Protein induction process and stochastic nature of cell commitment to proliferation and differentiation

A differential equation model is constructed to describe competition between trees with overlapping crowns. The model is based upon Thornley's mechanistic plant growth model which divides plant biomass into three components corresponding to storage material, degradable structural tissue and non-degradable structural tissue. The available incident radiation is partitioned among trees according to their sizes, with large trees intercepting more light than smaller neighbours. Analysis of the dynamic stability of the model reveals that suppression occurs over a wide range of parameter space. Typically, as canopy overlap increases and competition for light becomes intense, some trees are suppressed by their neighbours. The suppression-dominance phenomenon occurs even in stands of trees with identical parameter values. Model simulations are compared with data on the growth of Pinus radiata.     

The strength of competition among individual trees and the biomass-density trajectories of the cohort

We simulated the self-thinning of Rhizophora mangle mangrove forests with the spatially explicit simulation model KiWi. This model is an application of the field-of-neighbourhood (FON) approach, which describes an individual tree by a competition function defined on the zone of influence (ZOI) around the stem. The FON causes growth depression of the trees involved. Sustained growth depression results in tree death. We propose a subdivision of the biomass density trajectories (bdt), obtained during the thinning process, into four segments related to characteristic shapes of the stem diameter distribution of the cohort. A positive skewness of the stem diameter distribution, indicating that the majority of the individuals are small and hindered in growth, is necessary for the occurrence of a linear segment within the bdt, the so-called 'self-thinning line'. This segment is the third bdt segment according to our classification. It is reached when the positive skewness of the stem diameter distribution is maximal and ends when the skewness reaches its second zero transition. The thinning line is therefore linked to the homogenisation process, which forces the symmetry of the stem distribution. We show that the ongoing search for a universal slope for the linear segment of the biomass-density trajectory (bdt) cannot succeed, since it is species-specific and may also be site-dependent. The slope increases with increasing competition strength of the individuals. Nevertheless, the lower limit of the slope is pre-defined by geometrical constraints and modified by the actual strength of the neighbourhood competition. Although the simulations were all carried out with growth parameters of the mangrove species Rhizophora mangle, our results should be qualitatively valid and form a plausible theoretical framework to account for different biomass-density trajectories.     

Spatial pattern analysis and competition between Acacia karroo trees in humid savannas

It is unclear whether inter-tree competition plays a role in determining the woody plant cover of humid savannas. Spatial point-pattern analysis can give insights to the underlying processes affecting the individuals in a population. We assessed the spatial patterns of Acacia karroo trees from savannas in KwaZulu-Natal, using conventional nearest neighbour analysis and second-order spatial statistics such as Ripley??s K- and L-functions, and the univariate and bivariate O-ring statistics. We predicted that juvenile trees would be spatially aggregated, because of facilitation between shrubs when zones of overlap are relatively small, while adult trees would be regularly spaced because of the effects of density-dependent mortality (i.e. consistent with the honeycomb rippling model). We found that juvenile trees were more aggregated than expected by chance, and the overall spatial distribution of all trees was also found to be aggregated, with no evidence of regularity among large individuals. Nearest neighbour analysis, however, revealed significant positive correlations between the sum of the distances to the four nearest neighbours and the sum of the canopy diameters of the target tree and its four nearest neighbours, indicating the presence of competition. In sum, these findings suggest that competitive interactions between A. karroo trees at these sites are relatively weak, and result in decreased performance (smaller canopy diameters) rather than mortality, thus preventing a regular pattern of tree distribution. We advocate the use of both methods of detecting competitive interactions in the field, especially if the effects of competition are too subtle to result in differential mortality.     

Depth distribution of cherry (Prunus avium L.) tree roots as influenced by grass root competition

We investigated the effect of competition from grass roots (as controlled by herbicide application) on the depth distribution of white roots in cherry trees, grown with varying rates and frequency of application of N in an agroforestry system. Statistical summaries of distribution, namely mean and skewness, produced a concise and interpretable analysis of the data.There was a large increase in tree root numbers in the surface horizons after the herbicide had reduced grass root competition. Where the surrounding grass had not been reduced by herbicide, the average depth of tree roots increased with time, contrasting with a marked shift in the mode of distribution of root numbers to shallow depths when grass competition was removed. These findings are important in the understanding of plant root competition and for prescribing best practise for tree establishment in agroforestry systems.     

Differentiation and frequency distributions of body weights in plants and animals

The basic and simplest system that one can consider in ecology is a group of individuals of equal age and representing one species, that is, a cohort. This paper is an attempt to show that analysis of such a system may be of great importance to understanding basic ecological problems, such as, intraspecific competition and the dynamics of a single population. It is easy to observe that in even-aged populations individuals differ in weights. A close look can show that weight distributions in even-aged populations may have different skewness. Most common are distributions with coefficients of skewness greater than zero. Sometimes weight distributions are symmetrical or with skewness coefficients less than zero. In a cohort of growing individuals the coefficient of skewness changes with time: most often starting from zero (symmetrical distribution), it increases in time; sometimes after an initial increase it can decrease in the final stage of growth, which is related to an increased mortality of individuals. The rate of change in skewness, and the skewness itself depend on the density of individuals in a cohort and on food conditions. They are greater at higher densities and increase with deteriorating food conditions. Weight distributions are symmetrical at low densities and optimal food conditions. The differences in individual weights measured by variance of weight distributions or coefficient of variation follow the same pattern, but observed changes with time, density and food conditions are not so clear. These conclusions rest upon the review of numerous papers concerning both plants and animals, which is presented in this paper. In the past, the properties of weight distributions in even-aged populations were explained not by interactions between individuals, but rather as a natural outcome of the growth process of non-interacting individuals. The exponential equation of growth, with relative growth rate having a normal distribution in populations, was used to support this hypothesis. Obtained weight distributions were of positive skewness; however, this model, which in fact is able to describe the growth process only in its initial stage, cannot explain the changes of skewness of weight distributions with density and food conditions. A model has been developed which includes competitive interactions among members of even-aged populations to explain observed properties of weight distributions in them. The basic assumption is that intraspecific competition leads to uneven partitioning of resources, which are the object of competition. Functions describing resource partitioning among individuals are included into the model.(ABSTRACT TRUNCATED AT 400 WORDS)     

Modelling Growth-Competition Relationships in Trembling Aspen and White Spruce Mixed Boreal Forests of Western Canada

We examined the effect of competition on stem growth of Picea glauca and Populus tremuloides in boreal mixedwood stands during the stem exclusion stage. We combined traditional approaches of collecting competition data with dendrochronology to provide retrospective measurements of stem diameter growth. Several competition indices including stand basal area (BA), the sum of stem diameter at breast height (SDBH), and density (N) for the broadleaf and coniferous species, as well as similar indices considering only trees with diameters greater than each subject (BAGR, SDBHGR, and NGR), were evaluated. We used a nonlinear mixed model to characterize the basal area increment over the past 5, 10, 15, 20, 25, 30, and 35 years as a function of growth of nearby dominant trees, the size of the subject trees, deciduous and coniferous competition indices, and ecoregions. SDBHGR and BAGR were better predictors for spruce, and SDBHGR and NGR were better for aspen, respectively, than other indices. Results showed strongest correlations with long-term stem growth, as the best models integrated growth for 10–25 years for aspen and ≥25 for spruce. Our model demonstrated a remarkable capability (adjusted R²>0.67) to represent this complex variation in growth as a function of site, size and competition.     

Partitioning of root and shoot competition and the stability of savannas

A classic problem in coexistence theory is how grasses and trees coexist in savannas. A popular deterministic model of savannas, the rooting niche separation model, is based on an assumption that is not empirically supported in many savannas. Alternative models that do not rely on the rooting niche assumption invoke intricate stochastic mechanisms that limit their attractiveness as general models of savannas. In this article we develop an alternative deterministic model of grass-tree interactions and use it to analyze the conditions under which grass-tree coexistence is possible. The novel feature of this model is that it partitions aboveground and belowground competition and simulates the fact that fire and herbivory remove only aboveground biomass. The model predicts that stable coexistence of grasses and trees is possible, even when grasses and trees do not have separate rooting niches. We show that when aboveground competition is intense, grasses can be excluded by trees; under such conditions, fire can prevent grasses from exclusion and induce a stable savanna state. The model provides a general framework for exploring the interactive effects of competition, herbivory, and fire on savanna systems.     

Effect of climate and competition on radial growth of Pinus massoniana and Schima superba in China’s subtropical monsoon mixed forest

Tree growth is affected by many exogenous and endogenous factors, especially climate and competition. To address the issue of how these factors influence tree growth under global warming, dendroclimatology combined with competition analysis was used to examine the radial growth response of two major species – Pinus massoniana and Schima superba in subtropical monsoon mixed forests in southern China. For growth-climate relationship analysis, residual and ARSTAN chronologies of these two species were compared for the response function analysis over the past several decades. In terms of competition analysis, annual basal area increment (BAI) over several time intervals was calculated and linear mixed model techniques were employed. Several distance-independent competition indices were measured, including density (N), basal area (BA), and sum of diameter at breast height (SDBH). For competition trees with greater diameter (GR) than the subject tree, NGR, BAGR, SDBHGR were also calculated. Growth-climate relationship analysis suggested that tree growth varied in response to climate and was mostly correlated with minimum, mean and maximum air temperature as indicated by the adjusted R² value. Summer and winter temperatures had a negative effect on tree growth, while early spring temperature showed positive effects. Competition analysis suggested that subtropical trees had been affected by competition in varying degrees. Trees in the oldest forest had the most competition stress, while trees in younger forests were less affected by competition according to the adjusted R² value. Given that subtropical forests in China have been found to have more smaller trees with recent warming, it is expected that these forests will experience a decreasing effect of competition in near future. This can have profound effects on forest productivity and carbon sequestration potentials in Chinese subtropical forests.     

树木胸径大小对树干液流变化格局的偏度和时滞效应

通过分析具不同水力结构的马占相思、荷木和粉单竹液流变化格局的偏度和时滞,探讨液流的空间分布特征及对冠层蒸腾的影响。结果表明:荷木的液流格局偏度和时滞随树木胸径的增加呈减小的趋势,但马占相思由于冠层开阔和林分分化程度高而规律不明显,粉单竹液流偏度随胸径减少,由于冠幅较小,接受的光照较均匀,个体间的时滞差异不明显,但时滞值比胸径近似的荷木小。树干水分传输过程中存在液流再分配的现象,边材的导水效率可能是影响时滞的重要原因。冠层蒸腾的空间异质性与树木储存水有关,大树储存水较多,冠层蒸腾的异质性小;小树储存水较少,液流被优先分配到光照充足的东南方位,导致冠层蒸腾较高的异质性。旱季受土壤水分的限制,大树储存水对蒸腾的贡献大于湿季,而小树蒸腾由于受到储水容量的制约,储存水对蒸腾的贡献小于湿季。冠层接受光照的迟或早以及辐射量的大小是引起蒸腾时间变化格局和树干不同方位液流格局差异的重要原因,但液流的横向交换弱化了这种现象,往往是个体间的差异掩盖了方位的差异。湿季较小胸径的树木比偏值(枝下高与胸高处液流偏度的比值)大于旱季,而较大胸径的树木比偏值恰好相反,总体而言,比偏值随着胸径的增加而逐渐下降。     

Maximum Parsimony and the Skewness Test: A Simulation Study of the Limits of Applicability

The maximum parsimony (MP) method for inferring phylogenies is widely used, but little is known about its limitations in non-asymptotic situations. This study employs large-scale computations with simulated phylogenetic data to estimate the probability that MP succeeds in finding the true phylogeny for up to twelve taxa and 256 characters. The set of candidate phylogenies are taken to be unrooted binary trees; for each simulated data set, the tree lengths of all (2n − 5)!! candidates are computed to evaluate quantities related to the performance of MP, such as the probability of finding the true phylogeny, the probability that the tree with the shortest length is unique, the probability that the true phylogeny has the shortest tree length, and the expected inverse of the number of trees sharing the shortest length. The tree length distributions are also used to evaluate and extend the skewness test of Hillis for distinguishing between random and phylogenetic data. The results indicate, for example, that the critical point after which MP achieves a success probability of at least 0.9 is roughly around 128 characters. The skewness test is found to perform well on simulated data and the study extends its scope to up to twelve taxa.     

Effect of sex ratio,habitat factors and neighborhood competition on stem growth in the dioecious tree Fraxinus mandshurica

Growth rates of male and female trees are often different in a dioecious species. In this study, we analyzed sex ratios and the effect of gender, neighborhood competition and habitat factors on the stem growth of dioecious Fraxinus mandshurica trees in a secondary conifer and broad-leaved mixed forest in the Changbai Mountains of northeastern China. The sex ratio in the 5.2-ha study area does not deviate significantly from the expected 1:1 ratio, except for trees in the large diameter classes. For dbh >40 cm, the sex ratio is male-biased. This result suggests that males have a faster rate of stem growth than females, which is usually explained by the higher cost of reproduction in the fruit-bearing females. An analysis of the dbh distributions of two successive measurements showed that the rate of stem growth of the (27) females drops off with increasing dbh and remains below that of the (35) males. A causal model was used to analyze factors affecting the rate of stem growth, showing that these rates are affected significantly and positively by soil moisture and tree size in both genders and that within-gender competition is mainly for nitrogen. Our study suggests that neighborhood competition does not affect stem growth significantly, which is a rather surprising result.     

The Enemy of My Enemy Hypothesis: Why Coexisting with Grasses May Be an Adaptive Strategy for Savanna Trees

Savannas are characterized by the coexistence of trees and flammable grasses. Yet, tree–grass coexistence has been labeled as paradoxical—how do these two functional groups coexist over such an extensive area, despite being generally predisposed to excluding each other? For instance, many trees develop dense canopies that limit grass growth, and many grasses facilitate frequent/intense fires, increasing tree mortality. This study revisits tree–grass coexistence with a model of hierarchical competition between pyrogenic grasses, “forest trees” adapted to closed-canopy competition, and “savanna trees” that are inferior competitors in closed-canopy communities, but more resistant to fire. The assumptions of this model are supported by empirical observations, including a systematic review of savanna and forest tree community composition reported here. In general, the model simulations show that when savanna trees exert weaker competitive effects on grasses, a self-reinforcing grass community is maintained, which limits forest tree expansion while still allowing savanna trees to persist (albeit as a subdominant to grasses). When savanna trees exert strong competitive effects on grasses, savanna trees cover increases initially, but as grasses decline their inhibitory effect on forest trees weakens, allowing forest trees to expand and exclude grasses and savanna trees. Rather than paradoxical, these results suggest that having weaker competitive effects on grasses may be advantageous for savanna trees, leading to greater long-term abundance and stability. We label this the “enemy of my enemy hypothesis,” which might apply to species coexistence in communities defined by hierarchical competition or with species capable of generating strong ecological feedbacks.     

FREQUENCY DISTRIBUTIONS OF LENGTHS OF POSSIBLE NETWORKS FROM A DATA MATRIX

Abstract— It is common practice to attempt to find the minimum length tree (also known as the Wagner tree) for a given data matrix on a group of OTUs (taxa). However, little study has been made of the pattern of frequency distributions when the lengths of all possible networks (unrooted trees) are taken into consideration. A published real data matrix with eight OTUs was compared with randomly generated data, when the former showed a much larger variance and very marked skewness. A number of published data matrices with a larger number of OTUs were studied by random selection of 10240 out of the possible trees: these were compared with 32 randomly generated data sets with 13 OTUs, using the same program. An algorithm has been found for calculation of the expected mean, variance and skewness for random binary data with up to 13 OTUs, based on the number of characters representing each type of partition of the OTUs. The calculation requires listing of the possible topologies and their relative weighting, which are tabulated.     

High epitope expression levels increase competition between T cells

Both theoretical predictions and experimental findings suggest that T cell populations can compete with each other. There is some debate on whether T cells compete for aspecific stimuli, such as access to the surface on antigen-presenting cells (APCs) or for specific stimuli, such as their cognate epitope ligand. We have developed an individual-based computer simulation model to study T cell competition. Our model shows that the expression level of foreign epitopes per APC determines whether T cell competition is mainly for specific or aspecific stimuli. Under low epitope expression, competition is mainly for the specific epitope stimuli, and, hence, different epitope-specific T cell populations coexist readily. However, if epitope expression levels are high, aspecific competition becomes more important. Such between-specificity competition can lead to competitive exclusion between different epitope-specific T cell populations. Our model allows us to delineate the circumstances that facilitate coexistence of T cells of different epitope specificity. Understanding mechanisms of T cell coexistence has important practical implications for immune therapies that require a broad immune response.     

A Kramers-Moyal Approach to the Analysis of Third-Order Noise with Applications in Option Valuation

We propose the use of the Kramers-Moyal expansion in the analysis of third-order noise. In particular, we show how the approach can be applied in the theoretical study of option valuation. Despite Pawula’s theorem, which states that a truncated model may exhibit poor statistical properties, we show that for a third-order Kramers-Moyal truncation model of an option’s and its underlier’s price, important properties emerge: (i) the option price can be written in a closed analytical form that involves the Airy function, (ii) the price is a positive function for positive skewness in the distribution, (iii) for negative skewness, the price becomes negative only for price values that are close to zero. Moreover, using third-order noise in option valuation reveals additional properties: (iv) the inconsistencies between two popular option pricing approaches (using a “delta-hedged” portfolio and using an option replicating portfolio) that are otherwise equivalent up to the second moment, (v) the ability to develop a measure R of how accurately an option can be replicated by a mixture of the underlying stocks and cash, (vi) further limitations of second-order models revealed by introducing third-order noise.     

Density effect, self-thinning and size distribution in Pinus densiflora Sieb. et Zucc. stands

The competition-density (C-D) effect for given times and self-thinning over time in even-aged, natural, pure stands of Pinus densiflora Sieb. et Zucc. were analyzed with the reciprocal equation of the C-D effect in self-thinning stands, and the equation describing the time-trajectory of mean stem volume and stand density. The C-D effect and self-thinning were consistently well explained by the two equations. Differences in mean stem volume and in stand density among the stands tended to merge with increasing stand age. The self-thinning line with a slope of approximately –3/2 was reached by the higher density stand prior to the medium and lower density stands. The skewness of tree height distribution showed positive values, which means that the distribution is more or less L-shaped, and in addition the skewness decreased with increasing mean tree height, which indicates that smaller trees died as the stands grew. This trend is consistent with the asymmetric (one-sided) competition hypothesis that self-thinning is driven by competition for light. The tree height distribution was analyzed using the Weibull distribution. The location parameter h _min of the Weibull distribution increased with increasing stand age, and the scale parameter a tended to increase slightly with increasing stand age. The range of the shape parameter b of the Weibull distribution corresponded to that of the skewness.     

Morphological plasticity in mangrove trees: salinity-related changes in the allometry of Avicennia germinans

Key Message

Morphological plasticity helps plants to cope to environmental conditions. Allometric responses of the mangrove Avicennia germinans to increasing salinity are easily detectable when focusing on the top height trees.

Abstract

Several studies show that mangrove trees possess high species- and site-related trait allometry, suggesting large morphological plasticity that might be related to environmental conditions, but the causes of such variation are not clearly understood and systematic quantification is still missing. Both aspects are essential for a mechanistic understanding of the development and functioning of forests. We analyzed the role of salinity in the allometric relations of the mangrove Avicennia germinans, using: (1) the top height trees (trees with the largest diameters at breast height, which reflect forest properties at the maximum use of resources); (2) the slenderness coefficient (which indicates competition and environmental conditions); and (3) the crown to DBH ratio. These standard tools for forest scientists dealing with terrestrial forests are suitable to analyze the plastic responses of mangroves to salinity. First, the top height trees help to recognize structural forest properties that are not detectable when studying the whole stand. Second, we found that at salinities above 55 ‰, trees are less slender and develop wider crowns in relation to DBH than when growing at lower salinities. Our results suggest a significant change in allometric traits in relation to salinity, and reflect the plastic responses of tree traits in response to environmental variation. Understanding the plastic responses of plants to their environment can help to better model, predict, and manage forests in changing environments.     

Successions in forest coenoses after windfall: Models of tree competition

Based on the concept of competition for resources, the distribution of trees upon reforestation in windfall areas is studied. As a theoretical model for competition, a Zipf-Pareto model of ranking the distribution of resources is used. Analysis shows that the processes resulting from competitive interactions between the trees of different species proceed slowly in a windfall area where coniferous species get replaced by deciduous ones. In the territory where deciduous species initially dominated, competitive interactions between trees of different species turn out to be formed almost immediately upon natural reforestation after the windfall. By the time the ratio of species stabilizes and becomes a steady state, the ranks of individual species also stabilize. This result is obtained on the basis of a quantitative assessment of the change in leadership between competing species in time using Spearman’s rank correlation coefficient.     

Short- and long-term responses to seasonal drought in ponderosa pines growing at different plantation densities in Patagonia, South America

Trees drought responses could be developed in the short- or in the long-term, aiming at sustaining carbon fixation and water use efficiency (WUE). The objective of this study was to examine short- and long-term adjustments occurring in different size Pinus ponderosa Dougl. ex P. & C. Laws trees in response to seasonal drought when they are growing under different competition level. The following variables were studied: branch and stem hydraulic conductivity, canopy and stomatal conductance (gc, gs), transpiration (E), photosynthesis (A _max), wood δ¹³C (as a proxy of intrinsic WUE), leaf to sapwood area ratio (A _L:A _s) and growth in the biggest (B) and the smallest (S) trees of high (H) and low (L) density stands. A _L:A _s was positively correlated with tree size and negatively correlated with competition level, increasing leaf hydraulic conductance in H trees. Accordingly, higher gc and E per unit A _L were found in H than in L trees when soil water availability was high, but decreased abruptly during dry periods. BL trees maintained stable gc and E values even during the summer drought. The functional adjustments observed in H trees allow them to maintain their hydraulic integrity (no apparent k _s losses), but their stem and leaf growth were severely affected by drought events. _iWUE was similar between all tree groups in a wet season, whereas it significantly decreased in SH trees in a dry season suggesting that when radiation and water are co-limiting gas exchange, functional adjustments not only affect absolute growth, but also WUE.     

Competition for dead trees between humans and aye-ayes (<Emphasis Type="Italic">Daubentonia madagascariensis</Emphasis>) in central eastern Madagascar

The destruction and degradation of forest habitats are major threats to the sustainability of lemur populations in Madagascar. Madagascan landscapes often contain forest fragments that represent refuges for native fauna, while also being used for firewood and timber by local human populations. As undisturbed forest becomes increasingly scarce, understanding resource competition between humans and wildlife in disturbed habitats will be increasingly important. We tested the hypothesis that Malagasy and aye-ayes (Daubentonia madagascariensis) compete for the limited number of dead trees in rainforest fragments at Tsinjoarivo, Madagascar. We surveyed 2.16 ha within five fragments (range 5–228 ha) surrounding human settlements to quantify the density of dead trees and traces of both human and aye-aye activity. Neither aye-aye nor human traces were distributed according to the availability of particular trees species, and aye-ayes and Malagasy apparently preferred several different species. Although overlap was recorded in tree species used, human use tended to be positively correlated with a species’ desirability as firewood, while a negative relationship was seen for aye-ayes. Both consumers used trees of similar diameter at breast height, but those used by aye-ayes tended to be older, suggesting that human use might precede usefulness for aye-ayes. Finally, the density of dead trees and aye-aye traces were highest in smaller fragments, but human traces did not vary across fragment size. Although further study is needed to better quantify the aye-aye diet in this region, these data suggest that aye-ayes and local people compete for dead trees, and this competition could constitute a pressure on aye-aye populations.