BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. RESULTS: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. CONCLUSIONS: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

Needle removal by pine sawfly larvae increases branch-level VOC emissions and reduces below-ground emissions of Scots pine.

Climate warming is expected to increase the frequency of insect outbreaks in Boreal conifer forests. We evaluated how needle removal by the larvae of two diprionid sawfly species affects the composition and quantity of VOC emissions from Pinus sylvestris L. saplings. Feeding damage significantly increased the rate of localized VOC emissions from the damaged branch. The emissions of total monoterpenes (MTs) were dominating (96-98% of total VOCs) and increased by14-fold in Neodiprion sertifer-damaged branches and by 16-fold in Diprion pini-damaged branches compared to intact branches. Emissions of δ-3-carene, α-pinene, sabinene, and ß-phellandrene were most responsive. Feeding damage by N. sertifer larvae increased the emission rates of total sesquiterpenes by 7-fold (4% of total VOCs) and total green leaf volatiles by 13-fold (<1% of total VOCs). The VOC emissions from N. sertifer larvae constituted nearly 25% of the total branch emissions. N. sertifer feeding in the lower branches induced 4-fold increase in MT emissions in the top crown. Defoliation of Scots pine by D. pini significantly reduced the below-ground emissions of total MTs by approximately 80%. We conclude that defoliators could significantly increase total VOC emissions from the Scots pine canopy including MT emissions from resin storing sawfly larvae.

Density and composition of an insect population in a field trial of chitinase transgenic and wild-type silver birch (Betula pendula) clones.

Fifteen silver birch (Betula pendula Roth) lines carrying a sugar beet chitinase IV gene and eight wild-type birch clones were grown in a field trial. The composition and density of the insect population and the leaf damage caused by insects were monitored and compared between transgenic and wild-type trees. The most abundant insect group in all trees was aphids, and the variation in total insect densities was mainly explained by the variation in aphid densities. Insect densities were generally higher in the transgenic than in the control trees, indicating that the expression of the sugar beet chitinase IV gene had an influence on the suitability of birch leaves to aphids. The level of leaf damage was higher among transgenic than among control trees. Chewing damage was the most common type of leaf damage in all trees. The number of different damage types was higher among the wild-type clones than among the transgenic lines or their controls. The results indicate that the chitinase transgenic trees are more susceptible to aphids and suffer higher levels of leaf damage than the control trees. In the composition of the damage types, the control trees were more similar to the transgenic than to other wild-type trees, indicating that the composition was mostly linked to the genotype of the tree and not to the expression of the transgene. This study provides important information on the ecological interactions of chitinase transgenic trees in the field trial. No clear harmful effects of transgenic chitinase on the biodiversity of insect population were detected.

Cocoon predation on diprionid sawflies: the effect of forest fertility.

Predation by small mammals is thought to be one of the main regulators of outbreaking sawfly species. It has been suggested that predation may be lower in poor and dryish forests, and this is the reason why outbreaks often begin from this type of environment. We studied experimentally how fertility of the forest site affects cocoon predation experienced by two sawfly species, the common pine sawfly Diprion pini (Linnaeus) and the European pine sawfly Neodiprion sertifer (Geoffroy). We applied a fertilization treatment to selected pine-dominated barren forest sites in Finland, and 2-4 years later monitored predation on the sawfly cocoons in fertilized and control areas. The results did not support the idea that forest fertility was related to cocoon predation. We also could not verify that small mammal abundance was related to fertility of the forest. The most obvious pattern we observed was that the two sawfly species differed dramatically in predation experienced. N. sertifer has its cocoon phase in mid-summer and experienced only moderate predation (37%) whereas D. pini, with its cocoon phase in autumn, suffered from very heavy predation (96%). Our observations suggest that if predation is important in controlling the population dynamics of the species, its impact depends more on the sawfly species and season than on the fertility of the forest site.