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Agrilus planipennis, the emerald ash borer, is a species native to East Asia that was accidentally introduced to North America and Eastern Europe. In North America, it is responsible for tremendous damage. In Europe, its range has quickly expanded from the east where it was introduced in 2003, and it threatens the species of the genus Fraxinus. We developed an ensemble modelling approach to model the potential range of A. planipennis according to current climate conditions and four scenarios of climate change: SSP1–2.6, SSP2–4.5, SSP3–7.0 SSP5–8.5 in the period 2041–2060. We used three algorithms; random forest, boosted regression trees and Bayesian additive regression trees with occurrence data from both native and invaded ranges. The results indicate that most of the European continent is climatically suitable for A. planipennis. In Western Europe, the northern limit of the range is located in the British Isles and southern Scandinavia. The projection of the models according to estimates of future climate conditions shows that climate suitability would mostly remain unchanged in 2041–2060. During that period, the potential range is expected to slightly shrink in the south, around the Mediterranean Basin, and expand at its northern limit. Our results confirm that A. planipennis is, and will remain, a major threat to forest and ornamental ash tree health across Europe.

The pine processionary moth Thaumetopoea pityocampa is a defoliating lepidopter that develops during winter. The larvae are gregarious and bear urticating setae that are harmful to humans and vertebrates. They shelter in conspicuous silk tents that are easy to detect. We here present a dataset comprising tree characterization and tent counts from 3 agglomerations in France located in regions with different climatic environments. The studied trees belong to various conifer species that are potential hosts for the caterpillars. In each site, we defined clusters as one target tree and its 10–62 nearest neighbors, and surveyed each tree within the clusters by informing: tree species, coordinates, size, number of tents. We characterized a total of 3690 trees, including 2009 trees in Orléans (grouped in 68 clusters), 359 trees in La Baule (18 clusters) and 1322 trees in Montpellier (52 clusters). We provide the raw data characterizing each individual tree, graphs showing the prevalence and mean number of tents for the tree species included in the survey, and maps allowing to locate each tree. This dataset brings information about host preference of the pine processionary moth and will be useful as a baseline to study spatio-temporal variability of host-insect relationships. It can also be informative for decision-makers and managers of urban greenings to avoid trees that are likely to be heavily infested for plantation in proximity to vulnerable people.

Abstract Philaenus spumarius (Ps) is considered the main insect vector of the bacterium Xylella fastidiosa (Xf) in Europe. As such, it is a key actor of the Xf pathosystem on which surveillance and management strategies could be implemented. Although research effort has increased in the past years, the ecological factors shaping Ps abundance and distribution across landscapes are still poorly known in most regions of Europe. We selected 64 plots of 500m2 in Corsican semi-natural habitats in which we sampled nymphs and adults of Ps during three years. While local or surrounding vegetation structure (low or high scrubland) had little effect on Ps abundance, we highlighted a positive relationship between Ps abundance and the density of Cistus monspeliensis in the plots. We also found larger populations of Ps in cooler and moister plots. The pattern of host association highlighted here is unique, which calls for more studies on the ecology of Ps in Europe, to help designing surveillance and management strategy for Xf.

We describe the process by which the quarantine whitefly, Aleurocanthus spiniferus (Hemiptera, Aleyrodidae), was detected in France. The initial observation was made by a volunteer who reported a picture of an adult in the Inventaire National du Patrimoine Naturel (INPN Espèces), a citizen science resource developed by l’Office Français de la Biodiversité and the French Muséum National d’Histoire Naturelle. The specimen was suspected to be A. spiniferus from this picture by one of the expert entomologists in charge of the Hemiptera group validation. Once the species was identified, it was mounted on a slide and the information was officially passed on to the ministry in charge of agriculture via a communication channel set up in advance for this type of situation. The ministry then triggered the regulatory actions planned in the event of the suspected detection of quarantine organisms. Sampling was quickly carried out and the specimens collected on this occasion were formally identified as belonging to the species A. spiniferus. This led to the formalization of an outbreak in France. This sequence of decisions took just two months from the first observation to the implementation of a management plan. This case presents how incursion preparedness contributes to a rapid response. Furthermore, this case exemplifies how citizen science can contribute to the early detection of invasive species and highlights the importance of informing both the general public and professionals about major environmental issues.

Abstract Halyomorpha halys (Stål, 1855), the Brown Marmorated StinkBug (BMSB) is a highly successful invasive species native to eastern Asia that managed to spread into North America and Europe in recent decades. We set up a citizen science survey to monitor BMSB expansion in France in 2012 and analyzed the data it yielded between 2012 and 2019 to examine the local expansion of the insect. These data were gathered with occurrences form various sources (GBIF, literature) to calibrate a species niche model and assess potential current BMSB range. We evaluated the potential changes to the BMSB range due to climate change by projecting the model according to 6 global circulation models (GCM) and the shared socio-economic pathways SSP245 in two time periods 2021–2040 and 2041–2060. Citizen science allowed to track BMSB expansion in France and provided information about its phenology and its habitat preferences. The model highlighted the potential for further range expansion in Europe and illustrated the impact of climate change. These results could help managing the current BMSB invasion and the framework of this survey could contribute to a better preparedness of phytosanitary authorities either for the BMSB or other invasive pests.

Halyomorpha halys (Stål, 1855), the brown marmorated stinkbug (BMSB) is a highly successful invasive species native to eastern Asia. It has managed to spread into North America and Europe in recent decades, causing severe damage to various crops. BMSB has been detected in Europe in 2004 and has since expanded in more than 20 countries from Sweden to Greece and Spain to Turkey, the South European Territory of Russia (Krasnodar region) and Abkhazia. In 2012, we set up a citizen science survey to monitor BMSB expansion in France.The present crowdsourcing survey was initiated in 2012 and provided a large number of occurrence points of BMSB. These data allowed to track the expansion of the species in France from 2012 to 2019 and brought information about its phenology and distribution in various habitats. The dataset comprises both valid and invalid sightings thereby allowing to examine changes of citizen reports quality during the course of the survey. Despite a large proportion of misidentifications, the survey provided a large number of valid occurrences. Furthermore, valuable information on hemipterans of Pentatomidae and Coreidae families entering habitations were also gathered. The dataset also illustrates that, although designed for a large public, the Agiir application was mostly used by urban dwellers with very few sightings stemming from professionals of agricultural sectors.

The current climate change has marked impacts on the phenology of species, i.e., the timing of the various stages of their life cycle. Yet, to fully understand how phenological patterns are modified by the changes of temperature regimes, it is of prime importance to rely on high quality historical data. We here document a very valuable data set including the individual monitoring of the end of the larval phase and the date of adult emergence in the pine processionary moth Thaumetopoea pityocampa. A total of 46 479 caterpillars were followed between 1970 and 1984 in 6 sites along an altitudinal gradient in southern France. As optional prolonged diapause occurs in this species, i.e. some individuals experience one or more years of diapause before emerging, the caterpillars sampled any given year were monitored during up to 5 years. The goal was to give precise information about phenology in this species to further analyse its spatial and temporal patterns of variation.This dataset is unique by its richness and the type of data it contains. Phenology in the pine processionary moth is often monitored by the use of pheromone traps in the field, which does not provide all the necessary information because it is then not possible to trace back the exact origin of the moth trapped, nor to characterise other steps of the life cycle. More, as it corresponds to historical data dating back to the 70s and the 80s, it provides a historical baseline of trends in the pre-warming period.

Global change is expected to modify the threat posed by pathogens to plants. However, little is known regarding how a changing climate will influence the epidemiology of generalist vector-borne diseases. We developed a high-throughput screening method to test for the presence of a deadly plant pathogen, Xylella fastidiosa, in its insect vectors. Then, using data from a four-year survey in climatically distinct areas of Corsica (France), we demonstrated a positive correlation between the proportion of vectors positive to X. fastidiosa and temperature. Notably, a higher prevalence corresponded with milder winters. Our projections up to 2100 indicate an increased risk of outbreaks. While the proportion of vectors that carry the pathogen should increase, the climate conditions will remain suitable for the bacterium and its main vector, with possible range shifts towards a higher elevation. Besides calling for research efforts to limit the incidence of plant diseases in the temperate zone, this work reveals that recent molecular technologies could and should be used for massive screening of pathogens in vectors to scale-up surveillance and management efforts.

The brown marmorated stink bug (BMSB), Halyomorpha halys (Stål, 1855) is a hemipteran insect in the Pentatomidae family native to eastern Asia. This extremely polyphagous species is spreading rapidly worldwide. It is responsible for important economic damage to various agricultural crops, including wine grapes. Available data suggest that the current range of the BMSB is likely to expand in the near future which calls for more research and exploration of management options and biocontrol. Citizen science is a promising way forward on monitoring the BMSB expansion.

As a vector of Xylella fastidiosa (Wells, 1987) in Europe, the meadow spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Aphrophoridae) is a species of major concern. Therefore, tools and agents to control this ubiquitous insect that develops and feeds on hundreds of plant species are wanted. We conducted a field survey of P. spumarius eggs in Corsica and provide a first report of Ooctonus vulgatus Haliday, 1833 (Hymenoptera, Mymaridae) as a potential biocontrol agent of P. spumarius in Europe. To allow species identification, we summarized the main characters distinguishing O. vulgatus from other European species of Ooctonus and generated COI DNA barcodes. Parasitism rates were variable in the four localities included in the survey but could reach 69% (for an average number of eggs that hatched per locality of 109). Based on the geographic occurrences of O. vulgatus obtained from the literature, we calibrated an ecological niche model to assess its potential distribution in the Holarctic. Obviously, several questions need to be addressed to determine whether O. vulgatus could become an effective biocontrol agent of P. spumarius in Europe. So far, O. vulgatus has been reared only from P. spumarius eggs, but its exact host-range should be evaluated to ensure efficiency and avoid non-target effect. The top-down impact of the parasitoid on vector populations should also be assessed on large data sets. Finally, the feasibility of mass rearing should be tested. We hope this report serves as a starting point to initiate research on this parasitoid wasp to assess whether it could contribute to reduce the spread and impact of X. fastidiosa in Europe.

Forest trees are commonly used for ornamental purposes and are thus frequently encountered in non-forest landscapes where they represent an important component of the so-called trees outside forests (TOF). Little is known about the role of these trees in the connectivity between forest patches and their potential impact upon forest organisms’ dispersal. We focused on the tree species belonging to genera Pinus, Cedrus and Pseudotsuga, the potential hosts of the pine processionary moth Thaumetopoea pityocampa, a common defoliator in the western Mediterranean basin. We carried out an exhaustive inventory of trees in a 22 × 22 km sampling window located in the Beauce region (France) an agricultural territory where landscapes consist of intensively managed open-fields (mainly dedicated to cereal crops). The results showed that host trees suitable for the PPM are much more numerous than expected, and form small patches scattered across the study area. They are mostly ornamental trees planted in populated places such as villages. We conclude that hosts suitable for the PPM are available throughout agricultural landscapes. Various forest pests may benefit from TOF coverage that forms consistent ecological continuities linking forest areas. It appears that forest health should be addressed in a large context, encompassing non-forested areas, either agricultural lands or urbanized territories that play an overlooked role in large-scale spatial dynamics of forest pests and diseases.

The use of multiple sampling areas in landscape genetic analysis has been recognized as a useful way of generalizing the patterns of environmental effects on organism gene flow. It reduces the variability in inference which can be substantially affected by the scale of the study area and its geographic location. However, empirical landscape genetic studies rarely consider multiple sampling areas due to the sampling effort required. In this study, we explored the effects of environmental features on the gene flow of a flying long-horned beetle (Monochamus galloprovincialis) using a landscape genetics approach. To account for the unknown scale of gene flow and the multiple local confounding effects of evolutionary history and landscape changes on inference, we developed a way of resampling study areas on multiple scales and in multiple locations (sliding windows) in a single large-scale sampling design. Landscape analyses were conducted in 3*104 study areas ranging in scale from 220 to 1,000 km and spread over 132 locations on the Iberian Peninsula. The resampling approach made it possible to identify the features affecting the gene flow of this species but also showed high variability in inference among the scales and the locations tested, independent of the variation in environmental features. This method provides an opportunity to explore the effects of environmental features on organism gene flow on the whole and reach conclusions about general landscape effects on their dispersal, while limiting the sampling effort to a reasonable level.

Combining multivariable statistics and geostatistics with landscape metrics, we attempted to quantify the spatial pattern of urbanization in the city of Niamey, Niger. Landscape metrics provided local quantification of both landscape composition and physiognomy while the Principal Component Analysis (PCA) yielded a multivariable summary of the main source of landscape metrics variation across the city. We used the variogram (geostatistics) to analyze the spatial pattern of the PCA outcomes and to characterize the associated spatial scales of variation. In Niamey, the main urban structure corresponded to a gradient ranging from highly diversified, fragmented, and both wooded and built-up areas in the city center and along the Niger River, to less green zones gathering steel-roofed houses whose density diminished towards the periphery. This concentric structure centered on the Niger River clearly reflected the history of Niamey. PCA and geostatistics provided appealing quantitative estimates of spatial patterns, scales, anisotropy and intensity of urban structures. Although these different tools are known in landscape ecology, they are rarely used together. The present paper illustrates how they allow characterizing the marked spatial variation of the urban landscape of the fast-growing African city of Niamey (Niger). Such a quantification of the urban landscapes may be extremely useful for future correlative investigations in various fields of research and planning.

A serological survey of Toxoplasma gondii was conducted on 766 domestic and peridomestic rodents from 46 trapping sites throughout the city of Niamey, Niger. A low seroprevalence was found over the whole town with only 1.96% of the rodents found seropositive. However, differences between species were important, ranging from less than 2% in truly commensal Mastomys natalensis, Rattus rattus and Mus musculus, while garden-associated Arvicanthis niloticus displayed 9.1% of seropositive individuals. This is in line with previous studies on tropical rodents - that we reviewed here - which altogether show that Toxoplasma seroprevalence in rodent is highly variable, depending on many factors such as locality and/or species. Moreover, although we were not able to decipher statistically between habitat or species effect, such a contrast between Nile grass rats and the other rodent species points towards a potentially important role of environmental toxoplasmic infection. This would deserve to be further scrutinised since intra-city irrigated cultures are extending in Niamey, thus potentially increasing Toxoplasma circulation in this yet semi-arid region. As far as we are aware of, our study is one of the rare surveys of its kind performed in Sub-Saharan Africa and the first one ever conducted in the Sahel.

The paper describes rich, a new R package to perform species richness estimation and comparison. Species richness is the simplest surrogate for the more complex concept of species biodiversity. It is relatively easy to assess although estimations strongly depend on sampling intensity with the consequence that richness estimations should be standardized to perform valid comparisons. The R package rich allows such corrections as well as the computation of various statistics and implements different randomization tests to compare cumulative and average species richness of two communities. These tests are useful for ranking sites or communities which is a classical goal in restoration ecology and conservation biology.

Leptospirosis essentially affects human following contact with rodent urine-contaminated water. As such, it was mainly found associated with rice culture, recreational activities and flooding. This is also the reason why it has mainly been investigated in temperate as well as warm and humid regions, while arid zones have been only very occasionally monitored for this disease. In particular, data for West African countries are extremely scarce. Here, we took advantage of an extensive survey of urban rodents in Niamey, Niger, in order to look for rodent-borne pathogenic Leptospira species presence and distribution across the city. To do so, we used high throughput bacterial 16S-based metabarcoding, lipL32 gene-targeting RT-PCR, rrs gene sequencing and VNTR typing as well as GIS-based multivariate spatial analysis. Our results show that leptospires seem absent from the core city where usual Leptospira reservoir rodent species (namely R. rattus and M. natalensis) are yet abundant. On the contrary, L. kirschneri was detected in Arvicanthis niloticus and Cricetomys gambianus, two rodent species that are restricted to irrigated cultures within the city. Moreover, the VNTR profiles showed that rodent-borne leptospires in Niamey belong to previously undescribed serovars. Altogether, our study points towards the importance of market gardening in maintain and circulation of leptospirosis within Sahelian cities. In Africa, irrigated urban agriculture constitutes a pivotal source of food supply, especially in the context of the ongoing extensive urbanization of the continent. With this in mind, we speculate that leptospirosis may represent a zoonotic disease of concern also in arid regions that would deserve to be more rigorously surveyed, especially in urban agricultural settings.

Widely distributed species often show strong phylogeographic structure, with lineages potentially adapted to different biotic and abiotic conditions. The success of an invasion process may thus depend on the intraspecific identity of the introduced propagules. However, pest risk analyses are usually performed without accounting for intraspecific diversity. In this study, we developed bioclimatic models using MaxEnt and boosted regression trees approaches, to predict the potential distribution in Europe of six economically important Tephritid pests (Ceratitis fasciventris (Bezzi), Bactrocera oleae (Rossi), Anastrepha obliqua (Macquart), Anastrepha fraterculus (Wiedemann), Rhagoletis pomonella (Walsh) and Bactrocera cucurbitae (Coquillet)). We considered intraspecific diversity in our risk analyses by independently modeling the distributions of conspecific lineages. The six species displayed different potential distributions in Europe. A strong signal of intraspecific climate envelope divergence was observed in most species. In some cases, conspecific lineages differed strongly in potential distributions suggesting that taxonomic resolution should be accounted for in pest risk analyses. No models (lineage- and species-based approaches) predicted high climatic suitability in the entire invaded range of B. oleae-the only species whose intraspecific identity of invading populations has been elucidated-in California. Host availability appears to play the most important role in shaping the geographic range of this specialist pest. However, climatic suitability values predicted by species-based models are correlated with population densities of B. oleae globally reported in California. Our study highlights how classical taxonomic boundaries may lead to under- or overestimation of the potential pest distributions and encourages accounting for intraspecific diversity when assessing the risk of biological invasion.

Tree-ring datasets are used in a variety of circumstances, including archeology, climatology, forest ecology, and wood technology. These data are based on microdensity profiles and consist of a set of tree-ring descriptors, such as ring width or early/latewood density, measured for a set of individual trees. Because successive rings correspond to successive years, the resulting dataset is a ring variables × trees × time datacube. Multivariate statistical analyses, such as principal component analysis, have been widely used for extracting worthwhile information from ring datasets, but they typically address two-way matrices, such as ring variables × trees or ring variables × time. Here, we explore the potential of the partial triadic analysis (PTA), a multivariate method dedicated to the analysis of three-way datasets, to apprehend the space-time structure of tree-ring datasets. We analyzed a set of 11 tree-ring descriptors measured in 149 georeferenced individuals of European larch (Larix decidua Miller) during the period of 1967-2007. The processing of densitometry profiles led to a set of ring descriptors for each tree and for each year from 1967-2007. The resulting three-way data table was subjected to two distinct analyses in order to explore i) the temporal evolution of spatial structures and ii) the spatial structure of temporal dynamics. We report the presence of a spatial structure common to the different years, highlighting the inter-individual variability of the ring descriptors at the stand scale. We found a temporal trajectory common to the trees that could be separated into a high and low frequency signal, corresponding to inter-annual variations possibly related to defoliation events and a long-term trend possibly related to climate change. We conclude that PTA is a powerful tool to unravel and hierarchize the different sources of variation within tree-ring datasets.

Invasive rodents have been responsible for the diffusion worldwide of many zoonotic agents, thus representing major threats for public health. Cities are important hubs for people and goods exchange and are thus expected to play a pivotal role in invasive commensal rodent dissemination. Yet, data about urban rodents' ecology, especially invasive vs. native species interactions, are dramatically scarce. Here, we provide results of an extensive survey of urban rodents conducted in Niamey, Niger, depicting the early stages of rodent bioinvasions within a city. We explore the species-specific spatial distributions throughout the city using contrasted approaches, namely field sampling, co-occurrence analysis, occupancy modelling and indicator geostatistics. We show that (i) two species (i.e. rural-like vs. truly commensal) assemblages can be identified, and that (ii) within commensal rodents, invasive (Rattus rattus and Mus musculus) and native (Mastomys natalensis) species are spatially segregated. Moreover, several pieces of arguments tend to suggest that these exclusive distributions reflect an ongoing native-to-invasive species turn over. The underlying processes as well as the possible consequences for humans are discussed.

Mapping species spatial distribution using spatial inference and prediction requires a lot of data. Occurrence data are generally not easily available from the literature and are very time-consuming to collect in the field. For that reason, we designed a survey to explore to which extent large-scale databases such as Google maps and Google Street View could be used to derive valid occurrence data. We worked with the Pine Processionary Moth (PPM) Thaumetopoea pityocampa because the larvae of that moth build silk nests that are easily visible. The presence of the species at one location can therefore be inferred from visual records derived from the panoramic views available from Google Street View. We designed a standardized procedure allowing evaluating the presence of the PPM on a sampling grid covering the landscape under study. The outputs were compared to field data. We investigated two landscapes using grids of different extent and mesh size. Data derived from Google Street View were highly similar to field data in the large-scale analysis based on a square grid with a mesh of 16 km (96% of matching records). Using a 2 km mesh size led to a strong divergence between field and Google-derived data (46% of matching records). We conclude that Google database might provide useful occurrence data for mapping the distribution of species which presence can be visually evaluated such as the PPM. However, the accuracy of the output strongly depends on the spatial scales considered and on the sampling grid used. Other factors such as the coverage of Google Street View network with regards to sampling grid size and the spatial distribution of host trees with regards to road network may also be determinant.