The predator problem and PCR primers in molecular dietary analysis: Swamped or silenced; depth or breadth?

Dietary metabarcoding has vastly improved our ability to analyse the diets of animals, but it is hampered by a plethora of technical limitations including potentially reduced data output due to the disproportionate amplification of the DNA of the focal predator, here termed “the predator problem”. We review the various methods commonly used to overcome this problem, from deeper sequencing to exclusion of predator DNA during PCR, and how they may interfere with increasingly common multipredator-taxon studies. We suggest that multiprimer approaches with an emphasis on achieving both depth and breadth of prey detections may overcome the issue to some extent, although multitaxon studies require further consideration, as highlighted by an empirical example. We also review several alternative methods for reducing the prevalence of predator DNA that are conceptually promising but require additional empirical examination. The predator problem is a key constraint on molecular dietary analyses but, through this synthesis, we hope to guide researchers in overcoming this in an effective and pragmatic way

Assessing the impact of taxon resolution on network structure

Constructing ecological networks has become an indispensable approach in understanding how different taxa interact. However, the methods used to generate data in network research varies widely among studies, potentially limiting our ability to compare results meaningfully. In particular, methods of classifying nodes vary in their precision, likely altering the architecture of the network studied. For example, rather than being classified as Linnaean species, taxa are regularly assigned to morphospecies in observational studies, or to Molecular Operational Taxonomic Units (MOTUs) in molecular studies, with the latter defined based on an arbitrary threshold of sequence similarity. Although the use of MOTUs in ecological networks holds great potential, especially for allowing rapid construction of large datasets of interactions, it is unclear how the choice of clustering threshold can influence the conclusions obtained. To test the impact of taxonomic precision on network architecture, we obtained and analyzed 16 datasets of ecological interactions, inferred from metabarcoding and observations. Our comparisons of networks constructed under a range of sequence thresholds for assigning taxa demonstrate that even small changes in node resolution can cause wide variation in almost all key metric values. Moreover, relative values of commonly used metrics such as robustness were seen to fluctuate continuously with node resolution, thereby potentially causing error in conclusions drawn when comparing multiple networks. In observational networks, we found that changing node resolution could, in some cases, lead to substantial changes to measurements of network topology. Overall, our findings highlight the importance of classifying nodes to the greatest precision possible, and demonstrate the need for caution when comparing networks that differ with respect to node resolution, even where taxonomic groups and interaction types are similar. In such cases, we recommend that comparisons of networks should focus on relative differences rather than absolute values between the networks studied

Trap type affects dung beetle taxonomic and functional diversity in Bornean tropical forests

Baited pitfall traps (BPTs) and flight intercept traps (FITs) are the most common methods employed for sampling dung beetle communities. These methods vary in their efficacy and are affected by factors such as the bait types used and the dispersal abilities of different dung beetle species. We present the first quantitative comparison of the taxonomic and functional diversity, and community composition of dung beetles caught in BPTs and FITs in Bornean tropical forests. We show that BPTs and FITs captured complementary communities with different functional traits, and that BPTs captured more functionally diverse communities. We therefore recommend using a combination of both baited BPTs and FITs for studies assessing the composition of dung beetles across habitat types. Our results also highlight that it is important to consider how trap type affects the trait composition of communities when relating dung beetle communities and functional traits to ecological functioning. We suggest modifications to FITs based on the design of harp traps to increase their effectiveness in capturing larger-bodied beetles

Trap type affects dung beetle taxonomic and functional diversity in Bornean tropical forests

Baited pitfall traps (BPTs) and flight intercept traps (FITs) are the most common methods employed for sampling dung beetle communities. These methods vary in their efficacy and are affected by factors such as the bait types used and the dispersal abilities of different dung beetle species. We present the first quantitative comparison of the taxonomic and functional diversity, and community composition of dung beetles caught in BPTs and FITs in Bornean tropical forests. We show that BPTs and FITs captured complementary communities with different functional traits, and that BPTs captured more functionally diverse communities. We therefore recommend using a combination of both baited BPTs and FITs for studies assessing the composition of dung beetles across habitat types. Our results also highlight that it is important to consider how trap type affects the trait composition of communities when relating dung beetle communities and functional traits to ecological functioning. We suggest modifications to FITs based on the design of harp traps to increase their effectiveness in capturing larger-bodied beetles

Spatiotemporal and demographic variation in the diet of New Zealand lesser short-tailed bats (Mystacina tuberculata)

Variation in the diet of generalist insectivores can be affected by site‐specific traits including weather, habitat, and season, as well as demographic traits such as reproductive status and age. We used molecular methods to compare diets of three distinct New Zealand populations of lesser short‐tailed bats, Mystacina tuberculata. Summer diets were compared between a southern cold‐temperate (Eglinton) and a northern population (Puroera). Winter diets were compared between Pureora and a subtropical offshore island population (Hauturu). This also permitted seasonal diet comparisons within the Pureora population. Lepidoptera and Diptera accounted for >80% of MOTUs identified from fecal matter at each site/season. The proportion of orders represented within prey and the Simpson diversity index, differed between sites and seasons within the Pureora population. For the Pureora population, the value of the Simpson diversity index was higher in summer than winter and was higher in Pureora compared to Eglinton. Summer Eglinton samples revealed that juvenile diets appeared to be more diverse than other demographic groups. Lactating females had the lowest dietary diversity during summer in Pureora. In Hauturu, we found a significant negative relationship between mean ambient temperature and prey richness. Our data suggest that M. tuberculata incorporate a narrower diversity of terrestrial insects than previously reported. This provides novel insights into foraging behavior and ecological interactions within different habitats. Our study is the first from the Southern Hemisphere to use molecular techniques to examine spatiotemporal variation in the diet of a generalist insectivore that inhabits a contiguous range with several habitat types and climates

Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments - the poor cousins of primary forest. However, they are dynamic ecosystems that provide refugia for large amounts of biodiversity, so we cannot afford to underestimate their conservation value. Here, we present empirically defined thresholds for categorising the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation- relevant thresholds. First, lightly logged forests ( 68 %) of their biomass removed, and are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable, but they also reinforce the message that logged forests retain significant conservation value that should not be overlooked

Enhancing the ecological value of oil palm agriculture through set-asides

Agricultural expansion is the primary driver of ecological degradation across the tropics. Set-asides—uncultivated parts of agricultural landscapes, often on steep slopes and alongside rivers—may alleviate environmental impacts but can reduce the area cultivated. Here we model an approach to configuring set-asides aimed at optimizing ecological outcomes (biodiversity, above-ground carbon storage and nutrient cycling) without reducing net cultivation area. We compare set-asides in an oil palm landscape where all plantations adopt the same configuration (‘uniform’ approach) with a scenario where there can be variation in configuration among plantations (‘variable’ approach). We find that all set-aside configurations support substantial ecological values but that the best strategies involve set-asides, particularly alongside rivers, that are spatially targeted and variable among plantations. This ‘variable’ approach can increase ecological outcomes twofold over the ‘uniform’ approach without reducing net cultivation area. Our findings underscore the potential importance of well-planned set-asides for enhancing agricultural sustainability

A research agenda for microclimate ecology in human-modified tropical forests

Logging and habitat fragmentation impact tropical forest ecosystems in numerous ways, perhaps the most striking of which is by altering the temperature, humidity, and light environment of the forest—its microclimate. Because local-scale microclimatic conditions directly influence the physiology, demography and behavior of most species, many of the impacts of land-use intensification on the biodiversity and ecosystem functioning of tropical forests have been attributed to changes in microclimate. However, the actual pathways through which altered microclimatic conditions reshape the ecology of these human-modified ecosystems remain largely unexplored. To bridge this knowledge gap, here we outline an agenda for future microclimate research in human-modified tropical ecosystems. We focus specifically on three main themes: the role of microclimate in shaping (i) species distributions, (ii) species interactions, and (iii) ecosystem functioning in tropical forests. In doing so we aim to highlight how a renewed focus on microclimate can help us not only better understand the ecology of human-modified tropical ecosystems, but also guide efforts to manage and protect them