Macrofaunal Functional Diversity Provides Resilience to Nutrient Enrichment in Coastal Sediments

The degradation of ecosystems is often associated with losses of large organisms and the concomitant losses of the ecological functions they mediate. Conversely, the resilience of ecosystems to stress is strongly influenced by faunal communities and their impacts on processes. Denitrification in coastal sediments is a process that may provide ecosystem resilience to eutrophication by removing excess bioavailable nitrogen. Here, we conducted a large-scale field experiment to test the effect of macrofaunal community composition on denitrification in response to two levels of nutrient enrichment at 28 sites across a biologically heterogeneous sandflat. After 7 weeks of enrichment, we measured denitrification enzyme activity (DEA) along with benthic macrofaunal community composition and environmental variables. We normalised treatment site specific DEA values by those in ambient sediments (DEA_CN) to reveal the underlying response across the heterogeneous landscape. Nutrient enrichment caused reductions in DEA_CN as well as functional changes in the community; these were both more pronounced under the highest level of nutrient loading (on average DEA_CN was reduced by 34%). The degree of suppression of DEA_CN following moderate nitrogen loading was mitigated by a key bioturbating species, but following high nitrogen loading (which reduced the key species density) the abundance and diversity of other nutrient processing species were the most important factors alleviating negative effects. This study provides a prime example of the context-dependent role of biodiversity in maintaining ecosystem functioning, underlining that different elements of biodiversity can become important as stress levels increase. Our results emphasise that management and conservation strategies require a real-world understanding of the community attributes that facilitate nutrient processing and maintain resilience in coastal ecosystems.     

Time-Delayed Mutual Information of the Phase as a Measure of Functional Connectivity

We propose a time-delayed mutual information of the phase for detecting nonlinear synchronization in electrophysiological data such as MEG. Palus already introduced the mutual information as a measure of synchronization [1]. To obtain estimates on small data-sets as reliably as possible, we adopt the numerical implementation as proposed by Kraskov and colleagues [2]. An embedding with a parametric time-delay allows a reconstruction of arbitrary nonstationary connective structures – so-called connectivity patterns – in a wide class of systems such as coupled oscillatory or even purely stochastic driven processes [3]. By using this method we do not need to make any assumptions about coupling directions, delay times, temporal dynamics, nonlinearities or underlying mechanisms. For verifying and refining the methods we generate synthetic data-sets by a mutual amplitude coupled network of Rössler oscillators with an a-priori known connective structure. This network is modified in such a way, that the power-spectrum forms a power law, which is also observed in electrophysiological recordings. The functional connectivity measure is tested on robustness to additive uncorrelated noise and in discrimination of linear mixed input data. For the latter issue a suitable de-correlation technique is applied. Furthermore, the compatibility to inverse methods for a source reconstruction in MEG such as beamforming techniques is controlled by dedicated dipole simulations. Finally, the method is applied on an experimental MEG recording.     

多样性指标用于基因中剪切位点的识别

根据基因剪切位点处的碱基保守性特征,和附近位点的碱基组成和关联特征,应用多样性指标和二次判别分析,对几类模式生物的基因结构进行统一的分析和预测,能够较好地识别外显子和内含子及其边界.计算结果表明,对于4类物种,线虫(C.elegans),拟南芥(A.thaliana), 果蝇(D.melanogaster)和人类(human),核苷酸水平的识别精度为92.5%～97.1%,外显子水平的识别敏感性为83.7%～94.5%,特异性为87.8%～97.1%.预测能力优于GeneSplicer等剪切位点检测软件.     

Gene's Functional Arrangement as a Measure of thePhylogenetic Relationships of Microorganisms

With the development of genome sequencing more whole genomes of microorganisms were completed, many methods wereintroduced to reconstruct the phylogenetic tree of those microorganismswith the information extracted from the whole genomes through variousways of transforming or mapping the whole genome sequences into otherforms which can describe the evolutionary distance in a new way. We thinkit might be possible that there exists information buried in the wholegenome transferred along lineage, which remains stable and is moreessential than sequence conservation of individual genes or the arrangementof some genes of a selected set. We need to find one measurement that caninvolve as many phylogenetic features as possible that are beyond thegenome sequence itself. We converted each genome sequence of themicroorganisms into another linear sequence to represent the functionalstructure of the sequence, and we used a new information function tocalculate the discrepancy of sequences and to get one distance matrix of thegenomes, and built one phylogenetic tree with a neighbor joining method.The resulting tree shows that the major lineages are consistent with theresult based on their 16srRNA sequences. Our method discovered onephylogenetic feature derived from the genome sequences and the encodedgenes that can rebuild the phylogenetic tree correctly. The mapping of onegenome sequence to its new form representing the relative positions of thefunctional genes provides a new way to measure the phylogeneticrelationships, and with the more specific classification of gene functions theresult could be more sensitive.     

Plant Functional Group Diversity as a Mechanism for Invasion Resistance

A commonly cited mechanism for invasion resistance is more complete resource use by diverse plant assemblages with maximum niche complementarity. We investigated the invasion resistance of several plant functional groups against the nonindigenous forb Spotted knapweed (Centaurea maculosa). The study consisted of a factorial combination of seven functional group removals (groups singularly or in combination) and two C. maculosa treatments (addition vs. no addition) applied in a randomized complete block design replicated four times at each of two sites. We quantified aboveground plant material nutrient concentration and uptake (concentration × biomass) by indigenous functional groups: grasses, shallow‐rooted forbs, deep‐rooted forbs, spikemoss, and the nonindigenous invader C. maculosa. In 2001, C. maculosa density depended upon which functional groups were removed. The highest C. maculosa densities occurred where all vegetation or all forbs were removed. Centaurea maculosa densities were the lowest in plots where nothing, shallow‐rooted forbs, deep‐rooted forbs, grasses, or spikemoss were removed. Functional group biomass was also collected and analyzed for nitrogen, phosphorus, potassium, and sulphur. Based on covariate analyses, postremoval indigenous plot biomass did not relate to invasion by C. maculosa. Analysis of variance indicated that C. maculosa tissue nutrient percentage and net nutrient uptake were most similar to indigenous forb functional groups. Our study suggests that establishing and maintaining a diversity of plant functional groups within the plant community enhances resistance to invasion. Indigenous plants of functionally similar groups as an invader may be particularly important in invasion resistance.     

The Use of Discontinuities and Functional Groups to Assess Relative Resilience in Complex Systems

It is evident when the resilience of a system has been exceeded and the system qualitatively changed. However, it is not clear how to measure resilience in a system prior to the demonstration that the capacity for resilient response has been exceeded. We argue that self-organizing human and natural systems are structured by a relatively small set of processes operating across scales in time and space. These structuring processes should generate a discontinuous distribution of structures and frequencies, where discontinuities mark the transition from one scale to another. Resilience is not driven by the identity of elements of a system, but rather by the functions those elements provide, and their distribution within and across scales. A self-organizing system that is resilient should maintain patterns of function within and across scales despite the turnover of specific elements (for example, species, cities). However, the loss of functions, or a decrease in functional representation at certain scales will decrease system resilience. It follows that some distributions of function should be more resilient than others. We propose that the determination of discontinuities, and the quantification of function both within and across scales, produce relative measures of resilience in ecological and other systems. We describe a set of methods to assess the relative resilience of a system based upon the determination of discontinuities and the quantification of the distribution of functions in relation to those discontinuities.     

Functional Richness and Relative Resilience of Bird Communities in Regions with Different Land Use Intensities

Abstract Empirical estimates of the function and resilience of communities under different management regimes can provide valuable information for sustainable natural resource management, but such estimates are scarce to date. We quantified the functional richness and relative resilience of bird communities inhabiting five regions in southeastern Australia that represented different management regimes. First, we show that functional richness and relative resilience were reduced at species-poor sites in all regions. Second, we show that bird communities in agricultural regions had fewer body mass groups and fewer functional groups than expected by chance. This suggests that both the function and the resilience of bird communities in agricultural regions were reduced. The likely mechanisms for the observed loss of function and relative resilience are: (1) the simplification of landscape texture resulting in selective extinction of certain body mass groups; and (2) the selective extinction of certain functional groups that are particularly sensitive to intensive land use. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Drawing a Close to the Use of Human Figure Drawings as a Projective Measure of Intelligence

The practice of using children''s human figure drawings (HFDs) to assess their intellectual ability is pervasive among psychologists and therapists in many countries. Since the first systematic scoring system for HFDs was published in 1926, their continued popularity has led to the development of several revised versions of the test. Most recently, the Draw-A-Person Intellectual Ability Test for children, adolescents, and adults (DAP:IQ) was published. It is the most up-to-date form of HFD test designed to assess intellectual functioning across a wide age range. In the present study, we assessed the validity of the DAP:IQ as a screening measure of intelligence in both children and adults. In Experiment 1, 100 4- to 5-year-old children completed the DAP:IQ and the Wechsler Preschool and Primary Scale of Intelligence-Third Edition. In Experiment 2, 100 adults completed the DAP:IQ and the Wechsler Abbreviated Scale of Intelligence. In both experiments, we found only weak to modest correlations between scores on the DAP:IQ and the Wechsler tests. Furthermore, when we compared individual''s scores on the two tests, the DAP:IQ yielded high false positive and false negative rates when screening for borderline and superior intellectual functioning. Based on these findings, and based on the lack of validity of previous HFD tests, we conclude that practitioners should not rely on HFD tests as a projective measure of intelligence.     

Functional Diversity as a New Framework for Understanding the Ecology of an Emerging Generalist Pathogen

Emerging infectious disease outbreaks are increasingly suspected to be a consequence of human pressures exerted on natural ecosystems. Previously, host taxonomic communities have been used as indicators of infectious disease emergence, and the loss of their diversity has been implicated as a driver of increased presence. The mechanistic details in how such pathogen–host systems function, however, may not always be explained by taxonomic variation or loss. Here we used machine learning and methods based on Gower’s dissimilarity to quantify metrics of invertebrate functional diversity, in addition to functional groups and their taxonomic diversity at sites endemic and non-endemic for the model generalist pathogen Mycobacterium ulcerans, the causative agent of Buruli ulcer. Changes in these metrics allowed the rapid categorisation of the ecological niche of the mycobacterium’s hosts and the ability to relate specific host traits to its presence in aquatic ecosystems. We found that taxonomic diversity of hosts and overall functional diversity loss and evenness had no bearing on the mycobacterium’s presence, or whether the site was in an endemic area. These findings, however, provide strong evidence that generalist environmentally persistent bacteria such as M. ulcerans can be associated with specific functional traits rather than taxonomic groups of organisms, increasing our understanding of emerging disease ecology and origin.     

The Importance of Phytogenic Mounds (Nebkhas) for Restoration of Arid Degraded Rangelands in Northern Sinai

Abstract Natural accumulation of wind‐borne sediments within or around the canopies of plants plays an important role in the ecological and evolutionary dynamics of many coastal and desert ecosystems. The formation of such phytogenic mounds (nebkhas) creates patches that can strongly influence the spatial distribution of plant and soil resources. In land restoration of arid and semiarid environments it is important to study the potential role of such biological patchiness that may provide sites for coexistence of species with different life and growth forms. Our main objective was to test whether the nebkhas of a leguminous shrub, Retama raetam (white broom), promote restoration of herbaceous vegetation and soil in the degraded rangelands of northern Sinai. Vegetation and microclimatic and edaphic characteristics within the nebkhas, as well as within internebkha spaces, were compared for ungrazed and grazed sites. Abundance and richness of herbaceous plants were positively related to nebkha area, which explained more of the variance of abundance and richness in the grazed site than in the ungrazed one. Protection from grazing, especially on nebkhas, was associated with an increase in abundance and richness of herbaceous plants, improved soil microclimate, and increased soil fine particles and nutrient concentrations. The results suggest that management (in casu protection from grazing) of nebkhas of woody perennial shrubs changes rangeland conditions and improves the resource regulatory processes. Furthermore, nebkhas of unpalatable plants have the potential to preserve plant diversity in overgrazed plant communities, because they are effective in capturing and retaining water, soil materials, and propagules within and from nearby areas, resources that would otherwise be lost.     

Use of the Health and Activities Limitation Index as a Measure of Quality of Life in Obesity

Objective: Obesity reduces the quality of life (QOL); however, quantification of obesity's impact on QOL is cumbersome. Utility indices reduce QOL measurements to a single numerical value that can be used in the calculation of Quality‐Adjusted Life‐Years and the cost effectiveness for obesity treatment. The purpose of this investigation is to assess the sensitivity of the Health and Activities Limitation Index (HALex) utility index to obesity. Research Methods and Procedures: The answers to five questions regarding an individual's self‐perception of his or her health status and information about limitation in daily and work activities were collected from 32,440 adults in the 1998 National Health Information Survey. Answers to the questions were scored and converted to a utility index score ranging from 0 (near‐death state) to 1 (perfect health) with no limitations. Average values for indices corresponding to differing body mass indices were obtained and significance determined by ANOVA. Results: The utility index for normal weight males and females was 0.86 ± 0.19 and fell to 0.68 ± 0.27 for superobese males and 0.60 ± 0.28 in superobese females. Utility indices fell linearly with increasing body mass index and were lower for respondents having obesity‐related comorbid conditions known to reduce the quality of life. Discussion: There is a statistically significant decrease in the QOL with increasing obesity, slightly worse for women compared with men. The Health and Activities Limitation Index can quantitate the effect obesity and its complications have on quality of life.     

The Use of the Puzzle Box as a Means of Assessing the Efficacy of Environmental Enrichment

Environmental enrichment can dramatically influence the development and function of neural circuits. Further, enrichment has been shown to successfully delay the onset of symptoms in models of Huntington’s disease ^1-4, suggesting environmental factors can evoke a neuroprotective effect against the progressive, cellular level damage observed in neurodegenerative disorders. The ways in which an animal can be environmentally enriched, however, can vary considerably. Further, there is no straightforward manner in which the effects of environmental enrichment can be assessed: most methods require either fairly complicated behavioral paradigms and/or postmortem anatomical/physiological analyses. This protocol describes the use of a simple and inexpensive behavioral assay, the Puzzle Box ^5-7 as a robust means of determining the efficacy of increased social, sensory and motor stimulation on mice compared to cohorts raised in standard laboratory conditions. This simple problem solving task takes advantage of a rodent’s innate desire to avoid open enclosures by seeking shelter. Cognitive ability is assessed by adding increasingly complex impediments to the shelter’s entrance. The time a given subject takes to successfully remove the obstructions and enter the shelter serves as the primary metric for task performance. This method could provide a reliable means of rapidly assessing the efficacy of different enrichment protocols on cognitive function, thus paving the way for systematically determining the role specific environmental factors play in delaying the onset of neurodevelopmental and neurodegenerative disease.     

Limited Functional Redundancy in a High Diversity System: Single Species Dominates Key Ecological Process on Coral Reefs

Herbivory is a key process structuring plant communities in both terrestrial and aquatic ecosystems, with variation in herbivory often being related to shifts between alternate states. On coral reefs, regional reductions in herbivores have underpinned shifts from coral to dominance by leathery macroalgae. These shifts appear difficult to reverse as these macroalgae are unpalatable to the majority of herbivores, and the macroalgae suppress the recruitment and growth of corals. The removal of macroalgae is, therefore, viewed as a key ecological process on coral reefs. On the Great Barrier Reef, Sargassum is a dominant macroalgal species following experimentally induced coral–macroalgal phase-shifts. We, therefore, used Sargassum assays and remote video cameras to directly quantify the species responsible for removing macroalgae across a range of coral reef habitats on Lizard Island, northern Great Barrier Reef. Despite supporting over 50 herbivorous fish species and six macroalgal browsing species, the video footage revealed that a single species, Naso unicornis, was almost solely responsible for the removal of Sargassum biomass across all habitats. Of the 42,246 bites taken from the Sargassum across all habitats, N. unicornis accounted for 89.8% (37,982) of the total bites, and 94.6% of the total mass standardized bites. This limited redundancy, both within and across local scales, underscores the need to assess the functional roles of individual species. Management and conservation strategies may need to look beyond the preservation of species diversity and focus on the maintenance of ecological processes and the protection of key species in critical functional groups.     

Plant Functional Diversity and Species Diversity in the Mongolian Steppe

Background

The Mongolian steppe is one of the most important grasslands in the world but suffers from aridization and damage from anthropogenic activities. Understanding structure and function of this community is important for the ecological conservation, but has seldom been investigated.

Methodology/Principal Findings

In this study, a total of 324 quadrats located on the three main types of Mongolian steppes were surveyed. Early-season perennial forbs (37% of total importance value), late-season annual forbs (33%) and late-season perennial forbs (44%) were dominant in meadow, typical and desert steppes, respectively. Species richness, diversity and plant functional type (PFT) richness decreased from the meadow, via typical to desert steppes, but evenness increased; PFT diversity in the desert and meadow steppes was higher than that in typical steppe. However, above-ground net primary productivity (ANPP) was far lower in desert steppe than in the other two steppes. In addition, the slope of the relationship between species richness and PFT richness increased from the meadow, via typical to desert steppes. Similarly, with an increase in species diversity, PFT diversity increased more quickly in both the desert and typical steppes than that in meadow steppe. Random resampling suggested that this coordination was partly due to a sampling effect of diversity.

Conclusions/Significance

These results indicate that desert steppe should be strictly protected because of its limited functional redundancy, which its ecological functioning is sensitive to species loss. In contrast, despite high potential forage production shared by the meadow and typical steppes, management of these two types of steppes should be different: meadow steppe should be preserved due to its higher conservation value characterized by more species redundancy and higher spatial heterogeneity, while typical steppe could be utilized moderately because its dominant grass genus Stipa is resistant to herbivory and drought.     

The Resilience and Resistance of an Ecosystem to a Collapse of Diversity

Diversity is expected to increase the resilience of ecosystems. Nevertheless, highly diverse ecosystems have collapsed, as did Lake Victoria’s ecosystem of cichlids or Caribbean coral reefs. We try to gain insight to this paradox, by analyzing a simple model of a diverse community where each competing species inflicts a small mortality pressure on an introduced predator. High diversity strengthens this feedback and prevents invasion of the introduced predator. After a gradual loss of native species, the introduced predator can escape control and the system collapses into a contrasting, invaded, low-diversity state. Importantly, we find that a diverse system that has high complementarity gains in resilience, whereas a diverse system with high functional redundancy gains in resistance. Loss of resilience can display early-warning signals of a collapse, but loss of resistance not. Our results emphasize the need for multiple approaches to studying the functioning of ecosystems, as managing an ecosystem requires understanding not only the threats it is vulnerable to but also pressures it appears resistant to.     

Changes of Soil Bacterial Diversity as a Consequence of Agricultural Land Use in a Semi-Arid Ecosystem

Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years) of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE) analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes) correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.     

Leaf Dry Matter Content Predicts Herbivore Productivity,but Its Functional Diversity Is Positively Related to Resilience in Grasslands

This paper addresses whether the ecosystem service of animal production from grasslands depends upon plant functional identity, plant functional diversity or if the resilience of production is a function of this diversity. Using the results of nine grazing experiments the paper shows that productivity is highly dependent on one leaf trait, leaf dry matter content, as well as rainfall. Animal (secondary) productivity is not dependent on plant functional diversity, but the variability in productivity of grasslands is related to the functional diversity of leaf dry matter content. This and a range of independent studies have shown that functional diversity is reduced at high levels of grassland productivity, so it appears that there is a trade-off between productivity and the resilience of productivity in the face of environmental variation.