Exploring the connection between emergent animal personality and fitness using a novel individual-based model and decision tree approach

The connection between reproductive fitness and animal personality is not fully understood. Using computer simulations and machine learning, we found high accuracy rules that predict which personalities are associated with fitness for two correlated measures of components of fitness applied a posteriori for classificatory purposes: fitness component (1) in terms of survival and short-term reproductive success, and fitness component (2) in terms of long term reproductive success which is indirectly related to survival of the parents. Animals are represented in the abstract as individuals with a genome that through time develops into certain characteristic behaviors and personalities. To the best of our knowledge, this is the first simulation study of its kind that extracts rules to investigate the link between personality and fitness. Clearly separated behaviors between fit and non-fit individuals emerged through the evolution of the population over time without top-down processing. Moreover, we did not employ a pre-defined fitness function, in order to minimize any possible biases toward a specific type of behavior. With respect to fitness component (1), we found that individuals with one of two extreme values of a personality trait (either bold or fearful) tend to be most fit, which agrees with empirical studies. With respect to fitness component (2), we found that when resources are low, fit individuals search for food whereas if food is abundant, they focus on reproduction, thereby suggesting the context dependence of fitness related behaviors. Once again, these results agree with empirical studies.     

Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual-based approach

Changes in agricultural practices and forest fragmentation can have a dramatic effect on landscape connectivity and the dispersal of animals, potentially reducing gene flow within populations. In this study, we assessed the influence of woodland connectivity on gene flow in a traditionally forest-dwelling species--the European roe deer--in a fragmented landscape. From a sample of 648 roe deer spatially referenced within a study area of 55 x 40 km, interindividual genetic distances were calculated from genotypes at 12 polymorphic microsatellite loci. We calculated two geographical distances between each pair of individuals: the Euclidean distance (straight line) and the 'least cost distance' (the trajectory that maximizes the use of wooded corridors). We tested the correlation between genetic pairwise distances and the two types of geographical pairwise distance using Mantel tests. The correlation was better using the least cost distance, which takes into account the distribution of wooded patches, especially for females (the correlation was stronger but not significant for males). These results suggest that in a fragmented woodland area roe deer dispersal is strongly linked to wooded structures and hence that gene flow within the roe deer population is influenced by the connectivity of the landscape.     

The Symbiosis Interactome: a computational approach reveals novel components,functional interactions and modules in Sinorhizobium meliloti

Background  

Rhizobium-Legume symbiosis is an attractive biological process that has been studied for decades because of its importance in agriculture. However, this system has undergone extensive study and although many of the major factors underpinning the process have been discovered using traditional methods, much remains to be discovered.     

Individual variability and population regulation: an individual-based model

To study the influence of individual variability on population dynamics an individual-based model of the dynamics of a single population consisting of different individuals is constructed. The model is based on differences in individual assimilation rates due to intraspecific competition and variability of initial weights. The model exhibits "imperfect regulation", i.e., the number of individuals in the population oscillates and sooner or later the population becomes extinct. When individual variability is included, the model produces longer population extinction times than without individual variability. The average extinction time is not however a monotonic function of the degree of individual variability.     

Identify schizophrenia using resting-state functional connectivity: an exploratory research and analysis

ABSTRACT: BACKGROUND: Schizophrenia is a severe mental illness associated with the symptoms such as hallucination and delusion. The objective of this study was to investigate the abnormal resting-state functional connectivity patterns of schizophrenic patients which could identify furthest patients from healthy controls. METHODS: The whole-brain resting-state fMRI was performed on patients diagnosed with schizophrenia (n=22) and on age- and gender-matched, healthy control subjects (n=22). To differentiate schizophrenic individuals from healthy controls, the multivariate classification analysis was employed. The weighted brain regions were got by reconstruction arithmetic to extract highly discriminative functional connectivity information. RESULTS: The results showed that 93.2% (p<0.001) of the subjects were correctly classified via the leave-one-out cross-validation method. And most of the altered functional connections identified located within the visual cortical-, default-mode-, and sensorimotor network. Furthermore, in reconstruction arithmetic, the fusiform gyrus exhibited the greatest amount of weight. CONCLUSIONS: This study demonstrates that schizophrenic patients may be successfully differentiated from healthy subjects by using whole-brain resting-state fMRI, and the fusiform gyrus may play an important functional role in the physiological symptoms manifested by schizophrenic patients. The brain region of great weight may be the problematic region of information exchange in schizophrenia. Thus, our result may provide insights into the identification of potentially effective biomarkers for the clinical diagnosis of schizophrenia.     

An in situ, individual-based approach to quantify connectivity of marine fish: ontogenetic movements and residency of lingcod

As modern fishery assessments change in an effort to be more accurate and encompass the range of potential ecosystem interactions, critical information on the ecology of species including life history, intra and inter-specific competitive interactions and habitat requirements must be added to the standard fishery-dependent and independent data sets. One species whose movements and habitat associations greatly affects exploitation patterns is lingcod, Ophiodon elongatus, which support an economically important fishery along the coastal waters of the Pacific Coast of North America. High site fidelity and limited movements within nearshore areas are hypothesized to have resulted in high catchability, a major factor that has contributed to overfished stocks. Thus, assessing the level of movement and connectivity among lingcod subpopulations inhabiting nearshore habitats is a prerequisite to determining the condition of lingcod stocks. We used the Pacific Ocean Shelf Tracking (POST) Project acoustic receiver array in Alaska's Prince William Sound to monitor movements and residency of 21 acoustic-tagged lingcod for up to 16 months. Eight of sixteen lingcod (50%) initially aged at 2.5- to 3.5- years-old dispersed from their tag site. Dispersal was highly seasonal, occurring in two, five-week periods from mid-December through January and from mid-April through May. Dispersal in winter may be related to sexually immature lingcod or newly-mature male lingcod being displaced by territorial males. Spring dispersal may be indicative of the onset of migratory behavior where lingcod move out into Prince William Sound and possibly the offshore waters of the Gulf of Alaska. Our results reveal a pattern of ontogenetic dispersal as lingcod approach 4-years-old and exceed 50 cm total length. The large proportion of tagged fish migrating out of Port Gravina, their tagging site, reflects a high level of connectivity among Prince William Sound subpopulations. Our results also support the hypotheses that these subpopulations may be highly susceptible to overfishing because most fish show long residence times.     

General response patterns of fish populations to stress: an evaluation using an individual-based simulation model

General response patterns of fish populations tostress, originally proposed by Colby for fisheriesrehabilitation and later adapted by Munkittrick forcontaminants, were evaluated using an individual-basedsimulation model. General response patterns relatechanges in population-level variables to the type ofstress. The model follows the daily growth,mortality, and spawning of individual yellow perch andwalleye through their lifetime, and was corroboratedusing Oneida Lake data. Two versions of the model wereused: population (yellow perch only) and community(dynamic predation on yellow perch by walleye). Eightstresses were imposed on the population and communityversions of the model and 100-year simulations wereperformed. Response patterns were defined by changesin predicted yellow perch mean population abundance,mean age of adults, and mean adult growth (representedby mean length at age-7). Proposed response patternswere similar to those predicted using the populationversion of the model. Simulations using the communityversion of the model distorted the response patterns,either causing amplification, dampening, or reversalof many of the patterns. Predicted response patternsbecame unique when additional variables were included.Our model results suggest that caution is appropriatein interpreting general response patterns based onmean age, or when the population of interest plays amajor role in a relatively simple food web. The responsepattern approach may be better at identifying the lifestage impacted rather than the mechanism of the stress.     

Density distribution and size sorting in fish schools: an individual-based model

In fish schools the density varies per location and often individualsare sorted according to familiarity and/or body size. High densityis considered advantageous for protection against predatorsand this sorting is believed to be advantageous not only toavoid predators but also for finding food. In this paper, welist a number of mechanisms and we study, with the help of anindividual-based model of schooling agents, which spatial patternsmay result from them. In our model, schooling is regulated bythe following rules: avoiding those that are close by, aligningto those at intermediate distances, and moving towards othersfurther off. Regarding kinship/familiarity, we study patternsthat come about when agents actively choose to be close to relatedagents (i.e., ‘active sorting’). Regarding bodysize, we study what happens when agents merely differ in sizebut behave according to the usual schooling rules (‘sizedifference model’), when agents choose to be close tothose of similar size, and when small agents avoid larger ones(‘risk avoidance’). Several spatial configurationsresult: during ‘active sorting’ familiar agentsgroup together anywhere in the shoal, but agents of differentsize group concentrically, whereby the small agents occupy thecenter and the large ones the periphery (‘size differencemodel’ and ‘active sorting’). If small agentsavoid the risk of being close to large ones, however, smallagents end up at the periphery and large ones occupy the center(‘risk avoidance’). Spatial configurations are alsoinfluenced by the composition of the group, namely the percentageof agents of each type. Furthermore, schools are usually oblongand their density is always greatest near the front. We explainthe way in which these patterns emerge and indicate how resultsof our model may guide the study of spatial patterns in realanimals.     

Pc16a, the first characterized peptide from Conus pictus venom, shows a novel disulfide connectivity

A novel conotoxin, pc16a, was isolated from the venom of Conus pictus. This is the first peptide characterized from this South-African cone snail and it has only 11 amino acid residues, SCSCKRNFLCC*, with the rare cysteine framework XVI and a monoisotopic mass of 1257.6Da. Two peptides were synthesized with two possible conformations: globular (pc16a_1) and ribbon (pc16a_2). pc16a_1 co-eluted with the native peptide, which indicates a disulfide connectivity I-III, II-IV. The structure of pc16a_1 was determined by NMR. Both synthetic peptides were used to elucidate the biological activity. Bioassays were performed on crickets, ghost shrimps, larvae of the mealworm beetle and mice, but no effect was seen. Using two-electrode voltage clamp, a range of voltage-gated ion channels (Na(v) and K(v)) and nicotinic acetylcholine receptors were screened, but again no activity was found. Hence, the specific target of pc16a still remains to be discovered.     

Modelling the influence of landscape connectivity on animal distribution: a functional grain approach

Landscape change may reduce the connectivity of landscapes and impact the movement of animals. If movement processes have been influenced by landscape connectivity, we hypothesize that animals may distribute themselves in larger connected regions of the landscape in order to minimize the movement costs associated with obtaining required resources and avoiding predators. We adopt the term functional grain to describe a set of functionally connected regions. In this spatial pattern, each region describes a contiguous area of the landscape within which an animal may move freely below a threshold amount of movement cost. We used telemetry data from woodland caribou Rangifer tarandus caribou to test hypothetical functional grains where connectivity was determined by the spatial configuration of resource patches (patch only), by the resistance to movement presented by landscape features (resistance only), and by a combination of the two (patch + resistance). To identify these functional grains, we used a grains of connectivity approach, and introduced a novel lattice‐based variant of this method to build the resistance only model. We developed a measure of fit that describes caribou distribution with respect to larger functionally connected regions in the grain, and used this to ask: 1) are seasonal caribou locations consistent with a random functional grain, implying that landscape connectivity has not shaped their distribution? 2) Given a functional grain model, are seasonal caribou locations distributed in larger functionally connected regions than random points, implying a response to the shape, size, and location of the connected regions. We found support for landscape connectivity influencing animal distribution using grains based on a landscape resistance model, and that support varied between behaviourally defined seasons. We also discuss how our novel lattice approach may be valuable for highly mobile mammals and other species where the identification of resource patches is a limitation.     

Modelling the third dimension: Incorporating topography into the movement rules of an individual-based spatially explicit population model

A wide variety of topographical and environmental elements have been shown or proposed to influence the movement decisions of dispersing animals. Most real landscapes have topographical elements such as hills, valleys and urban developments, which can all act to modify a species’ perceptual range and directly influence movement behaviour. If a visual-based perceptual ability enables a dispersing individual to locate suitable habitat patches at a distance, then it is to be expected that topographical features would act to modify the overall success of this strategy. However, the majority of individual-based Spatially Explicit Population Models (SEPM) employ only two-dimensional landscapes.To investigate the effects of topographical elevation on dispersal patterns, a three-dimensional visual-based perceptual range algorithm was added to the dispersal rules of an individual-based SEPM. To explore the possible influences of a behavioural-based response to topography, an algorithm modelling valley-seeking behaviour was also developed. The performance of both algorithms was compared with that of a two-dimensional visual-based perceptual range algorithm. The overall consequences of dispersal under each algorithm were measured by recording population sizes in a target wood in the centre of a modelled, real landscape.The size of the population in the target wood, modelled using both of the three-dimensional algorithms, exhibited sensitivity to the direction of dispersal in interaction with perceptual range, which differed from that predicted by the two-dimensional approach. Population size was dependant on the spatial configuration of habitat patches and on the topography of the landscape, both of which could guide dispersers either towards or away from the target patch depending on the particular combinations of dispersal directions and perceptual ranges selected. Topography was found to have a greater effect on dispersal at shorter perceptual ranges, and thresholds in the results for all three algorithms suggested the existence of species and landscape dependant optimal perceptual ranges. It is recommended that both topography and topographical-based dispersal-altering algorithms, commensurate with the studied species’ behaviour, be incorporated into the movement rule-base of dispersal simulation models. The modelling of topography and its effects on movement in patchy landscapes are seen as essential ingredients in future landscape planning.     

Decoding unattended fearful faces with whole-brain correlations: an approach to identify condition-dependent large-scale functional connectivity

Processing of unattended threat-related stimuli, such as fearful faces, has been previously examined using group functional magnetic resonance (fMRI) approaches. However, the identification of features of brain activity containing sufficient information to decode, or "brain-read", unattended (implicit) fear perception remains an active research goal. Here we test the hypothesis that patterns of large-scale functional connectivity (FC) decode the emotional expression of implicitly perceived faces within single individuals using training data from separate subjects. fMRI and a blocked design were used to acquire BOLD signals during implicit (task-unrelated) presentation of fearful and neutral faces. A pattern classifier (linear kernel Support Vector Machine, or SVM) with linear filter feature selection used pair-wise FC as features to predict the emotional expression of implicitly presented faces. We plotted classification accuracy vs. number of top N selected features and observed that significantly higher than chance accuracies (between 90-100%) were achieved with 15-40 features. During fearful face presentation, the most informative and positively modulated FC was between angular gyrus and hippocampus, while the greatest overall contributing region was the thalamus, with positively modulated connections to bilateral middle temporal gyrus and insula. Other FCs that predicted fear included superior-occipital and parietal regions, cerebellum and prefrontal cortex. By comparison, patterns of spatial activity (as opposed to interactivity) were relatively uninformative in decoding implicit fear. These findings indicate that whole-brain patterns of interactivity are a sensitive and informative signature of unattended fearful emotion processing. At the same time, we demonstrate and propose a sensitive and exploratory approach for the identification of large-scale, condition-dependent FC. In contrast to model-based, group approaches, the current approach does not discount the multivariate, joint responses of multiple functional connections and is not hampered by signal loss and the need for multiple comparisons correction.     

Placing ocular mutants into a functional context: a chronobiological approach

The behavior of mammals is characterized by a 24-h cycle of rest and activity which is a fundamental adaption to the solar cycle of light and darkness. The pacemaker of this circadian clock is localized in the ventral part of the hypothalamus, the so-called suprachiasmatic nuclei (SCN), and is entrained by light signals mediated by the eye. The eye is directly connected via the retinohypothalamic tract (RHT) to the SCN. Light that reaches the retina elicits glutamate release at the synaptic terminals of the RHT and influences the neurons in the SCN in a manner that alters the behavioral state of the animal. A light pulse that reaches the retina at the beginning of the night elicits a delay of the clock phase, whereas a light pulse that reaches the retina at the end of the dark period leads to an advance of the clock phase. This advance or delay can be quantified by measuring the change in onset of wheel-running activity. Such measurements have, and continue to provide, a remarkably powerful assay of how light is detected and transduced to regulate circadian rhythms. The methods used for such measurements in mice are described in the following article.     

ZRANB2: structural and functional insights into a novel splicing protein

ZRANB2 was identified originally in a differential display experiment on 2-day and 10-day primary cultures of rat juxtaglomerular cells. During prolonged culture it was found to undergo down-regulation in concert with renin, the archetypical constituent of these cells. ZRANB2 has two zinc fingers that form a novel fold and show striking homology to Ran-binding protein domains. Human ZRANB2 mRNA is alternatively spliced to give two variants with different 3' ends. ZRANB2 has homologues across a range of species, the N-terminal end being particularly conserved. ZRANB2 is present in the nucleus of human cells. It binds to mRNA, as well as the essential splicing factors U170K and U2AF(35) and the novel splicing component SFRS17A (formerly known as XE7). ZRANB2 is one of 20 genes up-regulated in grade III ovarian serous papillary carcinoma. Here, we review current knowledge surrounding ZRANB2.     

Cirripede phylogeny using a novel approach: molecular morphometrics

We present a new method using nucleic acid secondary structure to assess phylogenetic relationships among species. In this method, which we term "molecular morphometrics," the measurable structural parameters of the molecules (geometrical features, bond energies, base composition, etc.) are used as specific characters to construct a phylogenetic tree. This method relies both on traditional morphological comparison and on molecular sequence comparison. Applied to the phylogenetic analysis of Cirripedia, molecular morphometrics supports the most recent morphological analyses arguing for the monophyly of Cirripedia sensu stricto (Thoracica + Rhizocephala + Acrothoracica). As a proof, a classical multiple alignment was also performed, either using or not using the structural information to realign the sequence segments considered in the molecular morphometrics analysis. These methods yielded the same tree topology as the direct use of structural characters as a phylogenetic signal. By taking into account the secondary structure of nucleic acids, the new method allows investigators to use the regions in which multiple alignments are barely reliable because of a large number of insertions and deletions. It thus appears to be complementary to classical primary sequence analysis in phylogenetic studies.     

Effects of piscivore-mediated habitat use on growth, diet and zooplankton consumption of roach: an individual-based modelling approach

SUMMARY 1. We used an individual based modelling approach for roach to (i) simulate observed diel habitat shifts between the pelagic and littoral zone of a mesotrophic lake; (ii) analyse the relevance of these habitat shifts for the diet, activity costs and growth of roach; and (iii) quantify the effects of a hypothetical piscivore-mediated (presence of pikeperch) confinement of roach to the littoral zone on roach diet, activity costs and growth.
2. The model suggests that in the presence of pikeperch, roach shifts from zooplankton as the primary diet to increased consumption of less nutritious food items such as macrophytes, filamentous algae and detritus.
3. The growth of roach between May and October was predicted to be significantly higher in the absence of pikeperch, although the net activity costs were about 60% higher compared with the scenario where pikeperch were present.
4. These modelling results provide quantitative information for interpreting diel horizontal migrations of roach as a result from a trade-off between food availability and predation risk in different habitats of a lake.
5. Altering the habitat selection mode of planktivorous roach by piscivore stocking has the potential to reduce zooplankton consumption by fish substantially, and could therefore be used as a biomanipulation technique complementing the reduction of zooplanktivorous fish.     

Comparing the plant virus spread patterns of non-persistently transmitted virus and persistently transmitted virus using an individual-based model

To compare the spread patterns between two types of plant viruses, non-persistent virus (NPV) and persistent virus (PV), we developed a spatially-explicit individual-based model. Our probability-based model is driven by the actions of insect vectors that are affected by interactions with host plants and plant viruses, considering both biological and behavioral components of their relationship. As a model system, we used potato virus y and potato leafroll virus, respectively for NPV and PV, potato for host plant, and Myzus persicae for the insect vector; empirical results from previous studies were acquired and adjusted to be used as our parameter values. Our simulation results showed that initial infection of PV in the field resulted in over 1.3 times greater number of insect vectors while causing approximately 7 times greater number of virus-infected plants compared to NPV by the end of simulation. Furthermore, spatial analysis showed that PV-infected plants showed greater aggregation in the field, forming larger patches compared to NPV-infected plants. Our results demonstrated the importance of host plant and insect vector manipulation by plant viruses as well as biological properties such as infectious period in the insect on the difference in overall spread pattern.