Optimizing sampling of flying insects using a modified window trap

High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method

Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.

Metabarcoding reveals that mixed forests mitigate negative effects of non-native trees on canopy arthropod diversity

Averting climate change-induced forest diebacks increasingly relies on tree species planted outside of their natural range and on the addition of non-native tree species to mixed-species forests. However, the consequences of such changes for associated biodiversity remain poorly understood, especially for the forest canopy as a largely understudied forest stratum. Here, we used flight interception traps and a metabarcoding approach to study the taxonomic and functional (trophic guilds) composition and taxon richness of canopy arthropods. We sampled 15 monospecific and mixed stands of native European beech, native Norway spruce-planted outside its natural range-and non-native Douglas fir in northwest Germany. We found that the diversity of arthropods was lower in non-native Douglas fir compared with native beech stands. Taxon richness of herbivores was reduced by both conifer species. Other functional guilds, however, were not affected by stand type. Arthropod composition differed strongly between native broadleaved beech and monospecific coniferous (native spruce or non-native Douglas fir) stands, with less pronounced differences between the native and non-native conifers. Beech-conifer mixtures consistently hosted intermediate arthropod diversity and community composition compared with the respective monospecific stands. Moreover, arthropod diversity had a positive relationship with the number of canopy microhabitats. Our study shows that considering arthropod taxa of multiple functional groups reveals the multifaceted impact of non-native tree species on forest canopy arthropod communities. Contrasting with previous studies that primarily focused on the forest floor, we found that native beech hosts a rich diversity of arthropods, compared with lower diversity and distinct communities in economically attractive, and especially in non-native, conifers with few canopy microhabitats. Broadleaf-conifer mixtures did not perform better than native beech stands, but mitigated the negative effects of conifers, making such mixtures a compromise to foster both forest-associated diversity and economic yield.

Camera-based automated monitoring of flying insects (Camfi). I. Field and computational methods

The ability to measure flying insect activity and abundance is important for ecologists, conservationists and agronomists alike. However, existing methods are laborious and produce data with low temporal resolution (e.g. trapping and direct observation), or are expensive, technically complex, and require vehicle access to field sites (e.g. radar and lidar entomology). We propose a method called "Camfi" for long-term non-invasive population monitoring and high-throughput behavioural observation of low-flying insects using images and videos obtained from wildlife cameras, which are inexpensive and simple to operate. To facilitate very large monitoring programs, we have developed and implemented a tool for automatic detection and annotation of flying insect targets in still images or video clips based on the popular Mask R-CNN framework. This tool can be trained to detect and annotate insects in a few hours, taking advantage of transfer learning. Our method will prove invaluable for ongoing efforts to understand the behaviour and ecology of declining insect populations and could also be applied to agronomy. The method is particularly suited to studies of low-flying insects in remote areas, and is suitable for very large-scale monitoring programs, or programs with relatively low budgets.

Forest gaps increase true bug diversity by recruiting open land species

Forests canopy gaps play an important role in forest ecology by driving the forest mosaic cycle and creating conditions for rapid plant reproduction and growth. The availability of young plants, which represent resources for herbivores, and modified environmental conditions with greater availability of light and higher temperatures, promote the colonization of animals. Remarkably, the role of gaps on insect communities has received little attention and the source of insects colonizing gaps has not been studied comprehensively. Using a replicated full-factorial forest experiment (treatments: Gap; Gap + Deadwood; Deadwood; Control), we show that following gap creation, there is a rapid change in the true bug (Heteroptera) community structure, with an increase in species that are mainly recruited from open lands. Compared with closed-canopy treatments (Deadwood and Control), open canopy treatments (Gap and Gap + Deadwood) promoted an overall increase in species (+ 59.4%, estimated as number of species per plot) and individuals (+ 76.3%) of true bugs, mainly herbivores and species associated to herbaceous vegetation. Community composition also differed among treatments, and all 17 significant indicator species (out of 117 species in total) were associated with the open canopy treatments. Based on insect data collected in grasslands and forests over an 11-year period, we found that the species colonizing experimental gaps had greater body size and a greater preference for open vegetation. Our results indicate that animal communities that assemble following gap creation contain a high proportion of habitat generalists that not occurred in closed forests, contributing significantly to overall diversity in forest mosaics.

Insect decline in forests depends on species' traits and may be mitigated by management

Insects are declining, but the underlying drivers and differences in responses between species are still largely unclear. Despite the importance of forests, insect trends therein have received little attention. Using 10 years of standardized data (120,996 individuals; 1,805 species) from 140 sites in Germany, we show that declines occurred in most sites and species across trophic groups. In particular, declines (quantified as the correlation between year and the respective community response) were more consistent in sites with many non-native trees or a large amount of timber harvested before the onset of sampling. Correlations at the species level depended on species' life-history. Larger species, more abundant species, and species of higher trophic level declined most, while herbivores increased. This suggests potential shifts in food webs possibly affecting ecosystem functioning. A targeted management, including promoting more natural tree species composition and partially reduced harvesting, can contribute to mitigating declines.

Optimizing low-cost sampling of pollinator insects in oilseed rape fields

Insects are key pollinators to ecosystem function, but much work remains to determine the most cost-effective, reliable scheme to monitor them. Pan traps (PT) and flight interception traps (FIT) are two of the most popular insect sampling methods used. However, their relative sampling performance and cost is poorly known for agroecosystems in China. We conducted a study across 18 oilseed rape fields in smallholder farmland in Zhejiang, China using these two traps. Our results showed that a single FIT had a greater sampling efficiency (more individuals and higher species richness) than a single PT, but controlling for cost, four PTs (the cost for four PTs is close to one FIT) showed a greater sampling efficiency than FITs. PTs collected more small-bodied individuals while FITs and PTs did not significantly differ in terms of monitoring pollinator insects with large body size. When exploring whether semi-natural habitat embedded in the agricultural landscape affected these results, results from both trap types shows that semi-natural habitat had a significant positive impact on wild pollinator diversity and rarefied species richness. Future studies that examine the effects of agricultural landscape on the wild pollinator community should combine PTs with netting or other active methods for long-term wild pollinator monitoring strategies.

Biodiversity response to forest management intensity, carbon stocks and net primary production in temperate montane forests

Managed forests are a key component of strategies aimed at tackling the climate and biodiversity crises. Tapping this potential requires a better understanding of the complex, simultaneous effects of forest management on biodiversity, carbon stocks and productivity. Here, we used data of 135 one-hectare plots from southwestern Germany to disentangle the relative influence of gradients of management intensity, carbon stocks and forest productivity on different components of forest biodiversity (birds, bats, insects, plants) and tree-related microhabitats. We tested whether the composition of taxonomic groups varies gradually or abruptly along these gradients. The richness of taxonomic groups was rather insensitive to management intensity, carbon stocks and forest productivity. Despite the low explanatory power of the main predictor variables, forest management had the greatest relative influence on richness of insects and tree-related microhabitats, while carbon stocks influenced richness of bats, birds, vascular plants and pooled taxa. Species composition changed relatively abruptly along the management intensity gradient, while changes along carbon and productivity gradients were more gradual. We conclude that moderate increases in forest management intensity and carbon stocks, within the range of variation observed in our study system, might be compatible with biodiversity and climate mitigation objectives in managed forests.

Patterns of richness across forest beetle communities-A methodological comparison of observed and estimated species numbers

Species richness is a frequently used measure of biodiversity. The compilation of a complete species list is an often unattainable goal. Estimators of species richness have been developed to overcome this problem. While the use of these estimators is becoming increasingly popular, working with the observed number of species is still common practice.To assess whether patterns of beetle communities based on observed numbers may be compared among each other, we compared patterns from observed and estimated numbers of species for beetle communities in the canopy of the Leipzig floodplain forest. These patterns were species richness and the number of shared species among three tree species and two canopy strata.We tested the applicability of the asymptotic Chao1 estimator and the estimate provided by the nonasymptotic rarefaction-extrapolation method for all tree species and both upper canopy and lower canopy. In the majority of cases, the ranking patterns of species richness for host tree species and strata were the same for the observed and estimated number of species. The ranking patterns of the number of species shared among host tree species and strata, however, were significantly different between observed and estimated values.Our results indicate that the observed number of species under-represents species richness and the number of shared species. However, ranking comparisons of published patterns based on the number of observed species may be acceptable for species richness but likely not reliable for the number of shared species. Further studies are needed to corroborate this conclusion. We encourage to use estimators and to provide open access to data to allow comparative assessments.

Sampling beetle communities: Trap design interacts with weather and species traits to bias capture rates

Globally, many insect populations are declining, prompting calls for action. Yet these findings have also prompted discussion about sampling methods and interpretation of long-term datasets. As insect monitoring and research efforts increase, it is critical to quantify the effectiveness of sampling methods. This is especially true if sampling biases of different methods covary with climate, which is also changing over time. We assess the effectiveness of two types of flight intercept traps commonly used for beetles, a diverse insect group responsible for numerous ecosystem services, under different climatic conditions in Norwegian boreal forest. One of these trap designs includes a device to prevent rainwater from entering the collection vial, diluting preservatives and flushing out beetles. This design is compared to a standard trap. We ask how beetle capture rates vary between these traps, and how these differences vary based on precipitation levels and beetle body size, an important species trait. Bayesian mixed models reveal that the standard and modified traps differ in their beetle capture rates, but that the magnitude and direction of these differences change with precipitation levels and beetle body size. At low rainfall levels, standard traps catch more beetles, but as precipitation increases the catch rates of modified traps overtake those of standard traps. This effect is most pronounced for large-bodied beetles. Sampling methods are known to differ in their effectiveness. Here, we present evidence for a less well-known but likely common phenomenon-an interaction between climate and sampling, such that relative effectiveness of trap types for beetle sampling differs depending on precipitation levels and species traits. This highlights a challenge for long-term monitoring programs, where both climate and insect populations are changing. Sampling methods should be sought that eliminate climate interactions, any biases should be quantified, and all insect datasets should include detailed methodological metadata.

Designing monitoring protocols to measure population trends of threatened insects: A case study of the cryptic, flightless grasshopper Brachaspis robustus

Statistically robust monitoring of threatened populations is essential for effective conservation management because the population trend data that monitoring generates is often used to make decisions about when and how to take action. Despite representing the highest proportion of threatened animals globally, the development of best practice methods for monitoring populations of threatened insects is relatively uncommon. Traditionally, population trend data for the Nationally Endangered New Zealand grasshopper Brachaspis robustus has been determined by counting all adults and nymphs seen on a single ~1.5 km transect searched once annually. This method lacks spatial and temporal replication, both of which are essential to overcome detection errors in highly cryptic species like B. robustus. It also provides no information about changes in the grasshopper’s distribution throughout its range. Here, we design and test new population density and site occupancy monitoring protocols by comparing a) comprehensive plot and transect searches at one site and b) transect searches at two sites representing two different habitats (gravel road and natural riverbed) occupied by the species across its remaining range. Using power analyses, we determined a) the number of transects, b) the number of repeated visits and c) the grasshopper demographic to count to accurately detect long term change in relative population density. To inform a monitoring protocol design to track trends in grasshopper distribution, we estimated the probability of detecting an individual with respect to a) search area, b) weather and c) the grasshopper demographic counted at each of the two sites. Density estimates from plots and transects did not differ significantly. Population density monitoring was found to be most informative when large adult females present in early summer were used to index population size. To detect a significant change in relative density with power > 0.8 at the gravel road habitat, at least seventeen spatial replicates (transects) and four temporal replicates (visits) were required. Density estimates at the natural braided river site performed poorly and likely require a much higher survey effort. Detection of grasshopper presence was highest (p_g > 0.6) using a 100 m x 1 m transect at both sites in February under optimal (no cloud) conditions. At least three visits to a transect should be conducted per season for distribution monitoring. Monitoring protocols that inform the management of threatened species are crucial for better understanding and mitigation of the current global trends of insect decline. This study provides an exemplar of how appropriate monitoring protocols can be developed for threatened insect species.

Automated flight-interception traps for interval sampling of insects

Recent debates on insect decline require sound assessments on the relative drivers that may negatively impact insect populations. Often, baseline data rely on insect monitorings that integrate catches over long time periods. If, however, effects of time-critical environmental factors (e.g., light pollution) are of interest, higher temporal resolution of insect data is required during very specific time intervals (e.g., between dusk and dawn). Conventional time-critical insect trapping is labour-intensive (manual activation/deactivation) and temporally inaccurate as not all traps can be serviced synchronically at different sites. Also, temporal shifts of environmental conditions (e.g., sunset/sunrise) are not accounted for. We present a battery-driven automated insect flight-interception trap which samples insects during seven user-defined time intervals. A commercially available flight-interception trap is fitted to a turntable containing eight positions, seven of them holding cups and one consisting of a pass-through hole. While the cups sample insects during period of interest, the pass-through hole avoids unwanted sampling during time-intervals not of interest. Comparisons between two manual and two automated traps during 71 nights in 2018 showed no difference in caught insects. A study using 20 automated traps during 104 nights in 2019 proved that the automated flight-interception traps are reliable. The automated trap opens new research and application possibilities as arbitrary insect-sampling intervals can be defined. The trap proves efficient, saving manpower and associated costs as activation/deactivation is required only every seven sampling intervals. In addition, the timing of the traps is accurate, as all traps sample at exactly the same intervals and ensure comparability. The automated trap is low maintenance and robust due to straightforward technical design. It can be controlled manually or via smartphone through a Bluetooth connection. Full construction details are given in Appendices.

What do tree-related microhabitats tell us about the abundance of forest-dwelling bats, birds, and insects?

Retaining trees during harvesting to conserve biodiversity is becoming increasingly common in forestry. To assess, select and monitor these habitat trees, ecologists and practitioners often use Tree-related Microhabitats (TreMs), which are assumed to represent the abundance and diversity of environmental resources for a wide range of forest-dwelling taxa. However, the relationship between TreMs and forest organisms is not fully understood. In this context, we attempted to identify and quantify the links between TreMs and three groups of forest organisms: insects, bats, and birds. Specifically, we tested whether species abundance is influenced by TreM abundance, either as direct predictor or as mediator of environmental predictors. We collected data in 86 temperate, 1-ha mixed forest plots and employed a hierarchical generalized mixed model to assess the influence of seven environmental predictors (aspect, number and height of standing dead trees, cover of herb and shrub layer, volume of lying deadwood, and terrain ruggedness index (TRI)) on the abundance of TreMs (15 groups) on potential habitat trees, insects (10 orders), bats (5 acoustic groups) and birds (29 species) as a function of seven environmental predictors: aspect, number and height of standing dead trees, cover of herb and shrub layer, volume of lying deadwood, and terrain ruggedness index (TRI). This allowed us to generate a correlation matrix with potential links between abundances of TreMs and co-occurring forest organisms. These correlations and the environmental predictors were tested in a structural equation model (SEM) to disentangle and quantify the effects of the environment from direct effects of TreMs on forest organisms. Four TreM groups showed correlations > |0.30| with forest organisms, in particular with insects and bats. Rot holes and concavities were directly linked with three insect groups and two bat groups. Their effect was smaller than effects of environmental predictors, except for the pairs "rot holes - Sternorrhyncha" and "rot holes - bats" of the Pipistrellus group. In addition, TreMs had indirect effects on forest organisms through mediating the effects of environmental predictors. We found significant associations between two out of fifteen TreM groups and five out of 44 forest organism groups. These results indicate that TreM abundance on potential habitat trees is not suited as a general indicator of the species abundance across broad taxonomic groups but possibly for specific target groups with proven links.

Evaluating the effectiveness of retention forestry to enhance biodiversity in production forests of Central Europe using an interdisciplinary, multi-scale approach

Retention forestry, which retains a portion of the original stand at the time of harvesting to maintain continuity of structural and compositional diversity, has been originally developed to mitigate the impacts of clear-cutting. Retention of habitat trees and deadwood has since become common practice also in continuous-cover forests of Central Europe. While the use of retention in these forests is plausible, the evidence base for its application is lacking, trade-offs have not been quantified, it is not clear what support it receives from forest owners and other stakeholders and how it is best integrated into forest management practices. The Research Training Group ConFoBi (Conservation of Forest Biodiversity in Multiple-use Landscapes of Central Europe) focusses on the effectiveness of retention forestry, combining ecological studies on forest biodiversity with social and economic studies of biodiversity conservation across multiple spatial scales. The aim of ConFoBi is to assess whether and how structural retention measures are appropriate for the conservation of forest biodiversity in uneven-aged and selectively harvested continuous-cover forests of temperate Europe. The study design is based on a pool of 135 plots (1 ha) distributed along gradients of forest connectivity and structure. The main objectives are (a) to investigate the effects of structural elements and landscape context on multiple taxa, including different trophic and functional groups, to evaluate the effectiveness of retention practices for biodiversity conservation; (b) to analyze how forest biodiversity conservation is perceived and practiced, and what costs and benefits it creates; and (c) to identify how biodiversity conservation can be effectively integrated in multi-functional forest management. ConFoBi will quantify retention levels required across the landscape, as well as the socio-economic prerequisites for their implementation by forest owners and managers. ConFoBi's research results will provide an evidence base for integrating biodiversity conservation into forest management in temperate forests.