Animal navigation: general properties of directed walks

The ability to locomote is a defining characteristic of all animals. Yet, all but the most trivial forms of navigation are poorly understood. Here we report and discuss the analytical results of an in-depth study of a simple navigation problem. In principle, there are two strategies for navigating a straight course. One is to use an external directional reference and to continually reorient with reference to it. The other is to monitor body rotations from internal sensory information only. We showed previously that, at least for simple representations of locomotion, the first strategy will enable an animal or mobile agent to move arbitrarily far away from its starting point, but the second strategy will not do so, even after an infinite number of steps. This paper extends and generalizes the earlier results by demonstrating that these findings are true even when a very general model of locomotion is used. In this general model, error components within individual steps are not independent, and directional errors may be biased. In the absence of a compass, the expected path of a directed walk in general approximates a logarithmic spiral. Some examples are given to illustrate potential applications of the quantitative results derived here. Motivated by the analytical results developed in this work, a nomenclature for directed walks is proposed and discussed. Issues related to path integration in mammals and robots, and measuring the curvature of a noisy path are also addressed using directed walk theory.     

Using pseudo amino acid composition to predict transmembrane regions in protein: cellular automata and Lempel-Ziv complexity

Summary. Transmembrane (TM) proteins represent about 20–30% of the protein sequences in higher eukaryotes, playing important roles across a range of cellular functions. Moreover, knowledge about topology of these proteins often provides crucial hints toward their function. Due to the difficulties in experimental structure determinations of TM protein, theoretical prediction methods are highly preferred in identifying the topology of newly found ones according to their primary sequences, useful in both basic research and drug discovery. In this paper, based on the concept of pseudo amino acid composition (PseAA) that can incorporate sequence-order information of a protein sequence so as to remarkably enhance the power of discrete models (Chou, K. C., Proteins: Structure, Function, and Genetics, 2001, 43: 246–255), cellular automata and Lempel-Ziv complexity are introduced to predict the TM regions of integral membrane proteins including both α-helical and β-barrel membrane proteins, validated by jackknife test. The result thus obtained is quite promising, which indicates that the current approach might be a quite potential high throughput tool in the post-genomic era. The source code and dataset are available for academic users at liml@scu.edu.cn. Authors’ address: Menglong Li, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P.R. China     

Evolutionary potential of morphological traits across different life‐history stages

Despite accumulating examples of selection acting on heritable traits in the wild, predicted evolutionary responses are often different from observed phenotypic trends. Various explanations have been suggested for these mismatches. These include within‐individual changes across lifespan that can create important variation in genetic architecture of traits and selection acting on them, but also potential problems with the methodological approach used to predict evolutionary responses of traits. Here, we used an 8‐year data set on tree swallow (Tachycineta bicolor) to first assess the effects of differences among three nestling life‐history stages on the genetic (co)variances of two morphological traits (body mass and primary feather length) and the selection acting on them over three generations. We then estimated the evolutionary potential of these traits by predicting their evolutionary responses using the breeder's equation and the secondary theorem of selection approaches. Our results showed variation in strength and direction of selection and slight changes in trait variance across ages. Predicted evolutionary responses differed importantly between both approaches for half of the trait–age combinations we studied, suggesting the presence of environmentally induced correlations between focal traits and fitness possibly biasing breeder's equation predictions. Our results emphasize that predictions of evolutionary potential for morphological traits are likely to be highly variable, both in strength and direction, depending on the life stage and method used, thus mitigating our capacity to predict adaptation and persistence of wild populations.     

Patch Time Allocation by the Parasitoid Diadegma semiclausum (Hymenoptera: Ichneumonidae). I. Effect of Interpatch Distance

We observed the foraging behavior of Diadegma semiclausum (Hymenoptera:Ichneumonidae), a larval parasitoid of the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae), in a wind tunnel to determine how interpatch distance affects patch time allocation. Individual female wasps were released onto an experimental patch infested with host larvae and were allowed freely to leave for an identically extrapatch placed upwind of the experimental patch with varying interpatch distances. The effects of interpatch distance and within-patch foraging experience on the patch-leaving tendency of the parasitoid were analyzed bymeans of the proportional hazards model. Increasing interpatch distance andunsuccessful host encounter as a result of host defense decreased the patch-leaving tendency, while successful oviposition and unsuccessful search time since last oviposition increased the patch-leaving tendency. Asa result, both patch residence time and number of ovipositions by D. semiclausum increased with increasing interpatch distance, which appears to agree with the general predictions of the marginal value theorem that a parasitoid should stay longer and parasitize more hosts with increasing interpatch distance.     

Joint phenotypes,evolutionary conflict and the fundamental theorem of natural selection

Multiple organisms can sometimes affect a common phenotype. For example, the portion of a leaf eaten by an insect is a joint phenotype of the plant and insect and the amount of food obtained by an offspring can be a joint trait with its mother. Here, I describe the evolution of joint phenotypes in quantitative genetic terms. A joint phenotype for multiple species evolves as the sum of additive genetic variances in each species, weighted by the selection on each species. Selective conflict between the interactants occurs when selection takes opposite signs on the joint phenotype. The mean fitness of a population changes not just through its own genetic variance but also through the genetic variance for its fitness that resides in other species, an update of Fisher''s fundamental theorem of natural selection. Some similar results, using inclusive fitness, apply to within-species interactions. The models provide a framework for understanding evolutionary conflicts at all levels.     

Failure of simple optimal foraging models to predict residence time when patch quality is uncertain

Blue jays (Cyanocitta cristata) were presented with a foragingsituation in which half of the patches they encountered containedno prey and half contained a single prey item. Experimentallydetermined probability distributions controlled prey arrivaltimes in those patches that contained prey. Patch residencein empty patches was studied during four experiments. In thefirst, prey arrival was exponentially distributed. Residencetimes increased with travel time as predicted by a rate-maximizationmodel, but the bird stayed in empty patches much longer thanpredicted. During the second experiment, prey arrival was uniformlydistributed. The jays again stayed longer than optimal, andpatch residence times increased as travel time increased, althoughthe residence time that maximized rate of intake was independentof travel time under these conditions. In the third experiment,exponential and uniform patches were randomly intermixed. Thejays showed larger travel-time effects in the exponential thanin the uniform patch. However, the travel-time effect in theuniform patch was contrary to rate-maximization predictions,and the birds again overstayed in both patch types. In the fourthexperiment, prefeeding at the start of each foraging bout slightlyincreased overstaying rather than decreasing overstaying, aswould be expected if overstaying were due to underestimatingenvironmental quality. Consistent and dramatic overstaying anda travel-time effect under conditions where travel time hasno effect on optimal residence times suggest that the rate-maximizationapproach does not apply to foraging problems involving patchuncertainty.     

Optimal patch use and metapopulation dynamics

Summary We compared the metapopulation dynamics of predator—prey systems with (1) adaptive global dispersal, (2) adaptive local dispersal, (3) fixed global dispersal and (4) fixed local dispersal by predators. Adaptive dispersal was modelled using the marginal value theorem, such that predators departed patches when the instantaneous rate of prey capture was less than the long-term rate of prey capture averaged over all patches, scaled to the movement time between patches. Adaptive dispersal tended to stabilize metapopulation dynamics in a similar manner to conventional fixed dispersal models, but the temporal dynamics of adaptive dispersal models were more unpredictable than the smooth oscillations of fixed dispersal models. Moreover, fixed and adaptive dispersal models responded differently to spatial variation in patch productivity and the degree of compartmentalization of the system. For both adaptive dispersal and fixed dispersal models, localized (stepping-stone) dispersal was more strongly stabilizing than global (island) dispersal. Variation among predators in the probability of dispersal in relation to local prey density had a strong stabilizing influence on both within-patch and metapopulation dynamics. These results suggest that adaptive space use strategies by predators could have important implications for the dynamics of spatially heterogeneous trophic systems.     

A threshold theorem for the general epidemic in discrete time

Summary A theorem, analogous to the continuous time Threshold Theorem of Kermack and McKendrick, is proved for a certain discrete time epidemic model. This model, in contrast to its continuous time analogue, leads to some solutions in which the total population of susceptibles may become infected in a finite time.     

An evolutionary Monte Carlo algorithm for predicting DNA hybridization

Many DNA-based technologies, such as DNA computing, DNA nanoassembly and DNA biochips, rely on DNA hybridization reactions. Previous hybridization models have focused on macroscopic reactions between two DNA strands at the sequence level. Here, we propose a novel population-based Monte Carlo algorithm that simulates a microscopic model of reacting DNA molecules. The algorithm uses two essential thermodynamic quantities of DNA molecules: the binding energy of bound DNA strands and the entropy of unbound strands. Using this evolutionary Monte Carlo method, we obtain a minimum free energy configuration in the equilibrium state. We applied this method to a logical reasoning problem and compared the simulation results with the experimental results of the wet-lab DNA experiments performed subsequently. Our simulation predicted the experimental results quantitatively.