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.     

Predictors of Introduction Success in the South Florida Avifauna

Biological invasions are an increasing global challenge, for which single-species studies and analyses focused on testing single hypotheses of causation in isolation are unlikely to provide much additional insight. Species interact with other species to create communities, which derive from species interactions and from the interactions of species with the scale specific elements of the landscape that provide suitable habitat and exploitable resources. I used logistic regression analysis to sort among potential intrinsic, community and landscape variables that theoretically influence introduction success. I utilized the avian fauna of the Everglades of South Florida, and the variables body mass, distance to nearest neighbor (in terms of body mass), year of introduction, presence of congeners, guild membership, continent of origin, distribution in a body mass aggregation or gap, and distance to body-mass aggregation edge (in terms of body mass). Two variables were significant predictors of introduction success. Introduced avian species whose body mass placed them nearer to a body-mass aggregation edge and further from their neighbor were more likely to become successfully established. This suggests that community interactions, and community level phenomena, may be better understood by explicitly incorporating scale.     

Ecological Resilience, Biodiversity, and Scale

We describe existing models of the relationship between species diversity and ecological function, and propose a conceptual model that relates species richness, ecological resilience, and scale. We suggest that species interact with scale-dependent sets of ecological structures and processes that determine functional opportunities. We propose that ecological resilience is generated by diverse, but overlapping, function within a scale and by apparently redundant species that operate at different scales, thereby reinforcing function across scales. The distribution of functional diversity within and across scales enables regeneration and renewal to occur following ecological disruption over a wide range of scales. Received 11 April 1997; accepted 9 July 1997.     

A Methodological Approach to Assess Cross-scale Relations and Interactions in Agricultural Ecosystems of Argentina

Agronomists, environmentalists, land managers, policy makers and development agents who make decisions at different levels (plot, farm, ecosystem, landscape, ecoregion, country) increasingly demand scientific information to understand cross-level links and interactions in systems that behave hierarchically. The purpose of this work is to study cross-scale relations and interactions in agricultural ecosystems of the Argentine Pampas. Based on public censuses and surveys from 1960 to 1996, data on crops cultivation, fossil energy (FE) consumption and energy productivity were used for the analysis. The whole region was divided into eight increasing geographic scales, and the impact of one scale on the broader ones was assessed through a simple analysis of energy productivity. Regression analysis was used to identify cross-scale linear slopes and to determine cross-scale interactions. We assume that non-parallel slopes in different years are attributable to cross-scale interactions. Given that the results show highly significant differences among inter-year slopes, we must accept that cross-scale interactions have occurred. Beyond any random behavior, it seems quite possible that decisions made at smaller scales may have a demonstrable effect on broader scales. Specific research is needed to elucidate key cause–effect relationships among scales. In principle, the possible interaction between intensification factors (for example, FE consumption) and spatial scales is a plausible hypothesis to be tested in the study area.     

Original Articles: Plant Attribute Diversity, Resilience, and Ecosystem Function: The Nature and Significance of Dominant and Minor Species

This study tested an hypothesis concerning patterns in species abundance in ecological communities. Why do the majority of species occur in low abundance, with just a few making up the bulk of the biomass? We propose that many of the minor species are analogues of the dominants in terms of the ecosystem functions they perform, but differ in terms of their capabilities to respond to environmental stresses and disturbance. They thereby confer resilience on the community with respect to ecosystem function. Under changing conditions, ecosystem function is maintained when dominants decline or are lost because functionally equivalent minor species are able to substitute for them. We have tested this hypothesis with respect to ecosystem functions relating to global change. In particular, we identified five plant functional attributes—height, biomass, specific leaf area, longevity, and leaf litter quality—that determine carbon and water fluxes. We assigned values for these functional attributes to each of the graminoid species in a lightly grazed site and in a heavily grazed site in an Australian rangeland. Our resilience proposition was cast in the form of three specific hypotheses in relation to expected similarities and dissimilarities between dominant and minor species, within and between sites. Functional similarity—or ecological distance—was determined as the euclidean distance between species in functional attribute space. The analyses provide evidence in support of the resilience hypothesis. Specifically, within the lightly grazed community, dominant species were functionally more dissimilar to one another, and functionally similar species more widely separated in abundance rank, than would be expected on the basis of average ecological distances in the community. Between communities, depending on the test used, two of three, or three of four minor species in the lightly grazed community that were predicted to increase in the heavily grazed community did in fact do so. Although there has been emphasis on the importance of functional diversity in supporting the flow of ecosystem goods and services, the evidence from this study indicates that functional similarity (between dominant and minor species, and among minor species) may be equally important in ensuring persistence (resilience) of ecosystem function under changing environmental conditions.     

The Use of RAPD Markers to Assess Catfish Hybridization

Taiwan's endemic catfish Clarias fuscus is gradually disappearing from its native habitat, and has been proposed for genebank preservation. Environmental pressures, including exotic species interference and habitat destruction, as well as possible competitive advantages of the hybrids over this species. In order to quickly and effectively provide a reliable DNA fingerprint for the pure strain of C. fuscus we used RAPD markers to assess C. fuscus, C. mossambicus, and C.batrachus. Of the 200 primers screened to prime PCR amplification of DNA from wild-caught C. fuscus, 16 yielded reproducible DNA bands. Unique RAPD markers generated from 3 PCR primers (#211, #245 and #287) are shown to be alleles present in the genomes of C. mossambicus but absent in the genome of C. fuscus. Hybrids of C. fuscus and C. mossambicus, therefore, could possibly be distinguished by the use of these specific molecular markers. Catfish caught from the Mingder Dam were then cautiously removed from the preserved stock because of the appearance of hybrid markers in their genomes.     

Functional Group Change within and across Scales following Invasions and Extinctions in the Everglades Ecosystem

Cross-scale resilience theory predicts that the combination of functional diversity within scales and functional redundancy across scales is an important attribute of ecosystems because it helps these systems resist minor ecological disruptions and regenerate after major disturbances such as hurricanes and fire. Using the vertebrate fauna of south Florida, we quantified how the loss of native species and invasion by nonnatives may alter functional group richness within and across scales. We found that despite large changes in species composition due to potential extinctions and successful invasions by nonnative species, functional group richness will not change significantly within scales, there will not be any significant loss of overall redundancy of ecology function across scales, and overall body mass pattern will not undergo substantial change. However, the types of functions performed will change, and this change may have profound effects on not only the Everglades ecosystem but on the entire landscape of south Florida. Received 14 November 2000; accepted 20 December 2001.     

The Use of Structured Imagery and Dispositional Measurement to Assess Situational Use of Mindfulness Skills

The recent proliferation of studies on mindfulness produced varying theoretical models, each based in part on how mindfulness is assessed. These models agree, however, that mindfulness encompasses moment-to-moment or situational experiences. Incongruence between dispositional and situational assessment would be problematic for theory and empirical research. In particular, it remains to be established whether situational measurement is an accurate method for mindfulness assessment and whether dispositional measures are able to accurately detect mindfulness skills in various situations. The association between dispositional and situational mindfulness processes (i.e., situational attention awareness and emotion acceptance) was examined in two studies. In Study 1 (N = 148), independent groups who reported high and low levels of dispositional mindfulness skills were compared on a continuous measure of situational mindfulness skills. In Study 2 (N = 317), dispositional mindfulness questionnaires were used to predict situational use of mindfulness skills. Results suggest not only that situational measures accurately detect use of mindfulness skills, but also that dispositional measures can predict one’s use of situational mindfulness skills. Findings from both studies were consistent across both positive and negative situations. Moreover, neither neuroticism nor extraversion was shown to have a moderating effect on the relationship between dispositional and situational use of mindfulness skills. The implications of these findings for clinical practice and future investigations pertaining to measurement validity in this area are discussed.     

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the "functional similarity" between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the "ortholog conjecture" (or, more properly, the "ortholog functional conservation hypothesis"). First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1) that GO annotations are often incomplete, potentially in a biased manner, and subject to an "open world assumption" (absence of an annotation does not imply absence of a function), and 2) that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the conclusions have a justifiable biological basis.     

The Use of Flow Cytometry to Assess the State of Chromatin in T Cells

During a proper immune response, quiescent T cells become activated upon antigen presentation to their antigen-specific T cell receptor. This leads to clonal proliferation of only those T cells that bear a receptor that recognizes the antigen. Chromatin decondensation is a hallmark of T cell activation and is required for T cells to acquire the ability to proliferate after antigen engagement. This change in chromatin condensation can be detected using antibodies raised against histone proteins. These antibodies cannot bind to their epitopes in naïve T cells as well as they can in activated T cells. We describe how to simultaneously stain T cell-specific surface markers, track viability with a fixable dead cell stain, and measure chromatin status via intracellular staining of Histone H3 proteins. Stained cells are analyzed by flow cytometry and chromatin condensation status is measured as the mean fluorescence intensity (MFI) of the Histone H3 stain. Chromatin decondensation during T cell activation is demonstrated as an increase in the MFI     

The Use of Fluorescent Probes to Assess Oxidative Processes in Isolated-Perfused Rat Heart Tissue

The formation of reactive oxygen species (ROS) in intact heart tissue has been assessed by direct ESR measurements, and indirectly by the formation of characteristic tissue products and the protective effects of various antioxidants. The development of lipid soluble esters of compounds which can be trapped intra-cellularly after hydrolysis, and which fluoresce after oxidation, has provided a new tool to investigate ROS in vitro. The utility of 2',7'-dichlorofluorescin diacetate (DCFDA) in isolated-perfused rat heart tissue was investigated in the present study. DCFDA and its deacetylated form were incubated with various levels of hydrogen peroxide or t-butylhydroperoxide (tBOOH). Conversion of the diacetate form to a fluorescent product required 4-5 h with hydrogen peroxide and up to 24 h with tBOOH. In contrast, the deacetylated form fluoresced at 80% of maximum levels 1 h after the addition of 100 mM tBOOH. DCFDA was loaded into heart tissue by infusing for lO min at a final concentration of 10,aM in Krebs-Henseleit bicarbonate buffer. After a lO min washout period, analysis of freeze-clamped heart tissue revealed that the trapped material was readily converted to a fluorescent product by tBOOH, indicating hydrolysis had occurred. Fluorescence of material trapped in heart tissue was approximately 24% of the maximum achieved after oxidation with lOOmM tBOOH. This value decreased to 18 and 13% when the loading and washout periods were from 0 to 20 or 10 to 30min of hypoxia, respectively. Similar results were obtained with the less readily oxidized dicarboxy derivative of DCFDA. Infusion of 500μM tBOOH increased the oxidation of DCFDA in heart tissue from 24 to 31%. These data demonstrate that DCFDA can be loaded into heart tissue and is capable of reflecting relative changes in the oxidative state of this organ.     

Measuring Functional Diversity in Plant Communities with MixedLife Forms: A Problem of Hardand Soft Attributes

This paper examines the functional relationships among species in an Australian rangeland community with mixed life forms. It follows a previous study (Walker and others 1999) that explored the role of dominant and minor species in maintaining functional diversity and resilience in a rangeland ecosystem. Unlike our previous results, which were based on estimates of five plant functional attributes, the dominant species in this second community apparently are functionally no more dissimilar to each other than to all other species. We suggest that the lack of clear results in mixed life form communities represents a confounding of the relationships between the “hard” attributes that actually govern how a plant performs in an ecosystem and the “soft” attributes that we use as surrogates. There are very few data on the hard functional attributes of plant species and consequently little information on precisely how the (soft) measurable traits are related to their imputed functions. What evidence there is shows that although the relationships are strong within life forms, they differ between life forms. This poses a problem for the development of research relating plant biodiversity to ecosystem function. Until such a database is developed, it will be very difficult to advance our understanding and measurement of functional diversity in mixed life form communities. Received 30 April 2001; Accepted 23 January 2002.     

广义Lyapunov函数与微分系统关于两种量度的相对稳定(Ⅱ)

利用广义Lyapunov函数来研究微分系统关于两种量度的相对稳定性,讨论它们之间的关系。得出微分系统关于两种量度的相对稳定性等价于广义Lyapunov函数具有某种相应的性质。     

The Use of Vital Dyes to Assess Embryonic Viability in the Hamster, Mesocricetus Auratus

Experiments were designed to assess the use of the vital dyes trypan blue and fluorescein diacetate as indicators of the viability of hamster ova and embryos. Exclusion of trypan blue and fluorescence with fluorescein diacetate showed high correlations with uptake of [³H]uridine by ova and further development of embryos in vitro. Ova killed by freezing and thawing incorporated [³H]uridine at background levels. Trypan blue exclusion and fluorescein diacetate uptake were highly correlated with each other (r = 0.99). Trypan blue and fluorescein diacetate serve as excellent indices of viability in ova and early embryos of hamsters.     

Plant Species Composition Effects on Belowground Properties and the Resistance and Resilience of the Soil Microflora to a Drying Disturbance

We hypothesised that plant species composition and richness would affect soil chemical and microbial community properties, and that these in turn would affect soil microbial resistance and resilience to an experimentally imposed drying disturbance. We performed a container experiment that manipulated the composition and species richness of common pasture plant species (Trifolium repens, Lolium perenne, and Plantago lanceolata) by growing them in monoculture, and in all the possible two and three-way combinations, along with an unplanted control soil. Experimental units were harvested at four different times over a 16-month period to determine the effect of plant community development and seasonal changes in temperature and moisture on belowground properties. Results showed that plant species composition influenced soil chemistry, soil microbial community properties and soil microbial resistance and resilience. Soil from planted treatments generally showed reduced soil microbial resistance to drying compared to unplanted control soils. Soils from under T. repens showed a higher resistance and resilience than the soils from under P. lanceolata, and a higher resistance than soils from under L. perenne. We suggest that differences across soils in either resource limitation or soil microbial community structure may be responsible for these results. Plant species richness rarely affected soil microbial community properties or soil microbial resistance and resilience, despite having some significant effects on plant community biomass and soil nitrogen contents in some harvests. The effect that treatments had for most variables differed between harvests, suggesting that results can be altered by the stage of plant community development or by extrinsic environmental factors that varied with harvest timing. These results in combination show that soil microbial resistance and resilience was affected by plant community composition, and the time of measurement, but was largely unrelated to plant species richness.     

The Use of Chemostats in Microbial Systems Biology

Cells regulate their rate of growth in response to signals from the external world. As the cell grows, diverse cellular processes must be coordinated including macromolecular synthesis, metabolism and ultimately, commitment to the cell division cycle. The chemostat, a method of experimentally controlling cell growth rate, provides a powerful means of systematically studying how growth rate impacts cellular processes - including gene expression and metabolism - and the regulatory networks that control the rate of cell growth. When maintained for hundreds of generations chemostats can be used to study adaptive evolution of microbes in environmental conditions that limit cell growth. We describe the principle of chemostat cultures, demonstrate their operation and provide examples of their various applications. Following a period of disuse after their introduction in the middle of the twentieth century, the convergence of genome-scale methodologies with a renewed interest in the regulation of cell growth and the molecular basis of adaptive evolution is stimulating a renaissance in the use of chemostats in biological research.     

The Use of Functional and Adaptive Criteria in Phylogenetic Systematics

SYNOPSIS. The controversy over whether functional data can contributeto phylogenetic inference has grown in recent years. Steps canbe taken toward its resolution if the relevance of functionaldata is judged for each component of phylogenetic analysis.These components are (1)recognizing of basic taxa (species orsupraspecific taxa), (2) formulating hypotheses of homologyfollowed by character analysis, (3) evaluating character phylogeny,(4) formulating phylogenetic hypotheses, and (5) evaluatingalternative phylogenetic hypotheses. It can be shown that functionaldata do not play a necessary or unique role in any of thesecomponents of phylogenetic analysis. Arguments to the contraryhave failed to provide a rigorous, repeatable methodto incorporatefunctional data; proponents of a functional approach to phylogeneticreconstruction rely too often on subjective, authoritarian argumentation. Students of functional evolutionary morphology frequently havefailed to understand the kinds of information necessary to studyor apply the causal process of adaptation via natural selection.This information, required by the very nature of the theoryitself, includes knowing the pattern of heredity of the phenotypiccharacters being studied, relating intrapopulational phenotypicvariability to variation in fitness, and knowing a sufficientamount about population structure to specify the componentsof natural selection. Studies within functional evolutionarymorphology are not designed to satisfy these requirements. Functionalevolutionary morphology uses the concepts of adaptation andnatural selection axiomatically, and thus such studies contributenothing to our understanding of the evolutionary process becausehypotheses about that process are not being evaluated. Thisalso suggests that, if functional evolutionary morphology wishesto engage in analyses of the evolutionary dynamics of the phenotype,a reorientation of its research strategy and goals will be necessary.     

The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain

Phytophthora is one of the most important and aggressive plant pathogenic genera in agriculture and forestry. Early detection and identification of its pathways of infection and spread are of high importance to minimize the threat they pose to natural ecosystems. eDNA was extracted from soil and water from forests and plantations in the north of Spain. Phytophthora-specific primers were adapted for use in high-throughput Sequencing (HTS). Primers were tested in a control reaction containing eight Phytophthora species and applied to water and soil eDNA samples from northern Spain. Different score coverage threshold values were tested for optimal Phytophthora species separation in a custom-curated database and in the control reaction. Clustering at 99% was the optimal criteria to separate most of the Phytophthora species. Multiple Molecular Operational Taxonomic Units (MOTUs) corresponding to 36 distinct Phytophthora species were amplified in the environmental samples. Pyrosequencing of amplicons from soil samples revealed low Phytophthora diversity (13 species) in comparison with the 35 species detected in water samples. Thirteen of the MOTUs detected in rivers and streams showed no close match to sequences in international sequence databases, revealing that eDNA pyrosequencing is a useful strategy to assess Phytophthora species diversity in natural ecosystems.