Biology subjects

Cruaud, A.

Publications and source records attributed to Cruaud, A..

10 recordsLinked to original sources

bioRxiv2025

Phylogenomics of Messor harvester ants (Hymenoptera: Formicidae: Stenammini) unravels their biogeographical origin and diversification patterns

As a major abiotic factor, climate change is expected to profoundly alter biological communities. On this basis, identifying how past temperature variations affected species diversification and distribution can help to predict the effects of the ongoing climate change. In this study, we focused on the harvester ant genus Messor which is mostly adapted to dry environments dominated by seed-producing plants. The phylogenetic analysis of 2,524 markers obtained from 58 Messor species/subspecies, supports their emergence in the Irano-Indian area approximately 20 Mya. Phylogenetic relationships uncovered in this study enabled us to redefine historical taxonomic groups, providing a solid basis for future revisions that encompass the entire genus diversity. Their diversification appears to be affected by temperature, with a higher speciation rate during warmer periods. This confirms that the ecological specialization of Messor makes them strongly dependent on thermal conditions. Our results highlight the importance of abiotic factors on diversification processes, especially for highly specialized species that may exhibit predictable evolutionary responses to climate changes.

evolutionary biology↗

bioRxiv2025

Phasing in and out of phytophagy: phylogeny and evolution of the family Eurytomidae (Hymenoptera: Chalcidoidea) based on Ultraconserved Elements

We present the first global molecular phylogenetic hypothesis for the family Eurytomidae, a group of chalcidoid wasps with diverse biology, with a representative sampling (197 ingroups and 11 outgroups) that covers all described subfamilies, and 70% of the known genera. Analyses of 962 Ultra-Conserved Elements (UCEs) with concatenation (IQ-TREE) and multispecies coalescent approaches (ASTRAL) resulted in highly supported topologies in recovering the monophyly of Eurytomidae and its four subfamilies. The taxonomy of Eurytomidae, and in particular the large subfamily Eurytominae, needs major revisions as most large genera are recovered as para- or polyphyletic, and the erection of multiple new genera is required in the future to accommodate these taxa. Here, we synonymize the genera Cathilaria (C. certa, C. globiventris, C. opuntiae, and C. rigidae) and the monotypic Aiolomorphus rhopaloides within Tetramesa syn. nov., Parabruchophagus (P. kazakhstanicus, P. nikolskaji, P. rasnitsyni, P. saxatilis, and P. tauricus) and Exeurytoma (E. anatolica, E. caraganae, and E. kebanensis) within Bruchophagus syn. nov.. We also provide 137 DNA barcode COI fragments extracted from the UCE contigs to aid in future identifications of Eurytomidae using this popular genetic marker. Eurytomidae most likely originated in South America with an estimated crown age of 83.37 Ma. Ancestral state reconstruction indicates that secondary phytophagy has evolved at least seven times within the subfamily Eurytominae, showcasing the evolutionary flexibility of these vastly understudied wasps.

zoology↗

bioRxiv2024

Insect-habitat-plant interaction networks provide guidelines to mitigate the risk of transmission of Xylella fastidiosa to grapevine in Southern France

O_LIXylella fastidiosa (Xf) is a xylem-limited bacterium that has been recorded in several European countries since its detection in 2013 in Apulia (Italy). Given the prominence of the wine industry in many southern European countries, a big threat is the development of Pierces disease in grapevines. Yet, the insect-habitat and insect-plant interaction networks in which xylem feeders, possible vectors of Xf, are involved around European vineyards are largely unknown. C_LIO_LIHere we describe these networks in three important wine-growing regions of southern France (Provence-Alpes-Cote dAzur, Occitanie, Nouvelle-Aquitaine) to identify the main source habitats of xylem feeders, and to gather information about their specialization degree at the habitat, plant family, and plant species levels. A total of 92 landscapes (and 700 sites) were studied over three sampling sessions in the fall 2020, the spring 2021, and the fall 2021. C_LIO_LIAmong the habitats sampled, meadows hosted the largest xylem feeder communities, followed by alfalfa fields. Vineyard headlands and inter-rows hosted slightly smaller xylem feeder communities, indicating that potential Xf vectors were thriving in the close vicinity of vulnerable plants. Finally woody habitats in general and grapevines in particular hosted very few xylem feeders, showing that transfer on vulnerable plants are rare, but not inexistent. In terms of specialization degrees, Philaenus spumarius, Aphrophora alni, Lepyronia coleoptrata, and Cicadella viridis were all similarly generalists at the habitat, plant family or plant species level. The only specialist was Aphrophora grp. salicina, which was restricted to riparian forests, and more specifically to Salicaceae. Neophilaenus spp. were extremely specialist at the plant family level (Poaceae), but rather generalist at the habitat and plant species levels. All 1017 insects screened for the presence of Xf tested negative, showing that Xf is not widespread in the studied regions. C_LIO_LIOur study provides new basic ecological information on potential vectors of Xf, especially on their specialization and feeding preferences, as well as practical information that may be relevant for the design of epidemiological surveillance plans. C_LI

ecology↗

bioRxiv2022

Endo-parasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endoparasitoid wasps (whose immature stages develop inside their hosts), the membrane-fusion property of double-stranded DNA viruses has been repeatedly domesticated following ancestral endogenizations. The endogenized genes provide female wasps with a delivery tool to inject virulence factors that are essential to the developmental success of their offspring. Because all known cases of viral domestication involve endoparasitic wasps, we hypothesized that this lifestyle, relying on a close interaction between individuals, may have promoted the endogenization and domestication of viruses. By analyzing the composition of 124 Hymenoptera genomes, spread over the diversity of this clade and including free-living, ecto- and endoparasitoid species, we tested this hypothesis. Our analysis first revealed that double-stranded DNA viruses, in comparisons with other viral genomic structures (ssDNA, dsRNA, ssRNA), are more often endogenized and domesticated (that is, retained by selection) than expected from their estimated abundance in insect viral communities. Secondly, our analysis indicates that the rate at which dsDNA viruses are endogenized is higher in endoparasitoids than in ectoparasitoids or free-living hymenopterans, which also translates into more frequent events of domestication. Hence, these results are consistent with the hypothesis that the endoparasitoid lifestyle has facilitated the endogenization of dsDNA viruses, in turn increasing the opportunities of domestications that now play a central role in the biology of many endoparasitoid lineages.

genomics↗

bioRxiv2022

The Chalcidoidea bush of life - a massive radiation blurred by mutational saturation

Capturing phylogenetic signal from a massive radiation can be daunting. The superfamily Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. Chalcidoidea are mostly parasitoid wasps that until now included 27 families, 87 subfamilies and as many as 500,000 estimated species. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 Ultra-Conserved Elements (UCEs) for 433 taxa including all extant families, over 95% of all subfamilies and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between molecular results and our collective morphological and biological knowledge, we detected insidious bias driven by the saturation of nucleotide data and highlighted morphological convergences. Our final results are based on a concatenated analysis of the least saturated exons and UCE data sets (2054 loci, 284,106 sites). Our analyses support a sister relationship with Mymarommatoidea. Seven of the previously recognized families were not monophyletic, so foundations for a new classification are discussed. Biology appears potentially more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a shift from smaller soft-bodied wasps to larger and more heavily sclerotized wasps. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a Middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea underwent a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about host taxa of chalcid wasps, their fossil record, and Earths paleogeographic history.

evolutionary biology↗

bioRxiv2022

Phylogenomics Illuminates the Evolutionary History of Wild Silkmoths in Space and Time (Lepidoptera: Saturniidae)

AO_SCPLOWBSTRACTC_SCPLOWWild silkmoths (Saturniidae) are one of the most emblematic and most studied families of moths. Yet, the absence of a robust phylogenetic framework based on a 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 described subfamilies, tribes, and genera. We investigated systematic biases in genomic data and performed dating and historical biogeographic analyses to reconstruct the evolutionary history of wild silkmoths in space and time. Using Gene Genealogy Interrogation, we showed that saturation of nucleotide sequence data blurred our understanding of early divergences and first biogeographic events. Our analyses support a Neotropical origin of saturniids, shortly after the Cretaceous-Paleogene extinction event (ca 64.0 [stem] - 52.0 [crown] Ma), and two independent colonization events of the Old World during the Eocene, presumably through the Bering Land Bridge. Early divergences strongly shaped the distribution of extant subfamilies as they showed very limited mobility across biogeographical regions, except for Saturniinae, a subfamily now present on all continents but Antarctica. Overall, our results provide a framework for in-depth investigations into the spatial and temporal dynamics of all saturniid lineages and for the integration of their evolutionary history into further global studies of biodiversity and conservation. Rather unexpectedly for a taxonomically well-known family such as Saturniidae, the proper alignment of taxonomic divisions and ranks with our phylogenetic results leads us to propose substantial rearrangements of the family classification, including the description of one new subfamily and two new tribes.

evolutionary biology↗

bioRxiv2018

Optimised DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol.

Enriching subsets of the genome prior to sequencing allows focusing effort on regions that are relevant to answer specific questions. As experimental design can be adapted to sequence many samples simultaneously, using such approach also contributes to reduce cost. In the field of ecology and evolution, target enrichment is increasingly used for genotyping of plant and animal species or to better understand the evolutionary history of important lineages through the inference of statistically robust phylogenies. Limitations to routine target enrichment by research laboratories are both the complexity of current protocols and low input DNA quantity. Thus, working with tiny organisms such as micro-arthropods can be challenging. Here, we propose easy to set up optimisations for DNA extraction and library preparation prior to target enrichment. Prepared libraries were used to capture 1432 Ultra-Conserved Elements (UCEs) from microhymenoptera (Chalcidoidea), which are among the tiniest insects on Earth and the most commercialized worldwide for biological control purposes. Results show no correlation between input DNA quantities (1.8-250ng, 0.4 ng with an extra whole genome amplification step) and the number of sequenced UCEs. Phylogenetic inferences highlight the potential of UCEs to solve relationships within the families of chalcid wasps, which has not been achieved so far. The protocol (library preparation + target enrichment), allows processing 96 specimens in five working days, by a single person, without requiring the use of expensive robotic molecular biology platforms, which could help to generalize the use of target enrichment for minute specimens.

evolutionary biology↗

bioRxiv2018

Revisiting the phylogeny of Ficus (Moraceae): When Next Generation Sequencing corroborates Past Generation Botanists

Despite their ecological and evolutionary importance, fig trees still lack a resolved phylogeny. We used multiple analytical approaches and 600 conserved RAD-seq loci collected across 40 representative species to infer phylogenetic relationships among the major clades of Ficus. Our results converged on a fully resolved phylogeny that contradicts previous hypotheses by not placing section Pharmacosycea sister to all other fig trees. Instead, we find that subgenus Sycomorus is sister to two clades, one comprising all other gynodioecious sections, and the other containing all monoecious sections. Our results corroborate earlier botanists hypotheses and provide a baseline for future classification. We infer the evolution of key traits (growth form, breeding system and pollination mode) and find that, contrary to previous hypotheses, the ancestor of extant fig trees was likely a gynodioecious and actively pollinated tree. Our results open new opportunities to explore diversification patterns in fig trees and better understand their mutualistic interaction with wasps.

evolutionary biology↗

bioRxiv2018

Climate change and the potential distribution of Xylella fastidiosa in Europe

The bacterium Xylella fastidiosa (Xf) is a plant endophyte native to the Americas that causes worldwide concern. Xf has been recently detected in several regions outside its natural range including Europe. In that context, accurate estimates of its response to climate change are required to design cost-efficient and environment-friendly control strategies. In the present study, we collected data documenting the native and invaded ranges of the three main subspecies of Xf: fastidiosa, pauca and multiplex, as well as two strains of Xf subsp. multiplex recently detected in southern France (ST6 and ST7). We fitted bioclimatic species distribution models (SDMs) to forecast their potential geographic range and impact in Europe under current and future climate conditions. According to model predictions, the geographical range of Xf as presently reported in Europe is small compared to the large extent of suitable areas. The European regions most threatened by Xf encompass the Mediterranean coastal areas of Spain, Greece, Italy and France, the Atlantic coastal areas of France, Portugal and Spain as well as the south-western regions of Spain and lowlands in southern Italy. Potential distribution of the different subspecies / strains are contrasted but all are predicted to increase by 2050, which could threaten several of the most economically important wine-, olive- and fruit-producing regions of Europe, warranting the design of control strategies. Bioclimatic models also predict that the subspecies multiplex might represent a threat to most of Europe under current and future climate conditions. These results may serve as a basis for future design of a spatially informed European-scale integrated management strategy, including early detection surveys in plants and insect vectors, quarantine measures as well as agricultural practices.

ecology↗

bioRxiv2018

Using insects to detect, monitor and predict the distribution of Xylella fastidiosa: a case study in Corsica

We sampled ca 2500 specimens of Philaenus spumarius throughout Corsica without a priori on the presence of symptoms on plants. We screened 448 specimens for the presence of Xylella fastidiosa (Xf) using qPCR and a custom nested PCR. qPCR appeared versatile and under-estimated the prevalence of Xf. Nested PCR showed that Xf was present in all populations. Molecular results were validated by prediction on the distribution of Xf made from tests conducted on plants, which shows the pertinence of using vectors in risk assessment studies. Xf was detected in tenerals and adults. Thus, P. spumarius could acquire Xf from its host plant, mostly Cistus monspeliensis in Corsica, which may act as reservoir for the next season. This contrasts with other observations and suggests that management strategies may have to be adapted on a case-by-case basis. At least two genetic entities and several variants of Xf not yet identified on plants were present in the insects, which suggests ancient introductions of Xf and a probable underestimation of the current diversity of the strains present in Corsica. Interestingly 6% of the specimens carried two subspecies. Studies are wanted to better characterize the strains present in Corsica and know how the disease was introduced, spread and why no sign of a potential epidemic was detected earlier. This study shows that, when sensitive enough methods are implemented, insects can be used to predict and better assess the exact distribution of Xf. Insects are indeed easy to collect, Xf multiply only in their foregut and does not become circulative, which facilitates its detection.\n\nKey messageO_LIInsect vectors can be used to detect, monitor and predict the distribution of Xylella fastidiosa\nC_LIO_LIThe widely used qPCR approach is not sensitive enough to detect low bacterial load\nC_LIO_LIDifferent strains/subspecies of Xf are widely distributed in Corsica which suggests old introduction(s)\nC_LIO_LIStrategies to manage Xf may need to be set up on a case-by-case basis\nC_LIO_LIThere is an urgent need to take stock of the situation in Europe to avoid unnecessary economic pressure on certain geographical areas and agricultural sectors.\nC_LI

ecology↗