Modelling the Coexistence of Annual and Perennial Plants in Temporally Varying Environments*

Abstract The long-term growth and coexistence of species with large mixed populations in varying environments were modelled for representative environments and life-history characteristics of annual and perennial plants. The effects of the relationships between the means, variances, and covariances of seed yield, establishment, and survival, were explored by Taylor's expansion. The main findings are: 1. Individual variation in reproductive success within generations has no effect on long-term growth, which is determined only by the mean growth rate of the individuals of the species. 2. In annual species with nonoverlapping generations and without seed banks, the species with the largest mean log of the annual growth rate Y, that is the product of the average seed yield per plant and the establishment probability per seed, will win in competition with other species, independent of the correlations between the growth rates of the different species. In this case there is a negative tradeoff between the mean and the variance. 3. In perennial species with a lottery type of equal access to vacant sites, a high annual survival probability allows stable coexistence between perennial species with independent or negatively correlated variance in their mean annual product of seed production and establishment Y. 4. The coexistence range and the likely number of coexisting perennial species increase as a function of the variance of the common species, and is decreased by the variance of the rare species. The coexistence range is decreased by the covariance between the growth rates of the species, and between the survival of the rare species and its growth rate. 5. If mortality in the community of long-lived perennials is synchronized, the generations become nonoverlapping, and the competitive dynamics become similar to that of annuals. 6. Coexistence between annual and perennial species is promoted if the covariances between the annual survival and the relative yield of perennials, and between the yields of perennials and annuals, decrease and become more negative. 7. Selection for seed yield and establishment in different conditions in annuals favours a generalist strategy with low variance between years which provides a moderate yield and establishment over a wide range of environmental conditions. In perennial plants, long-term growth rate is determined by the lifetime seed yield and establishment. Because of strong competition with annuals in the more common conditions, selection in perennials favours instead a specialist strategy, with a high seed yield and establishment at relatively rare occasions in space and time, in which there is only weak competition with annuals. 8. Coexistence of annual species with a long-lived seed bank in the soil is also made possible by independent variation in different years of the germination, seed yield and establishment of different species, analogous to the situation of perennial plants.     

Diurnal Rhythms Spatially and Temporally Organize Autophagy

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Temporally and Spatially Constrained ICA of fMRI Data Analysis

Constrained independent component analysis (CICA) is capable of eliminating the order ambiguity that is found in the standard ICA and extracting the desired independent components by incorporating prior information into the ICA contrast function. However, the current CICA method produces constraints that are based on only one type of prior information (temporal/spatial), which may increase the dependency of CICA on the accuracy of the prior information. To improve the robustness of CICA and to reduce the impact of the accuracy of prior information on CICA, we proposed a temporally and spatially constrained ICA (TSCICA) method that incorporated two types of prior information, both temporal and spatial, as constraints in the ICA. The proposed approach was tested using simulated fMRI data and was applied to a real fMRI experiment using 13 subjects who performed a movement task. Additionally, the performance of TSCICA was compared with the ICA method, the temporally CICA (TCICA) method and the spatially CICA (SCICA) method. The results from the simulation and from the real fMRI data demonstrated that TSCICA outperformed TCICA, SCICA and ICA in terms of robustness to noise. Moreover, the TSCICA method displayed better robustness to prior temporal/spatial information than the TCICA/SCICA method.     

Fitness, Flux and Phantoms in Temporally Variable Environments

The evolutionary problem of selection in temporally variable environments is addressed by investigating a metabolic model describing the approach to steady state of a flux emanating from a simple linear pathway of unsaturated enzymes catalyzing reversible monomolecular reactions. Analysis confirms previous claims that steps having no influence on the steady state flux may influence transient behavior, and that enzymes immune to natural selection at steady state may become subject to selection when fitness is a function of individual transient metabolic events. Indeed, calculations show that the β-galactosidase of Escherichia coli, which exerts a negligible effect on the steady state lactose flux, controls the approach to steady state. However, after 6 sec the lactose flux is within 0.1% of steady state, and so an ever changing environment must be invoked to continually expose β-galactosidase to selection. Analysis of the metabolic model undergoing multiple transient events reveals that fitness differences remain unaffected if enzyme activities remain constant and become minimized if enzyme activities differ among environments. Until suitable data become available, claims that metabolic behavior away from steady state necessarily exposes a far greater proportion of allozymes to natural selection should be treated with great skepticism.     

Performing Spatially and Temporally Explicit Ecological Exposure Assessments Involving Multiple Stressors

Ecological risk assessments have traditionally focused on estimating risk associated with a receptor's exposure to chemical stressors in abiotic (soil, water, etc.) and biotic (tissues, prey items) media. However, a free-living receptor is also constantly challenged to avoid or minimize adverse effects associated with those physical (e.g., loss of habitat) and biological (e.g., lack of adequate food) stressors that are already a consistent and natural part of its everyday existence. All three stressors, as well as their relative spatial and temporal positions with respect to each other and the receptor, may interact in ways that alter a chemical stressor's relative contribution to a receptor's overall risk. Evidence suggests that better representations of a chemical stressor's true contribution to overall risk would result if spatial, temporal, and multiple stressor interactions were more routinely considered and quantified. However, examples of this occurring in typical ecological risk assessments are rare, due, in part, to a lack of practical and accessible procedures for this purpose. This article outlines a procedure to give ecological risk assessment practitioners greater access to spatial, temporal, and multistressor techniques, describes an implementable spreadsheet-based model for performing calculations associated with this procedure, and discusses the types of ecological, life history, and landscape information needed to parameterize this model.     

Adult-Generated Hippocampal Neurons Allow the Flexible Use of Spatially Precise Learning Strategies

Despite enormous progress in the past few years the specific contribution of newly born granule cells to the function of the adult hippocampus is still not clear. We hypothesized that in order to solve this question particular attention has to be paid to the specific design, the analysis, and the interpretation of the learning test to be used. We thus designed a behavioral experiment along hypotheses derived from a computational model predicting that new neurons might be particularly relevant for learning conditions, in which novel aspects arise in familiar situations, thus putting high demands on the qualitative aspects of (re-)learning.In the reference memory version of the water maze task suppression of adult neurogenesis with temozolomide (TMZ) caused a highly specific learning deficit. Mice were tested in the hidden platform version of the Morris water maze (6 trials per day for 5 days with a reversal of the platform location on day 4). Testing was done at 4 weeks after the end of four cycles of treatment to minimize the number of potentially recruitable new neurons at the time of testing. The reduction of neurogenesis did not alter longterm potentiation in CA3 and the dentate gyrus but abolished the part of dentate gyrus LTP that is attributed to the new neurons. TMZ did not have any overt side effects at the time of testing, and both treated mice and controls learned to find the hidden platform. Qualitative analysis of search strategies, however, revealed that treated mice did not advance to spatially precise search strategies, in particular when learning a changed goal position (reversal). New neurons in the dentate gyrus thus seem to be necessary for adding flexibility to some hippocampus-dependent qualitative parameters of learning.Our finding that a lack of adult-generated granule cells specifically results in the animal''s inability to precisely locate a hidden goal is also in accordance with a specialized role of the dentate gyrus in generating a metric rather than just a configurational map of the environment. The discovery of highly specific behavioral deficits as consequence of a suppression of adult hippocampal neurogenesis thus allows to link cellular hippocampal plasticity to well-defined hypotheses from theoretical models.     

The LOX1 Gene of Arabidopsis Is Temporally and Spatially Regulated in Germinating Seedlings

We examined the temporal and spatial expression patterns of the LOX1 gene during the development of Arabidopsis thaliana seedlings. Measurements of steady-state LOX1 mRNA levels indicated that this gene is transiently expressed during germination. LOX1 mRNA was not detected in seed that had imbibed (T0) but reached a maximum level by 1 d in both light- and dark-grown seedlings. The induction of the LOX1 gene was not light dependent; however, mRNA levels were 4-fold greater in light-grown seedlings. Immunoblot analysis of lipoxygenase protein levels and measurements of enzyme activity suggested that the induction of the LOX1 gene resulted in the production of functional lipoxygenase enzyme. Lipoxygenase protein was not present in dry seed or seed that had imbibed, but was first detected by immunoblot analysis after 1 and 2 d of growth in the light and dark, respectively. In both cases, lipoxygenase protein levels remained high for 2 d and then declined. Lipoxygenase activity paralleled the changes in protein levels. In situ hybridization studies revealed that the LOX1 gene is transiently expressed in the epidermis and the aleurone layer during germination. LOX1 mRNA levels were particularly high in the epidermis of the radicle and the adaxial side of the cotyledons. These results suggest that the LOX1 gene product is produced specifically during early germination and plays a role in the functioning of the epidermis.     

Interaction Mechanisms of Cavitation Bubbles Induced by Spatially and Temporally Separated fs-Laser Pulses

The emerging use of femtosecond lasers with high repetition rates in the MHz regime together with limited scan speed implies possible mutual optical and dynamical interaction effects of the individual cutting spots. In order to get more insight into the dynamics a time-resolved photographic analysis of the interaction of cavitation bubbles is presented. Particularly, we investigated the influence of fs-laser pulses and their resulting bubble dynamics with various spatial as well as temporal separations. Different time courses of characteristic interaction effects between the cavitation bubbles were observed depending on pulse energy and spatio-temporal pulse separation. These ranged from merely no interaction to the phenomena of strong water jet formation. Afterwards, the mechanisms are discussed regarding their impact on the medical application of effective tissue cutting lateral to the laser beam direction with best possible axial precision: the mechanical forces of photodisruption as well as the occurring water jet should have low axial extend and a preferably lateral priority. Furthermore, the overall efficiency of energy conversion into controlled mechanical impact should be maximized compared to the transmitted pulse energy and unwanted long range mechanical side effects, e.g. shock waves, axial jet components. In conclusion, these experimental results are of great importance for the prospective optimization of the ophthalmic surgical process with high-repetition rate fs-lasers.     

Bacterial Community Composition of Stream Biofilms in Spatially Variable-Flow Environments

Streams are highly heterogeneous ecosystems, in terms of both geomorphology and hydrodynamics. While flow is recognized to shape the physical architecture of benthic biofilms, we do not yet understand what drives community assembly and biodiversity of benthic biofilms in the heterogeneous flow landscapes of streams. Within a metacommunity ecology framework, we experimented with streambed landscapes constructed from bedforms in large-scale flumes to illuminate the role of spatial flow heterogeneity in biofilm community composition and biodiversity in streams. Our results show that the spatial variation of hydrodynamics explained a remarkable percentage (up to 47%) of the variation in community composition along bedforms. This suggests species sorting as a model of metacommunity dynamics in stream biofilms, though natural biofilm communities will clearly not conform to a single model offered by metacommunity ecology. The spatial variation induced by the hydrodynamics along the bedforms resulted in a gradient of bacterial beta diversity, measured by a range of diversity and similarity indices, that increased with bedform height and hence with spatial flow heterogeneity at the flume level. Our results underscore the necessity to maintain small-scale physical heterogeneity for community composition and biodiversity of biofilms in stream ecosystems.Biofilms (attached and matrix-enclosed microbial communities) are an important form of microbial life in streams and rivers, where they can greatly contribute to ecosystem functions and even large-scale carbon fluxes (1, 3). Streams are inherently heterogeneous and are characterized by a largely unidirectional downstream flow of water that controls the dispersal of suspended microorganisms (21), biofilm community composition (7), architecture (2), and metabolism (13), for instance. However, we do not understand how diverse microorganisms assemble into biofilm communities based on flow heterogeneity and related dispersal in these ecosystems.Dispersal, as the propagation and immigration of biota, can have important consequences for biodiversity and ecosystem functioning in heterogeneous landscapes (18, 25). Landscape topography and turbulent transport affect dispersal, a relationship that is well studied in the dispersal of plant seeds (31) but not in the microbial world. Only recently have microbial ecologists begun to understand the role of dispersal in large-scale biogeographic patterns (29) and metacommunity ecology (24, 44). This growing body of research on microbial dispersal and its consequences for spatial patterns of community assembly and composition rests entirely on free-living bacteria, while no comparable data exist for microbial biofilms. The confirmation of detachment as an intrinsic behavior in many biofilms has led to the appreciation of dispersal as an insurance policy for these microbial communities to seed new habitats during resource limitation or aging of the parental biofilm (4). However, microbial ecology lacks conceptual models to predict postemigration processes, such as cell propagation, immigration, and community assembly during colonization of new surfaces. The perception of biofilms as microbial landscapes and, at the same time, as integrated parts of the landscape they inhabit offers the possibility to test models for habitat selection by dispersal cells (4). In this study, we focused on the assembly of biofilm communities by dispersal cells in spatially variable-flow environments; we did not measure dispersal as the emigration of cells from established biofilms. We adopted metacommunity ecology as a framework that encapsulates environmental heterogeneity and dispersal (18) to illuminate the mechanisms underlying community assembly.If the effects of microbial diversity on ecosystem functions are to be understood, we need to address the proper spatial resolution at which microorganisms assemble into communities and at which their functioning becomes manifest. In streams, this is typically at the level of habitats and microhabitats ranging from meters to centimeters, where characteristic geomorphological features (e.g., bedforms) and induced hydrodynamic fields develop and where spatial variations in biofilm metabolism become apparent (13). The ensemble of these small-scale variations translates into the landscape heterogeneity of the streambed.The aim of this study was to test whether spatial flow heterogeneity generating diverse microhabitats induces spatial species turnover and increases the biodiversity of microbial biofilms. Microbial metacommunity ecology predicts mass effects rather than species sorting to drive community composition in ecosystems with low residence time, such as streams (14, 18, 24). To test this prediction, we constructed six streambed landscapes from bedforms of defined dimensions differing in height; the mean flow (at flume scale) was kept constant, whereas the spatial heterogeneity of flow increased across the gradient of the six landscapes. The inoculum (i.e., the stream water and naturally contained microorganisms) and water chemistry were equal in all flumes. This allowed us to isolate flow heterogeneity as a potential driver of biofilm community composition in a high-energy ecosystem. We used terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA gene sequences from winter and summer communities and related bacterial community composition and microbial biomass to the hydrodynamics in representative microhabitats using causal modeling and forward selection of explanatory variables (9, 23).     

Adaptive Learning Networks: Developing Resource Management Knowledge through Social Learning Forums

The purpose of this paper is to explore adaptive learning networks as a contemporary means by which new resource management knowledge can develop through social learning forums. The paper draws upon recent discussions within two disparate literatures on indigenous knowledge and network theory and is grounded in fieldwork with two Anishinaabe First Nations in northwestern Ontario. The paper has three objectives. First, problematize the principle of representation as a basic way of including the knowledge of indigenous peoples within natural resource and environmental management. Second, utilize network theory as a way to weave together adaptive learning by individuals into a cross-cultural social learning process. Finally, propose an adaptive natural resources and environmental framework that brings together, through a social learning process, the different ways individuals, indigenous peoples and resource managers, perceive environmental change.     

Adaptive Spike Threshold Enables Robust and Temporally Precise Neuronal Encoding

Neural processing rests on the intracellular transformation of information as synaptic inputs are translated into action potentials. This transformation is governed by the spike threshold, which depends on the history of the membrane potential on many temporal scales. While the adaptation of the threshold after spiking activity has been addressed before both theoretically and experimentally, it has only recently been demonstrated that the subthreshold membrane state also influences the effective spike threshold. The consequences for neural computation are not well understood yet. We address this question here using neural simulations and whole cell intracellular recordings in combination with information theoretic analysis. We show that an adaptive spike threshold leads to better stimulus discrimination for tight input correlations than would be achieved otherwise, independent from whether the stimulus is encoded in the rate or pattern of action potentials. The time scales of input selectivity are jointly governed by membrane and threshold dynamics. Encoding information using adaptive thresholds further ensures robust information transmission across cortical states i.e. decoding from different states is less state dependent in the adaptive threshold case, if the decoding is performed in reference to the timing of the population response. Results from in vitro neural recordings were consistent with simulations from adaptive threshold neurons. In summary, the adaptive spike threshold reduces information loss during intracellular information transfer, improves stimulus discriminability and ensures robust decoding across membrane states in a regime of highly correlated inputs, similar to those seen in sensory nuclei during the encoding of sensory information.     

Bet-Hedging Diapause Strategies in Stochastic Environments

In many insect species, adult emergence spreads over several years because of the existence of prolonged diapause in certain individuals. From stochastic models, we show that diversified bet-hedging strategies (mixed strategies with emergence after 1 or 2 yr) are more fit than simple diapause strategy (emergence after 1 yr) or fixed prolonged diapause strategy (emergence after 2 yr) in isolated chestnut weevil populations. This conclusion applies to a large range of survival rates in prolonged diapause and is insensitive to initial conditions, magnitude of temporal autocorrelation, distribution of demographic parameters, and quoted values of population size limitation. However, the shape of the fitness distribution as a function of prolonged diapause frequency changes greatly in the absence of population size limitation. Whatever the survival rate during prolonged diapause, we find that there is no genotypic advantage to extending diapause for all chestnut weevil larvae to more than 1 yr. Our models predict selection of bet-hedging strategies over a large range of prolonged diapause frequencies. This result is consistent with the existence of several mixed strategies in a population. Emergences after 3 yr are not crucial for selection or for the dynamics of mixed strategies in the chestnut weevil.     

Peaking of the Pressure Pulse in Fluid-Filled Tubes of Spatially Varying Compliance

Calculations are made for a fluid-filled tube with characteristics approximately those found physiologically. The pressure variation, diameter, and compliance at the input end are as measured by Lawton for the abdominal aorta of a dog. After a 30 cm-long input section of constant k (=dp/dA), the tube is taken to stiffen by approximately the amount measured by Patel et al., i.e., k increases by a factor of 5 over the next 40 cm. The cross-section remains constant. Pressure and velocity wave forms are calculated at 8 stations spaced at 10-cm intervals down the tube. The pressure pulse leading edge is found to become steeper in the stiffening section. The peak height of the pressure pulse is found to increase by about 50% and the velocity pulse to decrease by about 30% as the disturbance propagates over a distance of 70 cm. These values agree qualitatively with the experimental physiological values given by McDonald. Most of the pressure peaking takes place upstream of the stiffening section.     

Asymptotic Distributions of Coalescence Times and Ancestral Lineage Numbers for Populations with Temporally Varying Size

The distributions of coalescence times and ancestral lineage numbers play an essential role in coalescent modeling and ancestral inference. Both exact distributions of coalescence times and ancestral lineage numbers are expressed as the sum of alternating series, and the terms in the series become numerically intractable for large samples. More computationally attractive are their asymptotic distributions, which were derived in Griffiths (1984) for populations with constant size. In this article, we derive the asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. For a sample of size n, denote by T_m the mth coalescent time, when m + 1 lineages coalesce into m lineages, and A_n(t) the number of ancestral lineages at time t back from the current generation. Similar to the results in Griffiths (1984), the number of ancestral lineages, A_n(t), and the coalescence times, T_m, are asymptotically normal, with the mean and variance of these distributions depending on the population size function, N(t). At the very early stage of the coalescent, when t → 0, the number of coalesced lineages n − A_n(t) follows a Poisson distribution, and as m → n, n(n ? 1)T_m/2N(0) follows a gamma distribution. We demonstrate the accuracy of the asymptotic approximations by comparing to both exact distributions and coalescent simulations. Several applications of the theoretical results are also shown: deriving statistics related to the properties of gene genealogies, such as the time to the most recent common ancestor (TMRCA) and the total branch length (TBL) of the genealogy, and deriving the allele frequency spectrum for large genealogies. With the advent of genomic-level sequencing data for large samples, the asymptotic distributions are expected to have wide applications in theoretical and methodological development for population genetic inference.     

Processing of DNA Polymerase-Blocking Lesions during Genome Replication Is Spatially and Temporally Segregated from Replication Forks

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The Genetical Response to Natural Selection by Varied Environments. IV. Gametic Disequilibrium in Spatially Varied Environments

Gametic disequilibria between allozyme loci were related to spatial variation of the environment in caged populations of Drosophila melanogaster . Two experiments, one with flies collected at "Chateau Tahbilk," South Australia, and the other with flies from "Groningen," The Netherlands, were sampled at generations 16 and 32. Spatial variation of the environment was stimulated using three food media. Eight polymorphic allozyme loci were used to estimate gametic disequilibria from digenic combinations of allotypes. All populations were duplicated within an environment and maintained at about 2500 adults. Standardized gametic disequilibria were compared by a weighted least squares analysis of the z-transformed statistical correlation of allele frequencies. Gametic disequilibria were strongly dependent upon food niche and food-niche interactions. The effects also varied with sampling time and were similar in duplicate populations. Gametic disequilibria were most often detected in the "Groningen"-derived populations and their strength was not strongly associated with recombination fraction. Many of the disequilibria concerned unlinked loci. The strength of selection was probably considerable and populations were evolving genetic architectures which reflected niche selection by the different foods without marked genetic isolation between foods; gene frequencies did not vary between niches within a population cage.     

Laminin and Type IV Collagen Isoform Substitutions Occur in Temporally and Spatially Distinct Patterns in Developing Kidney Glomerular Basement Membranes

Kidney glomerular basement membranes (GBMs) undergo laminin and type IV collagen isoform substitutions during glomerular development, which are believed to be required for maturation of the filtration barrier. Specifically, GBMs of earliest glomeruli contain laminin α1β1γ1 and collagen α1α2α1(IV), whereas mature glomeruli contain laminin α5β2γ1 and collagen α3α4α5(IV). Here, we used confocal microscopy to simultaneously evaluate expression of different laminin and collagen IV isoforms in newborn mouse GBMs. Our results show loss of laminin α1 from GBMs in early capillary loop stages and continuous linear deposition of laminin bearing the α5 chain thereafter. In contrast, collagen α1α2α1(IV) persisted in linear patterns into late capillary loop stages, when collagen α3α4α5(IV) first appeared in discontinuous, non-linear patterns. This patchy pattern for collagen α3α4α5(IV) continued into maturing glomeruli where there were lengths of linear, laminin α5-positive GBM entirely lacking either isoform of collagen IV. Relative abundance of laminin and collagen IV mRNAs in newborn and 5-week-old mouse kidneys also differed, with those encoding laminin α1, α5, β1, β2, and γ1, and collagen α1(IV) and α2(IV) chains all significantly declining at 5 weeks, but α3(IV) and α4(IV) were significantly upregulated. We conclude that different biosynthetic mechanisms control laminin and type IV collagen expression in developing glomeruli.