Evolutionary relationships between morphology, performance and habitat openness in the lizard genus Niveoscincus (Scincidae: Lygosominae)

Correlations between an animal's morphology and ecological parameters such as habitat characteristics emphasize the intimate link between phenotype and the environment, but are often difficult to interpret because the functional consequences of morphological variation are frequently unknown. We provide one of the few studies relating limb morphology, functional capabilities, and habitat in reptiles. We tested the hypothesis that species occupying open microhabitats would possess relatively longer limbs and faster sprint speeds than those occurring in more closed microhabitats. A number of morphological characteristics relevant to locomotion were quantified, including the length of the bones of the fore- and hindlimbs and body size. A phylogenetic analysis was then used to examine the evolutionary relationships between morphology, locomotor performance and microhabitat openness in seven species of Niveoscincus and one species of the closely related genus Pseudemoia. A significant evolutionary relationship was established between sprinting ability, morphology, and the openness of the microhabitat occupied by a species. The phylogenetic analysis demonstrated an evolutionary trend in Niveoscincus of species occupying open microhabitats (e.g. N. greeni, N ocellatus) being large with long limbs and high sprinting ability, while those occupying closed microhabitats (e.g. N coventryi, P. entrecasteauxii) art smaller with short limbs and much slower maximum sprint speeds.     

Nested reentrant and recurrent computation in early vision: a Bayesian neuromorphic model applied to hyperacuity

 Hyperacuity is demonstrated in a neuromorphic model of the early visual system. The model incorporates Bayesian principles which are embodied in the dynamics of reentrant and recurrent feedback processes. Each retinotopically mapped area in the model represents a transformation of data from the visual field. Sensory information propagates in a bottom-up direction from one area to the next, while information based on Bayesian priors propagates in a top-down direction through reentrant connections. The ‘bottom-up’ and ‘top-down’ information maintain a separate existence in distinct layers of the model, but they interact through local connections within each area. Transformations between one area and the next are defined by the reentrant synaptic connections between areas, while local prior probability maps are defined by local recurrent connections within layers. The representation of hyperacuity is accomplished using a model of functional multiplicity: the large ratio of neurons in striate cortex compared with the number of afferent fibers projecting from the lateral geniculate nucleus. High functional multiplicity, in conjunction with hierarchical reentrant processing, allows the model to represent a fine-grained restoration of the line structure of visual input. Received : 26 April 1995 / Accepted in revised form : 27 July 1996     

Diversity and geographic distribution of ciliates (Protista: Ciliophora)

About 4,500 free-living ciliate morphospecies have been described, applying an average synonymy rate of 20%. We estimate that 83–89% of the ciliate diversity is still undescribed, using the following probabilities: detailed habitat studies suggest that the described number of morphospecies must be doubled: 4,500 → 9,000; this figure has to be increased by about 50% due to species with similar interphase morphology but different resting cysts: 9,000 → 13,500; the genetic and molecular data suggest that this value must be doubled or trebled: 13,500 → 27,000 to 40,000 free-living, biological ciliate species. The knowledge on geographic distribution of ciliates heavily depends on flagship species and statistical analyses because reliable faunistic studies are rare and molecular data are still in its infancy. We present a list of 52 ciliate flagship species as a testable hypothesis, i.e., the hypothesis of restricted distribution of certain ciliate species must be refused when a considerable number of them is found in all or most biogeographic regions. Flagship species and statistical analyses consistently show Gondwanan and Laurasian ciliate communities, suggesting that the split of Pangaea deeply influenced ciliate distribution and rare species play a key role in geographic differentiation. However, there is also substantial evidence for continental, regional, and local endemism of free-living ciliates. The molecular studies usually show a high level of genetic diversity underlying ciliate morphospecies, suggesting that morphologic and molecular evolution may be decoupled in many ciliate species. Molecular studies on ciliate biogeography are at variance, possibly because most are still focusing on single molecular markers. In sum, the data indicate that ciliate biogeography is similar to that of plants and animals, but with an increased proportion of cosmopolites, favouring the moderate endemicity model. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

Hepatic respiratory compensation and haematological changes in the cave cyprinid, Phreatichthys andruzzii

In several ectotherms, including all members of the Osteichthyes studied so far, the spleen is capable of storing and releasing erythrocytes according to the animal's respiratory needs. The tropical cave cyprinid Phreatichthys andruzzii uses its liver rather than the spleen as the site of accumulation in the respiratory compensation process, like the amphibian Rana esculenta. The reversible process of erythrocyte accumulation in the liver is very evident in animals anaesthetized with chlorobutanol; MS-222, an anaesthetic widely used in lower vertebrates alters all the haematological parameters and is not suitable for studies on blood and respiration. The hepatic respiratory compensation mechanism is as efficient as the splenic one: in animals kept at 18 °C for 24 h the mean liver weight percentage was 70% higher than in specimens kept at 28 °C (2.43% of the body weight compared to 1.39%, in groups of six specimens) while mean red blood cell counts fell from 2.49 to 1.60 · 10¹² per l, in agreement with the haematocrit value and haemoglobin concentration; mean corpuscular volume remained constant (at about 177 fl). Accepted: 15 April 1997     

Relevance of nonlinear lumped-parameter models in the analysis of depth-EEG epileptic signals

In the field of epilepsy, the analysis of stereoelectroencephalographic (SEEG, intra-cerebral recording) signals with signal processing methods can help to better identify the epileptogenic zone, the area of the brain responsible for triggering seizures, and to better understand its organization. In order to evaluate these methods and to physiologically interpret the results they provide, we developed a model able to produce EEG signals from “organized” networks of neural populations. Starting from a neurophysiologically relevant model initially proposed by Lopes Da Silva et al. [Lopes da Silva FH, Hoek A, Smith H, Zetterberg LH (1974) Kybernetic 15: 27–37] and recently re-designed by Jansen et al. [Jansen BH, Zouridakis G, Brandt ME (1993) Biol Cybern 68: 275–283] the present study demonstrates that this model can be extended to generate spontaneous EEG signals from multiple coupled neural populations. Model parameters related to excitation, inhibition and coupling are then altered to produce epileptiform EEG signals. Results show that the qualitative behavior of the model is realistic; simulated signals resemble those recorded from different brain structures for both interictal and ictal activities. Possible exploitation of simulations in signal processing is illustrated through one example; statistical couplings between both simulated signals and real SEEG signals are estimated using nonlinear regression. Results are compared and show that, through the model, real SEEG signals can be interpreted with the aid of signal processing methods. Received: 3 January 2000 / Accepted: 24 March 2000     

Chaotic dynamics of information processing: The “magic number seven plus-minus two” revisited

In a well-known collection of his essays in cognitive psychology Miller (The Psychology of Communication. Penguin, 1974) describes in detail a number of experiments aiming at a determination of the limits (if any) of the human brain in processing information. He concludes that the ‘channel capacity’ of human subjects does not exceed a few bits or that the number of categories of (one-dimensional) stimuli from which unambiguous judgment can be made are of the order of ‘seven plus or minus two’. This ‘magic number’ holds also, Miller found, for the number of random digits a person can correctly recall on a row and also the number of sentences that can be inserted inside a sentence in a natural language and still be read through without confusion. In this paper we propose a dynamical model of information processing by a self-organizing system which is based on the possible use of strange attractors as cognitive devices. It comes as an amusing surprise to find that such a model can, among other things, reproduce the ‘magic number seven plus-minus two’ and also its variance in a number of cases and provide a theoretical justification for them. This justification is based on the optimum length of a code which maximizes the dynamic storing capacity for the strings of digits constituting the set of external stimuli. This provides a mechanism for the fact that the ‘human channel’, which is so narrow and so noisy (of the order of just a few bits per second or a few bits per category) possesses the ability of squeezing or ‘compressing’ practically an unlimited number of bits per symbol—thereby giving rise to a phenomenal memory.     

Dynamics of annual influenza A epidemics with immuno-selection

 The persistence of Influenza A in the human population relies on continual changes in the viral surface antigens allowing the virus to reinfect the same hosts every few years. The epidemiology of such a drifting virus is modeled by a discrete season-to-season map. During the epidemic season only one strain is present and its transmission dynamics follows a standard epidemic model. After the season, cross-immunity to next year's virus is determined from the proportion of hosts that were infected during the season. A partial analysis of this map shows the existence of oscillations where epidemics occur at regular or irregular intervals. Received: 16 February 2001 / Revised version: 11 June 2002 / Published online: 28 February 2003 Key words or phrases: Infectious disease – Influenza drift – Cross-immunity – Seasonal epidemics – Iterated map     

Impact of chronic and pulse dilution disturbances on metabolism and trophic structure in a saline Mediterranean stream

Non-diatom benthic algae from 104 streams in southern California were studied. We present a novel method for quantification of non-diatom algae that seeks to improve upon two important aspects of existing methods: separate processing of macroalgae and microalgae to avoid sample blending and consequent loss of macroalgal integrity, and for better viewing, counting a well-mixed microalgal subsample on a standard microscope slide instead of using a counting chamber. Our method provided high-quality taxonomic and quantitative data with low uncertainty. A total of 260 algal taxa were recorded, 180 of which were identified to species level. The median total algal biovolume per site was 22.7 mm³ cm⁻² (range: <0.001–836.9 mm³ cm⁻²), the median species number was 11 (range: 2–43). Total algal biovolume and species number correlated with canopy cover (negative) and water temperature (positive), but not with measured water chemistry constituents. The proportion of heterocystous cyanobacteria and Zygnemataceae were strongly negatively correlated with nitrate concentrations and TN. The proportion of red algae was negatively correlated with TP. Species optima calculations combined with indicator species analysis identified >40 algal species as potential indicators of nutrient conditions. Proposed here is a practical tool for non-diatom algal quantification that enhances its application to stream bioassessment.     

Predicting the buoyancy, equilibrium and potential swimming ability of giraffes by computational analysis

Giraffes (Giraffa camelopardalis) are often stated to be unable to swim, and while few observations supporting this have ever been offered, we sought to test the hypothesis that giraffes exhibited a body shape or density unsuited for locomotion in water. We assessed the floating capability of giraffes by simulating their buoyancy with a three-dimensional mathematical/computational model. A similar model of a horse (Equus caballus) was used as a control, and its floating behaviour replicates the observed orientations of immersed horses. The floating giraffe model has its neck sub-horizontal, and the animal would struggle to keep its head clear of the water surface. Using an isometrically scaled-down giraffe model with a total mass equal to that of the horse, the giraffe's proportionally larger limbs have much higher rotational inertias than do those of horses, and their wetted surface areas are 13.5% greater relative to that of the horse, thus making rapid swimming motions more strenuous. The mean density of the giraffe model (960 gm/l) is also higher than that of the horse (930 gm/l), and closer to that causing negative buoyancy (1000 gm/l). A swimming giraffe - forced into a posture where the neck is sub-horizontal and with a thorax that is pulled downwards by the large fore limbs - would not be able to move the neck and limbs synchronously as giraffes do when moving on land, possibly further hampering the animal's ability to move its limbs effectively underwater. We found that a full-sized, adult giraffe will become buoyant in water deeper than 2.8 m. While it is not impossible for giraffes to swim, we speculate that they would perform poorly compared to other mammals and are hence likely to avoid swimming if possible.     

Respiratory transfer impedance between 8and 384Hz in guinea pigs before and after bronchial challenge

Sobh, Jamil F., Craig M. Lilly, Jeffrey M. Drazen, andAndrew C. Jackson. Respiratory transfer impedance between 8 and384 Hz in guinea pigs before and after bronchial challenge. J. Appl. Physiol. 82(1): 172-181, 1997.We report a forced oscillatory technique for noninvasivelymeasuring respiratory transfer impedance (Ztr) between 8 and 384 Hz inguinea pigs. This technique uses a device consisting of two chambers:one surrounding the animal's head that is used as a plethysmograph tomeasured flow through the airway opening and the other that surroundsthe animal's body and is used to apply pressure oscillations to thebody surface. Ztr was measured in spontaneously breathing awake guineapigs and while the animals were anesthetized in normal andmethacholine-challenged conditions. An eight-element model consistingof an airway compartment separated from a tissue compartment by a shuntgas compression compartment was fit to the data. Anesthesia increasedcentral and peripheral airway resistance and bronchial airway wallcompliance by 13, 31, and 44%, respectively, whereas it decreasedtissue compliance by 37%. Compared with the unanesthetized condition, the methacholine challenge (20 µg/kg) resulted in an increase incentral and peripheral airway resistance (69 and 319%, respectively) and a decrease in bronchial airway wall and tissue compliance (37 and79%, respectively). This technique is capable of measuring Ztr inanesthetized and awake guinea pigs. Analysis of these data with thiseight-element model provides reasonable estimates of airway and tissueparameters.

     

An artificial modular neural network and its basic dynamical characteristics

This work contains a proposition of an artificial modular neural network (MNN) in which every module network exchanges input/output information with others simultaneously. It further studies the basic dynamical characteristics of this network through both computer simulations and analytical considerations. A notable feature of this model is that it has generic representation with regard to the number of composed modules, network topologies, and classes of introduced interactions. The information processing of the MNN is described as the minimization of a total-energy function that consists of partial-energy functions for modules and their interactions, and the activity and weight dynamics are derived from the total-energy function under the Lyapunov stability condition. This concept was realized by Cross-Coupled Hopfield Nets (CCHN) that one of the authors proposed. In this paper, in order to investigate the basic dynamical properties of CCHN, we offer a representative model called Cross-Coupled Hopfield Nets with Local And Global Interactions (CCHN-LAGI) to which two distinct classes of interactions – local and global interactions – are introduced. Through a conventional test for associative memories, it is confirmed that our energy-function-based approach gives us proper dynamics of CCHN-LAGI even if the networks have different modularity. We also discuss the contribution of a single interaction and the joint contribution of the two distinct interactions through the eigenvalue analysis of connection matrices. Received: 18 July 1995 / Accepted in revised form: 2 October 1997     

Enantioselective reduction of 3,4-methylene-dioxyphenylacetone using Candida famata and Zygosaccharomyces rouxii

In an effort to prepare 3,4-methylene-dioxyphenyl-(S)-isopropanol from 3,4-methylene-dioxyphenylacetone, an initial screen of microbes indicated that Candida famata could catalyze this reaction efficiently at low substrate concentration. A dilute, large-scale process was developed to provide experimental material for the chemical synthesis to be explored. However, the productivity number of this process [0.134 g product (g␣wet␣weight cells)⁻¹ day⁻¹ was too low to be practical. C.␣famata was also extremely sensitive to concentrations of both the ketone and the alcohol greater than 2 g/l. A more extensive screen of yeast and fungi revealed that Zygosaccharomyces rouxii was more tolerant to higher substrate concentrations and had a higher productivity number [0.8 g (g wet weight cells)⁻¹ day⁻¹]. These characteristics suggested that Z. rouxii could be used in a large-scale process at high substrate concentrations. Received: 8 July 1996 / Received revision: 9 September 1996 / Accepted: 18 September 1996     

Breakthrough to awareness: a preliminary neural network model of conscious and unconscious perception in word processing

 A neural network model is constructed to mimic the processing involved in semantic and working memory when subliminal effects are involved. These effects involve modifications of reaction time to later inputs, according to whether or not there has been conscious or unconscious processing of the earlier input. The model is constructed of two separate modules: one (a semantic memory module) allowing for processing at a semantic, but unconscious, level, and the other (a working memory module) for conscious experience. The latter module, although a replica of the earlier one, has different lateral connectivity and output function from the former. The model is shown to give a good fit to Marcel’s data on the processing of polysemous words. Further tests are suggested for the model, and a possible cortical implementation suggested. The relevance of the model to recent approaches to consciousness is also explored. Received: 7 February 1995/Accepted in revised form: 14 November 1995     

Intron Dynamics and the Evolution of Integrin β-Subunit Genes: Maintenance of an Ancestral Gene Structure in the Coral, Acropora millepora

We have determined the genomic structure of an integrin β-subunit gene from the coral, Acropora millepora. The coding region of the gene contains 26 introns, spaced relatively uniformly, and this is significantly more than have been found in any integrin β-subunit genes from higher animals. Twenty-five of the 26 coral introns are also found in a β-subunit gene from at least one other phylum, indicating that the coral introns are ancestral. While there are some suggestions of intron gain or sliding, the predominant theme seen in the homologues from higher animals is extensive intron loss. The coral baseline allows one to infer that a number of introns found in only one phylum of higher animals result from frequent intron loss, as opposed to the seemingly more parsimonious alternative of isolated intron gain. The patterns of intron loss confirm results from protein sequences that most of the vertebrate genes, with the exception of β4, belong to one of two β subunit families. The similarity of the patterns within each of the β1,2,7 and β3,5,6,8 groups indicates that these gene structures have been very stable since early vertebrate evolution. Intron loss has been more extensive in the invertebrate genes, and obvious patterns have yet to emerge in this more limited data set. Received: 5 March 2001 / Accepted: 17 May 2001     

A comparative analysis of the post‐cranial skeleton of fossorial and non‐fossorial gymnophthalmid lizards

Squamates are found in a wide range of habitats and show a corresponding diversity of morphologies that can often be correlated with locomotor mode. The evolution of a snake‐like body form, frequently associated with fossoriality, from a typical lacertiform morphology involves changes in the morphology of vertebrae, girdles, and limbs; the changes are mainly manifested by the reduction or loss of limbs and body elongation. In this study, we describe the axial and appendicular skeletons of six closely related gymnophthalmid species. Three of them show a lizard‐like morphology, with a four‐digit forelimb and a five‐digit hindlimb, and the other three show a snake‐like morphology associated with a burrowing habit, with reduced limbs and a longer body in comparison to the former three species. We show that vertebral morphology is similar among the six species, with the differences being accounted for by an increase in the number of vertebrae and by the structural reduction of girdles and limbs in the snake‐like species. Skeletal morphology provides valuable information on locomotion type, physiology, diet, and other biological features. The burrowing morphology usually involves accentuated reduction of girdle and limb elements, reflecting an undulating type of locomotion in which the limbs play little or no role in propelling the body; in contrast, well‐developed limbs and girdles indicate a greater reliance on the limbs for body propulsion. Limb reduction is frequent among vertebrates, but many different phenotypes are found in species exhibiting some kind of reduction, indicating that different mechanisms and evolutionary pressures may be involved in generating the diverse morphologies. J. Morphol. 274:845–858, 2013. © 2013 Wiley Periodicals, Inc.     

Pheromones and signature mixtures: defining species-wide signals and variable cues for identity in both invertebrates and vertebrates

Pheromones have been found in species in almost every part of the animal kingdom, including mammals. Pheromones (a molecule or defined combination of molecules) are species-wide signals which elicit innate responses (though responses can be conditional on development as well as context, experience, and internal state). In contrast, signature mixtures, in invertebrates and vertebrates, are variable subsets of molecules of an animal’s chemical profile which are learnt by other animals, allowing them to distinguish individuals or colonies. All signature mixtures, and almost all pheromones, whatever the size of molecules, are detected by olfaction (as defined by receptor families and glomerular processing), in mammals by the main olfactory system or vomeronasal system or both. There is convergence on a glomerular organization of olfaction. The processing of all signature mixtures, and most pheromones, is combinatorial across a number of glomeruli, even for some sex pheromones which appear to have ‘labeled lines’. Narrowly specific pheromone receptors are found, but are not a prerequisite for a molecule to be a pheromone. A small minority of pheromones act directly on target tissues (allohormone pheromones) or are detected by non-glomerular chemoreceptors, such as taste. The proposed definitions for pheromone and signature mixture are based on the heuristic value of separating these kinds of chemical information. In contrast to a species-wide pheromone, there is no single signature mixture to find, as signature mixtures are a ‘receiver-side’ phenomenon and it is the differences in signature mixtures which allow animals to distinguish each other.     

Depth cues, behavioural context, and natural illumination: some potential limitations of video playback techniques

By expanding on issues raised by D’Eath (1998), I address in this article three aspects of vision that are difficult to reproduce in the video- and computer-generated images used in experiments, in which images of conspecifics or of predators are replayed to animals. The lack of depth cues derived from binocular stereopsis, from accommodation, and from motion parallax may be one of the reasons why animals do not respond to video displays in the same way as they do to real conspecifics or to predators. Part of the problem is the difficulty of reproducing the closed-loop nature of natural vision in video playback experiments. Every movement an animal makes has consequences for the pattern of stimulation on its retina and this ”optic flow” in turn carries information about both the animal’s own movement and about the three-dimensional structure of the environment. A further critical issue is the behavioural context that often determines what animals attend to but that may be difficult to induce or reproduce in an experimental setting. I illustrate this point by describing some visual behaviours in fiddler crabs, in which social and spatial context define which part of the visual field a crab attends to and which visual information is used to guide behaviour. I finally mention some aspects of natural illumination that may influence how animals perceive an object or a scene: shadows, specular reflections, and polarisation reflections. Received: 23 November 1999 / Received in revised form: 9 February 2000 / Accepted: 10 February 2000     

Peering in mature, captive bonobos (Pan paniscus)

“Peering”—close-proximity staring at the mouth of another—was observed in ten (three males and seven females) mature (at least 7 years old) bonobos (Pan paniscus) living in three social groups at the San Diego Zoo and Wild Animal Park. Instantaneous scan samples, taken at 2-min intervals, over a three-and-a-half year period, yielded 617 observations of peering (1.4 per observation hour). Food was exchanged in only 15 of these scans. Peering was most often performed by younger animals and was primarily directed toward older females (“matrons”). In a given dyad, the animal more likely to peer at the other was also more like to both peer and be peered at if they frequently groomed and infrequently displayed aggression at a given female. An adolescent male showed the highest frequency of peering when living with two older females, but dropped to adult male levels when later housed with two younger (albeit mature) females. A reversal in which animal was more likely to peer, follow, and groom occurred in one female dyad, after the birth of the younger animal's first infant. After a similar birth in the other group, no such changes were observed. We discuss how these and related findings, in conjunction with what is known of the social structure of this species, suggest that one possible function of peering in bonobos may be as a signal acknowledging female status.     

The Eclipse of Species Ranges

This paper distinguishes four recognisably different geographical processes in principle causing species to die out. One of these processes, the one we dub “range eclipse”, holds that one range expands at the expense of another one, thereby usurping it. Channell and Lomolino (2000a, Journal of Biogeography 27: 169–179; 2000b, Nature 403: 84–87; see also Lomolino and Channell, 1995, Journal of Mammalogy 76: 335–347) measured the course of this process in terms of the proportion of the total range remaining in its original centre, thereby essentially assuming a homogeneous distribution of animals over the range. However, part of their measure seems mistaken. By giving a general, analytical formulation of eclipsing ranges, we estimate the exact course of this process. Also, our formulation does not partition a range into two spatially equal parts, its core and its edge, but it assumes continuity. For applying this model to data on the time evolution of species, individual time series should be available for each of them. For practical purposes we give an alternative way of plotting and interpreting such time series. Our approach, being more sensitive than Channell and Lomolino’s, gives a less optimistic indication of range eclipses than theirs once these have started.     

The central performance drop in texture segmentation: a simulation based on a spatial filter model

 This article presents a computational model of early visual information processing that attempts to account for the central performance drop (CPD) in texture segmentation. CPD is the finding that detection performance on short stimulus displays of line textures using orientation differences to set off the target is not maximal at the foveal center but in parafoveal areas. A comparison between a simulation and psychophysical experimental data supported the assumption that the CPD may be explained by properties of spatial frequency channels whose band-pass filter characteristics are not constant over the retina but differ with eccentricity in a defined manner. The model provided satisfactory predictions of experimental data based on densely or widely spaced line elements in texture fields. It is concluded that preattentive texture analysis might be performed by a relatively small number of simple spatial filters. Received: 14 November 1996 / Accepted in revised form: 3 June 1997