Cultivation of crops close to their wild relatives may jeopardise the integrity of wild genetic resources. Detecting cultivars among wild plants is necessary to characterise crop-wild gene flow, but can be challenging if cultivars and wild plants are phenotypically highly similar. Genomics tools can be used instead, but the selection of diagnostic loci for cultivar identification can be difficult if the wild and cultivated genepools are closely related. In Ethiopia, Arabica coffee cultivars resistant to coffee berry disease (CBD) occur near wild Coffea arabica plants and local landraces. However, the abundance and distribution of these cultivars across coffee sites remains unclear. Here, we present a new module of the SMAP package called SMAP relatedness pairwise to characterise pairwise genetic relationships between individuals based on haplotype calls and to identify diagnostic loci that distinguish (sets of) individuals from each other. Next, we estimate the relative abundance of CBD-resistant cultivars across 60 Ethiopian Arabica coffee sites using a genome-wide fingerprinting approach. We confirm the presence of these cultivars in around 75% of the coffee sites with a high agreement between a field survey and our DNA fingerprinting approach. At least 20 out of 60 sites with supposedly wild C. arabica individuals contain signatures of the cultivated genepool. Overall, we conclude that CBD-resistant cultivars are widespread in Ethiopian coffee sites. The development of SMAP relatedness pairwise opens opportunities to assess the distribution of coffee cultivars in other regions in Ethiopia and to apply similar screenings near wild relatives from other crops.

We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, Malaise trap samples were collected weekly (biweekly or monthly in the winter, when feasible) at 203 locations within 100 sites in Sweden and weekly at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of CO1 (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.

An increase in biotic interactions towards lower latitudes is one of the most consistent patterns in ecology. Higher temperatures and more stable climatic conditions at low latitudes are thought to enhance biotic interactions, accelerating biological evolution and leading to stronger anti-herbivore defences in plants. However, some studies report contradictory findings, highlighting the need for further investigation into the underlying mechanisms. We used a combination of field observations and feeding trials in controlled environments to investigate the effect of climate on chemical defences and insect herbivory in pedunculate oak (Quercus robur L.) throughout most of its geographic range in Europe, while controlling for physical defences. The concentration of lignin, flavonoids, and total phenolics increased significantly with temperature, whereas both field herbivory and weight of spongy moth (Lymantria dispar L.) larvae were negatively influenced by temperature. Lignin concentration positively influenced the weight of spongy moth larvae whereas it had no effect on field herbivory. We found no evidence of strong positive relationships between insect herbivory and larvae growth with leaf defences. Our study underscores the complexity of plant–herbivore interactions along climatic gradients and highlights the need for further research to disentangle these intricate relationships.

DNA metabarcoding of species-rich taxa is becoming a popular high-throughput method for biodiversity inventories. Unfortunately, its accuracy and efficiency remain unclear, as results mostly pertain to poorly known taxa in underexplored regions. This study evaluates what an extensive sampling effort combined with metabarcoding can tell us about the lepidopteran fauna of Sweden - one of the best-understood insect taxa in one of the most-surveyed countries of the world. We deployed 197 Malaise traps across Sweden for a year, generating 4749 bulk samples for metabarcoding, and compared the results to existing data sources. We detected more than half (1535) of the 2990 known Swedish lepidopteran species and 323 species not reported during the sampling period by other data providers. Full-length barcoding confirmed three new species for the country, substantial range extensions for two species and eight genetically distinct barcode variants potentially representing new species, one of which has since been described. Most new records represented small, inconspicuous species from poorly surveyed regions, highlighting components of the fauna overlooked by traditional surveying. These findings demonstrate that DNA metabarcoding is a highly efficient and accurate biodiversity sampling method, capable of yielding significant new discoveries even for the most well known of insect faunas.

Global change threatens a vast number of species with severe population declines or even extinction. The threat status of an organism is often designated based on geographic range, population size, or declines in either. However, invertebrates, which comprise the bulk of animal diversity, are conspicuously absent from global frameworks that assess extinction risk. Many invertebrates are hard to study, and it has been questioned whether current risk assessments are appropriate for the majority of these organisms. As the majority of invertebrates are rare, we contend that the lack of data for these organisms makes current criteria hard to apply. Using empirical evidence from one of the largest terrestrial arthropod surveys to date, consisting of over 33 000 species collected from over a million hours of survey effort, we demonstrate that estimates of trends based on low sample sizes are associated with major uncertainty and a risk of misclassification under criteria defined by the IUCN. We argue that even the most ambitious monitoring efforts are unlikely to produce enough observations to reliably estimate population sizes and ranges for more than a fraction of species, and there is likely to be substantial uncertainty in assessing risk for the majority of global biodiversity using species-level trends. In response, we discuss the need to focus on metrics we can currently measure when conducting risk assessments for these organisms. We highlight modern statistical methods that allow quantification of metrics that could incorporate observations of rare invertebrates into global conservation frameworks, and suggest how current criteria might be adapted to meet the needs of the majority of global biodiversity.

Societal Impact Statement: Arabica coffee grows in the forests and woodlands of Ethiopia. These Arabica coffee populations contain a reservoir of the highest genetic variation of this species, which is extremely valuable from a biodiversity conservation and coffee breeding point of view. Knowledge about the distribution of these populations, including how and to what extent they have been managed by local communities now and in the past, is limited. We reveal insights into the history, distribution, and management of Arabica coffee populations in the remaining forests of Ethiopia, which is essential for developing effective conservation policies for this globally important resource. Summary: To guide conservation of forest biodiversity in a broad sense, we need to understand the landscape-level variation in current and historical management practices of agroforestry systems. We collected data on coffee management practices across a large forested landscape in Ethiopia within Arabica coffee's indigenous distribution, using interviews in 11 villages and field surveys and interviews at 78 coffee sites in the forest. There was a gradient in coffee density (higher), liana cover (lower), and canopy cover (lower) from sites with high management intensity to sites without management. Recently, management intensity has increased in the forest edges. Interviews suggest that substantial areas of currently unmanaged coffee forests are a legacy of reforestation of abandoned (semi-) open landscapes in the late 19th century. Despite a dynamic history of coffee cultivation across these areas, the conservation of forest biodiversity, including unmanaged populations of genetically diverse Arabica coffee, should be a priority, given the few such remaining areas in Ethiopia and elsewhere in the world.

Ecological theory predicts that herbivory should be weaker on islands than on mainland based on the assumption that islands have lower herbivore abundance and diversity. However, empirical tests of this prediction are rare, especially for insect herbivores, and those few tests often fail to address the mechanisms behind island–mainland divergence in herbivory. In particular, past studies have not addressed the relative contribution of top-down (i.e. predator-driven) and bottom-up (i.e. plant-driven) factors to these dynamics. To address this, we experimentally excluded insectivorous vertebrate predators (e.g. birds, bats) and measured leaf traits associated with herbivory in 52 populations of 12 oak (Quercus) species in three island–mainland sites: The Channel Islands of California vs. mainland California, Balearic Islands vs. mainland Spain, and the island Bornholm vs. mainland Sweden (N = 204 trees). In each site, at the end of the growing season, we measured leaf damage by insect herbivores on control vs. predator-excluded branches and measured leaf traits, namely: phenolic compounds, specific leaf area, and nitrogen and phosphorous content. In addition, we obtained climatic and soil data for island and mainland populations using global databases. Specifically, we tested for island–mainland differences in herbivory, and whether differences in vertebrate predator effects or leaf traits between islands and mainland contributed to explaining the observed herbivory patterns. Supporting predictions, herbivory was lower on islands than on mainland, but only in the case of Mediterranean sites (California and Spain). We found no evidence for vertebrate predator effects on herbivory on either islands or mainland in any study site. In addition, while insularity affected leaf traits in some of the study sites (Sweden-Bornholm and California), these effects were seemingly unrelated to differences in herbivory. Synthesis. Our results suggest that vertebrate predation and the studied leaf traits did not contribute to island–mainland variation patterns in herbivory, calling for more nuanced and comprehensive investigations of predator and plant trait effects, including measurements of other plant traits and assessments of predation by different groups of natural enemies.

Aim: Climate is a major driver of large-scale variability in biodiversity, as a likely result of more intense biotic interactions under warmer conditions. This idea fuelled decades of research on plant-herbivore interactions, but much less is known about higher-level trophic interactions. We addressed this research gap by characterizing both bird diversity and avian predation along a climatic gradient at the European scale.

Location: Europe.

Taxon: Insectivorous birds and pedunculate oaks.

Methods: We deployed plasticine caterpillars in 138 oak trees in 47 sites along a 19° latitudinal gradient in Europe to quantify bird insectivory through predation attempts. In addition, we used passive acoustic monitoring to (i) characterize the acoustic diversity of surrounding soundscapes; (ii) approximate bird abundance and activity through passive acoustic recordings; and (iii) infer both taxonomic and functional diversity of insectivorous birds from recordings.

Results: The functional diversity of insectivorous birds increased with warmer climates. Bird predation increased with forest cover and bird acoustic activity but decreased with mean annual temperature and functional richness of insectivorous birds. Contrary to our predictions, climatic clines in bird predation attempts were not directly mediated by changes in insectivorous bird diversity or acoustic activity, but climate and habitat still had independent effects on predation attempts.

Main Conclusions: Our study supports the hypothesis of an increase in the diversity of insectivorous birds towards warmer climates but refutes the idea that an increase in diversity would lead to more predation and advocates for better accounting for activity and abundance of insectivorous birds when studying the large-scale variation in insect-tree interactions.

Urbanisation is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the 'urban facilitation model' suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the GLobal Urban Evolution project (GLUE), to study the effects of urbanisation on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of reduced Ne linked to urbanisation. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides the largest comprehensive test of the demographic effects of urbanisation. Our results contrast with the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.

Increasing temperatures and shifting precipitation patterns have major consequences for smallholder farmers, especially in the Global South. Our study examined spatial patterns and climatic drivers of farmers' perceptions of climate change, and how these perceptions translated into adaptation actions. We interviewed 56 farmers in southwestern Ethiopia and analyzed ERA5-Land reanalysis climate data from 1971 to 2020. The majority of farmers perceived the recorded temperature increase as well as a decrease and shift in the timing of rainfall. Perceived climate change varied with local climate factors and not with the rate of climate change itself. Farmers' adaptation practices showed associations with local temperature, but not with farmers’ perceptions of climate change. Our findings highlight that even if farmers perceive climate change, perceptions are most common in areas where climate action is already urgent, and perceptions may not translate into adaptation. Thus, targeted and timely information and extension programs are crucial.