Jérôme Morinière

Conserving the remaining primary forests and restoring forests on former agricultural lands are two key strategies to conserve biodiversity in the tropics. Natural regrowth of forest following the abandonment of agricultural land use is one way of forest restoration and thus, it is important to understand how biodiversity shifts with ongoing recovery and whether communities become more similar over time to those in old‐growth forests. We studied patterns of taxonomic, functional and phylogenetic diversity as well as community composition of Saturniidae, as one of the most conspicuous and well‐studied families of moths. Our study covered a forest recovery gradient from active agriculture via early and advanced stages of regrowth to old‐growth rainforests in the lowland Chocó region of Ecuador. Saturniidae diversity patterns did not follow the hypothesized increase from agriculture to old‐growth forest, but instead, the highest taxonomic and functional diversity was found in early regrowth, and the highest phylogenetic diversity in active agriculture. Diversity differences along the forest recovery gradient were overall weak and occurred mainly when focusing on common and dominant species, but community composition showed a gradual turnover with the strongest differences between old‐growth forest and active agriculture. Our results show that diverse Saturniidae communities are found in naturally recovering tropical forests. But although Saturniidae have been recommended as indicator species due to their well‐documented taxonomy, our results suggest that they are not well suited as indicators of forest recovery. Nevertheless, due to their striking appearance, Saturniidae could serve as flagship species for the conservation of tropical forests.

Autonomous monitoring of arthropod biodiversity is regularly based on a single trap type. However, the taxonomic composition of samples strongly depends on the trap type, and even the most widely used systems catch very different subsets of species from a local species pool. Metabarcoding of Malaise trap samples is a widely used approach. However, it is known that this trap type is strongly biased on dipterans and hymenopterans. We developed a combination of three trap types to show how the representativeness of local samples is improved and used them in 101 strict forest reserves (SFRs) in Germany for an overall survey. Separate analyses were conducted in two oak‐dominated and three beech‐dominated SFRs to show the different species composition of each trap type. COI sequences with high similarity were clustered into OTUs that can be assigned to BINs corresponding to taxonomic species. In the overall survey, we found 10 K OTUs that could be assigned to 2.4K species. In the oak forests, 400 species from 31 orders and, in the beech forests, 538 species from 27 orders could be identified. The four most important orders (Coleoptera, Diptera, Hymenoptera and Lepidoptera) together accounted for 85.5%–88.9% of all (BINs). The results confirm the dominance of Diptera and Hymenoptera in Malaise traps and of beetles in window and pitfall traps. The detection rate of our trap combination increased by 2.5% to 0.78% compared to the Malaise traps. We, therefore, estimate that about 12.8 K species live in German forests. The number of BINs increased by more than 29% in our combined traps compared to the Malaise‐only traps. With limited additional fieldwork, our trap combination reduced the taxonomic bias in the local samples compared to other studies relying only on Malaise traps, with the orders of the local fauna better represented. As the combined traps take about twice as long as the Malaise trap to set, we recommend the use of additional trap types in biodiversity monitoring and research to obtain a broader taxonomic and functional overview of changes in arthropod diversity.

Identifying key drivers of insect diversity decline in the Anthropocene remains a major challenge in biodiversity research. Metabarcoding has rapidly gained popularity for species identification, yet the lack of abundance data complicates accurate diversity metrics like sample coverage-standardized species richness. Additionally, the vast number of taxa lacks a unified phylogeny or trait database. We introduce a new workflow for metabarcoding insect data that constructs a phylogenetic tree for most insect families, standardizes sample coverage and assesses both taxonomic and phylogenetic diversity along the Hill series. Applying this workflow to Central Europe, we analysed insect diversity from 400 families across a land-use gradient. Our results show that land-use intensity significantly affects sample coverage, highlighting the necessity of biodiversity standardization. Taxonomic diversity declined by 27–44% and phylogenetic diversity by 13–29% across 39 000 operational taxonomic units, with diversity decreasing from forests to agricultural areas. When focusing on rare species communities exhibited greater phylogenetic diversity loss than taxonomic diversity, whereas dominant species experienced smaller phylogenetic losses but more pronounced declines in taxonomic diversity. Our findings underscore the detrimental effects of agriculture on insect taxa and reveal a dramatic loss of phylogenetic diversity among rare species with potential consequences for ecosystem stability.

The use of metabarcoding for insect species identification has grown rapidly, but the absence of abundance data hinders meaningful diversity metrics like sample coverage-standardized species richness. Additionally, the vast number of taxa often lacks a unified phylogeny or trait database. We present a framework for constructing a phylogenetic tree encompassing the majority of insect families, standardisation of sample coverage (an objective measure of sample completeness) and assessment of both taxonomic and phylogenetic diversity using the Hill series for metabarcoding data. Applied to central Europe, our framework analysed insect diversity from 400 families along a land-use gradient. Results revealed land-use intensity significantly affects sample coverage, emphasizing the need for biodiversity standardization. After standardization, taxonomic diversity declined by 27–44%, and phylogenetic diversity by 13–29% across 39,000 Operational Taxonomic Units, from forests to agricultural areas. Rare species exhibited greater phylogenetic diversity loss than taxonomic, while dominant species showed smaller phylogenetic losses but stronger declines in taxonomic diversity. Our findings underscore agriculture’s detrimental effects on specific insect taxa, even after adjusting for sample coverage, and provide new insights into the loss of functional diversity, as represented by phylogeny.

A comprehensive understanding of trophic interactions in terrestrial ecosystems is crucial for ecological research and conservation. Recent advances in non-invasive methods, such as environmental DNA (eDNA) metabarcoding, have enabled researchers to collect vast amounts of data on wild animal diets. However, sharing this data and metadata effectively and transparently presents new challenges. To address this, a new type of scholarly journal publication has emerged that aims to describe datasets rather than report research investigations. In this paper, we present a dataset of consumed prey species and parasites based on the metabarcoding of 113 faecal samples from the greater and lesser mouse-eared bats (Myotis myotis and Myotis blythii), along with a detailed description of the data sampling, laboratory analysis, and bioinformatics pipeline. Our dataset comprises 1018 unique Barcode Index Numbers (BINs) from 12 Classes and 43 Orders. In addition, we provide interactive Krona charts to visually summarize the taxonomic relationships and relative read abundance of the consumed prey species and parasites. This data can be used for meta-analysis, exploring new predator-prey and host-parasite interactions, studying inter- and intraspecific ecological interactions, and informing protected area management, among other applications. By sharing this dataset, we hope to encourage other researchers to use it to answer additional ecological questions and advance our understanding of trophic interactions in terrestrial ecosystems.

Despite their cosmopolitan occurrence and massive plankton sampling during expeditions, the genetic diversity within Pteropoda Cuvier, 1804 is still largely unexplored. In this study we present a next-generation environmental barcoding approach to zooplankton bulk samples, which were collected during the circumglobal 2010 Malaspina expedition to evaluate pteropod diversity. We introduce a technique that avoids destructive procedures and leaves material intact for further morphological investigations. We extracted DNA out of the dregs (organic material such as mucus or body parts) of 27 sample containers for molecular barcoding (average 100-260 bp of COI). We were able to identify 7128 operational taxonomic units corresponding to the species composition contained in the examined samples. Among them were three species of thecosome pteropods, Creseis acicula, Creseis virgula and Cavolinia inflexa, which are discussed with respect to their taxonomy and their geographic distribution. Unidentified gymnosomes were also present in our samples from warmer regions in oceanic waters of the southern Indian Ocean. To facilitate identification of species, it is beneficial to create a better database of pteropod COI barcodes. Furthermore, gathering environmental barcoding data on a broad global scale will help to better understand species abundance and distribution of pteropods in the world’s oceans, and potentially those of other planktonic organisms.

The effects of novel perennial energy crops on arthropod abundance and diversity were tested using three field trials in Bavaria. Established cup plant (Silphium perfoliatum), Virginia mallow (Sida hermaphrodita) and tall wheat grass (Thinopyrum ponticum) plots were sampled in autumn using a modified leaf blower and their arthropod faunas compared with that recorded in maize plots. At the time of sampling, maize, cup plant and Virginia mallow had already been harvested and samples from the remaining stubble were compared with those from open ground. Collembola were the most abundant group. The highest abundance and diversity of arthropods was recorded in tall wheat grass, with Hemiptera and Aranea especially benefitting from the green and taller vegetation. Post-harvest cup plant and Virginia mallow plots harboured a more diverse and more abundant arthropod assemblage than maize plots. Stubble was identified as a suitable habitat for arthropods in agricultural fields. In conclusion, the integration of perennial energy crops into existing biogas production systems could play an important role in supporting arthropods in agricultural landscapes by providing crucial structures and resources, such as the grassy vegetation of tall wheat grass in autumn and the long-lasting stubbles of cup plant and Virginia mallow.

Insecticides used to combat outbreaks of forest defoliators can adversely affect non‐target arthropods. Forestry insecticides typically suppress Lepidoptera larvae which are the cornerstone of the canopy community of deciduous oak forests. The abrupt removal of this dominant component of the food web could have far‐reaching implications for forest ecosystems, yet it is rarely investigated in practice owing to several methodological shortcomings. The taxonomic impediment and the biased nature of arthropod sampling techniques particularly impede the assessment of insecticide impacts on diverse communities. To tackle this issue, we propose an experimental approach combining sampling by pyrethrum knockdown and species determination via DNA metabarcoding, using community subsampling to derive estimates of species abundances. We applied this protocol to investigate the short‐term effects of the insecticides diflubenzuron (DFB) andBacillus thuringiensisvar.kurstaki(BTK) on canopy‐dwelling arthropod communities in German oak woodlands. Our approach allowed us to detect most of the diversity and integrate species abundances in our analyses. By classifying arthropod species into assemblages based on their expected sensitivity rather than coarse taxonomic groupings, we could unveil substantial effects of DFB across multiple taxa 5 weeks after application. Although strong effects on single species appear related to direct toxicity, substantial impacts of DFB on parasitoids and xylophagous beetles suggest that anti‐defoliator treatments can have previously unsuspected indirect effects on some components of forest arthropod communities. The impacts of BTK on community structure were consistent with that of DFB though much weaker. Synthesis and applications. Comparing diversity patterns in the arthropod communities of sprayed and unsprayed oak canopies, our results show that selective insecticides can alter species diversity in presumably non‐sensitive taxa. Even though the ecological significance of these impacts has yet to be assessed in an operational setting, their existence calls for increased regulatory scrutiny on indirect effects. As community approaches become more attainable with the rapid development of DNA metabarcoding, we suggest the inclusion of community‐level end points as regulatory requirements for the approval of forest‐use insecticides.