Opportunities to conduct large-scale field experiments are rare, but provide a unique opportunity to reveal the complex processes that operate within natural ecosystems. Here, we review the design of existing, large-scale forest fragmentation experiments. Based on this review, we develop a design for the Stability of Altered Forest Ecosystems (SAFE) Project, a new forest fragmentation experiment to be located in the lowland tropical forests of Borneo (Sabah, Malaysia). The SAFE Project represents an advance on existing experiments in that it: (i) allows discrimination of the effects of landscape-level forest cover from patch-level processes; (ii) is designed to facilitate the unification of a wide range of data types on ecological patterns and processes that operate over a wide range of spatial scales; (iii) has greater replication than existing experiments; (iv) incorporates an experimental manipulation of riparian corridors; and (v) embeds the experimentally fragmented landscape within a wider gradient of land-use intensity than do existing projects. The SAFE Project represents an opportunity for ecologists across disciplines to participate in a large initiative designed to generate a broad understanding of the ecological impacts of tropical forest modification.

The conversion of natural forest to oil palm plantation is a major current threat to the conservation of biodiversity in South East Asia. Most animal taxa decrease in both species richness and abundance on conversion of forest to oil palm, and there is usually a severe loss of forest species. The extent of loss varies significantly across both different taxa and different microhabitats within the oil palm habitat. The principal driver of this loss in diversity is probably the biological and physical simplification of the habitat, but there is little direct evidence for this. The conservation of forest species requires the preservation of large reserves of intact forest, but we must not lose sight of the importance of conserving biodiversity and ecosystem processes within the oil palm habitat itself. We urgently need to carry out research that will establish whether maintaining diversity supports economically and ecologically important processes. There is some evidence that both landscape and local complexity can have positive impacts on biodiversity in the oil palm habitat. By intelligent manipulation of habitat complexity, it could be possible to enhance not only the number of species that can live in oil palm plantations but also their contribution to the healthy functioning of this exceptionally important and widespread landscape.

Invertebrates are dominant species in primary tropical rainforests, where their abundance and diversity contributes to the functioning and resilience of these globally important ecosystems. However, more than one-third of tropical forests have been logged, with dramatic impacts on rainforest biodiversity that may disrupt key ecosystem processes. We find that the contribution of invertebrates to three ecosystem processes operating at three trophic levels (litter decomposition, seed predation and removal, and invertebrate predation) is reduced by up to one-half following logging. These changes are associated with decreased abundance of key functional groups of termites, ants, beetles and earthworms, and an increase in the abundance of small mammals, amphibians and insectivorous birds in logged relative to primary forest. Our results suggest that ecosystem processes themselves have considerable resilience to logging, but the consistent decline of invertebrate functional importance is indicative of a human-induced shift in how these ecological processes operate in tropical rainforests.

Background: During the past decade there has been a growing interest in bioenergy, driven by concerns about global climate change, growing energy demand, and depleting fossil fuel reserves. The predicted rise in biofuel demand makes it important to understand the potential consequences of expanding biofuel cultivation. A systematic review was conducted on the biodiversity impacts of three first-generation biofuel crops (oil palm, soybean, and jatropha) in the tropics. The study focused on the impacts on species richness, abundance (total number of individuals or occurrences), community composition, and ecosystem functions related to species richness and community composition. Methods: Literature was searched using an a priori protocol. Owing to a lack of available studies of biodiversity impacts from soybean and jatropha that met the inclusion criteria set out in the systematic review protocol, all analyses focused on oil palm. The impacts of oil palm cultivation on species richness, abundance, and community similarity were summarized quantitatively; other results were summarized narratively. Results: The searches returned 9143 articles after duplicate removal of which 25 met the published inclusion criteria and were therefore accepted for the final review. Twenty of them had been conducted in Malaysia and two thirds were on arthropods. Overall, oil palm plantations had reduced species richness compared with primary and secondary forests, and the composition of species assemblages changed significantly after forest conversion to oil palm plantation. Abundance showed species-specific responses and hence, the overall abundance was not significantly different between plantations and forest areas. Only one study reported how different production systems (smallholdings vs. industrial estates) affect biodiversity. No studies that examined the effects on ecosystem functions of reduced species richness or changes in community composition met the inclusion criteria. Neither were there studies that reported how areas managed under different standards (e.g. different certification systems) affect biodiversity and ecosystem function. Conclusions: Our review suggests that oil palm plantations have reduced species richness compared with primary and secondary forests, and the composition of species assemblage changes significantly after forest conversion to oil palm plantation. Effects of different production systems on biodiversity and ecosystem function are clear knowledge gaps that should be addressed in future research. Trial registration: CEE10-013