Reducing the babel in plant volatile communication: using the forest to see the trees

While plants of a single species emit a diversity of volatile organic compounds (VOCs) to attract or repel interacting organisms, these specific messages may be lost in the midst of the hundreds of VOCs produced by sympatric plants of different species, many of which may have no signal content. Receivers must be able to reduce the babel or noise in these VOCs in order to correctly identify the message. For chemical ecologists faced with vast amounts of data on volatile signatures of plants in different ecological contexts, it is imperative to employ accurate methods of classifying messages, so that suitable bioassays may then be designed to understand message content. We demonstrate the utility of ‘Random Forests’ (RF), a machine‐learning algorithm, for the task of classifying volatile signatures and choosing the minimum set of volatiles for accurate discrimination, using data from sympatric Ficus species as a case study. We demonstrate the advantages of RF over conventional classification methods such as principal component analysis (PCA), as well as data‐mining algorithms such as support vector machines (SVM), diagonal linear discriminant analysis (DLDA) and k‐nearest neighbour (KNN) analysis. We show why a tree‐building method such as RF, which is increasingly being used by the bioinformatics, food technology and medical community, is particularly advantageous for the study of plant communication using volatiles, dealing, as it must, with abundant noise.     

How to see the trees for the forest: introduction to a special issue on causation and disease

This paper summarizes the results from the first European Advanced Seminar in the Philosophy of the Life Sciences, which was held at the Brocher Foundation in Hermance (Switzerland) 6-10 September 2011. The Advanced Seminar brought together philosophers of the life sciences to discuss the topic of "Causation and Disease." The search for causes of disease in the biomedical sciences, we argue on the basis of the contributions to this conference, has not resulted in a simplification and unification of biomedical knowledge, as once hoped for by philosophers of science, but rather in its "complexification."     

Community invasibility and invasion by non-native Fraxinus pennsylvanica trees in a degraded tropical forest

Whether invasion of introduced plant species may be aided by certain community properties is poorly understood for species-rich ecosystems, such as tropical montane forests. In Kenya, the non-native tree Fraxinus pennsylvanica has invaded degraded montane forests. We used generalized linear mixed models to examine the relative importance of different community properties to Fraxinus invasion after agricultural abandonment and in the secondary forest. Fraxinus invasion was positively related to plant community species diversity and the abundance of tree saplings, shrubs, ferns, and herbs in the abandoned fallows, but negatively related to the same community properties in the secondary forest. The number of Fraxinus recruits declined with declining propagule pressure in the fallows, but not in the secondary forest. Although adult and saplings of Fraxinus were positively related to community diversity in the fallows, Fraxinus appeared to decrease diversity in the secondary forest. These results show that the success of non-native species invasion and the effects of an invader on the resident community may depend both on properties and degree of disturbance of the community. Plant community diversity and evenness appeared to determine the invasion success by increasing invasibility of the abandoned fallows, but decreasing invasibility of the secondary forest. Our results from a tropical degraded forest emphasize the importance of including habitat characteristics when predicting both the potential of non-native plant invasion and effects of invasives on the particular community.     

Biosafety in Populus spp. and other forest trees: from non-native species to taxa derived from traditional breeding and genetic engineering

Forest trees are fundamental components of our environment, mainly due to their long lifetime and important role in forest ecology. In the past, some non-native tree species and taxa from traditional breeding have induced severe environmental impacts such as biological invasion, changes in the ‘gene pool’, and spread of diseases in forestry. Genetically modified trees obtained in different research groups worldwide are particularly confronted with increased concerns regarding biosafety issues. In the light of current biosafety research worldwide, various threats facing forests and natural tree populations are evaluated in this review: biological invasions, horizontal gene transfer, vertical gene transfer and effects on other organisms. Results available from groups working in biosafety research and risk avoidance using forest trees, with emphasis on transgenic trees, are reviewed. Independent biosafety research as well as the establishment of biosafety research programs for forest trees financed by national and international authorities is now more important than ever before. Biosafety problems detected in the past clearly show the importance of a prior case-by-case evaluation of non-native species, new taxa and also genetically modified trees according to the precautionary principle before their release to avoid risks to the environment and human health.     

Cladistic analysis of cassiduloid echinoids: trying to see the phylogeny for the trees

Using DNA fingerprinting we estimated the reproductive success of 49 adult birds belonging to 16 breeding groups of the sexually monomorphic brown skua (Calharacta lonnbergi) from the Chatham Islands (New Zealand). This population has a variable mating system, breeding in both monogamous and polyandrous groups. The parentage of 45 chicks produced over three breeding seasons was unequivocally determined using the multilocus probes 33.15 and 33.6. We found no evidence of either extra-pair or extra-group fertilization and there was no evidence to suggest egg dumping by females in any breeding group. Consequently, in the case of pairs, parentage of all chicks was assigned to the resident adult birds. In addition, band sharing analysis indicated that members of communal groups were not close relatives. In the 10 communally breeding groups examined, multiple paternity within a clutch was recorded on two of the 12 occasions in which two chicks were reared. Analysis of the parentage of offspring belonging to different groups, from different years, demonstrated that the number of chicks produced by some adult males varied considerably between seasons. In contrast, the reproductive success of other individuals was constant; for example, one male produced two chicks in each of the three seasons it was studied, while other males in communal groups did not produce any chicks during the course of this study. Fitness is a lifetime parameter, and any assessment of it requires studies over at least the average lifetime of an individual. The findings presented in this study suggest that, for brown skuas, there are significant differences in the reproductive success of some adult males in different breeding seasons. These results indicate that estimates of reproductive fitness based on only a single breeding season's data can be seriously inaccurate. Should temporal changes in paternity (and/or maternity) be shown to be common phenomena in other species, then such results would have major implications for the interpretation of parentage studies.     

Effects of non-native plants on the native insect community of Delaware

Due to the lack of a co-evolutionary history, the novel defenses presented by introduced plants may be insurmountable to many native insects. Accordingly, non-native plants are expected to support less insect biomass than native plants. Further, native insect specialists may be more affected by introduced plants than native generalist herbivores, resulting in decreased insect diversity on non-native plants due to the loss of specialists. To test these hypotheses, we used a common garden experiment to compare native insect biomass, species richness, and the proportion of native specialist to native generalist insects supported by 45 species of woody plants. Plants were classified into three groupings, with 10 replicates of each species: 15 species native to Delaware (Natives), 15 non-native species that were congeneric with a member of the Native group (Non-native Congeners), and 15 non-native species that did not have a congener present in the United States (Aliens). Native herbivorous insects were sampled in May, June, and July of 2004 and 2005. Overall, insect biomass was greater on Natives than Non-native Congeners and Aliens, but insect biomass varied unpredictably between congeneric pair members. Counter to expectations, Aliens held more insect biomass than did Non-native Congeners. There was no difference in species richness or the number of specialist and generalist species collected among the three plant groupings in either year, although our protocol was biased against sampling specialists. If these results generalize to other studies, loss of native insect biomass due to introduced plants may negatively affect higher trophic levels of the ecosystem.     

Exploring the impact of a non-native seed predator on the seed germination of its non-native host

Biological Invasions - Novel interactions between introduced and native species commonly occur and can even be predicted from existing native interactions in a certain area. However, novel...     

Neuroimaging: seeing the trees for the forest

New functional imaging studies demonstrate that it is possible to decode a sensory visual pattern, and even an internal perceptual state, by combining seemingly insignificant feature selective signal biases present in a large number of voxels.     

Predicting forest site productivity in temperate lowland from forest floor, soil and litterfall characteristics using boosted regression trees

Aims

The aim of this study is on the one hand to identify the most determining variables predicting the site productivity of pedunculate oak, common beech and Scots pine in temperate lowland forests of Flanders; and on the other hand to test whether the accuracy of site productivity models based exclusively on soil or forest floor predictor variables is similar to the accuracy achieved by full ecosystem models, combining all soil, vegetation, humus and litterfall composition related variables.

Methods

Boosted Regression Trees (BRT) were used to model in a climatically homogeneous region the relationship between environmental variables and site productivity. A distinction was made between soil (soil physical and chemical), forest floor (vegetation and humus) and ecosystem (soil, forest floor and litterfall composition jointly) predictors.

Results

Our results have illustrated the strength of BRT to model the non-linear behaviour of ecological processes. The ecosystem models, based on all collected variables, explained most of the variability and were more accurate than those limited to either soil or forest floor variables. Nevertheless, both the soil and forest floor models can serve as good predictive models for many forest management practices.

Conclusions

Soil granulometric fractions and litterfall nitrogen concentrations were the most effective predictors of forest site productivity in Flanders. Although many studies revealed a fertilising effect of increased nitrogen deposition, nitrogen saturation seemed to reduce species’ productivity in this region.     

Landscape nutrition: seeing the forest instead of the trees

Recent theories suggest that herbivores forage across many scales and that foraging decisions are driven by the distribution of nitrogen. However, experimental tests of these predictions across large landscapes are rare and difficult. Pretorius et al. (2011) present an elegant experimental design to test how patch size, local nutrient density and total nutrient load are detected by foraging African elephants (Loxodonta africana) in the Colophospermum mopane shrub veld in South Africa. This experiment should serve as a model for investigations of how herbivores detect and respond to high nutrient patches of different size; it also raises questions for further research, such as the fate of high nutrient patches as elephants disperse nutrients from them in urine, faecal material and carcasses deposited elsewhere in the landscape.     

Economic impacts of non-native forest insects in the continental United States

Reliable estimates of the impacts and costs of biological invasions are critical to developing credible management, trade and regulatory policies. Worldwide, forests and urban trees provide important ecosystem services as well as economic and social benefits, but are threatened by non-native insects. More than 450 non-native forest insects are established in the United States but estimates of broad-scale economic impacts associated with these species are largely unavailable. We developed a novel modeling approach that maximizes the use of available data, accounts for multiple sources of uncertainty, and provides cost estimates for three major feeding guilds of non-native forest insects. For each guild, we calculated the economic damages for five cost categories and we estimated the probability of future introductions of damaging pests. We found that costs are largely borne by homeowners and municipal governments. Wood- and phloem-boring insects are anticipated to cause the largest economic impacts by annually inducing nearly $1.7 billion in local government expenditures and approximately $830 million in lost residential property values. Given observations of new species, there is a 32% chance that another highly destructive borer species will invade the U.S. in the next 10 years. Our damage estimates provide a crucial but previously missing component of cost-benefit analyses to evaluate policies and management options intended to reduce species introductions. The modeling approach we developed is highly flexible and could be similarly employed to estimate damages in other countries or natural resource sectors.     

From plants to birds: higher avian predation rates in trees responding to insect herbivory

BACKGROUND: An understanding of the evolution of potential signals from plants to the predators of their herbivores may provide exciting examples of co-evolution among multiple trophic levels. Understanding the mechanism behind the attraction of predators to plants is crucial to conclusions about co-evolution. For example, insectivorous birds are attracted to herbivore-damaged trees without seeing the herbivores or the defoliated parts, but it is not known whether birds use cues from herbivore-damaged plants with a specific adaptation of plants for this purpose. METHODOLOGY: We examined whether signals from damaged trees attract avian predators in the wild and whether birds could use volatile organic compound (VOC) emissions or net photosynthesis of leaves as cues to detect herbivore-rich trees. We conducted a field experiment with mountain birches (Betula pubescens ssp. czerepanovii), their main herbivore (Epirrita autumnata) and insectivorous birds. Half of the trees had herbivore larvae defoliating trees hidden inside branch bags and half had empty bags as controls. We measured predation rate of birds towards artificial larvae on tree branches, and VOC emissions and net photosynthesis of leaves. PRINCIPAL FINDINGS AND SIGNIFICANCE: The predation rate was higher in the herbivore trees than in the control trees. This confirms that birds use cues from trees to locate insect-rich trees in the wild. The herbivore trees had decreased photosynthesis and elevated emissions of many VOCs, which suggests that birds could use either one, or both, as cues. There was, however, large variation in how the VOC emission correlated with predation rate. Emissions of (E)-DMNT [(E)-4,8-dimethyl-1,3,7-nonatriene], beta-ocimene and linalool were positively correlated with predation rate, while those of highly inducible green leaf volatiles were not. These three VOCs are also involved in the attraction of insect parasitoids and predatory mites to herbivore-damaged plants, which suggests that plants may not have specific adaptations to signal only to birds.