Integral projection models for species with complex demography

Matrix projection models occupy a central role in population and conservation biology. Matrix models divide a population into discrete classes, even if the structuring trait exhibits continuous variation ( e. g., body size). The integral projection model ( IPM) avoids discrete classes and potential artifacts from arbitrary class divisions, facilitates parsimonious modeling based on smooth relationships between individual state and demographic performance, and can be implemented with standard matrix software. Here, we extend the IPM to species with complex demographic attributes, including dormant and active life stages, cross- classification by several attributes ( e. g., size, age, and condition), and changes between discrete and continuous structure over the life cycle. We present a general model encompassing these cases, numerical methods, and theoretical results, including stable population growth and sensitivity/ elasticity analysis for density- independent models, local stability analysis in density- dependent models, and optimal/ evolutionarily stable strategy life- history analysis. Our presentation centers on an IPM for the thistle Onopordum illyricum based on a 6- year field study. Flowering and death probabilities are size and age dependent, and individuals also vary in a latent attribute affecting survival, but a predictively accurate IPM is completely parameterized by fitting a few regression equations. The online edition of the American Naturalist includes a zip archive of R scripts illustrating our suggested methods

Evolution of complex flowering strategies: an age- and size-structured integral projection model

We explore the evolution of delayed age- and size-dependent flowering in the monocarpic perennial Carlina vulgaris, by extending the recently developed integral projection approach to include demographic rates that depend on size and age. The parameterized model has excellent descriptive properties both in terms of the population size and in terms of the distributions of sizes within each age class. In Carlina the probability of flowering depends on both plant size and age. We use the parameterized model to predict this relationship, using the evolutionarily stable strategy (ESS) approach. Despite accurately predicting the mean size of flowering individuals, the model predicts a step-function relationship between the probability of flowering and plant size, which has no age component. When the variance of the flowering-threshold distribution is constrained to the observed value, the ESS flowering function contains an age component, but underpredicts the mean flowering size. An analytical approximation is used to explore the effect of variation in the flowering strategy on the ESS predictions. Elasticity analysis is used to partition the agespecific contributions to the finite rate of increase (u) of the survival-growth and fecundity components of the model. We calculate the adaptive landscape that defines the ESS and generate a fitness landscape for invading phenotypes in the presence of the observed flowering strategy. The implications of these results for the patterns of genetic diversity in the flowering strategy and for testing evolutionary models are discussed. Results proving the existence of a dominant eigenvalue and its associated eigenvectors in general size- and age-dependent integral projection models are presented

Understanding Terrorist Organizations with a Dynamic Model

Terrorist organizations change over time because of processes such as recruitment and training as well as counter-terrorism (CT) measures, but the effects of these processes are typically studied qualitatively and in separation from each other. Seeking a more quantitative and integrated understanding, we constructed a simple dynamic model where equations describe how these processes change an organization's membership. Analysis of the model yields a number of intuitive as well as novel findings. Most importantly it becomes possible to predict whether counter-terrorism measures would be sufficient to defeat the organization. Furthermore, we can prove in general that an organization would collapse if its strength and its pool of foot soldiers decline simultaneously. In contrast, a simultaneous decline in its strength and its pool of leaders is often insufficient and short-termed. These results and other like them demonstrate the great potential of dynamic models for informing terrorism scholarship and counter-terrorism policy making.Comment: To appear as Springer Lecture Notes in Computer Science v2: vectorized 4 figures, fixed two typos, more detailed bibliograph

Atomic-Scale Variations of the Mechanical Response of 2D Materials Detected by Noncontact Atomic Force Microscopy

We show that noncontact atomic force microscopy (AFM) is sensitive to the local stiffness in the atomicscale limit on weakly coupled 2D materials, as graphene on metals. Our large amplitude AFM topography and dissipation images under ultrahigh vacuum and low temperature resolve the atomic and moiré patterns in graphene on Pt (111), despite its extremely low geometric corrugation. The imaging mechanisms are identified with a multiscale model based on density-functional theory calculations, where the energy cost of global and local deformations of graphene competes with short-range chemical and long-range van der Waals interactions. Atomic contrast is related with short-range tip-sample interactions, while the dissipation can be understood in terms of global deformations in the weakly coupled graphene layer. Remarkably, the observed moiré modulation is linked with the subtle variations of the local interplanar graphene-substrate interaction, opening a new route to explore the local mechanical properties of 2D materials at the atomic scaleWe thank the Marie Curie ITN Network “ACRITAS” (Grant No. FP7-PEOPLE-2012-ITN-317348) funded by the European Commission under the FP7 Marie Curie PEOPLE programme and the Spanish MINECO (Projects No. CSD2010-00024, No. MAT2011-23627, No. MAT2013-41636-P, and No. MAT2014-54484-P) for financial support. Computer time was provided by the Spanish Supercomputer Network (RES) at Marenostrum III (BSC, Barcelona) and Magerit (CesViMa, Madrid) computers. P. P. was supported by the Ramón y Cajal progra

Nutzung von Resistenzmechanismen verschiedener Rebarten als Alternative zum Einsatz von Kupfer im Ökoweinbau

Extrakte aus Wildreben bzw. Hybriden mit hoher Resistenz: Es war zu prüfen, ob durch die Applikation von Blattextrakten von Nicht-Vitis-vinifera-Rebsorten auf Qualitätsrebsorten Plasmopara viticola und andere Pathogene bekämpft, unterdrückt oder pflanzeneigene Abwehrmechanismen bei Qualitätsrebsorten durch in den Extrakten enthaltene Elicitoren aktiviert werden können resp. ob mit den Pflanzenextrakten eine direkte Bekämpfung dieser Problemschaderreger möglich ist. Kupferreduktionspotential bei Anbau neuer Vitis vinifera PIWI - Sorten: Der Anbau von PIWI’s ermöglicht einen weitgehenden Verzicht auf Pflanzenschutz und ist ökologisch und ökonomisch die nachhaltigste Form des Weinbaus überhaupt. Das Kupfereinsparungspotential durch den Anbau von PIWI’s ist vermutlich abhängig von der Resistenz der Sorte und von den klimatischen Bedingungen am Standort. Das für die jeweilige Sorte notwendige Maß an Pflanzenschutz soll in diesem Projekt erstmals ermittelt werden. Daraus lässt sich ein durchschnittliches Einsparpotential an Kupfer bestimmen. Orientierungsversuche mit geringen Stockzahlen im Freiland an Zuchtstämmen mit bereits pyramidisierten Plasmopara Resistenzen wurden in einer 2009 erstellten Prüfanlage mit Überkronenberegnung durchgeführt, in der beliebig hohe Befallsbedingungen für die Rebenperonospora geschaffen werden können

Assessment of the Al–Fe–Ti system

The Al–Fe–Ti system has been assessed and the limiting binary systems are shortly reviewed. Based on a thorough review of the literature, isotherms at 800, 900, and 1000 °C have been re-evaluated and a provisional isotherm at 1200 °C is presented for the first time. The effect of alloying the binary phases with the third component is reviewed with regard to the ternary homogeneity ranges, crystallography, order/disorder transformations, and site occupancies. Of the variously reported ternary compounds only the existence of “Al2FeTi” (τ2) and “Al8FeTi3” (τ3) is confirmed. The occurrence of the phases τ2*, τ′2, and of a new stacking variant of TiAl is still under discussion, while the existence of the phases Fe2AlTi (τ1) and Fe25Al69Ti6 (X) is ruled out. The presented reaction scheme corroborates the isothermal sections and also a representation of the liquidus surface is given. Magnetic, electrical, thermochemical, atomistic and diffusion data for Al–Fe–Ti alloys are summarised and an overview about studies on modelling of phase equilibria and phase transformations is given

Why so variable: can genetic variance in flowering thresholds be maintained by fluctuating selection?

We use integral projection models (IPMs) and individual-based simulations to study the evolution of genetic variance in two monocarpic plant systems. Previous approaches combining IPMs with an adaptive dynamics–style invasion analysis predicted that genetic variability in the size threshold for flowering will not be maintained, which conflicts with empirical evidence. We ask whether this discrepancy can be resolved by making more realistic assumptions about the underlying genetic architecture, assuming a multilocus quantitative trait in an outcrossing diploid species. To do this, we embed the infinitesimal model of quantitative genetics into an IPM for a size-structured cosexual plant species. The resulting IPM describes the joint dynamics of individual size and breeding value of the evolving trait. We apply this general framework to the monocarpic perennials Oenothera glazioviana and Carlina vulgaris. The evolution of heritable variation in threshold size is explored in both individual-based models (IBMs) and IPMs, using a mutation rate modifier approach. In the Oenothera model, where the environment is constant, there is selection against producing genetically variable offspring. In the Carlina model, where the environment varies between years, genetically variable offspring provide a selective advantage, allowing the maintenance of genetic variability. The contrasting predictions of adaptive dynamics and quantitative genetics models for the same system suggest that fluctuating selection may be more effective at maintaining genetic variation than previously thought

Natural variation in immune responses to neonatal mycobacterium bovis bacillus calmette-guerin (BCG) vaccination in a cohort of Gambian infants

Background There is a need for new vaccines for tuberculosis (TB) that protect against adult pulmonary disease in regions where BCG is not effective. However, BCG could remain integral to TB control programmes because neonatal BCG protects against disseminated forms of childhood TB and many new vaccines rely on BCG to prime immunity or are recombinant strains of BCG. Interferon-gamma (IFN-) is required for immunity to mycobacteria and used as a marker of immunity when new vaccines are tested. Although BCG is widely given to neonates IFN- responses to BCG in this age group are poorly described. Characterisation of IFN- responses to BCG is required for interpretation of vaccine immunogenicity study data where BCG is part of the vaccination strategy. Methodology/Principal Findings 236 healthy Gambian babies were vaccinated with M. bovis BCG at birth. IFN-, interleukin (IL)-5 and IL-13 responses to purified protein derivative (PPD), killed Mycobacterium tuberculosis (KMTB), M. tuberculosis short term culture filtrate (STCF) and M. bovis BCG antigen 85 complex (Ag85) were measured in a whole blood assay two months after vaccination. Cytokine responses varied up to 10 log-fold within this population. The majority of infants (89-98% depending on the antigen) made IFN- responses and there was significant correlation between IFN- responses to the different mycobacterial antigens (Spearman’s coefficient ranged from 0.340 to 0.675, p=10-6-10-22). IL-13 and IL-5 responses were generally low and there were more non-responders (33-75%) for these cytokines. Nonetheless, significant correlations were observed for IL-13 and IL-5 responses to different mycobacterial antigens Conclusions/Significance Cytokine responses to mycobacterial antigens in BCG-vaccinated infants are heterogeneous and there is significant inter-individual variation. Further studies in large populations of infants are required to identify the factors that determine variation in IFN- responses

Integrating evolution into ecological modelling: accommodating phenotypic changes in agent based models.

PMCID: PMC3733718This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Evolutionary change is a characteristic of living organisms and forms one of the ways in which species adapt to changed conditions. However, most ecological models do not incorporate this ubiquitous phenomenon. We have developed a model that takes a 'phenotypic gambit' approach and focuses on changes in the frequency of phenotypes (which differ in timing of breeding and fecundity) within a population, using, as an example, seasonal breeding. Fitness per phenotype calculated as the individual's contribution to population growth on an annual basis coincide with the population dynamics per phenotype. Simplified model variants were explored to examine whether the complexity included in the model is justified. Outputs from the spatially implicit model underestimated the number of individuals across all phenotypes. When no phenotype transitions are included (i.e. offspring always inherit their parent's phenotype) numbers of all individuals are always underestimated. We conclude that by using a phenotypic gambit approach evolutionary dynamics can be incorporated into individual based models, and that all that is required is an understanding of the probability of offspring inheriting the parental phenotype

Homophily and Contagion Are Generically Confounded in Observational Social Network Studies

We consider processes on social networks that can potentially involve three factors: homophily, or the formation of social ties due to matching individual traits; social contagion, also known as social influence; and the causal effect of an individual's covariates on their behavior or other measurable responses. We show that, generically, all of these are confounded with each other. Distinguishing them from one another requires strong assumptions on the parametrization of the social process or on the adequacy of the covariates used (or both). In particular we demonstrate, with simple examples, that asymmetries in regression coefficients cannot identify causal effects, and that very simple models of imitation (a form of social contagion) can produce substantial correlations between an individual's enduring traits and their choices, even when there is no intrinsic affinity between them. We also suggest some possible constructive responses to these results.Comment: 27 pages, 9 figures. V2: Revised in response to referees. V3: Ditt