An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae

Aim  Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersal-extinction-cladogenesis (DEC), against a parsimony-based method, dispersal-vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study.Location  World-wide.Methods  Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes-DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years.Results  Despite differences in the underlying biogeographical model, Bayes-DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events - which in Bayes-DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node.Main conclusions  By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide-spanning spatial and temporal model proposed here could prove useful for testing large-scale biogeographical patterns in plants.

Domain shuffling in a sensor protein contributed to the evolution of insect pathogenicity in plant-beneficial Pseudomonas protegens.

Pseudomonas protegens is a biocontrol rhizobacterium with a plant-beneficial and an insect pathogenic lifestyle, but it is not understood how the organism switches between the two states. Here, we focus on understanding the function and possible evolution of a molecular sensor that enables P. protegens to detect the insect environment and produce a potent insecticidal toxin specifically during insect infection but not on roots. By using quantitative single cell microscopy and mutant analysis, we provide evidence that the sensor histidine kinase FitF is a key regulator of insecticidal toxin production. Our experimental data and bioinformatic analyses indicate that FitF shares a sensing domain with DctB, a histidine kinase regulating carbon uptake in Proteobacteria. This suggested that FitF has acquired its specificity through domain shuffling from a common ancestor. We constructed a chimeric DctB-FitF protein and showed that it is indeed functional in regulating toxin expression in P. protegens. The shuffling event and subsequent adaptive modifications of the recruited sensor domain were critical for the microorganism to express its potent insect toxin in the observed host-specific manner. Inhibition of the FitF sensor during root colonization could explain the mechanism by which P. protegens differentiates between the plant and insect host. Our study establishes FitF of P. protegens as a prime model for molecular evolution of sensor proteins and bacterial pathogenicity.

Movement, impacts and management of plant distributions in response to climate change: insights from invasions

A major challenge in this era of rapid climate change is to predict changes in species distributions and their impacts on ecosystems, and, if necessary, to recommend management strategies for maintenance of biodiversity or ecosystem services. Biological invasions, studied in most biomes of the world, can provide useful analogs for some of the ecological consequences of species distribution shifts in response to climate change. Invasions illustrate the adaptive and interactive responses that can occur when species are confronted with new environmental conditions. Invasion ecology complements climate change research and provides insights into the following questions: i) how will species distributions respond to climate change? ii) how will species movement affect recipient ecosystems? and iii) should we, and if so how can we, manage species and ecosystems in the face of climate change? Invasion ecology demonstrates that a trait-based approach can help to predict spread speeds and impacts on ecosystems, and has the potential to predict climate change impacts on species ranges and recipient ecosystems. However, there is a need to analyse traits in the context of life-history and demography, the stage in the colonisation process (e.g., spread, establishment or impact), the distribution of suitable habitats in the landscape, and the novel abiotic and biotic conditions under which those traits are expressed. As is the case with climate change, invasion ecology is embedded within complex societal goals. Both disciplines converge on similar questions of "when to intervene?" and "what to do?" which call for a better understanding of the ecological processes and social values associated with changing ecosystems.

Transgenic plant factories for the production of biopolymers and plateform chemicals

In the mid-to long-term, resource constraints will force society to cover a significant share of the future demand for fuels, materials and chemicals by renewable resources. This trend is already visible in the increasing conversion of carbohydrates and plant oils to fuels, chemicals, and polymers. In this perspective, we discuss current efforts and ideas to produce platform chemicals and polymers directly in transgenic plants.

DNA banking for plant breeding, biotechnology and biodiversity evaluation.

The manipulation of DNA is routine practice in botanical research and has made a huge impact on plant breeding, biotechnology and biodiversity evaluation. DNA is easy to extract from most plant tissues and can be stored for long periods in DNA banks. Curation methods are well developed for other botanical resources such as herbaria, seed banks and botanic gardens, but procedures for the establishment and maintenance of DNA banks have not been well documented. This paper reviews the curation of DNA banks for the characterisation and utilisation of biodiversity and provides guidelines for DNA bank management. It surveys existing DNA banks and outlines their operation. It includes a review of plant DNA collection, preservation, isolation, storage, database management and exchange procedures. We stress that DNA banks require full integration with existing collections such as botanic gardens, herbaria and seed banks, and information retrieval systems that link such facilities, bioinformatic resources and other DNA banks. They also require efficient and well-regulated sample exchange procedures. Only with appropriate curation will maximum utilisation of DNA collections be achieved.

Stable isotope ecology of Miocene large mammals from Sandelzhausen, southern Germany

The carbon, oxygen, and strontium isotope composition of enamel from teeth of large Miocene herbivorous mammals from Sandelzhausen (MN5, late Early/early Middle Miocene) in the North Alpine foreland basin, were analyzed to infer diet and habitat. The mean enamel delta(13)C value of -11.4 +/- 1.0% (n = 53) for the nine taxa analyzed (including proboscideans, cervids, suids, chalicotheres, equids, rhinocerotids) indicates a pure C(3) plant diet for all mammals. (87)Sr/(86)Sr ratios of similar to 0.710 higher than those from teeth of the western Molasse Basin (0.708-0.709) seem to indicate preferential feeding of the mammals in the northeastern Molasse Basin. The sympatric herbivores have different mean delta(13)C and delta(18)O values which support diet partitioning and/or use of different habitats within a C(3) plant ecosystem. Especially the three sympatric rhinoceroses Plesiaceratherium fahlbuschi, Lartetotherium sansaniense, and Prosantorhinus germanicus show clear partitioning of plants and/or habitats. The palaeomerycid Germanomeryx fahlbuschi was a canopy folivore in moderately closed environments whereas Metaschizotherium bavaricum (Chalicotheriidae) and P. germanicus (Rhinocerotidae) were browsers in more closed forest environments. The horse Anchitherium aurelianense was probably a more generalized feeder than assumed from its dental morphology. The forest hog Hyotherium soemmeringi has the highest delta(13)C and lowest delta(18)O value of all analyzed taxa, possibly related to a frugivorous diet. Most taxa were water-dependent browsers that record meteoric water delta(18)O values of about -5.6 +/- 0.7% Vienna Standard Mean Ocean Water (VSMOW). Using a modern-day mean annual air temperature (MAT)-delta(18)OH(2)O relation a MAT of 19.3 +/- 1.5 degrees C can be reconstructed for Sandelzhausen. A Gomphotherium subtapiroideum tusk serially sampled for delta(18)O values does not record a clear pattern of seasonality. Thus most taxa were C(3) browsers in a forested and humid floodplain environment in the Molasse Basin, which experienced a warm-temperate to subtropical climate and possibly low seasonality.

Plant and arbuscular mycorrhizal fungal diversity - are we looking at the relevant levels of diversity and are we using the right techniques?

Fungal symbionts commonly occur in plants influencing host growth, physiology, and ecology (Carlile et al., 2001). However, while whole-plant growth responses to biotrophic fungi are readily demonstrated, it has been much more difficult to identify and detect the physiological mechanisms responsible. Previous work on the clonal grass Glyceria striata has revealed that the systemic fungal endophyte Epichloë glyceriae has a positive effect on clonal growth of its host (Pan & Clay, 2002; 2003). The latest study from these authors, in this issue (pp. 467- 475), now suggests that increased carbon movement in hosts infected by E. glyceriae may function as one mechanism by which endophytic fungi could increase plant growth. Given the widespread distribution of both clonal plants and symbiotic fungi, this research will have implications for our understanding of the ecology and evolution of fungus-plant associations in natural communities.

Biologia de Neotrioza tavaresi Crawford, 1925 (Hemiptera, Psyllidae), galhador da folha do araçazeiro (Psidium cattleianum)

Biology of the leaf gall inducer Neotrioza tavaresi Crawford, 1925 (Hemiptera, Psyllidae) on strawberry guava tree (Psidium cattleianum). A field study was conducted in Curitiba region, State of Paraná, southern Brazil, to describe the life cycle of Neotrioza tavaresi Crawford, 1925, a leaf galling insect in strawberry guava trees (Psidium cattleianum). Three cycles were observed (1997, 1998, 1999) during regular field trips and the insects were observed in Piraquara municipality, where 15 samples with 50 infested leaves were sampled in the 1997-98 cycle. Galls were dissected for detailed studies. Neotrioza tavaresi has a univoltine cycle in which adult individuals were found inside the galls from August onwards. The sexually mature insects with sex ratio 1, emerged from the galls after their dehiscence caused by feeding of the adult insects on the gall walls. Adult emergence started in early October and ended by early December, with its peak in November. Copulation took place as soon as adults exit the gall and egg laying started the next day. Females had more than 100 ovarioles containing 218.7±44.7 (n=50) fully formed eggs. This indicated the short sexual adult life-span (aprox. 5-7 days) of the species, also characterized by a concentrated oviposition. Adult individuals fed and laid their eggs on younger shoots of the plant. The bottoms of the yellowish eggs were inserted into the leaf tissue, mainly on its adaxial edge (78.1%). The nymphs hatched and, as they fed on the adaxial side of expanding leaves, modified the cell growth pattern and the round-shape galls developed on the adaxial side with one insect inside. The gall wall showed distinct layers, with the inner one suppliyng the food to the insects, and the outer layer supplying gall protection. Nymphs went through five instars and the exuviae remained stuck on a ball of wax inside the gall. All parasitoids found were Hymenoptera belonging to Chalcidoidea: Eulophidae (1 sp), Pteromalidae (2 spp) and Encyrtidae (3 spp). The findings suggest that leaf gall inducer and parasitoids insects and plant life cycles are closely connected and both leaf sprouting and gall opening seem to be triggered by the same environmental and plant conditions. The high abundance of shoots may favor insect performance as adult individuals can easily find an ideal place for feeding, copulating and laying eggs.

Spatial pattern of floral morphology: a possible insight into the effects of pollinators on plant distribution

Pollination syndromes involve convergent evolution towards phenotypes composed of specific scents, colours or floral morphologies that attract or restrict pollinator access to reward. How these traits might influence the distributions of plant species in interaction with pollinators has rarely been investigated. We sampled 870 vegetation plots in the western Swiss Alps and classified the plant species into seven blossom types according to their floral morphology (wind, disk, funnel, tube, bilabiate, head or brush). We investigated the environmental features of plots with functional diversity (FD) lower than expected by chance alone to detect potential pollination filtering and related the proportions of the seven blossom types to a combination of environmental descriptors. From these results, we inferred the potential effect of the pollinator on the spatial distribution of plant species. The vegetation plots with significantly lower FD of blossom types than expected by chance were found at higher altitudes, and the proportions of blossom types were strongly patterned along the same gradient. These results support a biotic filtering effect on plant species assemblages through pollination: disk blossoms became dominant at higher altitudes, resulting in a lower FD. In harsh conditions at high altitudes, pollinators usually decrease in activity, and the openness of the disk blossom grants access to any available pollinator. Inversely, bilabiate blossoms, which are mostly pollinated by bees, were more abundant at lower elevations, which are characterised by greater abundance and diversity of bees. Generalisation through openness of the blossom could be advantageous at high elevations, while specialisation could be a successful alternative strategy at lower elevations. The approach used in this study is purely correlative, and further investigations should be conducted to infer the nature of the causal relationship between plant and pollinator distributions.

Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds.

Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol-degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.chlorophenolicus on leaves of common bean (Phaseolus vulgaris) compared with growth on agar surfaces. In phyllosphere-grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf-induced expression of a subset of the so-called cph genes for the degradation of 4-chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3-oxoadipate, and was shown to be induced not only by 4-chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P.vulgaris by gas chromatography-mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere-based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation.

Genetic diversity in widespread species is not congruent with species richness in alpine plant communities.

The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, that is, ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesised to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies.

In vitro assessment of the pulmonary toxicity and gastric availability of lead-rich particles from a lead recycling plant

Epidemiological studies in urban areas have linked increasing respiratory and cardiovascular pathologies with atmospheric particulate matter (PM) from anthropic activities. However, the biological fate of metal-rich PM industrial emissions in urban areas of developed countries remains understudied. Lead toxicity and bioaccessibility assessments were therefore performed on emissions from a lead recycling plant, using complementary chemical acellular tests and toxicological assays, as a function of PM size (PM(10-2.5), PM(2.5-1) and PM(1)) and origin (furnace, refining and channeled emissions). Process PM displayed differences in metal content, granulometry, and percentage of inhalable fraction as a function of their origin. Lead gastric bioaccessibility was relatively low (maximum 25%) versus previous studies; although, because of high total lead concentrations, significant metal quantities were solubilized in simulated gastrointestinal fluids. Regardless of origin, the finest PM(1) particles induced the most significant pro-inflammatory response in human bronchial epithelial cells. Moreover, this biological response correlated with pro-oxidant potential assay results, suggesting some biological predictive value for acellular tests. Pulmonary effects from lead-rich PM could be driven by thiol complexation with either lead ions or directly on the particulate surface. Finally, health concern of PM was discussed on the basis of pro-inflammatory effects, accellular test results, and PM size distribution.

Role of Methyl Salicylate on Oviposition Deterrence in Arabidopsis thaliana.

Plants attacked by herbivores have evolved different strategies that fend off their enemies. Insect eggs deposited on leaves have been shown to inhibit further oviposition through visual or chemical cues. In some plant species, the volatile methyl salicylate (MeSA) repels gravid insects but whether it plays the same role in the model species Arabidopsis thaliana is currently unknown. Here we showed that Pieris brassicae butterflies laid fewer eggs on Arabidopsis plants that were next to a MeSA dispenser or on plants with constitutively high MeSA emission than on control plants. Surprisingly, the MeSA biosynthesis mutant bsmt1-1 treated with egg extract was still repellent to butterflies when compared to untreated bsmt1-1. Moreover, the expression of BSMT1 was not enhanced by egg extract treatment but was induced by herbivory. Altogether, these results provide evidence that the deterring activity of eggs on gravid butterflies is independent of MeSA emission in Arabidopsis, and that MeSA might rather serve as a deterrent in plants challenged by feeding larvae.

Study of the combined radial post-feeding dispersion of the blowflies Chrysomya megacephala (Fabricius) and C. albiceps (Wiedemann) (Diptera, Calliphoridae)

Blowflies use discrete and ephemeral substrates to feed their larvae. After they run out of food, the larvae begin to disperse in order to find adequate places for pupation or additional food sources, a process named post-feeding larval dispersion. Some important aspects of this process were studied in a circular arena allowing the combined radial post-feeding dispersion from the center of the arena of C. albiceps and C. megacephala larvae. To determine the location of each pupa, the arena was divided in 72 identical sections starting from the center. The distance from the center, the depth and weight of each pupa were evaluated. Statistical tests were done to verify the relation between weight, depth and distance for pupation. From the total an average of 976 larvae released (488 for each species) were collected considering both experiments 456 C. megacephala pupae and 488 of C. albiceps. This demonstrates that C. albiceps probably preyed on 32 C. megacephala larvae during post-feeding dispersion. The study of this dispersion process can be used to estimate the postmortem interval (PMI) of human cadavers in legal medicine.