Assumption validity in human optimal foraging: The Barí hunters of Venezuela as a test case

Optimal foraging theory is being used increasingly as a means of understanding human foraging behavior. One of the central assumptions of optimal foraging theory is that prey items or patches are encountered sequentially and as a Poisson process. Using empirical data gathered on the Barí hunters of Venezuela, we assess the validity of this central assumption. We compare our observed distribution of encounter frequencies with an expected Poisson distribution, utilizing chisquare tests and graphic representations. The results are strikingly consonant with the expected Poisson distribution and lend support to the applicability of optimal foraging models to human hunting behavior.     

An overview of the multispecies VPA — theory and applications

Summary Multispecies virtual population analysis is an attempt to take species interactions into account when assessing the status of fish stocks. It was introduced primarily with the aim of lowering the uncertainty in the natural mortality rate as used in single species VPA and to take account of variability between years and ages by calculating inside the model the part of the mortality rate caused by predation. The output of the MSVPA is therefore —in addition to stock sizes and fishing mortality rates as in single species VPA —the amounts consumed of the various species by the predators included in the analysis.The MSVPA model of the predation interactions results in a set of coupled non-linear equations which must be solved for each time step in the analysis. Key parameters in the model are the so-called suitability coefficients, measuring the relative suitability of one species as prey for another species. These parameters must be estimated inside the model and this estimation requires data on the stomach contents of the predators in the model. The MSVPA makes two key assumptions: constant ration size (i.e. independent of time for each species-age combination) and hence fixed weights-at-age and a model of prey selection which leads to a type ii functional feeding response. These assumptions do not hold for all areas and therefore limit the applicability of the MSVPA in its present form.The MSVPA is probably one of the more successful multispecies models in fisheries. Its main application to date has been to the North Sea, and although it has not been used directly as a management tool it has provided input values of parameters used in assessment models as well as valuable insights into the system. For example, it has demonstrated that an increase in mesh size can result in lower long-term yields, an effect opposite to what is predicted if species interactions are ignored. Such insights into the dynamics of the system are useful and MSVPA may therefore have an indirect role to play in management. Nevertheless, due to many uncertainties involved in multispecies modelling in general and MSVPA in particular, it seems doubtful that the use of MSVPA in fisheries management will be much greater in the immediate future than it is at present.     

An optimal degree of physical and chemical heterogeneity for the origin of life?

The accumulation of pure, concentrated chemical building blocks, from which the essential components of protocells could be assembled, has long been viewed as a necessary, but extremely difficult step on the pathway to the origin of life. However, recent experiments have shown that moderately increasing the complexity of a set of chemical inputs can in some cases lead to a dramatic simplification of the resulting reaction products. Similarly, model protocell membranes composed of certain mixtures of amphiphilic molecules have superior physical properties than membranes composed of single amphiphiles. Moreover, membrane self-assembly under simple and natural conditions gives rise to heterogeneous mixtures of large multi-lamellar vesicles, which are predisposed to a robust pathway of growth and division that simpler and more homogeneous small unilamellar vesicles cannot undergo. Might a similar relaxation of the constraints on building block purity and homogeneity actually facilitate the difficult process of nucleic acid replication? Several arguments suggest that mixtures of monomers and short oligonucleotides may enable the chemical copying of polynucleotides of sufficient length and sequence complexity to allow for the emergence of the first nucleic acid catalysts. The question of the origin of life may become less daunting once the constraints of overly well-defined laboratory experiments are appropriately relaxed.     

The derivation of D’Arcy Thompson’s theory of transformations from the theory of optimal design

It is shown informally that Cohn’s theory of Optimal Forms can be construed as a comparative theory, and that when this is done the celebrated theory of transformations of D’Arcy Thompson follows as a consequence. The implications of this type of theoretical foundation for the Thompson theory with regard to problems of comparative morphology are discussed, and some suggestions for the further implementation of the theory are described. This research was supported by the United States Air Force through the Air Force Office of Scientific Research of the Air Research and Development Command, under Contract No. AF 49(638)-917.     

The game of “gossip” analyzed by the theory of information

This paper deals with an analysis of a distributed model of the game of “gossip”, in which a message is passed through a line of individuals, and the final (in general, garbled) result is compared with the original ungarbled message. The deterioration of information (defined in the sense of Shannon and Wiener) along the line is calculated, and exact as well as asymptotic formulas suggesting approximate linear electric network analogues are obtained.     

Expansion and contraction of the cytotoxic T lymphocyte response—An optimal control approach

The kinetics of the cytotoxic T lymphocyte (CTL) response against intracellular pathogens has been found to have many stereotypical features that appear to be programmed early in the infection. We explain these findings here in terms of CTL response kinetics that minimize the probability that a pathological symptom will occur in association with the infection and its eradication. We assume that both the infection and the CTLs contribute to this pathology. We find that contraction kinetics is influenced by the relative pathogenicities of infection and CTLs, as well as on the virulence of the infection and the efficiency of the CTLs, but not by the magnitude of expansion or the dose and duration of infection. Our analysis explains the finding that the duration of the CTL expansion is highly stereotypical, with the maximum expansion of the CTL response dependent on the dose of the infection. Finally, we show that the stereotypical nature of CTL kinetics relies upon stringent regulation of the rates at which CTLs proliferate and die.     

A regional analysis of Barí land use intensification and its impact on landscape heterogeneity

Since pacification 30 years ago, the Barí of northwest Venezuela have aggregated in villages and have begun to produce cattle and some crops for sale in regional markets. This research analyzes satellite imagery to compare patterns of land use among Barí settlements that differ in their population size, cattle holdings, and distance to nearest marketplace. These comparisons indicate that settlement history mediates the effect of population pressure and herd sizes on land use. Moreover, intensification of land use is associated with greater deforestation and a more heterogeneous landscape, but less biodiversity in woody species.     

20 years since the introduction of DNA barcoding: from theory to application

Traditionally, taxonomic identification has relied upon morphological characters. In the last two decades, molecular tools based on DNA sequences of short standardised gene fragments, termed DNA barcodes, have been developed for species discrimination. The most common DNA barcode used in animals is a fragment of the cytochrome c oxidase (COI) mitochondrial gene, while for plants, two chloroplast gene fragments from the RuBisCo large subunit (rbcL) and maturase K (matK) genes are widely used. Information gathered from DNA barcodes can be used beyond taxonomic studies and will have far-reaching implications across many fields of biology, including ecology (rapid biodiversity assessment and food chain analysis), conservation biology (monitoring of protected species), biosecurity (early identification of invasive pest species), medicine (identification of medically important pathogens and their vectors) and pharmacology (identification of active compounds). However, it is important that the limitations of DNA barcoding are understood and techniques continually adapted and improved as this young science matures.     

Plant–insect chemical communication in ecological communities: An information theory perspective

Cross-species communication, where signals are sent by one species and perceived by others, is one of the most intriguing types of communication that functionally links different species to form complex ecological networks. Global change and human activity can affect communication by increasing fluctuations in species composition and phenology, altering signal profiles and intensity, and introducing noise. So far, most studies on cross-species communication have focused on a few specific species isolated from ecological communities. Scaling up investigations of cross-species communication to the community level is currently hampered by a lack of conceptual and practical methodologies. Here, we propose an interdisciplinary framework based on information theory to investigate mechanisms shaping cross-species communication at the community level. We use plants and insects, the cornerstones of most ecosystems, as a showcase and focus on chemical communication as the key communication channel. We first introduce some basic concepts of information theory, then we illustrate information patterns in plant–insect chemical communication, followed by a further exploration of how to integrate information theory into ecological and evolutionary processes to form testable mechanistic hypotheses. We conclude by highlighting the importance of community-level information as a means to better understand the maintenance and workings of ecological systems, especially during rapid global change.     

Should "handled" prey be considered? Some consequences for functional response, predator-prey dynamics and optimal foraging theory

Predator-prey models consider those prey that are free. They assume that once a prey is captured by a predator it leaves the system. A question arises whether in predator-prey population models the variable describing prey population shall consider only those prey which are free, or both free and handled prey together. In the latter case prey leave the system after they have been handled. The classical Holling type II functional response was derived with respect to free prey. In this article we derive a functional response with respect to prey density which considers also handled prey. This functional response depends on predator density, i.e., it accounts naturally for interference. We study consequences of this functional response for stability of a simple predator-prey model and for optimal foraging theory. We show that, qualitatively, the population dynamics are similar regardless of whether we consider only free or free and handled prey. However, the latter case may change predictions in some other cases. We document this for optimal foraging theory where the functional response which considers both free and handled prey leads to partial preferences which are not observed when only free prey are considered.     

Foraging decisions among Aché hunter-gatherers: New data and implications for optimal foraging models

This article summarizes 5 years of research on resource choice and foraging strategy among Ache foragers in eastern Paraguay. Successes and failures of simple models from optimal foraging theory (OFT) are discussed and revisions are suggested in order to bring the models in line with empirical evidence from the Ache. The following conclusions emerge: (1) Energetic returns from various alternative resources and foraging strategies is probably the best single predictor of foraging patterns. (2) Nutrient constraints should be added only when they significantly improve the predictive power of the model. Importance of meat versus vegetable resources may be one important modification based on nutrients that enhances the ability of OFT models to account for empirical reality in human foragers. (3) Men's and women's abilities and foraging patterns differ enough that they should be treated separately in all OFT analyses. (4) Opportunity costs associated with resources that are processed when foraging is not possible may be sufficiently low to predict that high processing time resources will be included in the optimal diet even when their associated return rates (including processing) are lower than mean foraging returns. (5) When food sharing is extensive and foraging bands include several adult males and females, foragers may not need to modify foraging strategies in other ways in order to reduce the risk of not eating on some days.     

Acanthamoeba and mimivirus interactions: the role of amoebal encystment and the expansion of the ‘Cheshire Cat’ theory

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How past and present influence the foraging of clonal plants?

Clonal plants spreading horizontally and forming a network structure of ramets exhibit complex growth patterns to maximize resource uptake from the environment. They respond to spatial heterogeneity by changing their internode length or branching frequency. Ramets definitively root in the soil but stay interconnected for a varying period of time thus allowing an exchange of spatial and temporal information. We quantified the foraging response of clonal plants depending on the local soil quality sampled by the rooting ramet (i.e. the present information) and the resource variability sampled by the older ramets (i.e. the past information). We demonstrated that two related species, Potentilla reptans and P. anserina, responded similarly to the local quality of their environment by decreasing their internode length in response to nutrient-rich soil. Only P. reptans responded to resource variability by decreasing its internode length. In both species, the experience acquired by older ramets influenced the plastic response of new rooted ramets: the internode length between ramets depended not only on the soil quality locally sampled but also on the soil quality previously sampled by older ramets. We quantified the effect of the information perceived at different time and space on the foraging behavior of clonal plants by showing a non-linear response of the ramet rooting in the soil of a given quality. These data suggest that the decision to grow a stolon or to root a ramet at a given distance from the older ramet results from the integration of the past and present information about the richness and the variability of the environment.     

Linear response theory: An alternative to PB and GB methods for the analysis of molecular dynamics trajectories?

We explore the use of classical Linear Response Theory (LRT) as an alternative strategy to the use of Molecular Mechanics/Poisson-Boltzmann strategies to compute the solvation free energy of macromolecules from molecular dynamics simulations using an explicit representation of solvent. The method reproduces well the free energy of solvation of standard amino acid side chains, small peptides, and proteins. The use of a fully discrete representation of solvent avoids the possible problems of continuum models to represent the solvation of systems containing tightly bound water molecules.     

Interaction of proteins of the adenylate cyclase complex: Area-limited mobility or movement along the whole membrane? Analysis with the application of the percolation theory

Extraction of the fluid lipid fraction from rat reticulocyte plasma membranes by phospholipase/BSA treatment leads to a reduction in the percentage of -adrenoreceptors complexed with the regulatory N-proteins and to a decrease of adenylate cyclase stimulation with a -agonist. Analysis of the data obtained on the basis of the percolation theory suggests that proteins of the adenylate cyclase complex move along the whole membrane.     

Are bird song complexity and song sharing shaped by habitat structure? An information theory and statistical approach

In songbirds, song complexity and song sharing are features of prime importance for territorial defence and mate attraction. These aspects of song may be strongly influenced by changes in social environment caused by habitat fragmentation. We tested the hypothesis that habitat fragmentation induced by human activities influences song complexity and song sharing in the skylark, a songbird with a very large repertoire and whose population recently underwent a large decline. We applied powerful mathematical and statistical tools to assess and compare song complexity and song sharing patterns of syllables and sequences of syllables in two populations: a declining population in a fragmented habitat, in which breeding areas are separated from each other by unsuitable surroundings, and a stable population in a continuous habitat. Our results show that the structure of the habitat influences song sharing, but not song complexity. Neighbouring birds shared more syllables and sequences of syllables in the fragmented habitat than in the continuous one. Habitat fragmentation seems thus to have an effect on the composition of elements in songs, but not on the number and complexity of these elements, which may be a fixed feature of song peculiar to skylarks.     

Equine endometrial biopsy: enhancement of clinical value by more extensive histopathology and application of new diagnostic techniques?

During the 1960s and 1970s, the clinical value of equine endometrial histopathology was firmly established after it was shown that fertility outcome was correlated with the presence and severity of specific microscopic lesions. The objective of this paper is to summarize reports from the veterinary literature published after the mid 1980s that describe new diagnostic methods of assessing equine uterine health using material collected by endometrial biopsy.     

Time spent exercising and obesity: An application of Lewbel’s instrumental variables method

This paper examines the role physical activity plays in determining body mass using data from the American Time Use Survey. Our work is the first to address the measurement error that arises when time use during a single day—rather than average daily time use over an extended period—is used as an explanatory variable. We show that failing to account for day-to-day variation in activities results in the effects of time use on a typical day being understated. Furthermore, we account for the possibility that physical activity and body mass are jointly determined by implementing Lewbel’s instrumental variables estimator that exploits first-stage heteroskedasticity rather than traditional exclusion restrictions. While averaging 30 min of transportation-related biking or walking per day lowers the BMI of men by 1.5, we find no effect of physically active leisure on the BMI of men in our sample. In contrast, 30 min of per day of either type of physical activity lowers the BMI of women by 1.