Nonequilibrium Population Research Articles

Variation in population structure across the ecological range of the Queensland fruit fly, Bactrocera tryoni

We sampled a pest fruit fly species, the Queensland fruit fly, Bactrocera tryoni, across its entire ecological range in eastern Australia, from ancestral high-density populations in tropical regions through to isolated outbreak populations in marginal arid areas. Using DNA microsatellite markers, we found that in ancestral areas, population differentiation was low and populations were genetically homogeneous over large distances. In more temperate areas, populations were far more genetically differentiated but there was no pattern of isolation-by-distance (no drift/migration equilibrium). Genetic drift appeared to be the major influence on population differentiation. The transition between these extremes was abrupt and unexpectedly far from the species border. Limited geographic structuring among the non-equilibrium populations was apparent from patterns of genetic differentiation, patterns of allelic richness and an ordination analysis. Our results also suggested that there might be recurring migration of flies into a neighbouring quarantine area.

Estimation and adjustment of microsatellite null alleles in nonequilibrium populations

AbstractNonamplified (null) alleles are a common feature of microsatellite genotyping and can bias estimates of allele and genotype frequencies, thereby hindering population genetic analyses. The frequency of microsatellite null alleles in diploid populations can be estimated for populations that are in Hardy–Weinberg equilibrium. However, many microsatellite data sets are from nonequilibrium populations, often with known inbreeding coefficients (F) or fixation indices (FIS or FST). Here, we propose a novel null allele estimator that can be used to estimate the null allele frequency and adjust visible allele frequencies in populations for which independent estimates of F, FIS or FST are available. The algorithm is currently available as an Excel macro that can be downloaded at no cost from http://www.microchecker.hull.ac.uk/ and will be incorporated into the software micro‐checker.

Ultrafast Chemistry: Using Time‐Resolved Vibrational Spectroscopy for Interrogation of Structural Dynamics

AbstractFor Abstract see ChemInform Abstract in Full Text.

Full Configuration Interaction Computer Simulation Study of the Thermodynamic and Kinetic Stability of Hydrated Dielectrons

The hydrated electron is a unique solvent-supported state comprised of an excess electron that is confined to a cavity by the surrounding water. Theoretical studies have suggested that two-electron solvent-supported states also can be formed; in particular, simulations indicate that two excess electrons could pair up and occupy a single cavity, forming a so-called hydrated dielectron. Although hydrated dielectrons have not been observed directly by experiment, their existence has been posited to explain the lack of an ionic strength effect in hydrated electron bimolecular annihilation [Schmidt, K. H.; Bartels, D. M. Chem. Phys. 1995, 190, 145]. To determine whether dielectrons may be created in the laboratory, we use thermodynamic integration (TI), combined with mixed quantum/classical molecular dynamics simulation, to examine the thermodynamic stability of hydrated electrons and dielectrons. For the dielectron calculations, we solve the two-electron quantum problem using full configuration interaction. Our results suggest that hydrated dielectrons are thermodynamically unstable relative to separated (single) hydrated electrons, although we also show that increasing the pressure could drive the equilibrium toward the formation of dielectrons. Because the simulations suggest that hydrated dielectrons are kinetically stable, we also examine a scenario for creating metstable, nonequilibrium populations of dielectrons, which involves the capture of a newly injected electron by a preexisting, equilibrated hydrated electron. These calculations, which allow for the full nonadiabatic relaxation of the injected electron, show that hydrated electrons may indeed act as trapping sites for unequilibrated electrons, so that capture may be a viable mechanism for creating dielectrons. We suggest possible experimental procedures to create such nonequilibrium hydrated dielectrons using either pulse radiolysis or ultrafast spectroscopic techniques.

Electron broadening of isolated lines with stationary non-equilibrium level populations

It is shown that a quantum kinetic theory approach to line broadening, extended to stationary non-equilibrium states, yields corrections to the standard electron impact widths of isolated lines that depend on the population of the radiator internal levels. A consistent classical limit from a general quantum treatment of the perturbing electrons also introduces corrections to the isolated line widths. Both effects are essential in preserving detailed-balance relations. Preliminary analysis indicates that these corrections may resolve existing discrepancies between theoretical and experimental widths of isolated lines. An experimental test of the results is proposed.

Decision-making in variable environments — a case of group selection and inter-generational conflict?

Suppose organisms need to engage in a particular action exactly once during some fixed period of time. Further suppose they can time this action to optimise their fitness based on the expected current payoff and the probability distribution of later payoffs. For an example we consider the timing of the annual nuptial flight in eusocial insects. Using two population genetics models, we ask whether stochasticity leads to evolutionary conflict between the queen and her offspring. We find that the winning phenotype is independent of who controls the timing. The best response to any non-equilibrium population strategy is the same in both control scenarios, a result that carries over to the diploid case. Although inter-generational conflict is therefore ruled out, the models support a previous observation that at equilibrium some of the offspring have a lower expected payoff than others. By measuring fitness in terms of relative reproductive success, we show that all individuals are in fact equally well off making group-selectionist arguments unnecessary. As such, the models should improve our understanding of the difficult conceptual problem of the unit of natural selection in stochastic environments.

Modeling and Simulation of Ionic Currents in Three-Dimensional Microfluidic Devices with Nanofluidic Interconnects

Electrokinetic fluid flow in nanocapillary array (NCA) membranes between vertically separated microfluidic channels offers an attractive alternative to using mechanical action to achieve fluidic communication between different regions of lab-on-a-chip devices. By adjusting the channel diameter, a, and the inverse Debye length, к, and applying the appropriate external potential, the nanochannel arrays, can be made to behave like digital fluidic switches, and the movement of molecules from one side of the array to the other side can be controlled. However, inherent differences in ionic mobility lead to non-equilibrium ion populations on the downstream side, which, in turn, shows up through transient changes in the microchannel conductance. Here we describe coupled calculations and experiments in which the electrical properties of a microfluidic–nanofluidic hybrid architecture are simulated by a combination of a compact model for the bulk electrical properties and iterative self-consistent solutions of the coupled Poisson, Nernst–Planck, and Navier–Stokes equations to recover the detailed ion motion in the nanopores. The transient electrical conductivity in the microchannel, after application of a forward bias pulse to the NCA membrane, is recovered in quantitative detail. The surface charge density of the nanopores and the capacitance of the membrane, which are critical determinants of electrokinetic flow through NCA, fall out of the analysis in a natural way, providing a clear mechanism to determine these critically important parameters.

Genetic Diversity and the Evolutionary History of Plant Immunity Genes in Two Species of Zea

Plant pathogenesis-related genes (PR genes) code for enzymes, enzyme inhibitors, and other peptides that confer resistance to pathogens and herbivores. Although several PR genes have been the subject of molecular population genetic analyses, a general understanding of their long-term evolutionary dynamics remains incomplete. Here we analyze sequence data from 17 PR genes from two closely related teosinte species of central Mexico. In addition to testing whether patterns of diversity at individual loci depart from expectations under a neutral model, we compared patterns of diversity at defense genes, as a class, to nondefense genes. In Zea diploperennis, the majority of defense genes have patterns of diversity consistent with neutral expectations while at least two genes showed evidence of recent positive selection consistent with arms-race models of antagonistic coevolution. In Zea mays ssp. parviglumis, by contrast, analyses of both defense and nondefense genes revealed strong and consistent departures from the neutral model, suggestive of nonequilibrium population dynamics or population structure. Nevertheless, we found a significant excess of replacement polymorphism in defense genes compared to nondefense genes. Although we cannot exclude relaxed selective constraint as an explanation, our results are consistent with temporally variable (transient or episodic) selection or geographically variable selection acting on parviglumis defense genes. The different patterns of diversity found in the two Zea species may be explained by parviglumis' greater distribution and population structure together with geographic variation in selection.

The energy-loss rate via polar-optical phonon scattering in quantum wires

The hot-electron energy-loss rate (ELR) conditioned by confined and interface polar-optical (PO) phonons for a quasi-one-dimensional cylindrical quantum wire embedded in a dielectric medium is investigated analytically. It is shown that the inclusion of the PO-phonon confinement effects is crucial for accurate calculation of the ELR in quantum wire. Taking into account the nonequilibrium phonon populations, the hot-electron ELR is derived by a model, which includes the lowest subband occupation and the phonon confinement effects. The contribution of intersubband transitions to electron ELR for the GaAs quantum wire embedded in Al x Ga 1− x As is estimated. The extrema on the ELR dependences on electron density are obtained.

Pure dephasing and phonon dynamics in GaAs- and GaN-based quantum dot structures: Interplay between material parameters and geometry

The pure dephasing of excitons in quantum dot structures due to their interaction with acoustic phonons as well as the spatiotemporal dynamics of the created nonequilibrium phonon population is studied theoretically. The theory is applied to GaAs- as well as GaN-based heterostructures. A detailed analysis of the interplay between different material parameters, different quantum dot geometries, and different electric fields is presented. The optical polarization induced by an ultrashort laser pulse exhibits a characteristic nonexponential behavior: it decays on a pico- or subpicosecond time scale to a value that strongly depends on temperature, structure, and material parameters and is then retained until, on a typically much longer time scale, it finally decays because of electron-hole recombination or transitions to other states. We find that, in general, the remnant optical polarization is much higher in the GaAs-based structures than in the GaN-based structure mainly because of the strongly enhanced piezoelectric coupling in GaN quantum dots. The optical excitation also leads to the buildup of a phonon population consisting of a polaron part that remains localized in the region of the quantum dot and a traveling part that leaves the dot region at the speed of sound. This traveling part exhibits characteristic anisotropies reflecting both the anisotropy of the quantum dot structure and of the coupling matrix elements.

ULTRAFAST CHEMISTRY: Using Time-Resolved Vibrational Spectroscopy for Interrogation of Structural Dynamics

Time-resolved infrared (IR) and Raman spectroscopy elucidates molecular structure evolution during ultrafast chemical reactions. Following vibrational marker modes in real time provides direct insight into the structural dynamics, as is evidenced in studies on intramolecular hydrogen transfer, bimolecular proton transfer, electron transfer, hydrogen bonding during solvation dynamics, bond fission in organometallic compounds and heme proteins, cis-trans isomerization in retinal proteins, and transformations in photochromic switch pairs. Femtosecond IR spectroscopy monitors the site-specific interactions in hydrogen bonds. Conversion between excited electronic states can be followed for intramolecular electron transfer by inspection of the fingerprint IR- or Raman-active vibrations in conjunction with quantum chemical calculations. Excess internal vibrational energy, generated either by optical excitation or by internal conversion from the electronic excited state to the ground state, is observable through transient frequency shifts of IR-active vibrations and through nonequilibrium populations as deduced by Raman resonances.

Metastable hydrogen absorption in ejecta close to $\mathsf{\eta}$ Carinae

Spectroscopy with the high spatial resolution of the Hubble Space Telescope (HST) reveals narrow absorption in the hydrogen Balmer lines in spectra of Eta Carinae and the nearby nebular-scattered starlight. While hydrogen Balmer absorption lines are seen in stellar photospheres and winds, we are not aware of such being seen in galactic nebulae. This exceptional case is caused by intense stellar UV radiation acting on high-density neutral clumps of gas in the close vicinity of the central source. The interaction of the UV radiation with hydrogen results in photo-ionization and photo-excitation leading to a non-equilibrium population of the metastable 2s S-2 level. This occurs throughout the equatorial region surrounding eta Carinae in sufficient quantity to produce strong narrow absorption on top of the broad P Cygni emission profile. This absorption can be considered to be a probe of the very non-uniform ejecta in the disk region surrounding eta Carinae. (Less)

Nonequilibrium conditions following landscape rearrangement: the relative contribution of past and current hydrological landscapes on the genetic structure of a stream‐dwelling fish

Interpreting patterns of population structure in nature is often challenging, especially in dynamic landscapes where population genetic connectivity evolves over time. In this study, we document the absence of migration-drift equilibrium in a stream-dwelling euryhaline fish resulting from past fine-scale drainage rearrangements and evaluate the relative contribution of past and current hydrological landscapes on observed population structure. Based on allelic variation at nine microsatellite loci, genetic relationships among 12 populations of brook charr, Salvelinus fontinalis, from Gros Morne National Park of Canada (GMNP, Newfoundland, Canada) did not reflect current stream hierarchical structure. In addition, we observed no correlation between population differentiation and contemporary landscape features (waterway distance and sums of altitudinal differences). Instead, population relationships were consistent with historical hydrological structure predicted a priori based on geomorphological and biogeographical evidences. Also, population differentiation was strongly correlated with inferred historical landscape features. Contemporary barriers have apparently preserved the signature of past genetic connectivity by constraining gene flow. Based on the relationships between population differentiation and current and past landscape features at various spatial scales, we suggest that brook charr genetic diversity in GMNP is mostly the result of small distance migrations at the time of colonization and subsequent differentiation through drift. This study highlights the potential of approaching landscapes from a combination of contemporary and historical perspectives when interpreting nonequilibrium population structures resulting from landscape rearrangement.

New Branch of Intersubband Plasmons in a Nonequilibrium Two-Layer System

The plasma oscillation spectrum for 2D electrons in a double quantum well is calculated. It is shown that an additional branch of intersubband plasmons can exist without experiencing Landau damping in the case of nonequilibrium population of subbands. In an asymmetric structure, this branch is responsible for both the emergence of instabilities and the possibility of amplification of plasma waves.

Allozyme variation, differentiation, and inbreeding in populations ofPinus mugoin Bulgaria

Genetic variation of 17 populations of Pinus mugo Turra was studied using 10 polymorphic allozyme loci. Polymorphism and gene diversity in these populations were comparable to mean values for gymnosperm species, but slightly lower than in pines with large and continuous ranges. We did not find significant interpopulation differentiation (FST= 0.041) or isolation by distance, suggesting that gene flow might be extensive or that the time elapsed since the species range became fragmented has been too short for genetic differentiation to arise via genetic drift. We detected moderate and statistically significant levels of inbreeding (mean FIS= 0.252) for all loci in all populations. Although there are many possible explanations for this nonequilibrium population structure, we propose that the main reasons for its ubiquity are the peculiar growth form and reproductive biology of P. mugo, which promote excessive near-neighbor pollinations. Populations in Vitosha Mountain and western Stara Planina had the highest levels of inbreeding and the lowest observed heterozygosities. All populations in these mountains are small and isolated, but none of them is under a special regime of protection. Thus, the conservation status of P. mugo populations in Vitosha Mountain and western Stara Planina may deserve reevaluation. Future gene conservation efforts should focus on obtaining information on the genetic variation of adaptive traits in P. mugo.

Field-free charge polarization of mesoscopic rings

We investigate the electron dynamics in a one-dimensional mesoscopic ring under the influence of short, linearly polarized half-cycle electromagnetic pulses. It is shown that the pulses induce a nonequilibrium coherent population of electronic states such that a time-dependent charge polarization of the ring is induced. The time-dependent charge oscillations persist after the pulses have diminished and decay on a time scale determined by the relaxation time. The overall duration of the charge polarization can be controlled by applying an appropriate train of half-cycle pulses. Furthermore, we show that the emission spectrum associated with the pulse-induced charge oscillations can be modulated appropriately by tuning the parameters of the driving pulses. It is shown theoretically how the induced charge polarization can in principle be utilized to measure experimentally the relaxation time of the system in a field-free manner.

Chirped pulse control of long range electron transfer

We have studied the capabilities of intense ultrashort chirped pulses for controlling the long range electron transfer in systems strongly coupled to a polar medium. We considered a two state electronic donor/acceptor system, possessing a large difference of permanent dipole moments between donor and acceptor states, with relaxation treated as a diffusion on electronic potential energy surfaces. This relaxation model has enabled us to trace continuously the transition from a coherent population transfer to incoherent one. In addition to the field controlled electron transfer, we take into account a possibility of the direct optical transition between electronic states under study as well. We have introduced the generalized Rabi frequency that enabled us to extend the concepts and ideas of population transfer, developed for optical transitions, to the electron transfer (radiationless process) controlled with strong electromagnetic field. We have shown that it is possible to realize the “radiationless” analogies to π-pulse excitation, adiabatic rapid passage and pump–dump process. We have obtained a physically clear picture of the analogy to the adiabatic rapid passage for the chirped controlled long-range electron transfer by studying vibrationally non-equilibrium populations behavior and careful examination of all the conditions needed for adiabatic rapid passage.

Adaptive evolution of asexual populations under Muller's ratchet.

We study the population genetics of adaptation in nonequilibrium haploid asexual populations. We find that the accumulation of deleterious mutations, due to the operation of Muller's ratchet, can considerably reduce the rate of fixation of advantageous alleles. Such reduction can be approximated reasonably well by a reduction in the effective population size. In the absence of Muller's ratchet, a beneficial mutation can only become fixed if it creates the best possible genotype; if Muller's ratchet operates, however, mutations initially arising in a nonoptimal genotype can also become fixed in the population, since the loss of the least-loaded class implies that an initially nonoptimal background can become optimal. We show that, while the rate at which adaptive mutations become fixed is reduced, the rate of fixation of deleterious mutations due to the ratchet is not changed by the presence of beneficial mutations as long as the rate of their occurrence is low and the deleterious effects of mutations (s(d)) are higher than the beneficial effects (s(a)). When s(a) > s(d), the advantage of a beneficial mutation can outweigh the deleterious effects of associated mutations. Under these conditions, a beneficial allele can drag to fixation deleterious mutations initially associated with it at a higher rate than in the absence of advantageous alleles. We propose analytical approximations for the rates of accumulation of deleterious and beneficial mutations. Furthermore, when allowing for the possible occurrence of interference between beneficial alleles, we find that the presence of deleterious mutations of either very weak or very strong effect can marginally increase the rate of accumulation of beneficial mutations over that observed in the absence of such deleterious mutations.

The classical metapopulation theory and the real, natural world: a critical appraisal

Die klassische Metapopulations-Theorie (CM) betrachtet das Überdauern der Arten in der Landschaft als einen Turnover von Aussterben—(Re-)Kolonisieren geeigneter Habitat-Patches in jeder Generation. Deshalb wird die Metapopulations-Dynamik durch binäre Veränderung im Status individueller Patches approximiert. Dieser Ansatz erlaubte eine rigorose mathematische Analyse von Metapopulations-Dynamiken und stellte Verbindungen zu generellen ökologischen Gesetzmäßigkeiten her oder führte zur Ableitung anwendbarer Konzepte in der Naturschutzbiologie. Ein kritischer Review der Literatur zeigt jedoch, dass nur wenige räumlich strukturierte Populationen entsprechend der CM-Theorie funktionieren. Darüber hinaus konzentrieren sich empirische Studien der CM normalerweise auf (1) Arten am Rande ihres Verbreitungsgebietes, (2) Arten mit kleinen oder extrem kleinen lokalen Populationsgrößen und (3) Arten, die im Untersuchungsgebiet abnehmen (in einem Fall zunehmen). Solche Populationssysteme im Ungleichgewicht sind weit von der Gleichgewichtswelt entfernt, wie sie in CM-Modellen idealisiert werden. Darüber hinaus zeigen empirische Vergleiche von Metapopulationen in stark fragmentierten Landschaften, dass die Aussterbe-(Re)-Kolonisations-Dynamik nur dann derjenigen entspricht, die die Theorie vorhersagt, wenn die lokalen Populationen sehr klein sind. Die fehlende Übereinstimmung zwischen der CM-Theorie und der realen, natürliche Welt könnte erklären, warum die Modelle und Konzepte, die aus dieser Theorie abgeleitet werden, nicht bei der Population-Viability-Analyse oder Naturschutzstrategien verwendet werden. Die endgültige Botschaft dieser Veröffentlichung ist dreifach: (1) ausschließliche und implizite Angleichung von räumlich strukturierten Populationen an klassische Metapopulationen sollte vermieden werden, (2) den Versuchen irgendeine Population entsprechend der CM-Theorie zu managen sollte eine sorgfältige Beobachtung der Übereinstimmung zwischen der Feldsituation und den Annahmen der Theorie vorangehen (besonders bezüglich der großen Rate des Turnover lokaler Populationen und dem Gleichgewichtszustand der Metapopulation) und (3) sollten Theoretiker vermeiden, die CM-Theorie und abgeleitete Konzepte als Patentrezepte für die Bewahrung von Populationen zu präsentieren, die mit Habitatverlusten und Fragementierung konfrontiert sind.

The structural dynamics of myoglobin

Conformational fluctuations in proteins were initially invoked to explain the observation that diffusion of small ligands through the matrix is a global phenomenon. Small globular proteins contain internal cavities that play a role not only in matrix dynamics but also in controlling function, tracing a pathway for the diffusion of the ligand to and from the active site. This is the main point addressed in this Review, which presents pertinent information obtained on myoglobin (Mb). Mb, a simple globular heme protein which binds reversibly oxygen and other ligands. The bond between the heme Fe(II) and gaseous ligands can be photodissociated by a laser pulse, generating a non-equilibrium population of protein structures that relaxes on a picosecond to millisecond time range. This process is associated with migration of the ligand to internal cavities of the protein, which are known to bind xenon. Some of the results obtained by laser photolysis, molecular dynamics simulations, and X-ray diffraction of intermediate states of wild-type and mutant myoglobins are summarized. The extended relaxation of the globin moiety directly observed by Laue crystallography reflects re-equilibration among conformational substates known to play an essential role in controlling protein function.