The interpretation of process from pattern using two-dimensional spectral analysis: modelling single species patterns in vegetation

Two-dimensional spectral analyses of spatial patterns are made using (i) the autocorrelation function, (ii) the periodogram, and its polar summary (iii) the R-spectrum and (iv) the -spectrum. Together these give a sensitive analysis of both the complete range of scales of pattern and directional components which exist in data sets and we illustrate how the significance of observed spectral features can be assessed.We investigate the spatial pattern of Calluna vulgaris in a regenerating woodland and of Epilobium angustifolium spreading in a woodland following the thinning of trees. Evidence in the spectra is found for directional, clumping and inhibition patterns, and is discussed in relation to spectra obtained from simulations of known pattern generating processes. Hypotheses about the important biological, environmental and management influences on the structure of the communities are examined.We gratefully acknowledge the Swedish Coniferous Biome Project and Dr P. J. Diggle for access to the heather data.     

Shared Pattern of Endocranial Shape Asymmetries among Great Apes,Anatomically Modern Humans,and Fossil Hominins

Anatomical asymmetries of the human brain are a topic of major interest because of their link with handedness and cognitive functions. Their emergence and occurrence have been extensively explored in human fossil records to document the evolution of brain capacities and behaviour. We quantified for the first time antero-posterior endocranial shape asymmetries in large samples of great apes, modern humans and fossil hominins through analysis of “virtual” 3D models of skull and endocranial cavity and we statistically test for departures from symmetry. Once based on continuous variables, we show that the analysis of these brain asymmetries gives original results that build upon previous analysis based on discrete traits. In particular, it emerges that the degree of petalial asymmetries differs between great apes and hominins without modification of their pattern. We indeed demonstrate the presence of shape asymmetries in great apes, with a pattern similar to modern humans but with a lower variation and a lower degree of fluctuating asymmetry. More importantly, variations in the position of the frontal and occipital poles on the right and left hemispheres would be expected to show some degree of antisymmetry when population distribution is considered, but the observed pattern of variation among the samples is related to fluctuating asymmetry for most of the components of the petalias. Moreover, the presence of a common pattern of significant directional asymmetry for two components of the petalias in hominids implicates that the observed traits were probably inherited from the last common ancestor of extant African great apes and Homo sapiens.These results also have important implications for the possible relationships between endocranial shape asymmetries and functional capacities in hominins. It emphasizes the uncoupling between lateralized activities, some of them well probably distinctive to Homo, and large-scale cerebral lateralization itself, which is not unique to Homo.     

A model of neural network for spatiotemporal pattern recognition

A model of neural network to recognize spatiotemporal patterns is presented. The network consists of two kinds of neural cells: P-cells and B-cells. A P-cell generates an impulse responding to more than one impulse and embodies two special functions: short term storage (STS) and heterosynaptic facilitation (HSF). A B-cell generates several impulses with high frequency as soon as it receives an impulse. In recognizing process, an impulse generated by a P-cell represents a recognition of stimulus pattern, and triggers the generation of impulses of a B-cell. Inhibitory impulses with high frequency generated by a B-cell reset the activities of all P-cells in the network.Two examples of spatiotemporal pattern recognition are presented. They are achieved by giving different values to the parameters of the network. In one example, the network recognizes both directional and non-directional patterns. The selectivities to directional and non-directional patterns are realized by only adjusting excitatory synaptic weights of P-cells. In the other example, the network recognizes time series of spatial patterns, where the lengths of the series are not necessarily the same and the transitional speeds of spatial patterns are not always the same. In both examples, the HSF signal controls the total activity of the network, which contributes to exact recognition and error recovery. In the latter example, it plays a role to trigger and execute the recognizing process. Finally, we discuss the correspondence between the model and physiological findings.     

Coupling traction force patterns and actomyosin wave dynamics reveals mechanics of cell motion

Motile cells can use and switch between different modes of migration. Here, we use traction force microscopy and fluorescent labeling of actin and myosin to quantify and correlate traction force patterns and cytoskeletal distributions in Dictyostelium discoideum cells that move and switch between keratocyte‐like fan‐shaped, oscillatory, and amoeboid modes. We find that the wave dynamics of the cytoskeletal components critically determine the traction force pattern, cell morphology, and migration mode. Furthermore, we find that fan‐shaped cells can exhibit two different propulsion mechanisms, each with a distinct traction force pattern. Finally, the traction force patterns can be recapitulated using a computational model, which uses the experimentally determined spatiotemporal distributions of actin and myosin forces and a viscous cytoskeletal network. Our results suggest that cell motion can be generated by friction between the flow of this network and the substrate.     

Directional biases and resource-dependence in dispersal generate spatial patterning in a consumer-producer model

Directional dispersal plays a large role in shaping ecological processes in diverse systems such as rivers, coastlines and vegetation communities. We describe an instability driven by directional dispersal in a spatially explicit consumer-producer model where spatial patterns emerge in the absence of external environmental variation. Dispersal of the consumer has both undirected and directed components that are functions of producer biomass. We demonstrate that directional dispersal is required for the instability, while undirected diffusive dispersal sets a lower bound to the spatial scale of emerging patterns. Furthermore, instability requires indirect feedbacks affecting consumer per capita dispersal rates, and not activator-inhibitor dynamics affecting production and mortality as is described in previous theory. This novel and less-restrictive mechanism for generating spatial patterns can arise over realistic parameter values, which we explore using an empirically inspired model and data on stream macroinvertebrates.     

In vivo analysis of a fluorescent SUMO fusion in transgenic Drosophila

Sumoylation, the covalent attachment of SUMO, a 90 amino acid peptide related to ubiquitin, is a major modulator of protein functions. Fluorescent SUMO protein fusions have been used in cell cultures to visualize SUMO in vivo but not in multicellular organisms. We generated a transgenic line of Drosophila expressing an mCherry-SUMO fusion. We analyzed its pattern in vivo in salivary gland nuclei expressing Venus-HP1 to recognize the different chromatin components (Chromocenter, chromosome IV). We compared it to SUMO immunostaining on squashed polytene chromosomes and observed similar patterns. In addition to the previously reported SUMO localizations (chromosome arms and chromocenter), we identify 2 intense binding sites: the fourth chromosome telomere and the DAPI-bright band in the region 81F.     

Efflux patterns for organic molecules from the CNS of the tobacco hornworm. Manduca sexta

The efflux of nicotine and its CNS metabolites from the nerve cord of the nicotine-insensitive tobacco hornworm is simpler (two efflux components) than from the nerve cord of the nicotine-sensitive cockroach (three components). This paper looks at the question of whether this disparity is merely a fortuitous species difference, or whether it may have regulatory significance. It is found that Manduca and Periplaneta cords display strikingly similar tripartite efflux patterns of leucine efflux, and that this pattern also characterises efflux of three extracellular markers from Manduca CNS. Efflux of the alkaloid, atropine, and the basic amino acid, arginine, from Manduca CNS follow different patterns from both nicotine/metabolite efflux and the other substances tested. These data support the notion that the simple efflux pattern for nicotine/metabolites in Manduca reflects the activity of special physiological processes, and is not simply imposed by factors such as tissue geometry.     

Mitochondria : I. Fine Structure of the Complex Patterns in the Mitochondria of Pelomyxa carolinensis Wilson (Chaos chaos L.)

Some of the mitochondria in the free-living giant ameba Pelomyxa carolinensis (Chaos chaos) exhibit unusual and strikingly complex morphological patterns. A study of serial sections of these mitochondria reveals that the patterns are formed by the organization and packing of minute villi (cristae mitochondriales). The form of the individual villus is a regular soft zigzag (or wave) with a bulbous enlargement at each point of inflection ("elbow") on the wave. The pattern of the mitochondria may become increasingly complex as a result of branching and fusing of the wavy villi. Densely packed fibrillar material is sometimes present in the stroma of the mitochondria.     

Search strategy of sex pheromone-stimulated male German cockroaches

Stimulation of the male German cockroach, Blattella germanica, with contact sex pheromone releases courtship behaviour and then area-restricted local search. Servosphere-recorded search patterns, compared to pre-stimulus pathways, are characterised by increased looping and path crossing and a relatively high rate of turning. Search behaviour can be performed in the absence of visual cues, including information relative to the site of stimulation. Information controlling search motor patterns is at least in part genetic; certain pattern components are generally similar from trial to trial, whereas specific pattern components vary widely.     

Mark-mark scatterplots improve pattern analysis in spatial plant ecology

Point process statistics provides valuable tools for many ecological studies, where ‘points’ are commonly determined to represent the locations of plants or animals and ‘marks’ are additional items such as species or size. In the statistical analysis of marked point patterns, various correlation functions are used such as the mark variogram or the mark correlation function. Often the interpretation of these functions is not easy and the non-spatial ecologist is in need of support. In order to make the analysis of spatial point patterns more accessible to ecologists, we introduced and tested a new graphical method, the mark-mark scatterplot. This plot visualises the marks of point pairs of inter-point distances r smaller than some small distance r_max. We tested the application of the mark-mark scatterplot by reconsidering three quite different tree patterns: a pattern of longleaf pine trees from the southern US which was strongly influenced by fires, a tropical tree pattern of the species Shorea congestiflora from Sri Lanka and a Scots pine pattern from Siberia (Russia). The new method yielded previously undetected cause-effect information on mark behaviour at short inter-point distances and thus improved the analysis with mark correlation functions as well as complemented the information they provided. We discovered important new correlations in clusters of trees at close proximity. The application of the mark-mark scatterplot will facilitate the interpretation of point process summary statistics and will make point process analysis more accessible to ecologists not specialized in point process statistics.     

Measuring Spatially- and Directionally-varying Light Scattering from Biological Material

Light interacts with an organism''s integument on a variety of spatial scales. For example in an iridescent bird: nano-scale structures produce color; the milli-scale structure of barbs and barbules largely determines the directional pattern of reflected light; and through the macro-scale spatial structure of overlapping, curved feathers, these directional effects create the visual texture. Milli-scale and macro-scale effects determine where on the organism''s body, and from what viewpoints and under what illumination, the iridescent colors are seen. Thus, the highly directional flash of brilliant color from the iridescent throat of a hummingbird is inadequately explained by its nano-scale structure alone and questions remain. From a given observation point, which milli-scale elements of the feather are oriented to reflect strongly? Do some species produce broader "windows" for observation of iridescence than others? These and similar questions may be asked about any organisms that have evolved a particular surface appearance for signaling, camouflage, or other reasons.In order to study the directional patterns of light scattering from feathers, and their relationship to the bird''s milli-scale morphology, we developed a protocol for measuring light scattered from biological materials using many high-resolution photographs taken with varying illumination and viewing directions. Since we measure scattered light as a function of direction, we can observe the characteristic features in the directional distribution of light scattered from that particular feather, and because barbs and barbules are resolved in our images, we can clearly attribute the directional features to these different milli-scale structures. Keeping the specimen intact preserves the gross-scale scattering behavior seen in nature. The method described here presents a generalized protocol for analyzing spatially- and directionally-varying light scattering from complex biological materials at multiple structural scales.     

A model for generating aspects of zebra and other mammalian coat patterns

A model is put forward which is capable of generating chemical maps whose concentration contours are similar to the patterns seen on the flanks of zebras, cats and other mammals. The model derives from the reaction-diffusion kinetics invented by Turing (1952) and it is assumed that the necessary molecular apparatus is present in each cell of a two-dimensional array and that the cells are in diffusion contact. The model was expressed in differential equation form and solved digitally under a range of different initial, boundary and other conditions. The main forms of pattern that the model generated were spots of variable complexity, rings, and both vertical and horizontal stripes. If morphogen concentration levels are assumed to act as melanin-production switches, then a common basic mechanism is capable of generating a variety of skin patterns. Simple spots such as those found in the fallow deer or the serval, F. serval, are generated if the kinetics are initiated simultaneously in each cell and interpretation depends only on the presence or absence of morphogen, which is assumed for the deer to be an activator and for the cat a suppressor of pigment formation. The reticulated pattern of the giraffe is generated if there is a single high-value threshold. Complex spots typical of the leopards can be produced if there are different concentration thresholds for different colours. Rings of pattern typical of those found on cat tails are generated if the cellular array is a very narrow cylinder. Horizontal stripes are generated if the kinetics in each cell are initiated by a diffusion gradient whose source is the dorsal line of cells and these stripes may break up into spots to give a pattern very similar to that of, for example, the fishing cat, F. viverina. The vertical stripes of the caffre cat, F. caffra, or the zebras are formed if the kinetics are initiated by a vertically-moving constant-velocity wave which also allows morphogen diffusion between previously uncoupled cells. Thus far, the mechanism has generated neither the triradii that are commonly found on forelimbs nor the rings often observed on mammalian limbs. It does however incorporate the randomness that characterizes skin pattern, its operation is of the scale required in embryogenesis, it can be made stable to growth and it can explain certain degenerate patterns. Analysis of a spotted zebra in the light of the model provides evidence that zebra stripes arise from the inhibition rather than the stimulation of melanin; their pattern is thus of white stripes on a black background.     

The Additivity of Contrast in the Human Eye

Using the method of binocular brightness matching, simultaneous brightness contrast effects were measured on two observers. The effects of a given pattern were invariably smaller than the summation of the effects of the pattern's components. This failure of additivity was valid both for patterns with isolated components as well as for those with components exactly contiguous with one another. This failure was more pronounced the farther the inducing patterns were from the test patch. These findings are interpreted as indicating that in the human (just as in the Limulus) eye, the amount of inhibition exerted by a given region on its neighbors depends upon the inhibition exerted against it as well as its excitation state.     

Assortative mating,sexual selection,and their consequences for gene flow in Littorina

When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.     

Dental evolution in Neophanomys (Rodentia, Octodontidae) from the late Miocene of central Argentina

The evolutionary pattern of the molar morphology of the small caviomorph (Octodontidae) Neophanomys from the late Miocene Cerro Azul Formation of central Argentina is analyzed. Two new species (chronomorphs) are recognized, which constitute an anagenetically evolving lineage with a gradual and directional pattern of increasing molar hypsodonty. Dental changes related to increasing hypsodonty are comparable to those of the octodontid lineage Chasichimys also recovered from the Cerro Azul Formation. However, Neophanomys shows comparatively less variation in gross morphology and there are no evidences that this lineage achieved euhypsodonty. In contrast, important changes in enamel microstructure (schmelzmuster) are observed among different populations of Neophanomys, supporting the hypothesis that these changes can occur at least partially independently from modifications in dental gross morphology. The patterns of dental evolution detected in the Neophanomys and Chasichimys-Xenodontomys lineages and the unequivocal polarity of the changes involved, related to increasing hypsodonty, reinforce the hypothesis that chronological differences exist among late Miocene outcroppings of Cerro Azul Formation in central Argentina.     

Towards more predictable and consistent landscape metrics across spatial scales

Habitat change and fragmentation are considered key drivers of environmental change and biodiversity loss. To understand and mitigate the effects of such spatial disturbances on biological systems, it is critical to quantify changes in landscape pattern. However, the characterization of spatial patterns remains complicated in part because most widely used landscape metrics vary with the amount of usable habitat available in the landscape, and vary with the scale of the spatial data used to calculate them. In this study, we investigate the nature of the relationship between intrinsic characteristics of spatial pattern and extrinsic scale-dependent factors that affect the characterization of landscape patterns. To do so, we used techniques from modern multivariate statistics to disentangle widely used landscape metrics with respect to four landscape components: extent (E), resolution (R), percentage of suitable habitat cover (P), and spatial autocorrelation level (H). Our results highlight those metrics that are less sensitive to change in spatial scale and those that are less correlated. We found, however, significant and complex interactions between intrinsic and extrinsic characteristics of landscape patterns that will always complicate researcher's ability to isolate purely landscape pattern driven effects from the effects of changing spatial scale. As such, our study illustrates the need for a more systematic investigation of the relationship between intrinsic characteristics and extrinsic properties to accurately characterize observed landscape patterns.     

Cuttlefish camouflage: context-dependent body pattern use during motion

It is virtually impossible to camouflage a moving target against a non-uniform background, but strategies have been proposed to reduce detection and targeting of movement. Best known is the idea that high contrast markings produce ‘motion dazzle’, which impairs judgement of speed and trajectory. The ability of the cuttlefish Sepia officinalis to change its visual appearance allows us to compare the animal''s choice of patterns during movement to the predictions of models of motion camouflage. We compare cuttlefish body patterns used during movement with those expressed when static on two background types; one of which promotes low-contrast mottle patterns and the other promotes high-contrast disruptive patterns. We find that the body pattern used during motion is context-specific and that high-contrast body pattern components are significantly reduced during movement. Thus, in our experimental conditions, cuttlefish do not use high contrast motion dazzle. It may be that, in addition to being inherently conspicuous during movement, moving high-contrast patterns will attract attention because moving particles in coastal waters tend to be of small size and of low relative contrast.     

The Role of Wheel Running in the Coupling of Two Simultaneous Circadian Rhythms of Motor Activity in the Rat

Motor activity is among the non-photic stimuli that act on the internal clock. We have tested the role of motor activity in the circadian pattern of rats under conditions near the lower limits of entrainment, that induce circadian rhythm dissociation. Three groups of 8 rats each were used: a) rats kept individually in 25×25×15 cm cages, b) rats in 50×25×15 cm cages, and c) rats in 50×25×15 cm cages with access to a running wheel. All the rats were kept under light-dark cycles of 22 hours (T22, 11L:11D) for 50 days, after which they were transferred to constant darkness. All the rats without a running wheel showed a motor activity pattern with two statistically significant circadian rhythms in the periodogram of Sokolove and Bushell: one circadian component entrained by the LD cycle, and another free-running. The rats with access to a running wheel showed several patterns: 5 rats showed only one rhythm entrained to the LD cycle, 2 rats showed circadian rhythm dissociation, and 1 showed only a free running rhythm. We believe that the simultaneous manifestation of two circadian components reflects the functional dissociation of the oscillators population that constitutes the circadian pacemaker, of the rat. Physical exercise acts on the pacemaker reinforcing the strongest group of oscillators, which, depending on the structure of the circadian system of the rat, is usually the one entrained to the LD cycle. This study supports the hypothesis that motor activity couples the oscillators that form the circadian system of the rat.     

The Role of Wheel Running in the Coupling of Two Simultaneous Circadian Rhythms of Motor Activity in the Rat

Motor activity is among the non-photic stimuli that act on the internal clock. We have tested the role of motor activity in the circadian pattern of rats under conditions near the lower limits of entrainment, that induce circadian rhythm dissociation. Three groups of 8 rats each were used: a) rats kept individually in 25×25×15 cm cages, b) rats in 50×25×15 cm cages, and c) rats in 50×25×15 cm cages with access to a running wheel. All the rats were kept under light-dark cycles of 22 hours (T22, 11L:11D) for 50 days, after which they were transferred to constant darkness. All the rats without a running wheel showed a motor activity pattern with two statistically significant circadian rhythms in the periodogram of Sokolove and Bushell: one circadian component entrained by the LD cycle, and another free-running. The rats with access to a running wheel showed several patterns: 5 rats showed only one rhythm entrained to the LD cycle, 2 rats showed circadian rhythm dissociation, and 1 showed only a free running rhythm. We believe that the simultaneous manifestation of two circadian components reflects the functional dissociation of the oscillators population that constitutes the circadian pacemaker, of the rat. Physical exercise acts on the pacemaker reinforcing the strongest group of oscillators, which, depending on the structure of the circadian system of the rat, is usually the one entrained to the LD cycle. This study supports the hypothesis that motor activity couples the oscillators that form the circadian system of the rat.