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1. Testing the radiation cascade in postglacial radiations of whitefish and their parasites: founder events and host ecology drive parasite evolution.

Author

Brabec, Jan, Gauthier, Jérémy, Selz, Oliver M, Knudsen, Rune, Bilat, Julia, Alvarez, Nadir, Seehausen, Ole, Feulner, Philine G D, Præbel, Kim, and Blasco-Costa, Isabel

Subjects
*ADAPTIVE radiation, *BIOLOGICAL evolution, *GENETIC drift, *HABITAT selection, *POPULATION genetics
Abstract

Reciprocal effects of adaptive radiations on the evolution of interspecific interactions, like parasitism, remain barely explored. We test whether the recent radiations of European whitefish (Coregonus spp.) across and within perialpine and subarctic lakes promote its parasite Proteocephalus fallax (Platyhelminthes: Cestoda) to undergo host repertoire expansion via opportunity and ecological fitting, or adaptive radiation by specialization. Using de novo genomic data, we examined P. fallax differentiation across lakes, within lakes across sympatric host species, and the contributions of host genetics versus host habitat use and trophic preferences. Whitefish intralake radiations prompted parasite host repertoire expansion in all lakes, whereas P. fallax differentiation remains incipient among sympatric fish hosts. Whitefish genetic differentiation per se did not explain the genetic differentiation among its parasite populations, ruling out codivergence with the host. Instead, incipient parasite differentiation was driven by whitefish phenotypic radiation in trophic preferences and habitat use in an arena of parasite opportunity and ecological fitting to utilize resources from emerging hosts. Whilst the whitefish radiation provides a substrate for the parasite to differentiate along the same water-depth ecological axis as Coregonus spp. the role of the intermediate hosts in parasite speciation may be overlooked. Parasite multiple-level ecological fitting to both fish and crustacean intermediate hosts resources may be responsible for parasite population substructure in Coregonus spp. We propose parasites' delayed arrival was key to the initial burst of postglacial intralake whitefish diversification, followed by opportunistic tapeworm host repertoire expansion and a delayed nonadaptive radiation cascade of incipient tapeworm differentiation. At the geographical scale, dispersal, founder events, and genetic drift following colonization of spatially heterogeneous landscapes drove strong parasite differentiation. We argue that these microevolutionary processes result in the mirroring of host–parasite phylogenies through phylogenetic tracking at macroevolutionary and geographical scales. [ABSTRACT FROM AUTHOR]

Published
2024
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2. New Caledonian rovers and the historical biogeography of a hyper‐diverse endemic lineage of South Pacific leaf beetles.

Author

Platania, Leonardo, Cardoso, Anabela, Anderson, Mark, Fikáček, Martin, Gauthier, Jérémy, Hendrich, Lars, Mille, Christian, Morii, Yuta, Reid, Chris A. M., Seidel, Matthias, Morgan‐Richards, Mary, Trewick, Steven A., Toussaint, Emmanuel F. A., and Gómez‐Zurita, Jesús

Subjects
CHRYSOMELIDAE, MOLECULAR phylogeny, MOLECULAR evolution, BIOGEOGRAPHY, PALEOGENE
Abstract

South Pacific archipelagos are central in the biogeographic debate on the relative importance of vicariance and dispersal in shaping the distribution of species. However, each taxonomic group was subject to different processes and histories, and here, we reveal the historical biogeography of the diverse Eumolpinae leaf beetles, widely distributed in the region. Extensive taxon sampling focusing on South Pacific Eumolpinae was used to infer the first molecular phylogeny of the group using three single‐copy protein‐coding nuclear and two mitochondrial markers. Upon assessing the clade of interest for lineage‐specific variation in substitution rates, the age of the most recent common ancestors was estimated using out‐group calibration and multi‐gamma site models (MGSMs). Biogeographic analyses used standard event‐based inferences also incorporating phylogenetic uncertainty. Zealandian Eumolpinae are monophyletic and appear to have split from their global relatives in the transition from the Cretaceous to the Paleogene. Variation in the rates of molecular evolution affected the in‐group stem branch, with a significant drop in the substitution rate, and the MGSM correction recovered the crown age of Zealandian Eumolpinae during the Late Eocene–Oligocene transition. Biogeographic inference resolved the origin of the radiation in New Caledonia, favouring a null model without island age constraints, and repeated dispersal events to the other islands, including three independent but synchronous colonisations of New Zealand during the Miocene. New Caledonia, with a highly diverse Eumolpinae fauna of uncertain origin, acted as a hub and pump of biodiversity of these beetles in the entire South Pacific region, sending migrants to other islands through long‐distance dispersal with lineages establishing when land became available. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

Author

Gauthier, Jérémy, Boulain, Hélène, van Vugt, Joke J. F. A., Baudry, Lyam, Persyn, Emma, Aury, Jean-Marc, Noel, Benjamin, Bretaudeau, Anthony, Legeai, Fabrice, Warris, Sven, Chebbi, Mohamed A., Dubreuil, Géraldine, Duvic, Bernard, Kremer, Natacha, Gayral, Philippe, Musset, Karine, Josse, Thibaut, Bigot, Diane, Bressac, Christophe, Moreau, Sébastien, Periquet, Georges, Harry, Myriam, Montagné, Nicolas, Boulogne, Isabelle, Sabeti-Azad, Mahnaz, Maïbèche, Martine, Chertemps, Thomas, Hilliou, Frédérique, Siaussat, David, Amselem, Joëlle, Luyten, Isabelle, Capdevielle-Dulac, Claire, Labadie, Karine, Merlin, Bruna Laís, Barbe, Valérie, de Boer, Jetske G., Marbouty, Martial, Cônsoli, Fernando Luis, Dupas, Stéphane, Hua-Van, Aurélie, Le Goff, Gaelle, Bézier, Annie, Jacquin-Joly, Emmanuelle, Whitfield, James B., Vet, Louise E. M., Smid, Hans M., Kaiser, Laure, Koszul, Romain, Huguet, Elisabeth, Herniou, Elisabeth A., and Drezen, Jean-Michel

Published
2021
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6. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

Author

Gauthier, Jérémy, Boulain, Hélène, van Vugt, Joke J. F. A., Baudry, Lyam, Persyn, Emma, Aury, Jean-Marc, Noel, Benjamin, Bretaudeau, Anthony, Legeai, Fabrice, Warris, Sven, Chebbi, Mohamed A., Dubreuil, Géraldine, Duvic, Bernard, Kremer, Natacha, Gayral, Philippe, Musset, Karine, Josse, Thibaut, Bigot, Diane, Bressac, Christophe, Moreau, Sébastien, Periquet, Georges, Harry, Myriam, Montagné, Nicolas, Boulogne, Isabelle, Sabeti-Azad, Mahnaz, Maïbèche, Martine, Chertemps, Thomas, Hilliou, Frédérique, Siaussat, David, Amselem, Joëlle, Luyten, Isabelle, Capdevielle-Dulac, Claire, Labadie, Karine, Merlin, Bruna Laís, Barbe, Valérie, de Boer, Jetske G., Marbouty, Martial, Cônsoli, Fernando Luis, Dupas, Stéphane, Hua-Van, Aurélie, Le Goff, Gaelle, Bézier, Annie, Jacquin-Joly, Emmanuelle, Whitfield, James B., Vet, Louise E. M., Smid, Hans M., Kaiser, Laure, Koszul, Romain, Huguet, Elisabeth, Herniou, Elisabeth A., and Drezen, Jean-Michel

Published
2021
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8. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies

Author

Gauthier, Jérémy, Meier, Joana, Legeai, Fabrice, Mcclure, Melanie, Whibley, Annabel, Bretaudeau, Anthony, Boulain, Hélène, Parrinello, Hugues, Mugford, Sam T., Durbin, Richard, Zhou, Chenxi, Mccarthy, Shane, Wheat, Christopher W., Piron‐prunier, Florence, Monsempes, Christelle, François, Marie‐christine, Jay, Paul, Noûs, Camille, Persyn, Emma, Jacquin‐joly, Emmanuelle, Meslin, Camille, Montagné, Nicolas, Lemaitre, Claire, Elias, Marianne, Gauthier, Jérémy, Meier, Joana, Legeai, Fabrice, Mcclure, Melanie, Whibley, Annabel, Bretaudeau, Anthony, Boulain, Hélène, Parrinello, Hugues, Mugford, Sam T., Durbin, Richard, Zhou, Chenxi, Mccarthy, Shane, Wheat, Christopher W., Piron‐prunier, Florence, Monsempes, Christelle, François, Marie‐christine, Jay, Paul, Noûs, Camille, Persyn, Emma, Jacquin‐joly, Emmanuelle, Meslin, Camille, Montagné, Nicolas, Lemaitre, Claire, and Elias, Marianne

Abstract

The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual pheromones, colour pattern and perhaps hostplant could drive reproductive isolation. However, no reference genome was available for Ithomiini, which has hindered further exploration on the genetic architecture of these candidate traits, and more generally on the genomic patterns of divergence. Here, we generated high-quality, chromosome-scale genome assemblies for two Melinaea species, M. marsaeus and M. menophilus, and a draft genome of the species Ithomia salapia. We obtained genomes with a size ranging from 396 to 503 Mb across the three species and scaffold N50 of 40.5 and 23.2 Mb for the two chromosome-scale assemblies. Using collinearity analyses we identified massive rearrangements between the two closely related Melinaea species. An annotation of transposable elements and gene content was performed, as well as a specialist annotation to target chemosensory genes, which is crucial for host plant detection and mate recognition in mimetic species. A comparative genomic approach revealed independent gene expansions in ithomiines and particularly in gustatory receptor genes. These first three genomes of ithomiine mimetic butterflies constitute a valuable addition and a welcome comparison to existing biological models such as Heliconius, and will enable further understanding of the mechanisms of adaptation in butterflies.

Published
2023
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9. Museomics reveals evolutionary history of Oreina alpine leaf beetles (Coleoptera: Chrysomelidae).

Author

Gauthier, Jérémy, Borer, Matthias, Toussaint, Emmanuel F. A., Bilat, Julia, Kippenberg, Horst, and Alvarez, Nadir

Subjects
*CHRYSOMELIDAE, *BEETLES, *HOST plants, *PLANT evolution, *SPECIES, *BIOGEOGRAPHY, *MUSEUM studies
Abstract

The monophyletic status of the genus Oreina as well as its phylogenetic relation to the closely related genera Chrysolina, Crosita and Cyrtonus has been debated for several decades. To assess the status of the genus and understand its evolutionary history, we performed a museomics study on 148 museum specimens belonging to 25 of the 28 described Oreina species as well as 19 other chrysomelid species, mainly from the genus Chrysolina. Using innovative molecular methods relying on hyRAD hybridization capture, we succeeded in recovering 2235 shared nuclear loci. Phylogenomic analyses clearly demonstrated that Oreina species form a clade separated from Chrysolina. These analyses also revealed the position of Chrysolina fastuosa outside of the genus Chrysolina, supporting the following taxonomic status updates: Fastastat. rev., Fasta fastuosacomb. nov. Within the genus Oreina, we further propose the synonymization of Oreina (Frigidorina) syn. n. and Oreina (Virgulatorina) syn. n. with Oreina (Chrysochloa). Divergence time and ancestral range estimations suggested that Oreina originated approximately 53 Ma in the Alps. Ancestral host plant reconstruction revealed key shifts during Oreina diversification. Overall, our study reinforces the importance of museum collections for molecular analysis and the effectiveness of hybridization capture approaches for conducting phylogenomic studies and finely investigating controversial taxonomic debates. [ABSTRACT FROM AUTHOR]

Published
2023
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10. Figure 3 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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11. Figure 5 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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12. Figure 15 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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13. Figure 21 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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14. Figure 8 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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15. Figures 29-32 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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16. Figure 4 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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17. Figure 6 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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18. Figure 7 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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19. Figures 24-26 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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20. Figure 9 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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21. Supplementary material 2 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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23. Supplementary material 1 from: Landry B, Bilat J, Hayden J, Solis MA, Lees DC, Alvarez N, Léger T, Gauthier J (2023) The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens. ZooKeys 1146: 1-42. https://doi.org/10.3897/zookeys.1146.96099

Author

Landry, Bernard, primary, Bilat, Julia, additional, Hayden, James, additional, Solis, M. Alma, additional, Lees, David C., additional, Alvarez, Nadir, additional, Léger, Théo, additional, and Gauthier, Jérémy, additional

Published
2023
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24. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies

Author

Gauthier, Jérémy, primary, Meier, Joana, additional, Legeai, Fabrice, additional, McClure, Melanie, additional, Whibley, Annabel, additional, Bretaudeau, Anthony, additional, Boulain, Hélène, additional, Parrinello, Hugues, additional, Mugford, Sam T., additional, Durbin, Richard, additional, Zhou, Chenxi, additional, McCarthy, Shane, additional, Wheat, Christopher W., additional, Piron‐Prunier, Florence, additional, Monsempes, Christelle, additional, François, Marie‐Christine, additional, Jay, Paul, additional, Noûs, Camille, additional, Persyn, Emma, additional, Jacquin‐Joly, Emmanuelle, additional, Meslin, Camille, additional, Montagné, Nicolas, additional, Lemaitre, Claire, additional, and Elias, Marianne, additional

Published
2023
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29. Dynamic evolution of size and colour in the highly specialized Zodarion ant-eating spiders.

Author

Ortiz, David, Pekár, Stano, Bilat, Julia, Shafaie, Sepideh, Alvarez, Nadir, and Gauthier, Jérémy

Subjects
BODY size, COLOR, ANTS, SPIDERS, PHYLOGENY, DESIGN techniques, MUSEUM studies
Abstract

Ecological specialists constitute relevant case studies for understanding the mechanisms, potential and limitations of evolution. The species-rich and strictly myrmecophagous spiders of the genus Zodarion show diversified defence mechanisms, including myrmecomorphy of different ant species and nocturnality. Through Hybridization Capture Using RAD Probes (hyRAD), a phylogenomic technique designed for sequencing poorly preserved specimens, we reconstructed a phylogeny of Zodarion using 52 (approx. a third of the nominal) species that cover its phylogenetic and distributional diversity. We then estimated the evolution of body size and colour, traits that have diversified noticeably and are linked to defence mechanisms, across the group. Our genomic matrix of 300 loci led to a well-supported phylogenetic hypothesis that uncovered two main clades inside Zodarion. Ancestral state estimation revealed the highly dynamic evolution of body size and colour across the group, with multiple transitions and convergences in both traits, which we propose is likely indicative of multiple transitions in ant specialization across the genus. Our study will allow the informed targeted selection of Zodarion taxa of special interest for research into the group's remarkable adaptations to ant specialization. It also exemplifies the utility of hyRAD for phylogenetic studies using museum material. [ABSTRACT FROM AUTHOR]

Published
2023
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32. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): comparative models for mimicry genetic studies

Author

GAUTHIER, Jérémy, primary, Meier, Joana, additional, Legeai, Fabrice, additional, McClure, Melanie, additional, Whibley, Annabel, additional, Bretaudeau, Anthony, additional, Boulain, Hélène, additional, Parrinello, Hugues, additional, Mugford, Sam, additional, Durbin, Richard, additional, Zhou, Chenxi, additional, McCarthy, Shane, additional, Wheat, Christopher, additional, Piron-Prunier, Florence, additional, Monsempes, Christelle, additional, François, Marie-Christine, additional, Jay, Paul, additional, Nous, Camille, additional, Persyn, Emma, additional, Jacquin-Joly, Emmanuelle, additional, Meslin, Camille, additional, Montagné, Nicolas, additional, Lemaitre, Claire, additional, and Elias, Marianne, additional

Published
2022
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33. Life-history traits drive spatial genetic structuring in Dinaric cave spiders

Author

Pavlek, Martina, Gauthier, Jérémy, Tonzo, Vanina, Bilat, Julia, Arnedo, Miquel A., and Alvarez, Nadir

Subjects
Ecology, cave-dwelling spiders, Dinarides, subterranean dispersal, subterranean gene flow, HyRAD, population genomics, Biology, Ecology, Evolution, Behavior and Systematics
Abstract

The subterranean ecosystem exerts strong selection pressures on the organisms that thrive in it. In response, obligate cave-dwellers have developed a series of morphological, physiological, and behavioral adaptations, such as eye reduction, appendage elongation, low metabolic rates or intermittent activity patterns, collectively referred to as troglomorphism. Traditionally, studies on cave organisms have been hampered by the difficulty of sampling (i.e., small population sizes, temporal heterogeneity in specimen occurrence, challenges imposed by the difficult-to-access nature of caves). Here, we circumvent this limitation by implementing a museomics approach. Specifically, we aim at comparing the genetic population structures of five cave spider species demonstrating contrasting life histories and levels of troglomorphism across different caves in the northern Dinarides (Balkans, Europe). We applied a genome-wide hybridization-capture approach (i.e., HyRAD) to capture DNA from 117 historical samples. By comparing the population genetic structures among five species and by studying isolation by distance, we identified deeper population structuring and more pronounced patterns of isolation by distance in the highly troglomorphic Parastalita stygia and Stalita pretneri ground dwellers, while the three web-building Troglohyphantes species, two of which can occasionally be found in surface habitats, showed less structured populations compatible with higher dispersal ability. The spatial distribution of genetic groups revealed common phylogeographic breaks among lineages across the studied species, which hint at the importance of environmental features in driving dispersal potential and shaping underground diversity.

Published
2022

34. The identity of Argyria lacteella (Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species revealed by morphology and DNA capture in type specimens.

Author

Landry, Bernard, Bilat, Julia, Hayden, James, Solis, M. Alma, Lees, David C., Alvarez, Nadir, Léger, Théo, and Gauthier, Jérémy

Subjects
GENETIC barcoding, BIOLOGICAL classification, LEPIDOPTERA, SPECIES, SYNONYMS
Abstract

In this study the aim was to resolve the taxonomy of several species of Argyria Hübner (Pyraloidea, Crambinae) with previously unrecognised morphological variation. By analysing the DNA barcode (COI-5P) in numerous specimens, the aim was to reconstruct phylogenetic relationships between species, to provide better evidence for synonymies, and to circumscribe their geographical distribution. Using an innovative DNA hybridisation capture protocol, the DNA barcode of the lectotype of Argyria lacteella (Fabricius, 1794) was partially recovered for comparison with the 229 DNA barcode sequences of Argyria specimens available in the Barcode of Life Datasystems, and this firmly establishes the identity of the species. The same protocol was used for the following type specimens: the Argyria abronalis (Walker, 1859) holo-type, thus confirming the synonymy of this name with A. lacteella, the holotype of A. lusella (Zeller, 1863), syn. rev., the holotype of A. multifacta Dyar, 1914, syn. nov. newly synonymised with A. lacteella, and a specimen of Argyria diplomochalis Dyar, 1913, collected in 1992. In addition, nine specimens of A. lacteella, A. diplomochalis, A. centrifugens Dyar, 1914 and A. gonogramma Dyar, 1915, from North to South America were sampled using classical COI amplification and Sanger sequencing. Argyria gonogramma Dyar, described from Bermuda, is the name to be applied to the more widespread North American species formerly identified as A. lacteella. Following morphological study of its holotype, Argyria vestalis Butler, 1878, syn. nov. is also synonymised with A. lacteella. The name A. pusillalis Hübner, 1818, is considered a nomen dubium associated with A. gonogramma. The adult morphology is diagnosed and illustrated, and distributions are plotted for A. lacteella, A. diplomochalis, A. centrifugens, and A. gonogramma based on slightly more than 800 specimens. For the first time, DNA barcode sequences are provided for the Antillean A. diplomochalis. This work provides a modified, improved protocol for the efficient hybrid capture enrichment of DNA barcodes from 18th and 19th century type specimens in order to solve taxonomic issues in Lepidoptera. [ABSTRACT FROM AUTHOR]

Published
2023
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35. Phylogenomic study of Amorphophallus (Alismatales; Araceae): When plastid DNA gene sequences help to resolve the backbone subgeneric delineation.

Author

Pouchon, Charles, Gauthier, Jérémy, Pitteloud, Camille, Claudel, Cyrille, and Alvarez, Nadir

Subjects
*AMORPHOPHALLUS, *ARACEAE, *DNA sequencing, *CURRENT distribution, *MIGRATORY birds, *GLUCOMANNAN
Abstract

Encompassing ca. 200 species distributed in paleotropical Africa and Asia, Amorphophallus is one of the largest genera of Araceae. In spite of the great economic interest in its glucomannan production, only a few studies have attempted to grasp the evolutionary history of this genus. In the current state of knowledge, four main clades, mostly linked to biogeographical delineation, have been identified from phylogenies based on a few genes. However, relationships among and within these clades still remain unclear, due to the rapid radiation that occurred during the early evolutionary history of the genus. Here, we generated genome skimming libraries for 43 specimens from 36 species distributed across the 4 clades, which allowed us to produce a phylogenetic matrix for a set of 71 plastid genes. Our phylogenies confirm the monophyly of these clades but show a new and well‐resolved arrangement among these clades. Our analyses therefore provide a new scenario and timeline for the evolution of the main Amorphophallus clades, consistent with the morphological characteristics of the clades. The inferred scenario is also in agreement with climate dynamics and the onset of long‐distance dispersal by the earliest migratory birds near the Oligocene/Miocene transition around 23 million years ago. Our study provides an up‐to‐date baseline to understand biogeographic and ecological processes that shaped the current diversity and distribution of Amorphophallus, paving the way for larger‐scale phylogenomic studies based on plastid and nuclear genomes. [ABSTRACT FROM AUTHOR]

Published
2023
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36. Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly—The Ithomiini Melinaea marsaeus

Author

Piron‐Prunier, Florence, primary, Persyn, Emma, additional, Legeai, Fabrice, additional, McClure, Melanie, additional, Meslin, Camille, additional, Robin, Stéphanie, additional, Alves‐Carvalho, Susete, additional, Mohammad, Ammara, additional, Blugeon, Corinne, additional, Jacquin‐Joly, Emmanuelle, additional, Montagné, Nicolas, additional, Elias, Marianne, additional, and Gauthier, Jérémy, additional

Published
2021
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38. DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

Author

Gauthier, Jérémy, Mouden, Charlotte, Suchan, Tomasz, Alvarez, Nadir, Arrigo, Nils, Riou, Chloé, Lemaitre, Claire, Peterlongo, Pierre, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), W. Szafer Institute of Botany, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Natural History Museum [Geneva], Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université de Lausanne = University of Lausanne (UNIL), CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Polska Akademia Nauk (PAN), and Dpt of Ecology and Evolution [Lausanne]

Subjects
Insertions, Bioinformatics, Reference-free, lcsh:R, Variants, lcsh:Medicine, Genomics, De novo variant calling, RAD-seq, Next-generation sequencing, Deletions, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Population genomics, Molecular Biology, SNPs
Abstract

International audience; Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets.

Published
2020

39. Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes

Author

Gauthier, Jérémy, BOULAIN, Hélène, van Vugt, Joke J.F.A., Baudry, Lyam, Persyn, Emma, Aury, Jean-Marc, Noel, Benjamin, Bretaudeau, Anthony, Legeai, Fabrice, Warris, Sven, Chebbi, Mohamed Amine, Dubreuil, Géraldine, Duvic, Bernard, Kremer, Natacha, Gayral, Philippe, Musset, Karine, Josse, Thibaut, Bigot, Diane, Bressac, Christophe, Moreau, Sébastien, Periquet, Georges, Harry, Myriam, Montagne, Nicolas, Boulogne, Isabelle, Sabeti-Azad, Mahnaz, Maïbèche, Martine, Chertemps, Thomas, Hilliou, Frédérique, Siaussat, David, Amselem, Joëlle, Luyten, Isabelle, Capdevielle-Dulac, Claire, Labadie, Karine, Merlin, Bruna Laís, Barbe, Valérie, de Boer, Jetske, Marbouty, Martial, Cônsoli, Fernando Luis, Vet, Louise E.M., Cônsoli, Fernando, Dupas, Stéphane, Hua Van, Aurélie, Le Goff, Gaëlle, Bézier, Annie, Jacquin-Joly, Emmanuelle, Whitfield, James, Vet, Louise, Smid, Hans, Kaiser-Arnault, Laure, Koszul, Romain, Huguet, Elisabeth, Herniou, Elisabeth, Drezen, Jean-Michel, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), France Génomique (UMS CNRS 3628 - INRAE 1396 - Inserm 026), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nederlands Instituut Voor Ecologie - NIOO (NETHERLANDS), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Collège doctoral [Sorbonne universités], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Nice Sophia Antipolis (... - 2019) (UNS), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, 0303 health sciences, food.ingredient, Host (biology), [SDV]Life Sciences [q-bio], fungi, Duurzame gewasbescherming, Parasitism, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Genome, Virus, Wespen, Parasitoid wasp, Parasitoid, 03 medical and health sciences, food, Evolutionary biology, Bracovirus, Gene, 030304 developmental biology
Abstract

Most endogenous viruses, an important proportion of eukaryote genomes, are doomed to slowly decay. Little is known, however, on how they evolve when they confer a benefit to their host. Bracoviruses are essential for the parasitism success of parasitoid wasps, whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome, for the first time at a chromosomal scale, that symbiotic bracovirus genes spread to and colonized all the chromosomes. Moreover, large viral clusters are stably maintained suggesting strong evolutionary constraints. Genomic comparison with another wasps revealed that this organization was already established ~53 mya. Transcriptomic analyses highlight temporal synchronization of viral gene expression, leading to particle production. Immune genes are not induced, however, indicating the virus is not perceived as foreign by the wasp. This recognition suggests that no conflicts remain between symbiotic partners when benefits to them converge.

Published
2020
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43. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone

Author

Gauthier, Jérémy, primary, Silva, Donna Lisa, additional, Gompert, Zachariah, additional, Whibley, Annabel, additional, Houssin, Céline, additional, Le Poul, Yann, additional, McClure, Melanie, additional, Lemaitre, Claire, additional, Legeai, Fabrice, additional, Mallet, James, additional, and Elias, Marianne, additional

Published
2020
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44. Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes

Author

Gauthier, Jérémy, primary, Boulain, Hélène, additional, van Vugt, Joke J.F.A., additional, Baudry, Lyam, additional, Persyn, Emma, additional, Aury, Jean-Marc, additional, Noel, Benjamin, additional, Bretaudeau, Anthony, additional, Legeai, Fabrice, additional, Warris, Sven, additional, Chebbi, Mohamed Amine, additional, Dubreuil, Géraldine, additional, Duvic, Bernard, additional, Kremer, Natacha, additional, Gayral, Philippe, additional, Musset, Karine, additional, Josse, Thibaut, additional, Bigot, Diane, additional, Bressac, Christophe, additional, Moreau, Sébastien, additional, Periquet, Georges, additional, Harry, Myriam, additional, Montagné, Nicolas, additional, Boulogne, Isabelle, additional, Sabeti-Azad, Mahnaz, additional, Maïbèche, Martine, additional, Chertemps, Thomas, additional, Hilliou, Frédérique, additional, Siaussat, David, additional, Amselem, Joëlle, additional, Luyten, Isabelle, additional, Capdevielle-Dulac, Claire, additional, Labadie, Karine, additional, Merlin, Bruna Laís, additional, Barbe, Valérie, additional, de Boer, Jetske G., additional, Marbouty, Martial, additional, Cônsoli, Fernando Luis, additional, Dupas, Stéphane, additional, Hua Van, Aurélie, additional, Le Goff, Gaëlle, additional, Bézier, Annie, additional, Jacquin-Joly, Emmanuelle, additional, Whitfield, James B., additional, Vet, Louise E.M., additional, Smid, Hans M., additional, Kaiser-Arnault, Laure, additional, Koszul, Romain, additional, Huguet, Elisabeth, additional, Herniou, Elisabeth A., additional, and Drezen, Jean-Michel, additional

Published
2020
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45. Shintō et altérité

Author

Le Blanc-Gauthier, Jérémy and Vecoli, Fabrizio

Subjects
Religion japonaise, Japon, Shintoism, Japan, Bouddhisme, Alterity, Kitabatake Chikafusa, Shintoïsme, Shintō, Buddhism, Japanese religions
Abstract

Il est généralement, et probablement trop facilement, admis que le Japon a connu des formes de distanciation de l’étranger tout au long de son histoire; que l’on pense à la fermeture supposément hermétique du sakoku 鎖国 (Pays enchainé/fermé) de l’ère Edo (1603-1868), à la résistance face aux invasions mongoles (1274; 1281) ou à la réticence de se laisser imbriquer dans le système tributaire chinois. En effet, face à ce repli national du Japon pouvant difficilement être relativisé pour l’ensemble de sa «proto-modernité» (Edo-jidai), de sa modernité et de sa contemporanéité (Meiji-jidai jusqu'à nos jours), bien des tentatives d’explications historiques furent entreprises, passant d’un essentialisme japonais à un particularisme lié à une géographie insulaire. À une pléthore de théories vint s’en greffer une, issue de l’histoire des religions, comme quoi le Japon aurait une mythologie qui, pour des raisons obscures, vint à se composer comme non pas une cosmogénèse universelle, mais comme une genèse nationale. De ce fait, là où la mythologie comparée a habitué les chercheurs à relever une forte récurrence, pour ne pas dire «une règle», de l’occurrence d’une cosmogénèse expliquant la création du monde, les textes dits mythologiques du Japon nous offrent une genèse qui, de prime abord, semble se limiter à l’archipel japonais et à sa réalité immédiate, le reste du monde semblant pratiquement occulté. Sommairement, de là viendrait peut-être une passation, au travers des âges, d’une compréhension mythologique du monde fondant et perpétuant un ethnocentrisme japonais. De par une telle perception ethnocentrique de la mythologie japonaise, le questionnement à savoir comment cette dernière, ou la religion japonaise plus globalement, «gérait» les relations entre le Japon et l’altérité peut facilement poindre. Donc, est-il possible de relever qu’elle fut, tout au long de l’histoire, le rapport de la religion japonaise à l’altérité ? De là point la problématique du rapport du shintō (voie des dieux) – doctrine qui, traditionnellement est reconnue comme indigène au Japon – à l’altérité. C’est par la mise en commun de trois cas historiques sélectionnés (l’importation de la notion de transcendance au Japon, l’idéologie impériale de la restauration du Namboku-cho (1333-1392) et l’introduction du christianisme au sein de l’archipel) que l’on peut entrevoir que le caractère authentiquement indigène du shintō serait plus de l’ordre d’une réinterprétation historique s’élaborant d’Edo-jidai à nos jours que d’une réalité constante tout au long de l’histoire japonaise., It is commonly accepted, although probably too casually, that through its history Japan has remained detached from anything foreign; whether we think of the so-called hermetic closed views of the sakoku 鎖国 (the lockedown/closed state) of the Edo era (1603-1868), the resistance to the Mongolian invasions (1274; 1281) or the reluctance to be incorporated in the Chinese tributary system. Indeed, in regard to this national fall-back which could hardly be relativized to the sum of its “proto-modernism” (Edo-jidai), its modern and contemporary aspect (Meiji-jidai up to nowadays), many different historical explanations were put forward, from a Japanese essentialism to a particularism tied to their insular geography. From a diverse set of theories, one emerges, birthed out of the history of religions, advancing the idea that Japan has a mythology which, for obscure reasons, would compose itself from a national genesis instead of a cosmological genesis. Consequently, where comparative mythology has accustomed researchers to notice strong repetitions, short of calling it a “rule”, of a cosmogenesis to explain the creation of the world, the so-called Japanese mythological texts offer a genesis which seems, at first glance, to limit itself to the Japanese archipelagos and its immediate reality, effectively occulting the rest of the world as it seems. Succinctly, according to this idea, this mythological understanding of the world, enduring through time, could be seen as the founding and perpetuating factor of the Japanese ethnocentrism. According to this perception of its ethnocentric character, one might wonder how this mythology, or the Japanese religion in general, would negotiate the relationship between Japan and various forms of otherness. Henceforth, could we look through Japanese history and analyze this relationship? At this point the problem of the Shinto (way of the Gods) – a doctrine traditionally recognized as originating from Japan – emerges as to how it relates to this very concept of otherness. Through the conjuncture of three selected historical cases (the importation of the transcendental in Japan, the imperial ideologie of the Namboku-cho restauration (1333-1392) and the christian introduction in the archipelago), we can see that the authentic indigenous character of the Shinto is the fruit of a historical reinterpretation stemming from the Edo-jidai to the present more than an enduring reality throughout Japanese history.

Published
2019

46. Relative influence of host, Wolbachia, geography and climate on the genetic structure of the Sub-saharan parasitic wasp Cotesia sesamiae

Author

Branca, Antoine, Le Ru, Bruno, Calatayud, Paul-André, Obonyo, Julius, Musyoka, Boaz, Capdevielle-Dulac, Claire, Kaiser-Arnauld, Laure, Silvain, Jean-François, Gauthier, Jérémy, Paillusson, Corentin, Gayral, Philippe, Herniou, Elisabeth, Dupas, Stéphane, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Évolution, génomes, comportement et écologie (EGCE), Centre National de la Recherche Scientifique (CNRS)-IRD-Université Paris-Sud - Paris 11 (UP11), International Centre of Insect Physiology and Ecology (ICIPE), ICIPE, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université de Tours-Centre National de la Recherche Scientifique (CNRS), and Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV]Life Sciences [q-bio], [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Cotesia sesamiae, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, specialization, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, host, parasitic diseases, genetic structure, host specialization, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, parasitoid, ComputingMilieux_MISCELLANEOUS, Wolbachia
Abstract

International audience; The parasitoid lifestyle represents one of the most diversified life history strategies on earth. There are however very few studies on the variables associated with intraspecific diversity of parasitoid insects, especially regarding the relationship with spatial, biotic and abiotic ecological factors. Cotesia sesamiae is a Sub-Saharan stenophagous parasitic wasp that parasitizes several African stemborer species with variable developmental success. The different host-specialized populations are infected with different strains of Wolbachia, an endosymbiotic bacterium widespread in arthropods that is known for impacting life history traits, notably reproduction, and consequently species distribution. In this study, first we analyzed the genetic structure of C. sesamiae across Sub-Saharan Africa, using 8 microsatellite markers. We identified five major population clusters across Sub-Saharan Africa, which probably originated in the East African Rift region and expanded throughout Africa in relation to host genus and abiotic factors, such as Köppen-Geiger climate classification. Using laboratory lines, we estimated the incompatibility between the different strains of Wolbachia infecting C. sesamiae. We observed that incompatibility between Wolbachia strains was asymmetric, expressed in one direction only. Based on these results, we assessed the relationships between the direction of gene flow and Wolbachia infections in the genetic clusters. We found that host specialization was more influential on genetic structure than Wolbachia-induced reproductive incompatibility, which in turn was more influential than geography and current climatic conditions. These results are discussed in the context of African biogeography, and co-evolution between Wolbachia, virus parasitoid and host, in the perspective of improving biological control efficiency through a better knowledge of biological control agents' evolutionary ecology.

Published
2019

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