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[hal-05302513] An ambrosia beetle recently introduced in Europe shows specific association with a yeast fungus
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Cecile Robin) 07 Oct 2025
https://hal.science/hal-05302513v1
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[hal-05499984] Guix-HPC Activity Report 2025
<div><p>Guix-HPC is a collaborative effort to bring reproducible software deployment to scientific workflows and high-performance computing (HPC). Guix-HPC builds upon the GNU Guix software deployment tools and aims to make them useful for HPC practitioners and scientists concerned with dependency graph control and customization and, uniquely, reproducible research.</p> <p>Guix-HPC started as a joint software development project involving three research institutes: Inria , the Max Delbrück Center for Molecular Medicine (MDC) and the Utrecht Bioinformatics Center (UBC). Guix for HPC and reproducible research has since received contributions from many individuals and organizations, including CNRS , Université Paris Cité , the University of Tennessee Health Science Center (UTHSC), Cornell University, and AMD. HPC remains a conservative domain but over the years, we have reached out to many organizations and people who share our goal of improving upon the status quo when it comes to software deployment.</p> <p>This report—our eighth report!—highlights key achievements of Guix-HPC between our previous report a year ago and today, February 2026. This year was marked by exciting developments for HPC and reproducible workflows. Significant advances were made in integrating Guix into the complex software landscape of HPC, taking the roles of software manager, workflow execution engine, backend for generating container images, or provider for the complete operating system layer. </p> <p>This year was also marked by the migration to Codeberg, a non-profit and community-led European platform whose main objective is to facilitate the expansion of the contributor community. Finally, support for reproducing computations from the past was also much improved. And, as usual, we have been using Guix for research, and teaching other researchers how to get started. </p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Céline Acary-Robert) 09 Feb 2026
https://hal.science/hal-05499984v1
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[hal-02819728] Impacts of climate change on temperate forests and interaction with management
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ano.nymous@ccsd.cnrs.fr.invalid (Denis Loustau) 06 Jun 2020
https://hal.inrae.fr/hal-02819728v1
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[hal-02629243] Global rise in emerging alien species results from increased accessibility of new source pools
Our ability to predict the identity of future invasive alien species is largely based upon knowledge of prior invasion history. Emerging alien species-those never encountered as aliens before-therefore pose a significant challenge to biosecurity interventions worldwide. Understanding their temporal trends, origins, and the drivers of their spread is pivotal to improving prevention and risk assessment tools. Here, we use a database of 45,984 first records of 16,019 established alien species to investigate the temporal dynamics of occurrences of emerging alien species worldwide. Even after many centuries of invasions the rate of emergence of new alien species is still high: Onequarter of first records during 2000-2005 were of species that had not been previously recorded anywhere as alien, though with large variation across taxa. Model results show that the high proportion of emerging alien species cannot be solely explained by increases in well-known drivers such as the amount of imported commodities from historically important source regions. Instead, these dynamics reflect the incorporation of new regions into the pool of potential alien species, likely as a consequence of expanding trade networks and environmental change. This process compensates for the depletion of the historically important source species pool through successive invasions. We estimate that 1-16% of all species on Earth, depending on the taxonomic group, qualify as potential alien species. These results suggest that there remains a high proportion of emerging alien species we have yet to encounter, with future impacts that are difficult to predict.
ano.nymous@ccsd.cnrs.fr.invalid (Hanno Seebens) 27 May 2020
https://hal.inrae.fr/hal-02629243v1
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[hal-01607783] No saturation in the accumulation of alien species worldwide
Although research on human-mediated exchanges of species has substantially intensified during the last centuries, we know surprisingly little about temporal dynamics of alien species accumulations across regions and taxa. Using a novel database of 45,813 first records of 16,926 established alien species, we show that the annual rate of first records worldwide has increased during the last 200 years, with 37% of all first records reported most recently (1970-2014). Inter-continental and inter-taxonomic variation can be largely attributed to the diaspora of European settlers in the nineteenth century and to the acceleration in trade in the twentieth century. For all taxonomic groups, the increase in numbers of alien species does not show any sign of saturation and most taxa even show increases in the rate of first records over time. This highlights that past efforts to mitigate invasions have not been effective enough to keep up with increasing globalization.
ano.nymous@ccsd.cnrs.fr.invalid (Hanno Seebens) 27 May 2020
https://hal.science/hal-01607783v1
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[hal-02736174] Consequences of fluvial maintenance operations on the biodiversity and landscape in the Mareau-aux-Prés islands (National Reserve of Saint-Mesmin, Loire River, France)
This sandy-gravelly bar is an ideal field support for studying long-term ecological issues. A multidisciplinary research programme (‘BioMareau’ project) is currently being conducted from 2012 to 2019, focusing on interactions and feedbacks between biotic and abiotic components and, since 2017, on landscape evolution and perception. The project involves researchers and local stakeholders (national reserve, environmental group), in interaction with institutional actors.
ano.nymous@ccsd.cnrs.fr.invalid (Marc Villar) 02 Jun 2020
https://hal.inrae.fr/hal-02736174v1
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[hal-02787851] Rapid spread of the invasive box tree moth throughout Europe : assessing its flight performance and growth rate.
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Audrey Bras) 05 Jun 2020
https://hal.inrae.fr/hal-02787851v1
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[hal-02787977] WP1 Impacts on biodiversity - French site
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Christophe Bouget) 05 Jun 2020
https://hal.inrae.fr/hal-02787977v1
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[hal-02627470] New species of leaf-mining Phyllonorycter (Lepidoptera Gracillariidae) from Siberia feeding on Caragana (Fabaceae)
During a DNA barcoding campaign of leaf-mining Gracillariidae from the Asian part of Russia, a new species of Phyllonorycter Hubner, feeding on the Siberian pea shrub, Caragana arborescens Lam. (Fabaceae) was discovered in Siberia. Here, this taxon is described as Phyllonorycter ivani sp. n. Among Fabaceae-feeding Phyllonorycter, so far only P. caraganella (Ermolaev) has been known to develop on Caragana. Phyllonorycter ivani and P. caraganella show a large divergence in morphology (external and male genitalia) and barcode region of the mtDNA-COI gene (8.6%). They feed on different host plants species and have different ranges in Russia. We show that DNA barcode data weakly supports the Fabaceae-feeding species groups. In addition, we show that morphologically (strongly) and genetically (weakly), P. ivani has affinity to the haasi species group, a West Palearctic group with asymmetrical male genitalia.
ano.nymous@ccsd.cnrs.fr.invalid (Natalia Kirichenko) 26 May 2020
https://hal.inrae.fr/hal-02627470v1
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[hal-02736217] Five-year study of consequences of fluvial maintenance operations on the biodiversity in the Mareau-aux-Prés islands (National Reserve of Saint-Mesmin, Loire River, France)
The Mareau-aux-Prés islands, along the Loire river, are characterized by a multiple channel pattern, where natural limestone riffles influence the morphology and spatial distribution of vegetated islands, secondary channels and alluvial bars. In September 2012, within these islands, the vegetation of the central 3 ha sandy-gravelly bar was uprooted and the bar level lowered in order to maintain the flow capacity of the river. A new sandy-gravelly bar appeared in spring 2013, ideal field support to study long-term ecological issues. A multidisciplinary research programme (‘BioMareau’ project) is currently being conducted from 2012 to 2019, focusing on physical and biological compartments. Field measurements on annual basis were performed on hydrosedimentary processes. Biotic components focus on colonization dynamics by Populus nigra seedlings (studying small-scale DNA spatial genetic structure and through plot survey), by native and invasive flora (through seed bank and summer inventories), by community assemblages of ground beetles Coleoptera Carabidae, by gravel nesting birds and on the consequence of the modification of the feeding habitat by the European beaver (as the island constituted the main source of wood). We will present 5 years of results after fluvial maintenance operations. The applied objectives of such study are to guide river managers in order to perform optimal useful management operations with a minimum loss of biodiversity.
ano.nymous@ccsd.cnrs.fr.invalid (Marc Villar) 02 Jun 2020
https://hal.inrae.fr/hal-02736217v1
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[hal-02734096] Does forest biodiversity respond to pulses of saproxylic microhabitats induced by tree dieback: a case study in mountain French silver fir forests
Forest diebacks are likely to increase in response to climate change, with increased frequency and intensity of droughts. In line with climate change scenarios, ecoclimatic modelling predicts a decrease in the range of silver fir, a drought-sensitive species, in its southern limit in the French Pyrenees. Diebacks are expected to induce a pulse of resources potentially favorable to certain forest species, e.g. tree-related microhabitats (TreM) for saproxylic species. The impact of forest dieback on biodiversity has nonetheless been poorly studied. As part of the international Climtree project, we set up a balanced sampling design of 56 plots crossing the intensity of local silver fir dieback and the salvage logging of weakened or dead trees. Detailed stand structure metrics and insect communities sampled by Malaise traps (insect MOTUs) or flight-interception traps (saproxylic beetles) have been measured. The structure of fir stands was affected by the level of decline, and to a lesser extent by salvage logging. We indeed observed a slight increase in CWD and in some TreM-bearing trees (crown deadwood, annual polypores , trunk rot holes) with dieback intensity, and a slight decrease in some TreM-bearing trees (crown deadwood, annual polypores) in salvaged compared with unharvested plots. However, these stand changes did not strongly affect local insect assemblages. Guilds of TreM-associated insects did not increase in abundance or richness with dieback-induced increase in resources. In conclusion, forest changes through dieback result in habitat and resource changes with still hard-to-predict impacts at the stand scale on a major reservoir of biodiversity.
ano.nymous@ccsd.cnrs.fr.invalid (Christophe Bouget) 02 Jun 2020
https://hal.inrae.fr/hal-02734096v1
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[hal-02617801] Exploring species diversity and host plant associations of leaf-mining micromoths (Lepidoptera: Gracillariidae) in the Russian Far East using DNA barcoding
The Russian Far East (RFE) is an important hotspot of biodiversity whose insect fauna remains understudied, particularly its Microlepidoptera. Here we explore the diversity of leaf-mining micromoths of the family Gracillariidae, their distribution and host plant associations in RFE using a combination of field observations and sampling, DNA barcoding, morphological analysis and literature review. We collected 91 gracillariid specimens (45 larvae, 9 pupae and 37 adults) in 12 localities across RFE and identified 34 species using a combination of DNA barcoding and morphology. We provide a genetic library of 57 DNA barcodes belonging to 37 Barcode Index Numbers (BINs), including four BINs that could potentially represent species new to science. Leaf mines and leaf shelters are described and illustrated for 32 studied species, male or female genitalia as well as forewing patterns of adults are shown, especially for those species identified based on morphology. Three species, Micrurapteryx caraganella (Hering), Callisto insperatella (Nickerl), and Phyllonorycter junoniella (Zeller) are newly recorded from RFE. Five species previously known from some regions of RFE, were found for the first time in Amurskaya Oblast: Phyllonorycter populifoliella (Treitschke), Primorskii Krai: Ph. sorbicola Kumata and Sahkalin Island: Caloptilia heringi Kumata, Ph. ermani (Kumata) and Ph. ulmifoliella (Hubner). Eight gracillariid-plant associations are novel to science: Caloptilia gloriosa Kumata on Acer pseudosieboldianum, Cameraria niphonica Kumata on A. caudatum subsp. ukurundense, Parornix ermolaevi Kuznetzov on Corylus sieboldiana, Phyllonorycter ermani (Kumata) on Betula platyphylla, Ph. nipponicella (Issiki) on Quercus mongolica, Ph. orientalis (Kumata) and Ph. pseudojezoniella Noreika on Acer saccharum, Ph. sorbicola on Prunus maakii. For the first time we documented the "green island" phenotype on Phyllonorycter cavella (Zeller) mines on Betula platyphylla. Two pestiferous species have been recorded during our surveys: Micrurapteryx caraganella on ornamental Caragana arborescens in urban plantations in Amurskaya Oblast, and the lime leafminer Phyllonorycter issikii (Kumata), a species known to be native to RFE and invasive elsewhere in Russia and in European countries. A revised checklist of RFE gracillariids has been compiled. It accounts for 135 species among which 17 species (13%) are only known to occur in RFE. The gracillariid fauna of RFE is more similar to the Japanese fauna (49%), than to the fauna of the rest of Russia (i.e European part and Siberia) (32%).
ano.nymous@ccsd.cnrs.fr.invalid (Natalia Kirichenko) 25 May 2020
https://hal.inrae.fr/hal-02617801v1
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[hal-02622748] Census and contemporary effective population size of two populations of the protected Spanish Moon Moth (Graellsia isabellae)
Graellsia isabellae is a protected lepidopteran both in France and Spain; however, there has been considerable debate over its conservation status. Recent literature emphasised the need of monitoring population size in the different mountain ranges where this iconic species occurs. We used mark-capture-recapture and genotypes of nine molecular microsatellite markers to estimate the census (N) and contemporary effective population size (N-e) of two Spanish populations extending over similar size areas (10-15 km(2)): Puebla (Eastern Spain) and Ordesa (Western Pyrenees). Only adult males were captured and analysed, as sampling was based on the use of the synthesised female sex pheromone. Estimates of N were rather different in the two populations: 3398 males in Puebla (95% CI = 2875-4145) and 1500 in Ordesa (95% CI = 1229-1932), although the area occupied by the populations was larger and more densely forested in Ordesa than in Puebla. Several lines of evidence pointed to a moderate-large contemporary N-e at Puebla (173-178 individuals) and a one-order of magnitude lower N-e at Ordesa (27-49). Thus, N-e/N ratios were very low (0.026 and 0.01 respectively). We recommend G. isabellae to be classified as of Least Concern under the IUCN criteria; however, the high temporal fragmentation index and the very low values of the N-e/N ratios obtained for this species, as compared with those recorded for most others, are usually taken as indicators of actual threat for their conservation. As a cautionary measure, managers should aim at maintaining gene flow by ensuring connectivity of Pinus sylvestris in these areas.
ano.nymous@ccsd.cnrs.fr.invalid (Neus Mari-Mena) 26 May 2020
https://hal.inrae.fr/hal-02622748v1
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[hal-03655839] Molecular basis and evolution of gall-inducing in Caloptilia (Gracillariidae)
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Carlos Lopez-Vaamonde) 30 Apr 2022
https://hal.inrae.fr/hal-03655839v1
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[hal-03655838] Estudio integrado del genero Vesperus Dejean, 1821 (Coleoptera: Cerambycidae) y elaboración de una biblioteca de ADN de referencia
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Miguel Angel) 30 Apr 2022
https://hal.inrae.fr/hal-03655838v1
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[hal-03607573] R script for the potential spread of Vespa velutina in Europe. https://zenodo.org/record/1193663
https://zenodo.org/record/1193663 R script to simulate the potential spread of the yellow-legged hornet in Europe (notably in some islands) and the data needed to do these simulations. This study was conducted in the frame of the project "FRELON" (2012-2014), which was supported by a French regional grant of Region Centre (France)
ano.nymous@ccsd.cnrs.fr.invalid (Christelle Robinet) 14 Mar 2022
https://hal.inrae.fr/hal-03607573v1
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[hal-01310179] Force balance in the take-off of a pierid butterfly: relative importance and timing of leg impulsion and aerodynamic forces
Up to now, the take-off stage has remained an elusive phase of insect flight that was relatively poorly explored compared with other maneuvers. An overall assessment of the different mechanisms involved in force production during take-off has never been explored. Focusing on the first downstroke, we have addressed this problem from a force balance perspective in butterflies taking off from the ground. In order to determine whether the sole aerodynamic wing force could explain the observed motion of the insect, we have firstly compared a simple analytical model of the wing force with the acceleration of the insect's center of mass estimated from video tracking of the wing and body motions. Secondly, wing kinematics were also used for numerical simulations of the aerodynamic flow field. Similar wing aerodynamic forces were obtained by the two methods. However, neither are sufficient, nor is the inclusion of the ground effect, to predict faithfully the body acceleration. We have to resort to the leg forces to obtain a model that best fits the data. We show that the median and hind legs display an active extension responsible for the initiation of the upward motion of the insect's body, occurring before the onset of the wing downstroke. We estimate that legs generate, at various times, an upward force that can be much larger than all other forces applied to the insect's body. The relative timing of leg and wing forces explains the large variability of trajectories observed during the maneuvers.
ano.nymous@ccsd.cnrs.fr.invalid (Gaëlle Bimbard) 03 May 2016
https://hal.science/hal-01310179v1
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[hal-02626409] Taxonomic revision of Neotropical Phyllocnistis Zeller, 1848 (Lepidoptera: Gracillariidae), with descriptions of seven new species and host plant associations
Until now, 20 species of leaf-mining micromoths of the genus Phyllocnistis Zeller (Lepidoptera, Gracillariidae) have been known to occur in the Neotropical region. Here we revise the previously known species and describe seven new species: four from French Guiana, P. kawakitai Brito & Lopez-Vaamonde, sp. nov., P. norak Brito & Lopez-Vaamonde, sp. nov., P. ohshimai Brito & Lopez-Vaamonde, sp. nov., P. petronellii Brito & Lopez-Vaamonde, sp. nov.; and, three from Brazil, P. helios Brito & Moreira, sp. nov., P. jupiter Brito & Moreira, sp. nov. and P. xylopiella Brito & Becker, sp. nov. Lectotypes are designated for P. aurilinea Zeller, 1877; P. citrella Stainton, 1856; P. rotans and P. sexangula Meyrick, 1915. Detailed descriptions of the pattern of forewing fasciae are provided for all species. Host plant associations, photographs of adults and illustrations of genitalia, when available, are provided for the described species of Neotropical Phyllocnistis. In addition, DNA barcodes were used for the delimitation of some species.
ano.nymous@ccsd.cnrs.fr.invalid (Rosangela Brito) 26 May 2020
https://hal.inrae.fr/hal-02626409v1
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[hal-02625499] Systematics of Phyllocnistis leaf-mining moths (Lepidoptera, Gracillariidae) feeding on dogwood (Cornus spp.) in Northeast Asia, with the description of three new species
During an ongoing DNA-barcoding campaign of the leaf-mining moths that feed on woody plants in Northeast Asia, four lineages of the genus Phyllocnistis (Gracillariidae, Phyllocnistinae) were discovered on dogwood (Cornus spp): P. cornella Ermolaev, 1987 on C. controversa Hemsl. (Japan: Hokkaido) and three new species - one feeding on C. controversa, C. florida L. and C. macrophylla Wall. in Japan (Honshu, Shikoku, Kyushu), a second species on C. macrophylla in China (Yunnan) and a third on Siberian dogwood Cornus alba L. in Russia (Siberia). All these species showed differences in morphology, in the barcode region of the cytochrome c oxidase I gene and in two nuclear genes (histone H3 and 28S ribosomal RNA). No correlation was found between the deep mitochondrial splits observed and the Wolbachia infection pattern. Based on both morphological and molecular evidence, the three recently discovered lineages are described here as new species: P. indistincta Kobayashi & Triberti, sp. n. (Japan), P. saepta Kirichenko, Ohshima & Huang, sp. n. (China) and P. verae Kirichenko, Triberti & Lopez-Vaamonde, sp. n. (Russia). In addition, the authors re-describe the adult morphology of P. cornella, provide the first record of this species from Japan and highlight the diagnostic characters that allow these Cornus-feeding Phyllocnistis species to be distinguished.
ano.nymous@ccsd.cnrs.fr.invalid (Natalia Kirichenko) 26 May 2020
https://hal.inrae.fr/hal-02625499v1
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[hal-04186507] Caractérisation des communautés d'invertébrés des cavités d'arbres par génomique environnementale
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ano.nymous@ccsd.cnrs.fr.invalid (Lucas Sire) 23 Aug 2023
https://hal.inrae.fr/hal-04186507v1
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[hal-04236365] Biosurveillance et suivis des insectes avec les codes barres ADN
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ano.nymous@ccsd.cnrs.fr.invalid (Carlos Lopez-Vaamonde) 10 Oct 2023
https://hal.inrae.fr/hal-04236365v1
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[hal-04236301] The evolutionary history of capital-breeding moths through the lens of wild silkmoths (Saturniidae) phylogenomics
Wild silkmoths (Saturniidae) are large capital-breeding insects with non-feeding adults that have short lifespan entirely devoted to reproduction. They exhibit a dazzling diversity of sizes, forms, and life-histories inviting questions about the role that key traits may have played in spurring out species diversification and biogeographical movements in organisms with such extreme reproductive strategy. Yet, the absence of a robust phylogenetic framework based on comprehensive taxonomic sampling impedes our understanding of their evolutionary history. We analyzed 1,024 ultraconserved elements (UCEs) and their flanking regions to infer the relationships among 338 species of Saturniidae representing all subfamilies, tribes, and genera. We performed dating and historical biogeographic analyses to reconstruct their evolutionary history in space and time. Rather unexpectedly for a taxonomically well-known family such as Saturniidae, the alignment of taxonomic divisions and ranks with our phylogenetic results led us to propose substantial rearrangements of the family classification. Saturniids most likely originated in the Neotropics, shortly after the Cretaceous-Paleogene extinction event (ca 64.0-52.0 Ma). Old World lineages stemmed from two independent colonization events during the Eocene, presumably through the Bering-Land-Bridge. Extant subfamilies showed limited mobility across biogeographical regions, except for Saturniinae, a subfamily now present on all continents but Antarctica. These results provide a framework for the integration of saturniid evolutionary history into further global studies of biodiversity and conservation, as well as for in-depth investigations of the spatial and temporal dynamics in all lineages and of the role that key innovations played in driving species diversification of these capital-breeding moths.
ano.nymous@ccsd.cnrs.fr.invalid (Rodolphe Rougerie) 10 Oct 2023
https://hal.inrae.fr/hal-04236301v1
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[hal-03655943] CLIMTREE: Quantifying changes in flying insect diversity and soil fauna along a gradient of climate induced forest decline using DNA metabarcoding
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Lucas Sire) 30 Apr 2022
https://hal.inrae.fr/hal-03655943v1
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[hal-03698341] Systematics of Slovenian Dahlica Enderlein, 1912, subgenus Brevantennia Sieder, 1953 (Lepidoptera, Psychidae)
The subgenus Brevantennia Sieder, 1953 of the genus Dahlica Enderlein, 1912 (Psychidae: Dahlicini) is represented by a group of 10 bagworm moth species, distributed in southwest and southeast Europe northwards to the Alps and Carpathians. This study is a revision of the subgenus Brevantennia species occurring in Slovenia based on our own comprehensive field studies, DNA barcoding and morphological analysis. Dahlica (B.) santicensis (Sieder, 1957) is established as bona spec. and D. (B.) gorskikotarica Weidlich, 2015, syn. nov. is synonymised with D. (B.) santicensis. Both D. (B.) adriatica (Rebel, 1919) and D. (B.) triglavensis (Rebel, 1919) are confirmed to occur in Slovenia. D. (B.) styriaca (Meier, 1957) is excluded from the checklist of Slovenian Lepidoptera fauna.
ano.nymous@ccsd.cnrs.fr.invalid (Jurij Rekelj) 17 Jun 2022
https://hal.inrae.fr/hal-03698341v1
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[hal-04236256] Population genomics and niche modeling of the Alpine populations of Graellsia isabellae
Graellsia isabellae (Lepidoptera, Saturniidae) is an emblematic threatened Lepidoptera species, found in mountain ranges of Spain and Alps. This moth is potentially impacted by climate change and dieback of its main host plant Scots pine (Pinus sylvestris). Our study was focused on the French Alpine population, because of its isolation and low genetic diversity as shown in a previous analysis based on mitochondrial DNA and microsatellite data. In order to better characterize the French population for conservation, a RADseq approach was used for 62 individuals, making it possible to obtain a large number of nuclear loci. The genetic variations analyzed (3,644 SNPs) confirm the strong isolation between the Pyrenean (n=8) and the Alpine (n=53) populations, but also reveal a sub-structure in the Alps. Basic genetic statistics also confirmed the low genetic diversity of the French population. To assess the environmental constraints affecting its distribution, a niche modeling approach was used, by incorporating climatic variables as well as the distribution of its host plant. This revealed that the potential distribution area is currently relatively limited. Projections of the evolution of its niche in the future, up to 2050, show a change in niche suitability that could have negative consequences for the survival of the French population and implications for the conservation strategy.
ano.nymous@ccsd.cnrs.fr.invalid (Flora Lambert-Auger) 10 Oct 2023
https://hal.inrae.fr/hal-04236256v1
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[hal-02609829] Dépérissement et diversité des insectes forestiers - une étude de cas dans les sapinières pyrénéennes
En raison de changements climatiques profonds, on constate une augmentation de fréquence et d'intensité des sécheresses dans certaines parties du globe (dont l'Europe) avec des conséquences déjà visibles sur les forêts. Dans ce contexte, le projet Climtree porte sur les Impacts écologiques et socio-économiques du dépérissement des arbres induit par les changements climatiques dans les forêts de montagne. Grâce à l'étude de 56 placettes dans 2 régions des Pyrénées, nous analysons ici la réponse de la diversité des assemblages entomologiques (i) à l'intensité du dépérissement local de la sapinière, (ii) au niveau de dépérissement des sapinières dans le paysage ? et (iii) aux coupes de récupération mises en oeuvre dans les peuplements dépérissants. Les premiers résultats montrent que le niveau de dépérissement local affecte la structure des sapinières, la composition générale des communautés d'insectes, l'abondance moyenne des xylo- et saproxylophages de résineux mais pas le nombre moyen d'espèces de coléoptères saproxyliques. Le niveau régional de dépérissement montre un effet significatif sur l'abondance des xylophages potentiels ravageurs de faiblesse, sur la richesse des xylo- et saproxylo-phages de résineux, l'abondance et la richesse moyenne des espèces rares et l'abondance moyenne des espèces cavicoles et fongicoles. La coupe de récupération ne provoque pas d'érosion générale de la diversité des assemblages de coléoptères saproxyliques et provoque de faibles changements de composition des communautés d'insectes.
ano.nymous@ccsd.cnrs.fr.invalid (Christophe Bouget) 16 May 2020
https://hal.inrae.fr/hal-02609829v1
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[hal-02318844] Origin of gall-inducing from leaf-mining in Caloptilia micromoths (Lepidoptera, Gracillariidae)
In insects, the gall-inducing life-style has evolved independently many times. Several evolutionary pathways leading to this lifestyle have been proposed. While there is compelling evidence supporting surface-feeders and stem-borers as ancestral states of insect gall-inducers, an evolutionary pathway from leaf-miners remains hypothetical. Here we explored this question by comparing the developmental processes of two micromoths, a gall-inducer Caloptilia cecidophora (Lep., Gracillariidae), and its non-gall-inducing relative C. ryukyuensis. Like other Caloptilia, the first and second instars of C. cecidophora are leaf-miners and the gall is initiated inside the leaf mine by the third instar, thus suggesting leaf-mining as an ancestral, plesiomorphic state in this case. This is the first example of an insect species switching from leaf-mining to gall-inducing during larval development. The first two leaf-mining instars of C. cecidophora exhibit an absence of growth and a reduced time duration compared to C. ryukyuensis. The shortening of the duration of leaf-mining stages is apparently compensated in C. cecidophora by a larger egg size than C. ryukyuensis, and an additional larval instar during the gall phase.
ano.nymous@ccsd.cnrs.fr.invalid (Antoine Guiguet) 17 Oct 2019
https://hal.science/hal-02318844v1
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[hal-02136833] Subterranean termites in the Centre-Val de Loire region: distribution patterns and invasion risks
This study presents research concerning subterranean termites found in the Centre-Val de Loire region. More specifically, we examined the geographical distribution of Reticulitermes flavipes, a globally invasive species. This work was conducted in collaboration with both social and life science specialists in order to better understand the factors mediating its spatial distribution. Using geomatics and the spatial analysis of R. flavipes' distribution, we were able to define geographical areas favorable to the termite. This geographical study and the diversity of players involved in this research underscore a growing awareness of termite invasion risks in society at large.
ano.nymous@ccsd.cnrs.fr.invalid (Dominique Andrieu) 26 May 2020
https://hal.science/hal-02136833v1
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[hal-02736320] DNA Metabarcoding to quantify the response of insect diversity to mountain forest die-offs in the French Pyrenees
Mountain forests suffer from an increase in frequency and severity of summer droughts and infestations of pathogens and insects. Those factors are causing high mortality of some keystone tree species (forest die-offs). Yet, how tree diebacks and associated changes in forest composition will affect local diversity and ecosystem functions remains unknown. Here, we aim at quantifying the impact of climate-induced forest decline on biodiversity by measuring changes in taxonomic structure of invertebrate communities along gradients of silver fir (Abies alba) dieback in the French Pyrenees. We use DNA metabarcoding to analyse 224 samples of Malaise traps placed on 56 silver fir dominated plots in the French Pyrenees from May to September 2017. Samples were sequenced using Illumina MiSeq and analysed using the DAMe twin-tagging pipeline approach. We conducted taxonomic assignment against reference DNA barcode libraries to streamli ne identification and recover biological information for ecological analysis. We discuss the results of our metabarcoding analysis and the utility of our approach to conduct biomonitoring across a large geographical scale.
ano.nymous@ccsd.cnrs.fr.invalid (Lucas Sire) 02 Jun 2020
https://hal.inrae.fr/hal-02736320v1
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[hal-00550576] Increasing demands and vanishing expertise in insect integrative biology
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ano.nymous@ccsd.cnrs.fr.invalid (Jérome Casas) 28 Dec 2010
https://hal.science/hal-00550576v1
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[hal-03846951] A large-scale dataset reveals taxonomic and functional specificities of wild bee communities in urban habitats of Western Europe
Wild bees are declining, mainly due to the expansion of urban habitats that have led to land-use changes. Effects of urbanization on wild bee communities are still unclear, as shown by contrasting reports on their species and functional diversities in urban habitats. To address this current controversy, we built a large dataset, merging 16 surveys carried out in 3 countries of Western Europe during the past decades, and tested whether urbanization influences local wild bee taxonomic and functional community composition. These surveys encompassed a range of urbanization levels, that were quantified using two complementary metrics: the proportion of impervious surfaces and the human population density. Urban expansion, when measured as a proportion of impervious surfaces, but not as human population density, was significantly and negatively correlated with wild bee community species richness. Taxonomic dissimilarity of the bee community was independent of both urbanization metrics. However, occurrence rates of functional traits revealed significant differences between lightly and highly urbanized communities, for both urbanization metrics. With higher human population density, probabilities of occurrence of above-ground nesters, generalist and small species increased. With higher soil sealing, probabilities of occurrence of above-ground nesters, generalists and social bees increased as well. Overall, these results, based on a large European dataset, suggest that urbanization can have negative impacts on wild bee diversity. They further identify some traits favored in urban environments, showing that several wild bee species can thrive in cities.
ano.nymous@ccsd.cnrs.fr.invalid (Arthur Fauviau) 10 Nov 2022
https://hal.science/hal-03846951v1
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[hal-04169148] Molecular biosurveillance of wood-boring cerambycid beetles using DNA metabarcoding
Individual sorting and identification of thousands of insects collected in mass trapping biosurveillance programs is a labor intensive and time-consuming process. Metabarcoding, which allows for the simultaneous identification of multiple individuals in a single mixed sample, has the potential to expedite this process. However, detecting all the species present in a bulk sample can be challenging. In this study, we quantified the effectiveness of metabarcoding at detecting all species in six different mock communities of xylophagous cerambycid beetles. No significant differences in the number of species detected were observed between MinION, Illumina, and IonTorrent sequencing technologies. However, a greater number of individuals was detected and identified to species using MinION. In addition, the proportion of reads assigned to the species level was higher with Illumina technology. The three sequencing technologies also showed similar results in detecting and identifying closely related species and species at low abundance. The capture method greatly influences sample preservation and detection. Indeed, individuals captured using monopropylene and water had both lower DNA concentration and species detection rates compared to individuals killed using just an insecticide without any collection medium.
ano.nymous@ccsd.cnrs.fr.invalid (Lois Veillat) 24 Jul 2023
https://hal.inrae.fr/hal-04169148v1
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[hal-04168930] Landscape genetics of the protected Spanish Moon Moth in core, buffer, and peripheral areas of the Ordesa y Monte Perdido National Park (Central Pyrenees, Spain)
Conservation managers need to know the degree of connectivity showed by the populations to be preserved, especially when protected areas and/or species are involved. One of the conservation projects carried out by the Ordesa y Monte Perdido National Park (Central Pyrenees, Spain) is the monitoring of the protected Spanish Moon Moth, Graellsia isabellae (Lepidoptera, Saturniidae), in several sites within the actual park, buffer zone, and peripheral area. Here we studied the genetic diversity, geographical structure, and connectivity of this iconic insect in those areas with the aim of producing evidence-based recommendations that might help the National Park staff in their decision-making. For this, we non-lethally sampled 402 adult moths from 17 sites and worked at two geographic scales: Western/Central Pyrenees and the area monitored by the staff of the National Park. The multilocus genotypes obtained for nine nuclear microsatellite markers allowed us to quantify genetic variation, investigate population structure, and calculate recent migration rates. Our results revealed a large-scale (ca. 125 km) west–east cline in allele frequencies that causes low overall genetic differentiation ( F ST = 0.038) and similar levels of diversity among sites. Habitat connectivity revealed as an important element determining dispersal for G. isabellae , given the patchy distribution of the host plant ( Pinus sylvestris ) in the study area. Gene flow within and outside the National Park was proved, with a particular site of the buffer zone (Bujaruelo) acting as a source of migrants to other localities within and outside the National Park. This finding underlines the importance of considering buffer zones to preserve genetic diversity within protected areas, and that safeguarding the connectedness of pine patches is key to the conservation of this iconic moth.
ano.nymous@ccsd.cnrs.fr.invalid (Inés González-Castellano) 22 Jul 2023
https://hal.inrae.fr/hal-04168930v1
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[hal-03656003] Saturniidae and Sphingidae as models for the study of insect diversity and macroecology
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ano.nymous@ccsd.cnrs.fr.invalid (Carlos Lopez-Vaamonde) 30 Apr 2022
https://hal.inrae.fr/hal-03656003v1
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[hal-03656001] Global patterns of insect diversity, distribution and evolutionary distinctness
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ano.nymous@ccsd.cnrs.fr.invalid (Carlos Lopez-Vaamonde) 30 Apr 2022
https://hal.inrae.fr/hal-03656001v1
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[hal-03655983] Non-Destructive DNA metabarcoding of insects for forest biomonitoring
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ano.nymous@ccsd.cnrs.fr.invalid (Lucas Sire) 30 Apr 2022
https://hal.inrae.fr/hal-03655983v1
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[hal-04236342] Landscape genetics of the protected Spanish Moon Moth in core, buffer, and peripheral areas of the Ordesa y Monte Perdido National Park (Central Pyrenees, Spain)
One of the conservation projects carried out by the Ordesa y Monte Perdido National Park is the monitoring of the protected Spanish Moon Moth, Graellsia isabellae (Saturniidae), in several sites within the actual park, buffer zone, and peripheral area. Here we studied the genetic diversity, geographical structure, and connectivity of this iconic insect in those areas with the aim of producing evidence-based recommendations that might help the National Park staff in their decision-making. For this, we non-lethally sampled 402 adult moths from 17 sites and worked at two geographic scales: Western/Central Pyrenees and the area monitored by the staff of the National Park. The multilocus genotypes obtained for nine nuclear microsatellite markers allowed us to quantify genetic variation, investigate population structure, and calculate recent migration rates. Our results revealed a large-scale (ca. 125 km) west–east cline in allele frequencies that causes low overall genetic differentiation (FST = 0.038) and similar levels of diversity among sites. Habitat connectivity revealed as an important element determining dispersal for G. isabellae, given the patchy distribution of the host plant (Pinus sylvestris) in the study area. Gene flow within and outside the National Park was proved, with a particular site of the buffer zone (Bujaruelo) acting as a source of migrants to other localities within and outside the National Park. This finding underlines the importance of considering buffer zones to preserve genetic diversity within protected areas, and that safeguarding the connectedness of pine patches is key to the conservation of this iconic moth.
ano.nymous@ccsd.cnrs.fr.invalid (Marta Vila) 10 Oct 2023
https://hal.inrae.fr/hal-04236342v1
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[hal-04273563] Patterns of speciation in a parapatric pair of Saturnia moths as revealed by target capture
The focus of this study has been to understand the evolutionary relationships and taxonomy of a widely distributed parapatric species pair of wild silk moths in Europe: Saturnia pavonia and Saturnia pavoniella (Lepidoptera: Saturniidae). To address species delimitation in these parapatric taxa, target enrichment and mtDNA sequencing was employed alongside phylogenetic, admixture, introgression, and species delimitation analyses. The dataset included individuals from both species close to and farther away from the contact zone as well as two hybrids generated in the lab. Nuclear markers strongly supported both S. pavonia and S. pavoniella as two distinct species, with hybrids forming a sister group to S. pavoniella. However, the Maximum Likelihood (ML) tree generated from mtDNA sequencing data presented a different picture, showing both taxa to be phylogenetically intermixed. This inconsistency is likely attributable to mitonuclear discordance, which can arise from biological factors (e.g., introgressive hybridization and/or incomplete lineage sorting). Our analyses indicate that past introgressions have taken place, but that there is no evidence to suggest an ongoing admixture between the two species, demonstrating that the taxa have reached full postzygotic reproductive isolation and hence represent two distinct biological species. Finally, we discuss our results from an evolutionary point of view taking into consideration the past climatic oscillations that have likely shaped the present dynamics between the two species. Overall, our study demonstrates the effectiveness of the target enrichment approach in resolving shallow phylogenetic relationships under complex evolutionary circumstances and that this approach is useful in establishing robust and well-informed taxonomic delimitations involving parapatric taxa.
ano.nymous@ccsd.cnrs.fr.invalid (Maria Khan) 07 Nov 2023
https://hal.inrae.fr/hal-04273563v2
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[hal-01595189] Consequences of fluvial maintenance operations on the sediment morphodynamic and the associated BIOdiversity in the mosaic of MAREAU-aux-prés islands.
The Mareau-aux-Prés islands are characterized by a multiple channel pattern affected by an incision of the main channel of 0.6m between 1979 and 2002. In this area, natural limestone riffles influence the morphology and spatial distribution of vegetated islands, secondary channels and alluvial bars. The latter bars are colonized by woody pioneer trees, such as native black poplar (Populus nigra L.). Within these islands, the central 3 ha sandy-gravelly bar is currently beeing surveyed since 2007. In a first study from 2007 to 2012, a multidisciplinary approach has been conducted to understand sediment dynamics and morphological evolution into an island style, mainly governed by sedimentary vertical accretion and presence of woody pionner vegetation (Wintenberger et al. 2015a,b). In september 2012, the vegetation of such island was uprooted and the bar level lowered in order to maintain the flow capacity of the river. A new sandy-gravelly bar appeared in spring 2013, ideal field support for studying long-term ecological issues. A second research programme from 2013 to 2015 was conducted in a multidisciplinary approach, focusing on physical and biological compartments. Field measurements on annual basis were performed on hydro-sedimentary processes to compare with the 2007-2012 period. Biotic components focus on colonization dynamics by Populus nigra seedlings (studying small-scale spatial genetic structure), by native and invasive flora (through seed bank and summer inventories), by community assemblages of ground beetles Coleoptera Carabidae, and on the consequence of the modification of the feeding habitat by the European beaver (as the central island constituted the main source of wood). A new project (2016-2019) has been elaborated, allowing to follow this long term survey, and also incorporating new technologies, such as satellite remote sensing. References : Wintenberger, C., et al. 2015a. Geomorphology, 246 : 305-320 Wintenberger, C., et al. 2015b. Geomorphology 248 : 185-204
ano.nymous@ccsd.cnrs.fr.invalid (Marc Villar) 26 Sep 2017
https://hal.science/hal-01595189v1
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[hal-03206694] Climate-induced forest dieback drives compositional change in insect communities that is concentrated amongst rare species
Marked decline in insect species richness, abundance and biomass have recently been quantified in Europe. We metabarcoded 224 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging have an impact on flying insects (ca. 3000 insect species) in silver fir Pyrenean forests. We found no evidence that climate-induced forest dieback impacted species richness of flying insects but revealed compositional turnover patterns consistent with those seen during natural forest succession, given that the key covariates explaining compositional variation were canopy openness versus microhabitat diversity and deadwood amount at local and landscape scales, respectively. Importantly, most change was driven by rare species. In contrast, observed levels of salvage logging did not explain change in species richness or composition. Hence, although forest dieback appears to cause changes in species assemblages mimicking natural forest succession, it also increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.
ano.nymous@ccsd.cnrs.fr.invalid (Lucas Sire) 23 Apr 2021
https://univ-tours.hal.science/hal-03206694v1
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[hal-03655787] The study of taxonomic diversity of leaf-mining moths Gracillariidae on woody plants in siberia using molecular genetic tools
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ano.nymous@ccsd.cnrs.fr.invalid (Natalia Kirichenko) 30 Apr 2022
https://hal.inrae.fr/hal-03655787v1
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[hal-03643553] Modeling the relationship between temperature and development of the pine processionary moth to predict its phenology
Insect development is heavily impacted by temperature and the development time could vary across life-stages. In the literature, two types of model are generally used to simulate insect development: 1) linear models that are easy to use but not reliable near developmental limits and 2) non linear models that are more robust but need substantial datasets to be correctly parameterized. The good practice is to test both types of models and compare their predictions to find the best model. The pine processionary moth (PPM), Thaumetopoea pityocampa, is an important forest pest in Europe currently expanding its range with climate warming. Due to its univoltine development, this species is also suspected to respond to climate change with shifts of its life cycle depending on climatic features. To simulate PPM phenology, we built three phenology models: 1) a linear model based on degree-days needed to achieve the development of each life stage, 2) a non-linear model based on the thermal performance curve (TPC) of each stage considering hourly mean temperatures, and 3) a non-linear model also based on the TPC of each stage but considering daily mean temperatures. To compare the accuracy of each model, their predictions were compared to phenological observation data. The non-linear model with daily mean temperatures was found to best fit the observations. This model was used to explore the effects of climate warming on PPM phenology.
ano.nymous@ccsd.cnrs.fr.invalid (Laura Poitou) 15 Apr 2022
https://hal.inrae.fr/hal-03643553v1
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[hal-03655926] Historical herbaria to study past distribution and invasion history of phyllophagous insects
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ano.nymous@ccsd.cnrs.fr.invalid (Natalia Kirichenko) 30 Apr 2022
https://hal.inrae.fr/hal-03655926v1
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[hal-03655922] Evolution of gall-induction and host-plant associations in Phyllanthaceae-feeding Caloptilia (Lepidoptera: Gracillariidae)
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ano.nymous@ccsd.cnrs.fr.invalid (Antoine Guiguet) 30 Apr 2022
https://hal.inrae.fr/hal-03655922v1
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[hal-03655905] DNA barcoding of wild and edible insects to sustain forests and fight malnutrition in Madagascar
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ano.nymous@ccsd.cnrs.fr.invalid (Brian Fisher) 30 Apr 2022
https://hal.inrae.fr/hal-03655905v1
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[hal-03319291] Climate Change Alters Temperate Forest Canopies and Indirectly Reshapes Arthropod Communities
Global change challenges the adaptive potential of forests. Large-scale alterations of forest canopies have been reported across Europe, and further modifications are expected in response to the predicted changes in drought and windstorm regimes. Since forest canopies are dynamic interfaces between atmosphere and land surface, communities of canopy-dwelling insects are at the forefront of major changes in response to both direct and indirect effects of climate change. First, we briefly introduce the factors shaping arthropod communities in the canopy of temperate forests. Second, we cover the significant impacts of a forest decline on canopy structure and functioning, and more specifically its contrasted effects on insect microhabitats, trophic resources and forest microclimates. Deleterious effects may be expected for several guilds of leaf-dwelling insects. Nonetheless, a forest decline could also lead to transient or long-lasting resource pulses for other canopy-dwelling guilds, especially saproxylic species depending on deadwood substrates and tree-related microhabitats. The novel microclimates may also become more favorable for some particular groups of insects. We pinpoint current knowledge gaps and the technological locks that should be undone to improve our understanding of the canopy biotope and biodiversity in temperate forests. We highlight the need for integrative approaches to reveal the mechanisms at play. We call for cross-scale studies and long-term collaborative research efforts, involving different disciplines such as community and disturbance ecology, plant and insect ecophysiology, and thermal ecology, to better anticipate ongoing functional and conservation issues in temperate forest ecosystems.
ano.nymous@ccsd.cnrs.fr.invalid (Aurélien Sallé) 05 Oct 2021
https://hal.inrae.fr/hal-03319291v1
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[hal-04186404] Mécatronique et deep learning au service de l’automatisation des suivis de biodiversité en forêt
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ano.nymous@ccsd.cnrs.fr.invalid (Christophe Bouget) 23 Aug 2023
https://hal.inrae.fr/hal-04186404v1
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[hal-05119119] Modélisation des capacités d'invasion et d'expansion de bioagresseurs forestiers
<div><p>La modélisation est un outil qui peut permettre, d'une part, de tester des hypothèses que l'on ne pourrait pas tester facilement sur le terrain dans le but de mieux comprendre le mécanisme en jeu, et, d'autre part, de faire des simulations et des prédictions. Dans le cadre des invasions biologiques, différents types de modèles ont été développés. Ils s'intéressent aux différentes étapes d'une invasion : l'arrivée d'une espèce invasive, son établissement et son expansion. Dans ce chapitre, nous présentons un modèle décrivant la probabilité d'entrée d'un bioagresseur forestier avec l'importation de bois, des modèles de distribution qui permettent d'identifier les territoires dans lesquels il pourrait s'établir, des modèles de dispersion, et des modèles d'expansion qui décrivent à la fois les capacités de dispersion, d'établissement et de croissance des populations. Enfin, nous terminons sur une approche plus prospective. En dehors de l'étape d'entrée, les autres types de modèles peuvent être appliqués aussi bien à des espèces exotiques envahissantes qu'à des espèces natives en expansion.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Christelle Robinet) 18 Jun 2025
https://hal.inrae.fr/hal-05119119v1
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[hal-04758162] Isotrias hybridana (Hübner, [1817]) et Isotrias rectifasciana (Haworth, [1811]) sont une même espèce (Lepidoptera : Tortricidae)
Des difficultés pour différencier les mâles d’Isotrias hybridana de ceux d’I. rectifasciana ont été rencontrées lors de l’inventaire des lépidoptères sur plusieurs sites d’Occitanie. Afin de résoudre ce problème, une série d’individus d’Isotrias a été analysée. L’analyse a pris en compte des critères de morphologie externe, de structures génitales et de séquences code-barre ADN. Les résultats de l’analyse morphologique indiquent que les deux taxons ne peuvent pas être distingués, non seulement pour les mâles mais également pour les femelles, car le critère habituellement utilisé pour les différencier n’est pas discriminant. Les codes-barres ADN disponibles à l’échelle européenne suggèrent aussi qu’il n’y a qu’une seule espèce.
ano.nymous@ccsd.cnrs.fr.invalid (Gérard Labonne) 20 Dec 2024
https://hal.inrae.fr/hal-04758162v1
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[hal-02740183] Conséquences des travaux d'entretien du lit de la Loire sur plusieurs composantes de la biodiversité au sein de la mosaïque des îles de Mareau-aux-Prés (Loiret).
Ce projet de recherche a étudié les conséquences des travaux d’entretien du lit de la Loire sur plusieurs composantes de la biodiversité (faune et flore) au sein de la mosaïque d’ilots de 13 hectares de Mareau-aux-Prés (inclus dans la Réserve Naturelle Nationale de St-Mesmin, Loiret). Suite aux travaux (dévégétalisation et reprofilage), un nouvel assemblage de communautés s’est mis progressivement en place. Ce projet est centré sur cette nouvelle dynamique de recolonisation: la biodiversité intra et interspécifique a été étudiée pendant 3 ans avant et après travaux (via l’acquisition de données in situ et d’analyses génétiques et spatialisées) autour de quatre compartiments biologiques : (1) végétation herbacée, arbustive et arborescente, autochtone et exotique (2) entomofaune coléoptère Carabidae (3) avifaune nicheuse des grèves (4) castor d’Europe. Nous avons pu observer et mesurer une succession quasi primaire alimentée par le flux de populations provenant des autres ilots, îles et berges.
ano.nymous@ccsd.cnrs.fr.invalid (Marc M. Villar) 03 Jun 2020
https://hal.inrae.fr/hal-02740183v1
