Cutting the forest to see a single tree?

The development of single-molecule tools has significantly impacted the way we think about biochemical processes. Watching a single protein in action allows us to observe kinetic details and rare subpopulations that are hidden in ensemble-averaging techniques. I will discuss here the pros and cons of the single-molecule approach in studying ligand binding in macromolecular systems and how these techniques can be applied to characterize the behavior of large multicomponent biochemical systems.     

Can the theory of critical distances predict the failure of shape memory alloys?

Components made from shape memory alloys (SMAs) such as nitinol often fail from stress concentrations and defects such as notches and cracks. It is shown here for the first time that these failures can be predicted using the theory of critical distances (TCDs), a method which has previously been used to study fracture and fatigue in other materials. The TCD uses the stress at a certain distance ahead of the notch to predict the failure of the material due to the stress concentration. The critical distance is believed to be a material property which is related to the microstructure of the material. The TCD is simply applied to a linear model of the material without the need to model the complication of its non-linear behaviour. The non-linear behaviour of the material at fracture is represented in the critical stress. The effect of notches and short cracks on the fracture of SMA NiTi was studied by analysing experimental data from the literature. Using a finite element model with elastic material behaviour, it is shown that the TCD can predict the effect of crack length and notch geometry on the critical stress and stress intensity for fracture, with prediction errors of less than 5%. The value of the critical distance obtained for this material was L?=?90?μm; this may be related to its grain size. The effects of short cracks on stress intensity were studied. It was shown that the same value of the critical distance (L?=?90?μm) could estimate the experimental data for both notches and short cracks.     

Do fitness-equalizing tradeoffs lead to neutral communities?

Neutral theory in ecology is aimed at describing communities where species coexist due to similarities rather than the classically posited niche differences. It assumes that all individuals, regardless of species identity, are demographically equivalent. However, Hubbell suggested that neutral theory may describe even niche communities because tradeoffs equalize fitness across species which differ in their traits. In fact, tradeoffs can involve stabilization as well as fitness equalization, and stabilization involves different dynamics and can lead to different community patterns than neutral theory. Yet the important question remains if neutral theory provides a robust picture of all fitness-equalized communities, of which communities with demographic equivalence are one special case. Here, I examine Hubbell’s suggestion for a purely fitness-equalizing interspecific birth–death tradeoff, expanding neutral theory to a theory describing this broader class of fitness-equalized communities. In particular, I use a flexible framework allowing examination of the influence of speciation dynamics. I find that the scaling of speciation rates with birth and death rates, which is poorly known, has large impacts on community structure. In most cases, the departure from the predictions of current neutral models is substantial. This work suggests that demographic and speciation complexities present a challenge to the future development and use of neutral theory in ecology as null model. The framework presented here will provide a starting point for meeting that challenge, and may also be useful in the development of stochastic niche models with speciation dynamics.     

Does sex matter? Gender‐specific responses to forest fragmentation in Neotropical bats

Understanding the consequences of habitat modification on wildlife communities is central to the development of conservation strategies. However, albeit male and female individuals of numerous species are known to exhibit differences in habitat use, sex‐specific responses to habitat modification remain little explored. Here, we used a landscape‐scale fragmentation experiment to assess, separately for males and females, the effects of fragmentation on the abundance of Carollia perspicillata and Rhinophylla pumilio, two widespread Neotropical frugivorous bats. We predicted that sex‐specific responses would arise from higher energetic requirements from pregnancy and lactation in females. Analyses were conducted independently for each season, and we further investigated the joint responses to local and landscape‐scale metrics of habitat quality, composition, and configuration. Although males and females responded similarly to a fragmentation gradient composed by continuous forest, fragment interiors, edges, and matrix habitats, we found marked differences between sexes in habitat use for at least one of the seasons. Whereas the sex ratio varied little in continuous forest and fragment interiors, females were found to be more abundant than males in edge and matrix habitats. This difference was more prominent in the dry season, the reproductive season of both species. For both species, abundance responses to local‐ and landscape‐scale predictors differed between sexes and again, differences were more pronounced in the dry season. The results suggest considerable sex‐mediated responses to forest disruption and degradation in tropical bats and complement our understanding of the impacts of fragmentation on tropical forest vertebrate communities.     

Can we produce carbon and climate neutral forest bioenergy?

Harvesting branches, stumps and unmercantable tops, in addition to stem wood, decreases the carbon input to the soil and consequently reduces the forest carbon stock. We examine the changes in the forest carbon cycle that would compensate for this carbon loss over a rotation period and lead to carbon neutral forest residue bioenergy systems. In addition, we analyse the potential climate impact of these carbon neutral systems. In a boreal forest, the carbon loss was compensated for with a 10% increase in tree growth or a postponing of final felling for 20 years from 90 to 110 years in one forest rotation period. However, these changes in carbon sequestration did not prevent soil carbon loss. To recover soil carbon stock, a 38% increase in tree growth or a 21% decrease in the decomposition rate of the remaining organic matter was needed. All the forest residue bioenergy scenarios studied had a warming impact on climate for at least 62 years. Nevertheless, the increases in the carbon sequestration from forest growth or reduction in the decomposition rate of the remaining organic matter resulted in a 50% smaller warming impact of forest bioenergy use or even a cooling climate impact in the long term. The study shows that carbon neutral forest residue bioenergy systems have warming climate impacts. Minimization of the forest carbon loss improves the climate impact of forest bioenergy.     

Can the theory of evolution be falsified?

In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called the theory of common descent), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.     

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.     

Can root traits predict communities of soil nematodes in restored northern prairies?

Plant and Soil - We examined how restoration affects the structure and function of grasslands belowground by relating changes in the morphology and architecture of root systems of dominant plants...     

Can phenological models predict tree phenology accurately in the future? The unrevealed hurdle of endodormancy break

The onset of the growing season of trees has been earlier by 2.3 days per decade during the last 40 years in temperate Europe because of global warming. The effect of temperature on plant phenology is, however, not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud endodormancy, and, on the other hand, higher temperatures are necessary to promote bud cell growth afterward. Different process‐based models have been developed in the last decades to predict the date of budbreak of woody species. They predict that global warming should delay or compromise endodormancy break at the species equatorward range limits leading to a delay or even impossibility to flower or set new leaves. These models are classically parameterized with flowering or budbreak dates only, with no information on the endodormancy break date because this information is very scarce. Here, we evaluated the efficiency of a set of phenological models to accurately predict the endodormancy break dates of three fruit trees. Our results show that models calibrated solely with budbreak dates usually do not accurately predict the endodormancy break date. Providing endodormancy break date for the model parameterization results in much more accurate prediction of this latter, with, however, a higher error than that on budbreak dates. Most importantly, we show that models not calibrated with endodormancy break dates can generate large discrepancies in forecasted budbreak dates when using climate scenarios as compared to models calibrated with endodormancy break dates. This discrepancy increases with mean annual temperature and is therefore the strongest after 2050 in the southernmost regions. Our results claim for the urgent need of massive measurements of endodormancy break dates in forest and fruit trees to yield more robust projections of phenological changes in a near future.     

What shapes cerambycid beetle communities in a tropical forest mosaic? Assessing the effects of host tree identity,forest structure,and vertical stratification

Due to anthropogenic activities, tropical rain forests face many challenges in sustaining biodiversity and maintaining global climates. This study explores how forest successional stage, tree composition, and stratum affect communities of saproxylic cerambycid beetles—concealed feeders that play important roles in forest nutrient cycling. Forty trees in five families (Fabaceae, Lecythidaceae, Malvaceae, Moraceae, and Sapotaceae) were sampled in a mosaic of old‐growth and secondary forest on the Osa Peninsula, Costa Rica. Bait branches yielded 3549 cerambycid individuals in 49 species. Species richness was almost identical in old‐growth and secondary forest, and both yielded specialists, but abundance was higher in old‐growth forest. Overall community structure was most strongly influenced by host plant species; within most plant families it was also impacted by forest successional status. Moraceae was the exception, presumably because the focal tree species was abundant in both old‐growth and secondary forest. Several host and old‐growth specialist species reached high densities within patches of old‐growth forest, but seldom colonized apparently suitable trees within secondary forest. This suggests that even small areas of old‐growth forest can act as refuges, but that secondary forest may act as a barrier to dispersal. The vulnerability of specialized saproxylic insects to land use change will be linked to the ability of their preferred hosts to disperse to and persist in successional habitats; rearing studies may provide the most accurate method to monitor community changes over time.     

Can the acoustic adaptation hypothesis predict the structure of Australian birdsong?

The acoustic adaptation hypothesis (AAH) predicts that long-distance signals will be structured so as to maximize their transmission fidelity. Previous studies testing the hypothesis on birdsong have provided equivocal support. The best support comes from large-scale comparative studies and those studies where habitat is characterized as open versus densely vegetated. In the first case, sufficient statistical power is present to detect even small effects on song structure, whereas in the later case the effect size of the habitat may be sufficiently large. Most studies have focused on Holarctic or Neotropical species, which may ultimately share a common evolutionary history. In this study, Australian birds were chosen for a phylogenetically independent test of key predictions of the AAH. Specifically, birds in open habitats were predicted to sing songs with higher frequencies, greater bandwidth, have a greater probability of having overtones, and be emitted at a quicker rate than birds inhabiting densely forested habitats. Acoustic measurements were made on commercially available recordings of 121 species of Australian birds from 41 different families. Analyses controlled for variation explained by body mass (using ANCOVA), and phylogeny (using genus pairs analyses). We found only modest support for the AAH. Our finding that birds in open habitats produced higher frequency vocalizations and greater bandwidth vocalizations is also consistent with hypotheses about signal structure facilitating auditory distance assessment. Forest birds may therefore rely on cues other than frequency-dependent attenuation for ranging.     

Can the pheromones of predators modulate responses to herbivore‐induced plant volatiles?

Biological control of greenhouse pests has been successfully developed and applied. In greenhouse crops, several entomophagous species (predators and parasitoids) are used simultaneously in the crop cycle. One important aspect of these crops, which represent modified ecosystems, is the interactions among complexes of species, including plants, phytophagous insects, and predators. The chemical relationships (semiochemicals: pheromones and kairomones) among these species likely play an important role in greenhouse crops; however, few studies have focused on these relationships. The aim of this study was to analyse the importance of semiochemicals. Three groups of laboratory trials were conducted with two predatory species: Nabis pseudoferus and Nesidiocoris tenuis (Hemiptera: Nabidae and Miridae, respectively). The results of the first group of trials indicated that the adult females of both species were more attracted to herbivore‐induced plant volatiles (HIPVs) than they were to the control plants or plants with artificial damage. Based on the second group of trials, pheromones triggered an attraction in adult females of both species for conspecifics. Finally, based on the interactions of the adult females of the same species, pheromones changed or modulated the predatory responses to HIPVs. The implications of these results for the biological control of pest species in greenhouses are further discussed.     

Reproductive performance of the invasive tree Ligustrum lucidum in a subtropical dry forest: does habitat fragmentation boost or limit invasion?

The spread of non-native invasive plants is closely linked to land use changes imposed by human activities such as the expansion of urbanizations and agricultural activities that result in the loss and fragmentation of native forests. While the conditions generated in fragmented forests may provide suitable new habitat for the arrival and establishment of invasive plant propagules, we know little about the reproductive performance of established invasive populations growing in fragmented conditions. We assess sexual reproduction of Ligustrum lucidum in continuous and fragmented forests across 2 years. We also measure soil quality parameters in 1 year to determine their relative influence in shaping its reproduction in both landscape conditions. We observed a strong decrease in reproductive success at the population level in fragmented habitats. However, reproduction at the individual level showed no differences in seed production per tree between landscape conditions, implying no changes in pollination service. Simultaneously, soils of continuous forests had higher water content, total nitrogen, organic matter and carbon. These soil quality parameters were positively correlated with seed production and seedling number per plot within the same year. Thus, reproductive failure in fragmented forests would not be the result of Allee effects but the consequence of less favorable abiotic soil conditions. In current dynamic and changing climatic scenarios imposed by human activities, water and nutrient demanding invasive plants like L. lucidum might be as likely as or even more susceptible to these changes than native ones. Climatic shifts acting in concert with land use changes may either ameliorate invasion spread in abiotically eroded fragmented habitats or boost invasion into novel environments, resulting in new distribution spread patterns.     

Can forest fragmentation disrupt a conditional mutualism? A case from central Amazon

This is the first study to investigate whether scatter-hoarding behavior, a conditional mutualism, can be disrupted by forest fragmentation. We examined whether acouchies (Myoprocta acouchy, Rodentia) and agoutis (Dasyprocta leporina, Rodentia) changed scatter-hoarding behavior toward seeds of Astrocaryum aculeatum (Arecaceae) as a consequence of a decrease in forest-patch area. Our study was conducted at the 30-year-old Biological Dynamics of Forest Fragments Project, in central Amazon, Brazil. We tested whether forest size affected the number of Astrocaryum seeds removed and scatter-hoarded (and likely dispersed) by acouchies and agoutis, as well as the distance that the seeds were hoarded. The study extended over three seasons: the peak of the rainy season (March–April), the transition between the rainy and the dry season (May–June), and the peak of the dry season (August–September). Our results revealed that the number of seeds removed was larger in smaller fragments, but that the percentage of seeds hoarded was much lower, and seeds eaten much higher, in 1-ha fragments. Moreover, fewer seeds were taken longer distances in fragments than in the continuous forest. Site affected the number of seeds removed and season affected the percentage of seeds hoarded: more seeds were removed from stations in one site than in two others, and hoarding was more important in April and September than in June. Our study reveals that scatter-hoarding behavior is affected by forest fragmentation, with the most important disruption in very small fragments. Fragmentation converts a largely mutualistic relationship between the rodents and this palm in large forest patches into seed predation in small fragments.     

Can life-history traits predict the response of forb populations to changes in climate variability?

1.  Climate change will cause changes in average temperature and precipitation as well as increased fluctuations around the mean, yet few studies have considered the impacts of altered climate variability on plant populations. We tested whether life-history traits (expected life span, generation time and seed size) can predict plant responses to increased environmental variability across similar plant species sharing the same habitat.
2.  We combined long-term demographic data on 10 prairie forb species with stochastic demography techniques to estimate the effects of potential changes in matrix element means and variances on the long-term stochastic population growth rate.
3.  For all 10 species, recruitment had higher contribution and elasticity values than survival, meaning that climate change is more likely to influence population growth through effects on recruitment than on survival for these relatively short-lived forbs. Species with longer generation times had lower elasticities to increases in matrix element variability.
4.   Synthesis. Our analysis of a unique, long-term data set suggests that longer-lived plant species will be less vulnerable to the effects of future increases in climate variability. While this relationship was previously reported for diverse taxa from many locations, our results show that it also applies within a guild of short-lived species from a single community. The generality of the pattern demonstrates the potential for using life-history traits to make predictions about which species may be the most vulnerable to climate change.     

Can measures of prey availability improve our ability to predict the abundance of large marine predators?

Apex marine predators can structure marine communities, so factors underlying their abundance are of broad interest. However, such data are almost completely lacking for large sharks. We assessed the relationship between tiger shark abundance, water temperature, and the availability of a variety of known prey over 5 years in Western Australia. Abundance of sharks in four size categories and the density of prey (cormorants, dugongs, sea snakes, sea turtles) were indexed using daily catch rates and transects, respectively. Across all sizes, thermal conditions were a determinant of abundance, with numerical peaks coinciding with periods of high water temperature. However, for sharks exceeding 300 cm total length, the inclusion of dugong density significantly improved temperature-based models, suggesting that use of particular areas by large tiger sharks is influenced by availability of this sirenian. We conclude that large marine predator population models may benefit from the inclusion of measures of prey availability, but only if such measures consider prey types separately and account for ontogenetic shifts in the diet of the predator in question. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.