreement with observational data. By combining the realistic structure of the magnetic field with the temperature structure of the quiet solar photosphere, the continuum formation level above the equipartition layer can be found. Preliminary results are shown of wave propagation through this magnetic structure. The observational consequences of the oscillations are examined in continuum intensity and in the Fe I 6302 angstrom magnetically sensitive line.

A topological algorithm for identification of structural domains of proteins

Background: Identification of the structural domains of proteins is important for our understanding of the organizational principles and mechanisms of protein folding, and for insights into protein function and evolution. Algorithmic methods of dissecting protein of known structure into domains developed so far are based on an examination of multiple geometrical, physical and topological features. Successful as many of these approaches are, they employ a lot of heuristics, and it is not clear whether they illuminate any deep underlying principles of protein domain organization. Other well-performing domain dissection methods rely on comparative sequence analysis. These methods are applicable to sequences with known and unknown structure alike, and their success highlights a fundamental principle of protein modularity, but this does not directly improve our understanding of protein spatial structure.

Collective decoherence of cold atoms coupled to a Bose-Einstein condensate

We examine the time evolution of cold atoms (impurities) interacting with an environment consisting of a degenerate bosonic quantum gas. The impurity atoms differ from the environment atoms, being of a different species. This allows one to superimpose two independent trapping potentials, each being effective only on one atomic kind, while transparent to the other. When the environment is homogeneous and the impurities are confined in a potential consisting of a set of double wells, the system can be described in terms of an effective spin-boson model, where the occupation of the left or right well of each site represents the two (pseudo)-spin states. The irreversible dynamics of such system is here studied exactly, i.e. not in terms of a Markovian master equation. The dynamics of one and two impurities is remarkably different in respect of the standard decoherence of the spin-boson system. In particular, we show: (i) the appearance of coherence oscillations, (ii) the presence of super and subdecoherent states that differ from the standard ones of the spin-boson model, and (iii) the persistence of coherence in the system at long times. We show that this behaviour is due to the fact that the pseudospins have an internal spatial structure. We argue that collective decoherence also prompts information about the correlation length of the environment. In a one-dimensional (1D) configuration, one can change even more strongly the qualitative behaviour of the dephasing just by tuning the interaction of the bath.

Red-shifts and red herrings in geographical ecology

I draw attention to the need for ecologists to take spatial structure into account more seriously in hypothesis testing. If spatial autocorrelation is ignored, as it usually is, then analyses of ecological patterns in terms of environmental factors can produce very misleading results. This is demonstrated using synthetic but realistic spatial patterns with known spatial properties which are subjected to classical correlation and multiple regression analyses. Correlation between an autocorrelated response variable and each of a set of explanatory variables is strongly biased in favour of those explanatory variables that are highly autocorrelated - the expected magnitude of the correlation coefficient increases with autocorrelation even if the spatial patterns are completely independent. Similarly, multiple regression analysis finds highly autocorrelated explanatory variables "significant" much more frequently than it should. The chances of mistakenly identifying a "significant" slope across an autocorrelated pattern is very high if classical regression is used. Consequently, under these circumstances strongly autocorrelated environmental factors reported in the literature as associated with ecological patterns may not actually be significant. It is likely that these factors wrongly described as important constitute a red-shifted subset of the set of potential explanations, and that more spatially discontinuous factors (those with bluer spectra) are actually relatively more important than their present status suggests. There is much that ecologists can do to improve on this situation. I discuss various approaches to the problem of spatial autocorrelation from the literature and present a randomisation test for the association of two spatial patterns which has advantages over currently available methods.

Compositional Divergence and Convergence in Local Communities and Spatially Structured Landscapes

Community structure depends on both deterministic and stochastic processes. However, patterns of community dissimilarity (e.g. difference in species composition) are difficult to interpret in terms of the relative roles of these processes. Local communities can be more dissimilar (divergence) than, less dissimilar (convergence) than, or as dissimilar as a hypothetical control based on either null or neutral models. However, several mechanisms may result in the same pattern, or act concurrently to generate a pattern, and much research has recently been focusing on unravelling these mechanisms and their relative contributions. Using a simulation approach, we addressed the effect of a complex but realistic spatial structure in the distribution of the niche axis and we analysed patterns of species co-occurrence and beta diversity as measured by dissimilarity indices (e.g. Jaccard index) using either expectations under a null model or neutral dynamics (i.e., based on switching off the niche effect). The strength of niche processes, dispersal, and environmental noise strongly interacted so that niche-driven dynamics may result in local communities that either diverge or converge depending on the combination of these factors. Thus, a fundamental result is that, in real systems, interacting processes of community assembly can be disentangled only by measuring traits such as niche breadth and dispersal. The ability to detect the signal of the niche was also dependent on the spatial resolution of the sampling strategy, which must account for the multiple scale spatial patterns in the niche axis. Notably, some of the patterns we observed correspond to patterns of community dissimilarities previously observed in the field and suggest mechanistic explanations for them or the data required to solve them. Our framework offers a synthesis of the patterns of community dissimilarity produced by the interaction of deterministic and stochastic determinants of community assembly in a spatially explicit and complex context.

Relative role of deterministic and stochastic determinants of soil animal community: a spatially explicit analysis of oribatid mites

1. Ecologists are debating the relative role of deterministic and stochastic determinants of community structure. Although the high diversity and strong spatial structure of soil animal assemblages could provide ecologists with an ideal ecological scenario, surprisingly little information is available on these assemblages.
2. We studied species-rich soil oribatid mite assemblages from a Mediterranean beech forest and a grassland. We applied multivariate regression approaches and analysed spatial autocorrelation at multiple spatial scales using Moran's eigenvectors. Results were used to partition community variance in terms of the amount of variation uniquely accounted for by environmental correlates (e.g. organic matter) and geographical position. Estimated neutral diversity and immigration parameters were also applied to a soil animal group for the first time to simulate patterns of community dissimilarity expected under neutrality, thereby testing neutral predictions.
3. After accounting for spatial autocorrelation, the correlation between community structure and key environmental parameters disappeared: about 40% of community variation consisted of spatial patterns independent of measured environmental variables such as organic matter. Environmentally independent spatial patterns encompassed the entire range of scales accounted for by the sampling design (from tens of cm to 100 m). This spatial variation could be due to either unmeasured but spatially structured variables or stochastic drift mediated by dispersal. Observed levels of community dissimilarity were significantly different from those predicted by neutral models.
4. Oribatid mite assemblages are dominated by processes involving both deterministic and stochastic components and operating at multiple scales. Spatial patterns independent of the measured environmental variables are a prominent feature of the targeted assemblages, but patterns of community dissimilarity do not match neutral predictions. This suggests that either niche-mediated competition or environmental filtering or both are contributing to the core structure of the community. This study indicates new lines of investigation for understanding the mechanisms that determine the signature of the deterministic component of animal community assembly.

Chase over the Nile: The Social Evolution of Riverine Landscape in Urban Egypt

Throughout its history, Cairo evolved as a regional metropolis that sprawls along the banks of the Nile accumulating narratives of evolving social landscape. Overlooking the Nile reflected a privileged social position and place for the urban elite. In spatial terms, the urban bourgeoisie tend to develop living havens in enclaves that are distant from the populace’s everyday life. Ironically, exclusive settlements only attract urban growth further in their direction. This chapter offers an analytical reading of the socio-spatial structure of Cairo following the emergence and decline of a series bourgeoisie quarters along the shores of the Nile. It reports urban narratives based on archival records, documents and investigation of historical texts and travelers’ accounts. This essay argues that cities are essentially social constructs in which hierarchy and connectivity are fundamental aspects of its economic and spatial logic. Through social ambition and desire for upgrade, middle class infiltrate into bourgeoisie havens and sometimes encircle it, seeking better living condition inscribed by social mobility and connectivity to centres of wealth and power. Being both natural barrier and cohesive spine, the Nile helped Cairo to develop successive nucleuses of highly crafted urban experiences that have left their imprints on the contemporary urban scene.

Contribution of rarity and commonness to patterns of species richness

There is little understanding in ecology as to how biodiversity patterns emerge from the distribution patterns of individual species. Here we consider the question of the contributions of rare (restricted range) and common (widespread) species to richness patterns. Considering a species richness pattern, is most of the spatial structure, in terms of where the peaks and troughs of diversity lie, caused by the common species or the rare species (or neither)? Using southern African and British bird richness patterns, we show here that commoner species are most responsible for richness patterns. While rare and common species show markedly different species richness patterns, most spatial patterning in richness is caused by relatively few, more common, species. The level of redundancy we found suggests that a broad understanding of what determines the majority of spatial variation in biodiversity may be had by considering only a minority of species.

Fractal species distributions do not produce power-law species-area relationships

We derive the species-area relationship (SAR) expected from an assemblage of fractally distributed species. If species have truly fractal spatial distributions with different fractal dimensions, we show that the expected SAR is not the classical power-law function, as suggested recently in the literature. This analytically derived SAR has a distinctive shape that is not commonly observed in nature: upward-accelerating richness with increasing area (when plotted on log-log axes). This suggests that, in reality, most species depart from true fractal spatial structure. We demonstrate the fitting of a fractal SAR using two plant assemblages (Alaskan trees and British grasses). We show that in both cases, when modelled as fractal patterns, the modelled SAR departs from the observed SAR in the same way, in accord with the theory developed here. The challenge is to identify how species depart from fractality, either individually or within assemblages, and more importantly to suggest reasons why species distributions are not self-similar and what, if anything, this can tell us about the spatial processes involved in their generation.