Detecting climate signals in populations across life histories.

Climate impacts are not always easily discerned in wild populations as detecting climate change signals in populations is challenged by stochastic noise associated with natural climate variability, variability in biotic and abiotic processes, and observation error in demographic rates. Detection of the impact of climate change on populations requires making a formal distinction between signals in the population associated with long-term climate trends from those generated by stochastic noise. The time of emergence (ToE) identifies when the signal of anthropogenic climate change can be quantitatively distinguished from natural climate variability. This concept has been applied extensively in the climate sciences, but has not been explored in the context of population dynamics. Here, we outline an approach to detecting climate-driven signals in populations based on an assessment of when climate change drives population dynamics beyond the envelope characteristic of stochastic variations in an unperturbed state. Specifically, we present a theoretical assessment of the time of emergence of climate-driven signals in population dynamics ( ToE pop ). We identify the dependence of ToE pop on the magnitude of both trends and variability in climate and also explore the effect of intrinsic demographic controls on ToE pop . We demonstrate that different life histories (fast species vs. slow species), demographic processes (survival, reproduction), and the relationships between climate and demographic rates yield population dynamics that filter climate trends and variability differently. We illustrate empirically how to detect the point in time when anthropogenic signals in populations emerge from stochastic noise for a species threatened by climate change: the emperor penguin. Finally, we propose six testable hypotheses and a road map for future research.

The kinship matrix: inferring the kinship structure of a population from its demography.

The familial structure of a population and the relatedness of its individuals are determined by its demography. There is, however, no general method to infer kinship directly from the life cycle of a structured population. Yet, this question is central to fields such as ecology, evolution and conservation, especially in contexts where there is a strong interdependence between familial structure and population dynamics. Here, we give a general formula to compute, from any matrix population model, the expected number of arbitrary kin (sisters, nieces, cousins, etc) of a focal individual ego, structured by the class of ego and of its kin. Central to our approach are classic but little-used tools known as genealogical matrices. Our method can be used to obtain both individual-based and population-wide metrics of kinship, as we illustrate. It also makes it possible to analyse the sensitivity of the kinship structure to the traits implemented in the model.

An Evolutionary and Ecological Community Model for Distribution of Phenotypes and Abundances among Competing Species.

AbstractHere, we propose a theory for the structure of communities of competing species. We include ecologically realistic assumptions, such as density dependence and stochastic fluctuations in the environment, and analyze how evolution caused by r- and K-selection will affect the packing of species in the phenotypic space as well as the species abundance distribution. Species-specific traits have the same matrix G of additive genetic variances and covariances, and evolution of mean traits is affected by fluctuations in population size of all species. In general, the model produces a shape of the distributions of log abundances that is skewed to the left, which is typical of most natural communities. Mean phenotypes of the species in the community are distributed approximately uniformly on the surface of a multidimensional sphere. However, environmental stochasticity generates selection that deviates species slightly from this surface; nonetheless, phenotypic distribution will be different from a random packing of species. This model of community evolution provides a theoretical framework that predicts a relationship between the structure of the phenotypic space and the form of species abundance distributions that can be compared against time series of variation in community structure.

Forest management affects seasonal source-sink dynamics in a territorial, group-living bird.

The persistence of wildlife populations is under threat as a consequence of human activities, which are degrading natural ecosystems. Commercial forestry is the greatest threat to biodiversity in boreal forests. Forestry practices have degraded most available habitat, threatening the persistence of natural populations. Understanding population responses is, therefore, critical for their conservation. Population viability analyses are effective tools to predict population persistence under forestry management. However, quantifying the mechanisms driving population responses is complex as population dynamics vary temporally and spatially. Metapopulation dynamics are governed by local dynamics and spatial factors, potentially mediating the impacts of forestry e.g., through dispersal. Here, we performed a seasonal, spatially explicit population viability analysis, using long-term data from a group-living territorial bird (Siberian jay, Perisoreus infaustus). We quantified the effects of forest management on metapopulation dynamics, via forest type-specific demography and spatially explicit dispersal, and how forestry impacted the stability of metapopulation dynamics. Forestry reduced metapopulation growth and stability, through negative effects on reproduction and survival. Territories in higher quality natural forest contributed more to metapopulation dynamics than managed forests, largely through demographic processes rather than dispersal. Metapopulation dynamics in managed forest were also less resilient to disturbances and consequently, may be more vulnerable to environmental change. Seasonal differences in source-sink dynamics observed in managed forest, but not natural forests, were caused by associated seasonal differences in dispersal. As shown here, capturing seasonal source-sink dynamics allows us to predict population persistence under human disturbance and to provide targeted conservation recommendations.

Density-dependent population dynamics of a high Arctic capital breeder, the barnacle goose.

Density regulation of the population growth rate occurs through negative feedbacks on underlying vital rates, in response to increasing population size. Here, we examine in a capital breeder how vital rates of different life-history stages, their elasticities and population growth rates are affected by changes in population size. We developed an integrated population model for a local population of Svalbard barnacle geese, Branta leucopsis, using counts, reproductive data and individual-based mark-recapture data (1990-2017) to model age class-specific survival, reproduction and number of individuals. Based on these estimates, we quantified the changes in demographic structure and the effect of population size on age class-specific vital rates and elasticities, as well as the population growth rate. Local density regulation at the breeding grounds acted to reduce population growth through negative effects on reproduction; however, population size could not explain substantial variation in survival rates, although there was some support for density-dependent first-year survival. With the use of prospective perturbation analysis of the density-dependent projection matrix, we show that the elasticities to different vital rates changed as population size increased. As population size approached carrying capacity, the influence of reproductive rates and early-life survival on the population growth rate was reduced, whereas the influence of adult survival increased. A retrospective perturbation analysis revealed that density dependence resulted in a positive contribution of reproductive rates, and a negative contribution of the numbers of individuals in the adult age class, to the realised population growth rate. The patterns of density dependence in this population of barnacle geese were different from those recorded in income breeding birds, where density regulation mainly occurs through an effect on early-life survival. This indicates that the population dynamics of capital breeders, such as the barnacle goose, are likely to be more reproduction-driven than is the case for income breeders.

Sexual Identity Disorder and Psychosis in Klinefelter Syndrome: A Synthesis of Literature and a Case Report.

Klinefelter syndrome (KS) 47, XXY is the most frequent chromosomal abnormality causing hypogonadism in humans. This chromosomal abnormality of number in its classical form called homogeneous (supernumerary X) is generally the result of a meiosis accident. Several studies have suggested that individuals with KS are at greater risk of developing various psychiatric disorders, including depression and schizophrenia. The diagnosis is made based on subnormal testosterone with high pituitary gonadotropins and confirmed by determining the karyotype on a blood simple. We did a literature review using an electronic search in three databases: Pubmed/MEDLINE, Google Scholar, and PsychInfo. We found that since 1989, seven case reports with KS and mental disorders with similar and different characteristics of our case illustration of a patient with KS and psychosis were published.

Trait level analysis of multitrait population projection matrices.

In most matrix population projection models, individuals are characterized according to, usually, one or two traits such as age, stage, size or location. A broad theory of multitrait population projection matrices (MPPMs) incorporating larger number of traits was long held back by time and space computational complexity issues. As a consequence, no study has yet focused on the influence of the structure of traits describing a life-cycle on population dynamics and life-history evolution. We present here a novel vector-based MPPM building methodology that allows to computationally-efficiently model populations characterized by numerous traits with large distributions, and extend sensitivity analyses for these models. We then present a new method, the trait level analysis consisting in folding an MPPM on any of its traits to create a matrix with alternative trait structure (the number of traits and their characteristics) but similar asymptotic properties. Adding or removing one or several traits to/from the MPPM and analyzing the resulting changes in spectral properties, allows investigating the influence of the trait structure on the evolution of traits. We illustrate this by modeling a 3-trait (age, parity and fecundity) population designed to investigate the implications of parity-fertilitytrade-offs in a context of fecundity heterogeneity in humans. The trait level analysis, comparing models of the same population differing in trait structures, demonstrates that fertility selection gradients differ between cases with or without parity-fertility trade-offs. Moreover it shows that age-specific fertility has seemingly very different evolutionary significance depending on whether heterogeneity is accounted for. This is because trade-offs can vary strongly in strength and even direction depending on the trait structure used to model the population.

Diffusion enhancement and autoparametric resonance.

The possibility of an autoparametric resonance in an isolated many-particle system induces a specific behavior of the particles in the presence of thermal noise. In particular, the variance associated with a resonant mode, and consequently that of the associated particles, is strongly increased compared to what it would have in the absence of parametric resonance. In this paper we consider a dimer submitted to a periodic potential for which there are only two modes, the center of mass motion and the internal vibration mode. This is the simplest system which is dynamically rich enough to exhibit an autoparametric excitation of the internal vibrations by the center of mass motion. The consequences of this autoparametric excitation on the particles diffusion will be discussed according to the stiffness of the interaction and to the initial energy of the dimer, the relevant parameters which characterize this dynamics.

Parametric resonance in a conservative system of coupled nonlinear oscillators.

We study a dimer in a periodic potential well, which is a conservative but nonintegrable system. This seemingly simple system exhibits a surprisingly rich dynamics. Using a systematic asymptotic analysis, we demonstrate that the translation mode of the dimer (center of mass motion) may induce a parametric resonance of the oscillatory mode. No external forcing occurs, thus this system belongs to the class of autoparametric systems. When the dimer energy is such that both particles are trapped in neighboring potential wells, we derive the relevant amplitude equations for the eigenmodes (center of mass motion and relative motion) and show that they are integrable. In the opposite limit, when the dimer slides along the external potential so that the center of mass motion is basically a translation, we also exhibit autoparametric amplification of the relative motion. In both cases our calculations provide reliable estimates of the relevant parameters for the autoparametric resonance to appear. Moreover, the comparison between the numerical integration of the actual system and the asymptotic analysis evidences an excellent quantitative agreement.

Motions of a dimer on a periodic potential.

A dimer on a periodic potential is a simple system that exhibits a surprisingly rich dynamics. This system is conservative, but it is nonlinear and nonintegrable. In a previous work, we evidenced the autoparametric excitation of the relative motion by the center of mass in two limiting cases (very small or very large initial energy, compared to the external potential depth). We extend these results for arbitrary initial energy. The relevant control parameters are the dimer initial energy and the stiffness of the link between the two particles. In this parameter plane, we build a behavior map which classifies the available dynamical regimes of the dimer. The parameters plane can be separated into domains in which the dimer particles are either trapped in adjacent potential wells, slide along the potential, or exhibit more complex motions in which the particles jumps to farthest well or in which the center-of-mass motion is neither monotonous nor periodic. We discuss the thresholds between these domains.

Evolutionary demographic models reveal the strength of purifying selection on susceptibility alleles to late-onset diseases.

Assessing the role played by purifying selection on a susceptibility allele to late-onset disease (SALOD) is crucial to understanding the puzzling allelic spectrum of a disease, because most alleles are recent and rare. This fact is surprising because it suggests that alleles are under purifying selection while those that are involved in post-menopause mortality are often considered neutral in the genetic literature. The aim of this article is to use an evolutionary demography model to assess the magnitude of selection on SALODs while accounting for epidemiological and sociocultural factors. We develop an age-structured population model allowing for the calculation of SALOD selection coefficients (1) for a large and realistic parameter space for disease onset, (2) in a two-sex model in which men can reproduce in old age and (3) for situations in which child survival depends on maternal, paternal and grandmaternal care. The results show that SALODs are under purifying selection for most known age-at-onset distributions of late-onset genetic diseases. Estimates regarding various genes involved in susceptibility to cancer or Huntington's disease demonstrate that negative selection largely overcomes the effects of drift in most human populations. This is also probably true for neurodegenerative or polycystic kidney diseases, although sociocultural factors modulate the effect of selection in these cases. We conclude that neutrality is probably the exception among alleles that have a deleterious effect in old age and that accounting for sociocultural factors is required to understand the full extent of the force of selection shaping senescence in humans.

New insights on mercury abatement and modeling in a full-scale municipal solid waste incineration flue gas treatment unit.

Modeling approaches are generally used to describe mercury transformations in a single step of flue gas treatment processes. However, less attention has been given to the interactions between the different process stages. Accordingly, the mercury removal performance of a full-scale solid waste incineration plant, equipped with a dry flue gas treatment line was investigated using two complementary modeling strategies: a thermochemical equilibrium approach to study the mercury transformation mechanisms and speciation in the flue gas, and a kinetic approach to describe the mercury adsorption process. The modeling observations were then compared to real-operation full-scale data. Considering the typical flue gas composition of waste incineration facilities (high concentrations of HCl compared to Hg), it was found that a process temperature decrease results in better mercury removal efficiencies, associated with a higher oxidation extent of Hg in HgCl2, and the enhancement of the sorbent capacity. Improvements can also be attained by increasing the sorbent injection rate to the process, or the solid/gas separation cycles. An empirical correlation to predict the mercury removal efficiency from the main operating parameters of dry flue gas treatment units was proposed, representing a useful tool for waste incineration facilities. The presented modeling approach proved to be suitable to evaluate the behavior of full-scale gas treatment units, and properly select the most adequate adjustments in operating parameters, in order to respect the increasingly constraining mercury emissions regulations.

Sound propagation in a constrained lattice of beads: high-frequency behavior and dispersion relation.

We report on acoustic wave propagation in a regular array of nominally identical beads under isotropic static stress. The weak polydispersity of the beads makes the contact lattice random. Time-frequency analysis of the acoustic signal is performed and allows measurement of the full lattice dispersion relation. Comparison with the theoretical prediction for a perfect triangular lattice gives an indication of the level of randomness in the contact lattice. The results extend, in a consistent way, a previous study restricted to long wavelength propagation [B. Gilles and C. Coste, Phys. Rev. Lett. 90, 174302 (2003)]: The contact lattice is ordered by increasing the stress, and the smaller the wavelength, the higher the stress required to get regular lattice behavior. Measurements involving ballistic propagation of the coherent wave, whatever its frequency, evidence reversible lattice behavior under compression and/or decompression. Nevertheless, correlations of short wavelength incoherent waves are a sensitive probe of disorder, and allow us to exhibit a small irreversible evolution of the lattice.

Enhancement of Brownian motion for a chain of particles in a periodic potential.

The transport of particles in very confined channels in which single file diffusion occurs has been largely studied in systems where the transverse confining potential is smooth. However, in actual physical systems, this potential may exhibit both static corrugations and time fluctuations. Some recent results suggest the important role played by this nonsmoothness of the confining potential. In particular, quite surprisingly, an enhancement of the Brownian motion of the particles has been evidenced in these kinds of systems. We show that this enhancement results from the commensurate effects induced by the underlying potential on the vibrational spectra of the chain of particles, and from the effective temperature associated with its time fluctuations. We will restrict our derivation to the case of low temperatures for which the mean squared displacement of the particles remains smaller than the potential period.

Transverse single-file diffusion and enhanced longitudinal diffusion near a subcritical bifurcation.

A quasi-one-dimensional system of repelling particles undergoes a configurational phase transition when the transverse confining potential decreases. Below a threshold, it becomes energetically favorable for the system to adopt one of two staggered raw patterns, symmetric with respect to the system axis. This transition is a subcritical pitchfork bifurcation for short range interactions. As a consequence, the homogeneous zigzag pattern is unstable in a finite zigzag amplitude range [h_{C1},h_{C2}]. We exhibit strong qualitative effects of the subcriticality on the thermal motions of the particles. When the zigzag amplitude is close enough to the limits h_{C1} and h_{C2}, a transverse vibrational soft mode occurs which induces a strongly subdiffusive behavior of the transverse fluctuations, similar to single-file diffusion. On the contrary, the longitudinal fluctuations are enhanced, with a diffusion coefficient which is more than doubled. Conversely, a simple measurement of the thermal fluctuations allows a precise determination of the bifurcation thresholds.

Interaction, coalescence, and collapse of localized patterns in a quasi-one-dimensional system of interacting particles.

We study the path toward equilibrium of pairs of solitary wave envelopes (bubbles) that modulate a regular zigzag pattern in an annular channel. We evidence that bubble pairs are metastable states, which spontaneously evolve toward a stable single bubble. We exhibit the concept of topological frustration of a bubble pair. A configuration is frustrated when the particles between the two bubbles are not organized in a modulated staggered row. For a nonfrustrated (NF) bubble pair configuration, the bubbles interaction is attractive, whereas it is repulsive for a frustrated (F) configuration. We describe a model of interacting solitary wave that provides all qualitative characteristics of the interaction force: It is attractive for NF systems and repulsive for F systems and decreases exponentially with the bubbles distance. Moreover, for NF systems, the bubbles come closer and eventually merge as a single bubble, in a coalescence process. We also evidence a collapse process, in which one bubble shrinks in favor of the other one, overcoming an energetic barrier in phase space. This process is relevant for both NF systems and F systems. In NF systems, the coalescence prevails at low temperature, whereas thermally activated jumps make the collapse prevail at high temperature. In F systems, the path toward equilibrium involves a collapse process regardless of the temperature.

Hysteretic and intermittent regimes in the subcritical bifurcation of a quasi-one-dimensional system of interacting particles.

In this article, we study the effects of white Gaussian additive thermal noise on a subcritical pitchfork bifurcation. We consider a quasi-one-dimensional system of particles that are transversally confined, with short-range (non-Coulombic) interactions and periodic boundary conditions in the longitudinal direction. In such systems, there is a structural transition from a linear order to a staggered row, called the zigzag transition. There is a finite range of transverse confinement stiffnesses for which the stable configuration at zero temperature is a localized zigzag pattern surrounded by aligned particles, which evidences the subcriticality of the bifurcation. We show that these configurations remain stable for a wide temperature range. At zero temperature, the transition between a straight line and such localized zigzag patterns is hysteretic. We have studied the influence of thermal noise on the hysteresis loop. Its description is more difficult than at T=0 K since thermally activated jumps between the two configurations always occur and the system cannot stay forever in a unique metastable state. Two different regimes have to be considered according to the temperature value with respect to a critical temperature T_{c}(τ_{obs}) that depends on the observation time τ_{obs}. An hysteresis loop is still observed at low temperature, with a width that decreases as the temperature increases toward T_{c}(τ_{obs}). In contrast, for T>T_{c}(τ_{obs}) the memory of the initial condition is lost by stochastic jumps between the configurations. The study of the mean residence times in each configuration gives a unique opportunity to precisely determine the barrier height that separates the two configurations, without knowing the complete energy landscape of this many-body system. We also show how to reconstruct the hysteresis loop that would exist at T=0 K from high-temperature simulations.

Thermal motion of a nonlinear localized pattern in a quasi-one-dimensional system.

We study the dynamics of localized nonlinear patterns in a quasi-one-dimensional many-particle system near a subcritical pitchfork bifurcation. The normal form at the bifurcation is given and we show that these patterns can be described as solitary-wave envelopes. They are stable in a large temperature range and can diffuse along the chain of interacting particles. During their displacements the particles are continually redistributed on the envelope. This change of particle location induces a small modulation of the potential energy of the system, with an amplitude that depends on the transverse confinement. At high temperature, this modulation is irrelevant and the thermal motion of the localized patterns displays all the characteristics of a free quasiparticle diffusion with a diffusion coefficient that may be deduced from the normal form. At low temperature, significant physical effects are induced by the modulated potential. In particular, the localized pattern may be trapped at very low temperature. We also exhibit a series of confinement values for which the modulation amplitudes vanishes. For these peculiar confinements, the mean-square displacement of the localized patterns also evidences free-diffusion behavior at low temperature.

Subcriticality of the zigzag transition: A nonlinear bifurcation analysis.

When repelling particles are confined by a transverse potential in quasi-one-dimensional geometry, the straight line equilibrium configuration becomes unstable at small confinement, in favor of a staggered row that may be inhomogeneous or homogeneous. This conformational phase transition is a pitchfork bifurcation called the zigzag transition. We study the zigzag transition in infinite and periodic finite systems with short-range interactions. We provide numerical evidence that in this case the bifurcation is subcritical since it exhibits phase coexistence and hysteretic behavior. The physical mechanism responsible for the change in the bifurcation character is the nonlinear coupling between the transverse soft mode at the transition and the longitudinal Goldstone mode linked to the translational or rotational invariance of the zigzag pattern. An asymptotic analysis, near the bifurcation threshold and assuming an infinite system, gives an explicit expression for the normal form of the bifurcation. We establish the subcriticality, and we describe with excellent precision the inhomogeneous zigzag patterns observed in the simulations. A direct test of the physical mechanism responsible for the bifurcation character evidences a quantitative agreement.