Trophic organisation defines the flow of energy through ecosystems and is a key component of community structure. Widespread and intensifying anthropogenic disturbance threatens to disrupt trophic organisation by altering species composition and relative abundances and by driving shifts in the trophic ecology of species that persist in disturbed ecosystems. We examined how intensive disturbance caused by selective logging affects trophic organisation in the biodiversity hotspot of Sabah, Borneo. Using stable nitrogen isotopes, we quantified the positions in the food web of 159 leaf-litter ant species in unlogged and logged rainforest and tested four predictions: (i) there is a negative relationship between the trophic position of a species in unlogged forest and its change in abundance following logging, (ii) the trophic positions of species are altered by logging, (iii) disturbance alters the frequency distribution of trophic positions within the ant assemblage, and (iv) disturbance reduces food chain length. We found that ant abundance was 30% lower in logged forest than in unlogged forest but changes in abundance of individual species were not related to trophic position, providing no support for prediction (i). However, trophic positions of individual species were significantly higher in logged forest, supporting prediction (ii). Consequently, the frequency distribution of trophic positions differed significantly between unlogged and logged forest, supporting prediction (iii), and food chains were 0.2 trophic levels longer in logged forest, the opposite of prediction (iv). Our results demonstrate that disturbance can alter trophic organisation even without trophically-biased changes in community composition. Nonetheless, the absence of any reduction in food chain length in logged forest suggests that species-rich arthropod food webs do not experience trophic downgrading or a related collapse in trophic organisation despite the disturbance caused by logging. These food webs appear able to bend without breaking in the face of some forms of anthropogenic disturbance.
Forests in Southeast Asia are rapidly being logged and converted to oil palm. These changes in land-use are known to affect species diversity but consequences for the functional diversity of species assemblages are poorly understood. Environmental filtering of species with similar traits could lead to disproportionate reductions in trait diversity in degraded habitats. Here, we focus on dung beetles, which play a key role in ecosystem processes such as nutrient recycling and seed dispersal. We use morphological and behavioural traits to calculate a variety of functional diversity measures across a gradient of disturbance from primary forest through intensively logged forest to oil palm. Logging caused significant shifts in community composition but had very little effect on functional diversity, even after a repeated timber harvest. These data provide evidence for functional redundancy of dung beetles within primary forest and emphasize the high value of logged forests as refugia for biodiversity. In contrast, conversion of forest to oil palm greatly reduced taxonomic and functional diversity, with a marked decrease in the abundance of nocturnal foragers, a higher proportion of species with small body sizes and the complete loss of telecoprid species (dung-rollers), all indicating a decrease in the functional capacity of dung beetles within plantations. These changes also highlight the vulnerability of community functioning within logged forests in the event of further environmental degradation.
In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA "superbarcodes" for testing hypotheses regarding global patterns of diversity.