A physiological analogy of the niche for projecting the potential distribution of plants

Aim  To develop a physiologically based model of the plant niche for use in species distribution modelling. Location  Europe. Methods  We link the Thornley transport resistance (TTR) model with functions which describe how the TTR’s model parameters are influenced by abiotic environmental factors. The TTR model considers how carbon and nutrient uptake, and the allocation of these assimilates, influence growth. We use indirect statistical methods to estimate the model parameters from a high resolution data set on tree distribution for 22 European tree species. Results  We infer, from distribution data and abiotic forcing data, the physiological niche dimensions of 22 European tree species. We found that the model fits were reasonable (AUC: 0.79–0.964). The projected distributions were characterized by a false positive rate of 0.19 and a false negative rate 0.12. The fitted models are used to generate projections of the environmental factors that limit the range boundaries of the study species. Main conclusions  We show that physiological models can be used to derive physiological niche dimensions from species distribution data. Future work should focus on including prior information on physiological rates into the parameter estimation process. Application of the TTR model to species distribution modelling suggests new avenues for establishing explicit links between distribution and physiology, and for generating hypotheses about how ecophysiological processes influence the distribution of plants.     

On computational efficiency of the hybrid Monte Carlo method applied to the multicanonical ensemble

Abstract

In the present paper, computational efficiency of the hybrid Monte Carlo (HMC) method applied to the multicanonical ensemble is studied; the HMC is an equation of motion guided Monte Carlo method. As in the standard HMC for the canonical ensemble, the multicanonical HMC calculations with high acceptance ratio show better efficiency; about 60% acceptance yields the best performance for the system examined.     

Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

We present an approach which can be used to identify native-like folds in a data base of protein conformations in the absence of any sequence homology to proteins in the data base. The method is based on a knowledge-based force field derived from a set of known protein conformations. A given sequence is mounted on all conformations in the data base and the associated energies are calculated. Using several conformations and sequences from the globin family we show that the native conformation is identified correctly. In fact the resolution of the force field is high enough to discriminate between a native fold and several closely related conformations. We then apply the procedure to several globins of known sequence but unknown three dimensional structure. The homology of these sequences to globins of known structures in the data base ranges from 49 to 17%. With one exception we find that for all globin sequences one of the known globin folds is identified as the most favorable conformation. These results are obtained using a force field derived from a data base devoid of globins of known structure. We briefly discuss useful applications in protein structural research and future development of our approach.     

Lipid vertical motion and related steric effects in bilayer membranes

We present a theoretical model of a lipid bilayer in its gel state which explicity couples the vertical displacements of the lipid chains to their conformational state. In this model the chains are free to move longitudinally under a potential due to the neighbouring chains. The potential is due to a restoring force with a force constant k and thus acts to keep them in the local plane as defined by their nearest neighbours. It is demonstrated that the force constant k is directly related to the internal bilayer pressure, , and that if a value =33 dynes/cm is assumed then k=17.3 dynes/cm. Steric effects are explicity included by allowing chains to twist into free volume created by the vertical displacement of neighbouring chains. The Hamiltonian is expressed in terms of the projection operators, P _ij , describing the displacement of chain i relative to a neighbour j, and G _ij describing the direction of a twist in chain i. The model is solved both analytically and via Monte Carlo simulations for a one-dimensional system. The possibility of phase-transitions in two-dimensions and the relevance to the bilayer pre-transition is discussed.This work was first presented in poster form at the Canadian Biochemical Society Conference held in Banff, Alberta, Canada, April 29–May 4, 1984Work supported in part by the Natural Sciences and Engineering Research Council of Canada, Le Fonds Formation des Chercheurs et Action a la Recherche du Quebec, and the Advisory Research Council of Queen's University     

Soluble metals in the atmosphere and their biological implications

Multivariate statistical analysis has been applied to time series measurements of aerosol elemental composition from PIXE analysis of filter samples, and principal components have been resolved that represent distinct particle types in an external mixture in the atmosphere. In this study, it is argued that a combination of chemical and statistical analyses of the data may be more powerful in determining chemical species in atmospheric aerosols than studies that employ mainly direct chemical analysis of chemical species in unresolved mixtures of aerosol particle samples. Sulfur is generally associated with mineral dust elements. It is reasoned that the association may represent sulfuric acid coatings on particles that can lead to mineral dissolution and solubilization of significant amounts of aluminum, iron, and other metals. Upon wet or dry deposition to the surface, the fluxes of these metals in biologically-available form may be sufficient to affect primary productivity in the world ocean and cause ecological damage in lakes. As a consequence, the fluxes of biogenic trace gases to the atmosphere may be changed, possibly leading to changes in the tropospheric concentration of ozone. The inputs to lakes of soluble aluminum, which is toxic to fish, may be partly by deposition directly from the atmosphere, thus not limited to leaching of soils by acid deposition. Human inhalation of soluble aluminum and other solulilized mineral metals may account, in part, for the observed geographic pattern of deaths attributed to chronic obstructive pulmonary disease (COPD) that show high rates in cities of the Western US and the southeast region, but low in most of the midwest and northeast.     

Computational sequence analysis of matrix metalloproteinases

Matrix metalloproteinases (MMP) play a cardinal role in the breakdown of extracellular matrix involved in a variety of biological and pathological processes. Research on MMPs has classified and characterized these enzymes according to their matrix substrate specificity, gene and protein domain structure, and regulation of activity and expression. However, the discovery of new MMPs has introduced a need for a more comprehensive and systematic method of classification and quantitative comparison of known and newly discovered members. This study compiles a sequence alignment, constructs a dendrogram, and calculates physical data and homology percentage assignments in order to obtain further insight into MMP structure-function relationships. Thorough analysis of MMP primary sequence domains, physical data patterns, and statistical analysis of sequence homology yields higher resolution in the similarities and differences that group MMP members.     

A protocol for classifying regional dynamics,exemplified by using woodland birds in southeastern Australia

Abstract Communities of forest and woodland birds are usually studied intensively at only one or a few locations. This provides a perspective that perhaps emphasizes local phenomena at the expense of placing local dynamics in the context of processes operating at the landscape or regional scale. The present paper seeks to redress partially this imbalance by studying the dynamics of individual bird species among several habitat types (all Eucalyptus-dominated forests or woodlands) over the annual cycle. This regional-scale (250km), continental study reveals that species exhibit idiosyncratic dynamics of various kinds: restricted or more ubiquitous occupation of habitats and three forms of seasonal dynamics at the regional scale (resident, migrant and itinerant). By using this classificatory scheme, it becomes evident that the bird communities found in different habitats consist of diverse collections of strategists and that the level of diversity differs among habitat types. The difficulties that many field workers have had in reconciling their observations with community theory most likely reflect the underlying dynamism of bird communities, especially in the temperate regions on continents where seasonal fluxes are pronounced.     

Detection of mining impacts on aquatic macroinvertebrate communities: Results of a disturbance experiment and the design of a multivariate BACIP monitoring programme at Coronation Hill,Northern Territory

Abstract Multivariate methods for the detection of impacts on communities are: (i) explored in the context of a disturbance experiment at a site of previous uranium mining in Kakadu National Park, Northern Territory; and (ii) applied to the design of a monitoring programme for a proposed mining development at nearby Coronation Hill. The disturbance experiment in Rockhole Mine Creek used a gravity-fed redirection of polluted water from the mine adit to create a point-source pollutant. Weekly samples of the macroinvertebrate communities were taken both before and after disturbance at the control and‘impact’ site, as part of a multivariate BACIP (Before-After-Control-Impact-Pairs) design. The results of the experiment show that the multivariate approach provided high sensitivity in detecting impacts on the community, with little difference in sensitivity between species and family level analyses. A simple procedure for deleting those taxa that show poor discrimination between pristine and presently disturbed areas further increased the sensitivity of the tests. In addition to the BACIP analyses, robust ordination of the community data suggested a time/treatment interaction effect. Application of the multivariate BACIP approach also was explored using baseline data for benthic communities from the South Alligator River near Coronation Hill. The method provides high statistical power for monitoring; a relatively small change in community dissimilarity would be detectable in a programme with 5 years of observations before and after commencement of mining. A robust ordination of the yearly samples for the control and potential-impact sites showed that, although samples varied along identifiable gradients over time, the two areas changed in parallel so that the difference between the areas was approximately constant over years. This result demonstrates that the multivariate BACIP approach can provide relative constancy of pre-impact difference values, a key requirement of BACIP designs that is difficult to satisfy using abundance data for a single species.     

Initial soil organic carbon stocks govern changes in soil carbon: Reality or artifact?

Changes in soil organic carbon (SOC) storage have the potential to affect global climate; hence identifying environments with a high capacity to gain or lose SOC is of broad interest. Many cross-site studies have found that SOC-poor soils tend to gain or retain carbon more readily than SOC-rich soils. While this pattern may partly reflect reality, here we argue that it can also be created by a pair of statistical artifacts. First, soils that appear SOC-poor purely due to random variation will tend to yield more moderate SOC estimates upon resampling and hence will appear to accrue or retain more SOC than SOC-rich soils. This phenomenon is an example of regression to the mean. Second, normalized metrics of SOC change—such as relative rates and response ratios—will by definition show larger changes in SOC at lower initial SOC levels, even when the absolute change in SOC does not depend on initial SOC. These two artifacts create an exaggerated impression that initial SOC stocks are a major control on SOC dynamics. To address this problem, we recommend applying statistical corrections to eliminate the effect of regression to the mean, and avoiding normalized metrics when testing relationships between SOC change and initial SOC. Careful consideration of these issues in future cross-site studies will support clearer scientific inference that can better inform environmental management.     

巢式设计的多元分析

本文把经典巢式设计的统计分析方法由单变量推广到多变量,使得试验或调查的多性状数据能综合在一起进行分析,以得出考虑了性状间相关性在内的统计结论并用一烟草栽培试验数据示明具体步骤。