The intermediate disturbance hypothesis--species diversity or functional diversity?

Phytoplankton dynamics in a shallow eutrophic lake were investigatedover a 3-year period with respect to environmental forces whichdrive species composition and diversity. Diversity was calculatedon the basis of species as well as on the basis of their functionalproperties (the C-R-S concept). Stratification and water columnmixing had a strong impact on phytoplankton composition. Applicationof a similarity–diversity model revealed that a high diversitywas a transient non-stable state, whereas drastic changes orlong-lasting stable environmental conditions are characterizedby low diversity. This effect was more pronounced when the diversitywas calculated on the basis of the phytoplankton species' functionalproperties. Thus, this functional approach supports the intermediatedisturbance hypothesis from field data.     

How many species are there in apple insect communities?: testing the resource diversity and intermediate disturbance hypotheses

Abstract.

• 1 In European and American apple orchards the insect species richness, calculated from our own, and published data, varied widely (30–940 species). The dominance of insect orders was similar to that found in natural communities.
• 2 To test the predictions of the‘resource diversity hypothesis’(RDH) and the‘intermediate disturbance hypothesis’(IDH) of insect diversity, we analysed the simultaneous impact of vegetational diversity and intensity of orchard management practice on the species richness of characteristic insect categories in six types of apple stands, over 5 years, in Hungary.
• 3 The more diverse was the vegetation adjacent to the orchard and the less intensively was the orchard managed, the greater was the total insect species richness, supporting both hypotheses.
• 4 The number of agricultural pest species found in the apple orchards depended above all on the diversity of adjacent agricultural vegetation, supporting only the RDH.
• 5 The species richness of specialized apple pests was limited only by the intensity of pest control, supporting only the IDH.
• 6 Within the category of generalist natural enemies species richness mainly varied with the diversity of adjacent vegetation, supporting the RDH.
• 7 The aeroentomofauna constituted a surprisingly high percentage (>50%) for both total species and agricultural pests, but was poorly represented within the natural enemies category, and absent from the specific apple pest category.
• 8 A general conclusion is that the number of insect species in perennial orchard-systems within agricultural areas is determined primarily by the regional extra-orchard vegetational diversity and secondly by the degree of local intra-orchard disturbances and plant diversity. Consequently, at the community level the predictions of both hypotheses can be simultaneously valid at different spatial scales and are not mutually exclusive. However, within the community, at the level of the different insect categories studied here, only one of the hypotheses proved to be valid.

     

Issues affecting the measurement of disturbance response patterns in herbaceous vegetation – A test of the intermediate disturbance hypothesis

The 'intermediate disturbance hypothesis' (IDH) predicts maximum species diversity at intermediate levels of disturbance. Disturbance levels are measured by intensity or frequency of disturbance or by the time since disturbance. The IDH has been tested over a wide range of studies and communities with results either accepting or rejecting the hypothesis. The objectives of this study were to determine how observed disturbance response patterns for the same herbaceous plant community are influenced by modelling techniques, particularly in relation to the expression of disturbance gradients, choice of species diversity indices, and time of assessment since disturbance. Response patterns were examined using a multi-factorial disturbance experiment involving grazing (absent and present); fire (absent and present); soil cultivation (none, 5 and 20 cm); and amendment (none, fertiliser, and fertiliser plus clover seeds). Generalized linear models with a b-spline function were used to define response patterns for five different disturbance gradients over a 24-month period using three indices of diversity. Seven basic disturbance response models were recognized ranging from the classical IDH bell-shaped pattern through increasing or decreasing trends, to a no-change model with increasing levels of disturbance. Only 6.7% of all models were consistent with the IDH. The no-change model was found in nearly half the cases investigated and increased in occurrence with time since disturbance. The choice of the disturbance intensity gradient, the species diversity index used and the time of assessment after disturbance significantly influenced the frequency of occurrence of the disturbance response models observed. Consequently, the responses of vegetation to disturbance gradients show many patterns depending on how they are defined and modelled rather than the simple bell-shaped curve as predicted by the IDH, but the ecological mechanisms supporting some of these patterns need to be further investigated.     

The protein folding problem: when will it be solved?

The protein folding problem can be viewed as three different problems: defining the thermodynamic folding code; devising a good computational structure prediction algorithm; and answering Levinthal's question regarding the kinetic mechanism of how proteins can fold so quickly. Once regarded as a grand challenge, protein folding has seen much progress in recent years. Folding codes are now being used to successfully design proteins and non-biological foldable polymers; aided by the Critical Assessment of Techniques for Structure Prediction (CASP) competition, protein structure prediction has now become quite good. Even the once-challenging Levinthal puzzle now seems to have an answer--a protein can avoid searching irrelevant conformations and fold quickly by making local independent decisions first, followed by non-local global decisions later.     

Can the intermediate disturbance hypothesis and information on species traits predict anuran responses to fire?

Fire is a common form of recurrent disturbance in many ecosystems, but ecological theory has a poor record of predicting animal responses to fire, at both species and assemblage levels. As a consequence, there is limited information to guide fire regime management for biodiversity conservation. We investigated a key research gap in the fire ecology literature; that is, the response of an anuran assemblage to variation in the fire return interval. We tested two hypotheses using a spatially‐explicit fire database collected over a 40 year period: 1) species richness would peak at intermediate levels of disturbance. 2) Species with traits which enabled them to escape fire – burrowing or canopy dwelling – would be better able to survive fires, resulting in higher levels of occurrence in frequently burned sites. We found no evidence for either a reduction in species richness at locations with short fire return intervals, or a peak in species richness at intermediate levels of disturbance. Although we found some support for individual species responses to fire return intervals, these were inconsistent with the interpretation of burrowing or climbing being functional traits for fire‐avoidance. Instead burrowing and climbing species may be more likely to be disadvantaged by frequent fire than surface dwelling frogs. More generally, our results show that many species in our study system have persisted despite a range of fire frequencies, and therefore that active management of fire regimes for anuran persistence may be unnecessary. The responses of anurans to fire in this location are unlikely to be predictable using simple life‐history traits. Future work should focus on understanding the mechanistic underpinnings of fire responses, by integrating information on animal behavior and species’ ecological requirements.     

Pharmacogenomics: will the promise be fulfilled?

Tools such as genome resequencing and genome-wide association studies have recently been used to uncover a number of variants that affect drug toxicity and efficacy, as well as potential drug targets. But how much closer are we to incorporating pharmacogenomics into routine clinical practice? Five experts discuss how far we have come, and highlight the technological, informatics, educational and practical obstacles that stand in the way of realizing genome-driven medicine.     

Prion hypothesis: the end of the controversy?

Forty-three years have passed since it was first proposed that a protein could be the sole component of the infectious agent responsible for the enigmatic prion diseases. Many discoveries have strongly supported the prion hypothesis, but only recently has this once heretical hypothesis been widely accepted by the scientific community. In the past 3 years, researchers have achieved the 'Holy Grail' demonstration that infectious material can be generated in vitro using completely defined components. These breakthroughs have proven that a misfolded protein is the active component of the infectious agent, and that propagation of the disease and its unique features depend on the self-replication of the infectious folding of the prion protein. In spite of these important discoveries, it remains unclear whether another molecule besides the misfolded prion protein might be an essential element of the infectious agent. Future research promises to reveal many more intriguing features about the rogue prions.     

Abundance, diversity and fidelity of macroinvertebrates sheltering beneath rocks during tidal emersion in an intertidal cobble field: Does the intermediate disturbance hypothesis hold for less exposed shores with smaller rocks?

The community structure of macroinvertebrates occurring beneath cobbles during tidal emersion was investigated in an intertidal cobble field on the east coast of the south island of New Zealand. In order to test whether the intermediate disturbance hypothesis (IDH) holds in less exposed shores comprised exclusively of smaller rocks (cobbles) we measured 1) the size frequency distribution of cobbles (mass and basal surface area), 2) the incidence of barnacle encrustation as an indirect measure of cobble disturbance, 3) the abundances of the dominant macroinvertebrates occurring beneath cobbles (the crab Hemigrapsus crenulatus, the chiton Sypharochiton pelliserpentis and the snail Diloma zealandica), and 4) macroinvertebrate fidelity beneath a range of cobble sizes. Only large cobbles were found to be encrusted with barnacles, indicative of their greater resistance to physical disturbance by waves and currents. Mark and relocate experiments indicated fidelity to a given cobble over two tidal cycles was 11-14% for crabs and did not vary with cobble size. In contrast, fidelity to medium and large cobbles was higher for chitons (26-45%) and snails (17-31%) and generally increased with increasing cobble size. In contrast to the predictions of the IDH, there was a positive correlation between increasing cobble size and increasing species diversity of organisms found under the cobbles. This pattern is not simply attributable to greater space available beneath large cobbles as there was a significantly greater density of macroinvertebrates beneath medium and large, compared to the small cobbles. Increasing species diversity with increasing cobble size appears to be independent of patterns of species recolonization associated with small cobbles being subject to high disturbance or interspecific competitive hierarchies associated with low disturbance beneath large cobbles. Instead, factors such as aggregative behaviors, and reducing vulnerability to predators and desiccation stress are likely to explain the relationship between cobbles and their associated macroinvertebrate communities.     

Complex memories in honeybees: can there be more than two?

Foraging honeybees are likely to learn visual and chemical cues associated with many different food sources. Here, we explore how many such sources can be memorized and recalled. Marked bees were trained to visit two (or three) sugar feeders, each placed at a different outdoor location and carrying a different scent. We then tested the ability of the bees to recall these locations and fly to them, when the training scents were blown into the hive, and the scents and food at the feeders were removed. When trained on two feeder locations, each associated with a different scent, the bees could correctly recall the location associated with each scent. However, this ability broke down when the number of scents and feeder locations was increased to three. Performance was partially restored when each of the three training feeders was endowed with an additional cue, namely, a distinct colour. Our results suggest that bees can recall a maximum of two locations when each is associated with a different scent. However, this number can be increased if the scent cues are augmented by visual cues. These findings have implications for the ways in which associations are established and laid down in honeybee memory.     

Where and when does a ring start and end? Testing the ring-species hypothesis in a species complex of Australian parrots

Speciation, despite ongoing gene flow can be studied directly in nature in ring species that comprise two reproductively isolated populations connected by a chain or ring of intergrading populations. We applied three tiers of spatio-temporal analysis (phylogeny/historical biogeography, phylogeography and landscape/population genetics) to the data from mitochondrial and nuclear genomes of eastern Australian parrots of the Crimson Rosella Platycercus elegans complex to understand the history and present genetic structure of the ring they have long been considered to form. A ring speciation hypothesis does not explain the patterns we have observed in our data (e.g. multiple genetic discontinuities, discordance in genotypic and phenotypic assignments where terminal differentiates meet). However, we cannot reject that a continuous circular distribution has been involved in the group's history or indeed that one was formed through secondary contact at the 'ring's' east and west; however, we reject a simple ring-species hypothesis as traditionally applied, with secondary contact only at its east. We discuss alternative models involving historical allopatry of populations. We suggest that population expansion shown by population genetics parameters in one of these isolates was accompanied by geographical range expansion, secondary contact and hybridization on the eastern and western sides of the ring. Pleistocene landscape and sea-level and habitat changes then established the birds' current distributions and range disjunctions. Populations now show idiosyncratic patterns of selection and drift. We suggest that selection and drift now drive evolution in different populations within what has been considered the ring.     

Testing the species--genetic diversity correlation in the Aegean archipelago: toward a haplotype-based macroecology?

A positive correlation between species diversity and genetic diversity has been proposed, consistent with neutral predictions in macroecology. We assessed the species--genetic diversity correlation in tenebrionid beetle communities of the Aegean archipelago on 15 islands of different sizes, distances to mainland, and ages of isolation. Alpha and beta diversity of species and haplotypes were assessed using sequences of > 1,000 individuals (mitochondrial cytochrome oxidase 1 and nuclear muscular protein 20). We show that (i) there is a strong species-area and haplotype-area relationship; (ii) species richness in island communities is correlated with intraspecific genetic diversity in the constituent species except when island size or distance to mainland is factored out in partial correlations; (iii) community similarity declines exponentially at an increasing rate when calculated on the basis of species, nuclear, and mtDNA haplotypes; and (iv) distance decay of community similarity is slower in dispersive sand-dwelling lineages compared with less dispersive lineages that are not sand obligate. Taken together, these correlated patterns at the species and haplotype level are consistent with individual-based stochastic dispersal proposed by neutral theories of biodiversity. The results also demonstrate the utility of haplotype data for exploring macroecological patterns in poorly known biota and predicting large-scale biodiversity patterns based on genetic inventories of local samples.     

Could nested PCR be applicable for the study of microbial diversity?

PCR-based methods for rRNA gene analysis have been widely used to study diversity of microbiology. However, the analysis would be difficult when the DNA content in samples is too low to be amplified by conventional PCR. Nested PCR comes up with the advantage of higher sensitivity. It can detect target DNA at several-fold lower concentrations than conventional PCR. However, the amplification bias and factors that potentially affect measurement of sample diversity associated with nested PCR method has received little attention. Here, nested PCR was compared to reconditioning PCR which is based on conventional PCR and it would reduce the formation of heteroduplex. We investigated the use of both nested and reconditioning PCR methods to construct clone libraries of 16S rRNA genes from four swimming pool water samples. Abundances of OTUs (operational taxonomic units) were correlated between the libraries (r ² = 0.88, P < 0.0005), and some OTUs had equivalent abundances in the two libraries using the Chi-square test. Differences in taxonomic groups, as well as diversity and richness estimators, were compared by paired t-test and the Wilcoxon test, respectively. There were no significant differences between clone libraries using these two PCR methods. The results of ∫-Libshuff analysis suggested that nested PCR have no particular biases in revealing OTU diversity of a bacterial community. Thus, nested PCR produce congruent pictures with reconditioning PCR in the microbial community analysis.     

Testing Thayer's hypothesis: can camouflage work by distraction?

One of the oldest theories of animal camouflage predicts that apparently conspicuous markings enhance concealment. Such 'distraction' marks are hypothesized to work by drawing the viewer's attention away from salient features, such as the body outline, that would otherwise reveal the animal. If distraction marks enhance concealment, then they offer a route for animals to combine camouflage markings with conspicuous signalling strategies, such as warning signals. However, the theory has never been tested and remains controversial. By using camouflaged artificial prey presented to wild avian predators, we test whether distractive markings enhance concealment. In contrast to predictions, we find that markings, both circular and irregular shapes, increase predation compared with unmarked targets. Markings became increasingly costly as their contrast against the prey increased. Our experiments failed to find any empirical support for the hypothesis that distraction markings are an important aspect of camouflage in animals.     

Does disturbance drive the collapse of biotic interactions at the severe end of a diversity–biomass gradient?

It has been recently proposed that the decrease in diversity towards the severe end of the humped-back diversity–biomass model of Grime was driven by a collapse of facilitation due to extreme conditions of either stress or physical disturbance. In order to test the hypothesis that disturbance is the primary direct factor driving the collapse of interactions occurring along environmental severity gradients, we conducted a removal experiment in the highly stressed French coastal dunes along a gradient of disturbance due to sand burial. Four dune species were used as targets and transplanted with and without neighbours in four communities along the gradient. The experiment was conducted twice, a dry and an average year. Results of the experiment showed that during the dry year the effect of the environment was prominent and only one species was facilitated for survival in the least disturbed community. During the average year, interactions for growth were important only in the same community, with positive or negative responses depending on the natural position of the target species within the coastal dune gradient. In accordance with our hypothesis, most interactions for both survival and growth were observed in the least disturbed community exhibiting the highest diversity. There were no interactions in the most disturbed community with the lowest diversity.     

Testing the ‘plant domestication-reduced defense’ hypothesis in blueberries: the role of herbivore identity

Domestication is predicted to reduce resistance of agricultural crops against insect herbivores; however, its impact on herbivores with different feeding modes and evolutionary histories needs investigation. To this end, we conducted greenhouse experiments to explore the effects of domestication of blueberries (Vaccinium corymbosum), a crop native to North America, on the performance of two chewing herbivores [the native Sparganothis fruitworm (Sparganothis sulfureana (Clemens)) and non-native gypsy moth (Lymantria dispar L.)], and one piercing-sucking herbivore [the blueberry aphid (Illinoia azaleae (Mason))]. Lymantria dispar performed better (i.e., larvae gained more mass, damaged more leaves, and had greater survival) on cultivated V. corymbosum than on its wild counterpart. In contrast, domestication had no impact on the native S. sulfureana larval mass, consumption, and survivorship. Domestication increased survivorship, but not offspring production, of the aphid I. azaleae. To examine changes in plant chemistry due to domestication, we measured phenolic and nutrient (macro- and micro-elements) content in wild and cultivated V. corymbosum leaves. Although there were no differences in total phenolic content, two compounds were absent, while two were at lower and one at higher concentration in domesticated than in wild plants. Wild V. corymbosum leaves had higher amounts of phosphorus, sulfur, and sodium than cultivated leaves; the opposite was found for aluminum. While our findings provide support for the ‘plant domestication-reduced defense’ hypothesis, the effects of domestication were dependent on feeding modes and adaptations of the herbivores such that the non-native chewing species was more positively affected than the chewing and the piercing-sucking natives.     

Lateral gene transfer: when will adolescence end?

The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fuelled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints probably stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Here, we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.     

Seed plant phylogeny: Demise of the anthophyte hypothesis?

Recent molecular phylogenetic studies indicate, surprisingly, that Gnetales are related to conifers, or even derived from them, and that no other extant seed plants are closely related to angiosperms. Are these results believable? Is this a clash between molecules and morphology?