Tree establishment along an ENSO experimental gradient in the Atacama desert

Questions: (1) What are the roles of regional climate and plant growth rate for seedling establishment during ENSO rainy pulses along the western coast of South America? (2) What is the water threshold for tree seedling establishment in these arid ecosystems? Location: Atacama Desert, western South America: Piura (5°10’ S, 80°37’ W), Mejia (17°00’ S, 71°59’ W), Fray Jorge (30°41'S,71°37'W). Methods: We experimentally simulated a gradient of ENSO rainfall in three locations encompassing the total extent of the Atacama Desert to test the relative importance of regional climate for seedling establishment during rainy pulses. We also carried out a common garden experiment to test the role of potential interspecific differences in growth rate among two Prosopis tree species. Results: Water threshold for seedling survival increased towards the south with less than 27 mm required in Piura, 100 mm in Mejia and 450 mm in Fray Jorge. We found that seedling survival and growth rate (shoots and roots) were much higher in Piura than in the other two sites for both Prosopis species. Conclusions: Our results indicate that tree establishment during rainy pulses is more likely to be successful in regions where rain falls during warm months and stimulates fast plant growth, and where loose soil texture facilitates deep root growth and therefore access to more stable water sources.     

Invasive grass litter facilitates native shrubs through abiotic effects

Questions: Plant invasions are considered one of the top threats to the biodiversity of native taxa, but clearly documenting the causal links between invasions and the decline of native species remains a major challenge of invasion biology. Most studies have focused on impacts of invaders' living biomass, rather than on mechanisms mediated by litter. However, invasive plant litter, which is often of a very different type and quantity than a system's native plant litter, can have multiple important effects on ecosystem processes – such as nitrogen cycling and soil microclimate – that may influence native plants. Location: We studied effects of litter of invasive grass species that are widespread throughout western North America on native shrubs in southern California's semi‐arid habitat of coastal sage scrub. Methods: We combined a 3‐year field manipulation of non‐native litter with structural equation modeling to understand interacting effects on non‐native grasses, native shrubs, soil nitrogen (available and total), and soil moisture. Results: Litter addition facilitated non‐native grass growth, revealing a positive feedback likely to enhance invasion success. Contrary to a major paradigm of invasion biology – that competition with invasive plant species causes declines of native plants – we found that litter also facilitated growth of the native dominant shrub, a result supported by observational trends. Structural equation models indicated that enhanced soil moisture mediated the positive effects of litter on shrub growth. Conclusions: We demonstrate that invasive plants, via their litter, can facilitate dominant native plants by altering soil moisture. Our results highlight that understanding the impacts and mechanisms of plant invasions may be enhanced by considering the role of invasive plant litter on native plants and ecosystem properties.     

Semi‐Markov Models with Phase‐Type Sojourn Distributions

Summary Continuous‐time multistate models are widely used for categorical response data, particularly in the modeling of chronic diseases. However, inference is difficult when the process is only observed at discrete time points, with no information about the times or types of events between observation times, unless a Markov assumption is made. This assumption can be limiting as rates of transition between disease states might instead depend on the time since entry into the current state. Such a formulation results in a semi‐Markov model. We show that the computational problems associated with fitting semi‐Markov models to panel‐observed data can be alleviated by considering a class of semi‐Markov models with phase‐type sojourn distributions. This allows methods for hidden Markov models to be applied. In addition, extensions to models where observed states are subject to classification error are given. The methodology is demonstrated on a dataset relating to development of bronchiolitis obliterans syndrome in post‐lung‐transplantation patients.     

Structure of biological soil crust communities in Callitris glaucophylla woodlands of New South Wales,Australia

Question: What is the nature of the relationships between cover, diversity and abundance of biological soil crusts, cover and diversity of vascular plants, and annual rainfall, soil texture and forestry practices in Callitris glaucophylla woodlands? Location: Arid and semi‐arid Callitris glaucophylla‐domi‐nated woodlands of eastern Australia. Methods: We documented soil crust‐forming mosses, lichens and liverworts at 83 woodland sites along a gradient of declining rainfall. Linear and non‐linear regression were used to examine relationships between soil crust species and attributes of vascular plant communities, and a similarity matrix (species abundance X sites) was subjected to Non‐metric Multi‐Dimensional Scaling (MDS), and Analysis of Similarities (ANOSIM) to show the degree of association between groups of taxa, and soil texture, rainfall classes and forestry practices. Results : We collected 86 taxa. Mosses were dominated by the family Pottiaceae, and lichens were dominated by squamulose forms. Average annual rainfall was highly correlated with soil crust community composition, and loamy soils supported a greater cover and diversity of taxa compared with sandy soils. Increases in tree cover were associated with significant, though weak, increases in abundance, but not diversity, of crusts. Crusts tended to be more diverse in areas that (1) had a sparse cover of ground‐storey plants; (2) were relatively stable ‐ as indicated by the proportion of perennial and/or native plants; (3) had more stable soil surfaces; and (4) were unlogged. Litter cover, overstorey thinning, and livestock grazing had no appreciable effect on crust diversity or cover. Conclusions : Callitris glaucophylla woodlands provide substantial habitat for soil crust organisms, and the dense tree cover and closed canopies of Callitris do not appear to have a major influence on the structure of biological crust communities. Unlike other woodland systems, relatively few patches would be required to reserve a high diversity of crust species.     

Dispersal,diversity and distribution patterns in pioneer vegetation: The role of river‐floodplain connectivity

Question: Are there changes in dispersal patterns in floodplain pioneer vegetation with effects on seedling number, species richness and species composition along a gradient of declining river‐floodplain connectivity? Location: Middle Elbe river floodplain, Germany. Methods: An experiment with five treatments was set up along a gradient of declining river‐floodplain connectivity, partitioning seedlings into three groups: (1) emerging solely from water dispersed seeds, (2) from wind/animal dispersed seeds and (3) from the soil diaspore bank. Two controls were established: without any manipulation and exclusion of all seeds. The results were compared with those of vegetation and soil sampling to evaluate the representativeness of the experimental sites in terms of species composition, diversity, seedling number and soil parameters. Results: Water dispersal and the soil diaspore bank were the major dispersal strategies shaping floodplain pioneer vegetation at the Middle Elbe river. The number of seedlings, species richness and the variation in species composition in these habitats depend on the degree of connectivity. The seedling number and species richness is highest in sites of permanent or almost permanent exchange with the main channel, where water dispersal additionally contributes to the number of seedlings grown from the soil seed bank. Conclusion: The results underline the importance of river‐floodplain ecotones as sink habitats for water‐dispersed seeds. Considering the strongly reduced river‐floodplain interactions due to dykes and other engineering structures, management strategies are necessary to improve connectivity and the renewal of fluvial land forms.     

Exploring spatial and temporal variations of cadmium concentrations in pacific oysters from british columbia

Oysters from the Pacific Northwest coast of British Columbia, Canada, contain high levels of cadmium, in some cases exceeding some international food safety guidelines. A primary goal of this article is the investigation of the spatial and temporal variation in cadmium concentrations for oysters sampled from coastal British Columbia. Such information is important so that recommendations can be made as to where and when oysters can be cultured such that accumulation of cadmium within these oysters is minimized. Some modern statistical methods are applied to achieve this goal, including monotone spline smoothing, functional principal component analysis, and semi-parametric additive modeling. Oyster growth rates are estimated as the first derivatives of the monotone smoothing growth curves. Some important patterns in cadmium accumulation by oysters are observed. For example, most inland regions tend to have a higher level of cadmium concentration than most coastal regions, so more caution needs to be taken for shellfish aquaculture practices occurring in the inland regions. The semi-parametric additive modeling shows that oyster cadmium concentration decreases with oyster length, and oysters sampled at 7 m have higher average cadmium concentration than those sampled at 1 m.     

Feature-based classification of native and non-native protein-protein interactions: Comparing supervised and semi-supervised learning approaches

Structural knowledge about protein-protein interactions can provide insights to the basic processes underlying cell function. Recent progress in experimental and computational structural biology has led to a rapid growth of experimentally resolved structures and computationally determined near-native models of protein-protein interactions. However, determining whether a protein-protein interaction is physiological or it is the artifact of an experimental or computational method remains a challenging problem. In this work, we have addressed two related problems. The first problem is distinguishing between the experimentally obtained physiological and crystal-packing protein-protein interactions. The second problem is concerned with the classification of near-native and inaccurate docking models. We first defined a universal set of interface features and employed a support vector machines (SVM)-based approach to classify the interactions for both problems, with the accuracy, precision, and recall for the first problem classifier reaching 93%. To improve the classification, we next developed a semi-supervised learning approach for the second problem, using transductive SVM (TSVM). We applied both classifiers to a commonly used protein docking benchmark of 124 complexes. We found that while we reached the classification accuracies of 78.9% for the SVM classifier and 80.3% for the TSVM classifier, improving protein-docking methods by model re-ranking remains a challenging problem.     

A test for spatial relationships between neighbouring plants in plots of heterogeneous plant density

Abstract. Maps of plant individuals in (x, y) coordinates (i.e. point patterns) are currently analysed through statistical methods assuming a homogeneous distribution of points, and thus a constant density within the study area. Such an assumption is seldom met at the scale of a field plot whilst delineating less heterogeneous subplots is not always easy or pertinent. In this paper we advocate local tests carried out in quadrats partitioning the plot and having a size objectively determined via a trade‐off between squared bias and variance. In each quadrat, the observed pattern of points is tested against complete spatial randomness (CSR) through a classical Monte‐Carlo approach and one of the usual statistics. Local tests yield maps of p‐values that are amenable to diversified subsequent analyses, such as computation of a variogram or comparison with co‐variates. Another possibility uses the frequency distribution of p‐values to test the whole point pattern against the null hypothesis of an inhomogeneous Poisson process. The method was demonstrated by considering computer‐generated inhomoge‐neous point patterns as well as maps of woody individuals in banded vegetation (tiger bush) in semi‐arid West Africa. Local tests proved able to properly depict spatial relationships between neighbours in spite of heterogeneity/clustering at larger scales. The method is also relevant to investigate interaction between density and spatial pattern in the presence of resource gradients.