Seasonality,species richness and poor dispersion mediate intraspecific trait variability in stonefly community responses along an elevational gradient

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应用DGGE研究微生物群落时的常见问题分析

变性梯度凝胶电泳(DGGE)是通过核酸片段对微生物群落进行研究,可以监测未培养细菌及其功能基因,被广泛地应用于微生物群落多样性和动态分析,并成为微生物分子生态学研究中的重要手段之一。文中论述了DGGE操作过程中遇到的常见问题,并提出了相应的解决方法。全面分析了样品预处理过程和PCR扩增效果对DGGE分析的影响,探讨了DGGE图谱的优化过程和图谱分析方法,并对DGGE的应用前景进行了综述。     

Toward molecular trait‐based ecology through integration of biogeochemical,geographical and metagenomic data

Using metagenomic ‘parts lists’ to infer global patterns on microbial ecology remains a significant challenge. To deduce important ecological indicators such as environmental adaptation, molecular trait dispersal, diversity variation and primary production from the gene pool of an ecosystem, we integrated 25 ocean metagenomes with geographical, meteorological and geophysicochemical data. We find that climatic factors (temperature, sunlight) are the major determinants of the biomolecular repertoire of each sample and the main limiting factor on functional trait dispersal (absence of biogeographic provincialism). Molecular functional richness and diversity show a distinct latitudinal gradient peaking at 20°N and correlate with primary production. The latter can also be predicted from the molecular functional composition of an environmental sample. Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait‐based biogeography and ecology.     

Functional traits explain phytoplankton community structure and seasonal dynamics in a marine ecosystem

A fundamental yet elusive goal of ecology is to predict the structure of communities from the environmental conditions they experience. Trait‐based approaches to terrestrial plant communities have shown that functional traits can help reveal the mechanisms underlying community assembly, but such approaches have not been tested on the microbes that dominate ecosystem processes in the ocean. Here, we test whether functional traits can explain community responses to seasonal environmental fluctuation, using a time series of the phytoplankton of the English Channel. We show that interspecific variation in response to major limiting resources, light and nitrate, can be well‐predicted by lab‐measured traits characterising light utilisation, nitrate utilisation and maximum growth rate. As these relationships were predicted a priori, using independently measured traits, our results show that functional traits provide a strong mechanistic foundation for understanding the structure and dynamics of ecological communities.     

Variations and Trade‐offs in Functional Traits of Tree Seedlings during Secondary Succession in a Tropical Lowland Rain Forest

The seedling stage is generally the most important bottleneck for the successful regeneration of trees in forests. The traits of seedlings, particularly biomass allocation and root traits, are more easily quantified than the traits of adults. In this study, we tested the hypothesis that seedling traits vary and trade‐off tracking the changing environment during secondary succession. We measured the major morphological traits of 27 dominant species and the major environmental factors in a chronosequence (30‐yr‐old fallow, 60‐yr‐old fallow, and old growth forest) after shifting cultivation in a tropical lowland rain forest on Hainan Island, China. The 30‐yr‐old fallow had higher light and nutrient availability, and the older forests had higher soil water content. Redundancy analysis based on species abundance and environmental factors revealed groups of seedlings that dominate in different stages of succession. Seedlings in different stages of succession had different strategies of biomass allocation for harvesting resources that varied in availability. Species characteristic of younger forest had higher allocation to roots and higher specific leaf area, while species characteristic of older forest had higher allocation to leaves. Our study suggests that the variations and trade‐offs in the major functional traits of tree seedlings among successional classes may reflect changes in environmental conditions during succession.     

Quantifying the effects of ecological constraints on trait expression using novel trait‐gradient analysis parameters

Complex processes related to biotic and abiotic forces can impose limitations to assembly and composition of plant communities. Quantifying the effects of these constraints on plant functional traits across environmental gradients, and among communities, remains challenging. We define ecological constraint (C_i) as the combined, limiting effect of biotic interactions and environmental filtering on trait expression (i.e., the mean value and range of functional traits). Here, we propose a set of novel parameters to quantify this constraint by extending the trait‐gradient analysis (TGA) methodology. The key parameter is ecological constraint, which is dimensionless and can be measured at various scales, for example, on population and community levels. It facilitates comparing the effects of ecological constraints on trait expressions across environmental gradients, as well as within and among communities. We illustrate the implementation of the proposed parameters using the bark thickness of 14 woody species along an aridity gradient on granite outcrops in southwestern Australia. We found a positive correlation between increasing environmental stress and strength of ecological constraint on bark thickness expression. Also, plants from more stressful habitats (shrublands on shallow soils and in sun‐exposed locations) displayed higher ecological constraint for bark thickness than plants in more benign habitats (woodlands on deep soils and in sheltered locations). The relative ease of calculation and dimensionless nature of C_i allow it to be readily implemented at various scales and make it widely applicable. It therefore has the potential to advance the mechanistic understanding of the ecological processes shaping trait expression. Some future applications of the new parameters could be investigating the patterns of ecological constraints (1) among communities from different regions, (2) on different traits across similar environmental gradients, and (3) for the same trait across different gradient types.     

Combining taxon‐by‐trait and taxon‐by‐site matrices for analysing trait patterns of macroinvertebrate communities: a rejoinder to Monaghan & Soares ()

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Wing morphology and flight behavior of pelecaniform seabirds

The selective pressures associated with flight are significant factors in shaping the morphology of volant forms. Tropical seabirds are of particular interest because of their long foraging bouts, which can last hundreds of kilometers in search of unpredictable (spatially and temporally) resources. Here, we contrast wing loading (WL), aspect ratio (AR), and planform shape among five pelecaniform seabirds and correlate morphological diversity with known differences in flight strategies. Overall, WL and AR scaled with body mass. The Great Frigratebird had lower WL than that predicted, whereas the Red-tailed Tropicbird had higher WL than that predicted. The tropicbird also exhibited a lower AR than that predicted. Visualization of planform shape was accomplished by using Thin-plate spline relative warp analysis (TPS/RWA), and three major regions of variations were discovered: wing base, mid-wing, and distal wing/wing tip. As expected, the three boobies were more similar than either the tropicbird or the frigatebird. The tropicbird had a broader distal wing and more rounded wing tip, associated with its greater use of flapping flight. The frigatebird showed the greatest deviation in the distal wing and wing tip associated with the high maneuverability required for aerial pursuit and kleptoparasitism. By using TPS/RWA, important differences were detected in planform shape that would have otherwise gone unnoticed when using only WL and AR. These differences correlated strongly with parameters such as maneuverability, flapping, and soaring flight.     

The ecology of differences: assessing community assembly with trait and evolutionary distances

Species enter and persist in local communities because of their ecological fit to local conditions, and recently, ecologists have moved from measuring diversity as species richness and evenness, to using measures that reflect species ecological differences. There are two principal approaches for quantifying species ecological differences: functional (trait‐based) and phylogenetic pairwise distances between species. Both approaches have produced new ecological insights, yet at the same time methodological issues and assumptions limit them. Traits and phylogeny may provide different, and perhaps complementary, information about species' differences. To adequately test assembly hypotheses, a framework integrating the information provided by traits and phylogenies is required. We propose an intuitive measure for combining functional and phylogenetic pairwise distances, which provides a useful way to assess how functional and phylogenetic distances contribute to understanding patterns of community assembly. Here, we show that both traits and phylogeny inform community assembly patterns in alpine plant communities across an elevation gradient, because they represent complementary information. Differences in historical selection pressures have produced variation in the strength of the trait‐phylogeny correlation, and as such, integrating traits and phylogeny can enhance the ability to detect assembly patterns across habitats or environmental gradients.     

Comparison of microbial community assays for the assessment of stream biofilm ecology

We investigated a range of microbiological community assays performed on scrapes of biofilms formed on artificial diffusing substrates deployed in 8 streams in eastern Scotland, with a view to using them to characterize ecological response to stream water quality. The assays considered were: Multiplex Terminal Restriction Fragment Length Polymorphism or M-TRFLP (a molecular method), Phospholipid Fatty Acid or PLFA analysis (a biochemical method) and MICRORESP^™ (a physiological method) alongside TDI, diatom species, and chlorophyll a content. Four of the streams were classified as of excellent status (3-6 μg/L Soluble Reactive Phosphorus (SRP)) with respect to soluble P content under the EU Water Framework Directive and four were of borderline good/moderate or moderate status (43-577 μg/L SRP). At each site, 3 replicates of 3 solute diffusion treatments were deployed in a Latin square design. Solute diffusion treatments were: KCl (as a control solute), N and P (to investigate the effect of nutrient enrichment), or the herbicide isoproturon (as a “high impact” control, which aimed to affect biofilm growth in a way detectable by all assays). Biofilms were sampled after 4 weeks deployment in a low flow period of early summer 2006.The chlorophyll a content of biofilms after 4 weeks was 2.0 ± 0.29 mg/m² (mean ± se). Dry matter content was 16.0 ± 13.1 g/m². The M-TRFLP was successfully used for generating community profiles of cyanobacteria, algae and bacteria and was much faster than diatom identification. The PFLA and TDI were successful after an increase in the sample size, due to low counts. The MICRORESP^™ assays were often below or near detection limit. We estimated the per-sample times for the successful assays as follows: M-TRFLP: 20 min, PLFA 40 min, TDI 90 min. Using MANOVA on the first 5 principal co-ordinates, all the assays except MICRORESP^™ showed significant differences between sites, but none of the assays showed a significant effect of either initial stream trophic status (as classified by the EU Water Framework Directive using chemical standards for soluble P), or of the diffusing solute treatment. Multiple Procrustes analysis on the ordination results showed that the diatom and M-TRFLP data sets hold distinct, though as yet unexplored, information about the ecological factors affecting stream biofilms. The diatom data were subjected to principal components analysis, to identify which taxa were more strongly influenced by site variables, trophic status or treatment effects. These were Acnanthes lanceolata, A. minutissimma, Nitzchia spp., Coccineis spp. and Navicula spp. Further experimentation and data analysis on a larger number of sites, to identify specific M-TRFLP bands that could be used as indicators linked to specific taxa, are desirable. Results highlight the need for a multifactorial approach to understanding controls on stream ecology.     

Sensitivity analysis of Repast computational ecology models with R/Repast

Computational ecology is an emerging interdisciplinary discipline founded mainly on modeling and simulation methods for studying ecological systems. Among the existing modeling formalisms, the individual‐based modeling is particularly well suited for capturing the complex temporal and spatial dynamics as well as the nonlinearities arising in ecosystems, communities, or populations due to individual variability. In addition, being a bottom‐up approach, it is useful for providing new insights on the local mechanisms which are generating some observed global dynamics. Of course, no conclusions about model results could be taken seriously if they are based on a single model execution and they are not analyzed carefully. Therefore, a sound methodology should always be used for underpinning the interpretation of model results. The sensitivity analysis is a methodology for quantitatively assessing the effect of input uncertainty in the simulation output which should be incorporated compulsorily to every work based on in‐silico experimental setup. In this article, we present R/Repast a GNU R package for running and analyzing Repast Simphony models accompanied by two worked examples on how to perform global sensitivity analysis and how to interpret the results.     

Diet,feeding behavior,and jaw architecture of Taï monkeys: Congruence and chaos in the realm of functional morphology

We review feeding and mandibular anatomy in a community of West African monkeys. We use field observations, food material property data, and skeletal specimens from the Ivory Coast's Taï Forest to explore the factors that shape mandibular architecture in colobines and cercopithecines. Despite excellent geographic control across our sample, the fit between bone form (as conventionally described) and functional activity (as we perceive it) is not spectacular. We present a thought experiment to assess how well we could reconstruct diet in the Taï monkeys if we only had skeletons and teeth to study. This exercise indicated that we would be correct about half the time. Our analyses reinforce the notion that diet is anything but a monolithic variable and that better success at relating mandibular form to food must incorporate information on ingestive and processing behavior, geometric and material properties of foods, and both material and structural data on jaws themselves.     

转大麻哈鱼生长激素基因鲤表型性状与体质量的相关性及通径分析

随机选取二龄转大麻哈鱼生长激素基因鲤和对照鲤各30尾,运用相关分析和通径分析的方法研究全长、体长、体高、尾柄高、尾柄长、头长、吻长、眼径、眼间距、体厚10个表型性状对体质量的影响程度,以此确定影响二龄转基因鲤和对照鲤体质量的主要表型参数.相关分析结果表明:转基因鲤和对照鲤的大部分表型性状与体质量间的相关系数均达到极显著水平(P<0.01).通径分析结果显示:体长和体高可以作为预测转基因鲤体质量的主要表型参数,转基因鲤体长对体质量的通径系数为0.572,体高对体质量的通径系数为0.415,体长和体高直接决定体质量;而体厚和头长可以作为预测对照鲤体质量的主要表型参数,对照鲤体厚对体质量的通径系数为0.610,头长对体质量的通径系数为0.377,体厚和头长对体质量具有决定作用.     

SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci

In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses of linkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large number of samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study with high efficiency. The platform has been well evaluated by several sets of real data.     

Predation, competition, and nutrient recycling: a stoichiometric approach with multiple nutrients

A model for two competing prey species and one predator is formulated in which three essential nutrients can limit growth of all populations. Prey take up dissolved nutrients and predators ingest prey, assimilating a portion of ingested nutrients and recycling or respiring the balance. For all species, the nutrient contents of individuals vary and growth is coupled to increasing content of the limiting nutrient. This model was parameterized to describe a flagellate preying on two bacterial species, with carbon (C), nitrogen (N), and phosphorus (P) as nutrients. Parameters were chosen so that the two prey species would stably coexist without predators under some nutrient supply conditions. Using numerical simulations, the long-term outcomes of competition and predation were explored for a gradient of N:P supply ratios, varying C supply, and varying preference of the predator for the two prey. Coexistence and competitive exclusion both occurred under some conditions of nutrient supply and predator preference. As in simpler models of competition and predation these outcomes were largely governed by apparent competition mediated by the predator, and resource competition for nutrients whose effective supply was partly governed by nutrient recycling also mediated by the predator. For relatively small regions of parameter space, more complex outcomes with multiple attractors or three-species limit cycles occurred. The multiple constraints posed by multiple nutrients held the amplitudes of these cycles in check, limiting the influence of complex dynamics on competitive outcomes for the parameter ranges explored.     

Interaction effects of cell diffusion,cell density and public goods properties on the evolution of cooperation in digital microbes

Microbial cooperation typically consists in the sharing of secreted metabolites (referred to as public goods) within the community. Although public goods generally promote population growth, they are also vulnerable to exploitation by cheating mutants, which no longer contribute, but still benefit from the public goods produced by others. Although previous studies have identified a number of key factors that prevent the spreading of cheaters, little is known about how these factors interact and jointly shape the evolution of microbial cooperation. Here, we address this issue by investigating the interaction effects of cell diffusion, cell density, public good diffusion and durability (factors known to individually influence costs and benefits of public goods production) on selection for cooperation. To be able to quantify these effects across a wide parameter space, we developed an individual‐based simulation platform, consisting of digital cooperator and cheater bacteria inhabiting a finite two‐dimensional continuous toroidal surface. Our simulations, which closely mimic microbial microcolony growth, revealed that: (i) either reduced cell diffusion (which keeps cooperators together) or reduced public good diffusion (which keeps the public goods closer to the producer) is not only essential but also sufficient for cooperation to be promoted; (ii) the sign of selection for or against cooperation can change as a function of cell density and in interaction with diffusion parameters; and (iii) increased public goods durability has opposing effects on the evolution of cooperation depending on the level of cell and public good diffusion. Our work highlights that interactions between key parameters of public goods cooperation give rise to complex fitness landscapes, a finding that calls for multifactorial approaches when studying microbial cooperation in natural systems.